diff options
753 files changed, 13600 insertions, 4205 deletions
@@ -19,5 +19,5 @@ # - F999: name name be undefined or undefined from star imports. # [flake8] -ignore = E221,E241,E731,F403,F821,F999,F405 +ignore = E129,E221,E241,E272,E731,F403,F821,F999,F405 max-line-length = 79 diff --git a/.gitignore b/.gitignore index 960b5b0035..b1215f0c7e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,7 @@ /var/spack/stage /var/spack/cache +/var/spack/repos/*/index.yaml +/var/spack/repos/*/lock *.pyc /opt *~ diff --git a/.travis.yml b/.travis.yml index 904143a00f..b376a33490 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,17 @@ language: python + python: - "2.6" - "2.7" +env: + - TEST_TYPE=unit + - TEST_TYPE=flake8 + +# Exclude flake8 from python 2.6 +matrix: + exclude: + - python: "2.6" + env: TEST_TYPE=flake8 # Use new Travis infrastructure (Docker can't sudo yet) sudo: false @@ -20,20 +30,13 @@ before_install: - git fetch origin develop:develop script: - # Regular spack setup and tests - - . share/spack/setup-env.sh - - spack compilers - - spack config get compilers - - spack install -v libdwarf - - # Run unit tests with code coverage - - coverage run bin/spack test - + # Run unit tests with code coverage plus install libdwarf + - 'if [ "$TEST_TYPE" = "unit" ]; then share/spack/qa/run-unit-tests; fi' # Run flake8 code style checks. - - share/spack/qa/run-flake8 + - 'if [ "$TEST_TYPE" = "flake8" ]; then share/spack/qa/run-flake8; fi' after_success: - - coveralls + - 'if [ "$TEST_TYPE" = "unit" ] && [ "$TRAVIS_PYTHON_VERSION" = "2.7" ]; then coveralls; fi' notifications: email: @@ -58,17 +58,24 @@ can join it here: ### Contributions -At the moment, contributing to Spack is relatively simple. Just send us -a [pull request](https://help.github.com/articles/using-pull-requests/). +Contributing to Spack is relatively. Just send us a +[pull request](https://help.github.com/articles/using-pull-requests/). When you send your request, make ``develop`` the destination branch on the [Spack repository](https://github.com/LLNL/spack). -Your contribution will need to pass all the tests run by the `spack test` -command, as well as the formatting checks in `share/spack/qa/run-flake8`. -You should run both of these before submitting your pull request, to -ensure that the online checks succeed. +Before you send a PR, your code should pass the following checks: -Spack is using a rough approximation of the [Git +* Your contribution will need to pass the `spack test` command. + Run this before submitting your PR. + +* Also run the `share/spack/qa/run-flake8` script to check for PEP8 compliance. + To encourage contributions and readability by a broad audience, + Spack uses the [PEP8](https://www.python.org/dev/peps/pep-0008/) coding + standard with [a few exceptions](https://github.com/LLNL/spack/blob/develop/.flake8). + +We enforce these guidelines with [Travis CI](https://travis-ci.org/LLNL/spack). + +Spack uses a rough approximation of the [Git Flow](http://nvie.com/posts/a-successful-git-branching-model/) branching model. The ``develop`` branch contains the latest contributions, and ``master`` is always tagged and points to the @@ -1,4 +1,5 @@ #!/usr/bin/env python +# flake8: noqa ############################################################################## # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. @@ -24,9 +25,10 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import sys -if not sys.version_info[:2] >= (2,6): +if not sys.version_info[:2] >= (2, 6): v_info = sys.version_info[:3] - sys.exit("Spack requires Python 2.6 or higher. This is Python %d.%d.%d." % v_info) + sys.exit("Spack requires Python 2.6 or higher. " + "This is Python %d.%d.%d." % v_info) import os @@ -62,7 +64,8 @@ for pyc_file in orphaned_pyc_files: try: os.remove(pyc_file) except OSError as e: - print "WARNING: Spack may fail mysteriously. Couldn't remove orphaned .pyc file: %s" % pyc_file + print ("WARNING: Spack may fail mysteriously. " + "Couldn't remove orphaned .pyc file: %s" % pyc_file) # If there is no working directory, use the spack prefix. try: @@ -128,6 +131,7 @@ if len(sys.argv) == 1: # actually parse the args. args = parser.parse_args() + def main(): # Set up environment based on args. tty.set_verbose(args.verbose) @@ -148,7 +152,7 @@ def main(): # If the user asked for it, don't check ssl certs. if args.insecure: - tty.warn("You asked for --insecure, which does not check SSL certificates.") + tty.warn("You asked for --insecure. Will NOT check SSL certificates.") spack.curl.add_default_arg('-k') # Try to load the particular command asked for and run it @@ -167,7 +171,8 @@ def main(): elif isinstance(return_val, int): sys.exit(return_val) else: - tty.die("Bad return value from command %s: %s" % (args.command, return_val)) + tty.die("Bad return value from command %s: %s" + % (args.command, return_val)) if args.profile: import cProfile diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index df9a3901bf..a42d941791 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -1159,7 +1159,7 @@ More than one spec may be placed on the command line here. Module Commands for Shell Scripts `````````````````````````````````` -Although Spack is flexbile, the ``module`` command is much faster. +Although Spack is flexible, the ``module`` command is much faster. This could become an issue when emitting a series of ``spack load`` commands inside a shell script. By adding the ``--shell`` flag, ``spack module find`` may also be used to generate code that can be diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 6e4cd338fe..22ca85abf9 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -29,8 +29,9 @@ import shutil import stat import errno import getpass -from contextlib import contextmanager, closing +from contextlib import contextmanager import subprocess +import fileinput import llnl.util.tty as tty @@ -85,13 +86,14 @@ def filter_file(regex, repl, *filenames, **kwargs): if ignore_absent and not os.path.exists(filename): continue - shutil.copy(filename, backup_filename) + # Create backup file. Don't overwrite an existing backup + # file in case this file is being filtered multiple times. + if not os.path.exists(backup_filename): + shutil.copy(filename, backup_filename) + try: - with closing(open(backup_filename)) as infile: - with closing(open(filename, 'w')) as outfile: - for line in infile: - foo = re.sub(regex, repl, line) - outfile.write(foo) + for line in fileinput.input(filename, inplace=True): + print(re.sub(regex, repl, line.rstrip('\n'))) except: # clean up the original file on failure. shutil.move(backup_filename, filename) @@ -104,6 +106,7 @@ def filter_file(regex, repl, *filenames, **kwargs): class FileFilter(object): """Convenience class for calling filter_file a lot.""" + def __init__(self, *filenames): self.filenames = filenames @@ -189,7 +192,7 @@ def install(src, dest): def install_tree(src, dest, **kwargs): - """Manually install a file to a particular location.""" + """Manually install a directory tree to a particular location.""" tty.debug("Installing %s to %s" % (src, dest)) shutil.copytree(src, dest, **kwargs) @@ -353,7 +356,8 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs): # When follow_nonexisting isn't set, don't descend into dirs # in source that do not exist in dest if follow_nonexisting or os.path.exists(dest_child): - tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs) # NOQA: ignore=E501 + tuples = traverse_tree( + source_root, dest_root, rel_child, **kwargs) for t in tuples: yield t @@ -420,14 +424,20 @@ def fix_darwin_install_name(path): libs = glob.glob(join_path(path, "*.dylib")) for lib in libs: # fix install name first: - subprocess.Popen(["install_name_tool", "-id", lib, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501 - long_deps = subprocess.Popen(["otool", "-L", lib], stdout=subprocess.PIPE).communicate()[0].split('\n') # NOQA: ignore=E501 + subprocess.Popen( + ["install_name_tool", "-id", lib, lib], + stdout=subprocess.PIPE).communicate()[0] + long_deps = subprocess.Popen( + ["otool", "-L", lib], + stdout=subprocess.PIPE).communicate()[0].split('\n') deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]] # fix all dependencies: for dep in deps: for loc in libs: if dep == os.path.basename(loc): - subprocess.Popen(["install_name_tool", "-change", dep, loc, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501 + subprocess.Popen( + ["install_name_tool", "-change", dep, loc, lib], + stdout=subprocess.PIPE).communicate()[0] break diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py index 63eb08d803..df32012e2d 100644 --- a/lib/spack/llnl/util/lang.py +++ b/lib/spack/llnl/util/lang.py @@ -24,7 +24,6 @@ ############################################################################## import os import re -import sys import functools import collections import inspect @@ -39,14 +38,15 @@ def index_by(objects, *funcs): Values are used as keys. For example, suppose you have four objects with attributes that look like this: - a = Spec(name="boost", compiler="gcc", arch="bgqos_0") - b = Spec(name="mrnet", compiler="intel", arch="chaos_5_x86_64_ib") - c = Spec(name="libelf", compiler="xlc", arch="bgqos_0") - d = Spec(name="libdwarf", compiler="intel", arch="chaos_5_x86_64_ib") + a = Spec(name="boost", compiler="gcc", arch="bgqos_0") + b = Spec(name="mrnet", compiler="intel", arch="chaos_5_x86_64_ib") + c = Spec(name="libelf", compiler="xlc", arch="bgqos_0") + d = Spec(name="libdwarf", compiler="intel", arch="chaos_5_x86_64_ib") - list_of_specs = [a,b,c,d] - index1 = index_by(list_of_specs, lambda s: s.arch, lambda s: s.compiler) - index2 = index_by(list_of_specs, lambda s: s.compiler) + list_of_specs = [a,b,c,d] + index1 = index_by(list_of_specs, lambda s: s.arch, + lambda s: s.compiler) + index2 = index_by(list_of_specs, lambda s: s.compiler) ``index1'' now has two levels of dicts, with lists at the leaves, like this: @@ -137,7 +137,7 @@ def get_calling_module_name(): finally: del stack - if not '__module__' in caller_locals: + if '__module__' not in caller_locals: raise RuntimeError("Must invoke get_calling_module_name() " "from inside a class definition!") @@ -173,11 +173,11 @@ def has_method(cls, name): class memoized(object): """Decorator that caches the results of a function, storing them in an attribute of that function.""" + def __init__(self, func): self.func = func self.cache = {} - def __call__(self, *args): if not isinstance(args, collections.Hashable): # Not hashable, so just call the function. @@ -187,12 +187,10 @@ class memoized(object): self.cache[args] = self.func(*args) return self.cache[args] - def __get__(self, obj, objtype): """Support instance methods.""" return functools.partial(self.__call__, obj) - def clear(self): """Expunge cache so that self.func will be called again.""" self.cache.clear() @@ -237,13 +235,21 @@ def key_ordering(cls): if not has_method(cls, '_cmp_key'): raise TypeError("'%s' doesn't define _cmp_key()." % cls.__name__) - setter('__eq__', lambda s,o: (s is o) or (o is not None and s._cmp_key() == o._cmp_key())) - setter('__lt__', lambda s,o: o is not None and s._cmp_key() < o._cmp_key()) - setter('__le__', lambda s,o: o is not None and s._cmp_key() <= o._cmp_key()) - - setter('__ne__', lambda s,o: (s is not o) and (o is None or s._cmp_key() != o._cmp_key())) - setter('__gt__', lambda s,o: o is None or s._cmp_key() > o._cmp_key()) - setter('__ge__', lambda s,o: o is None or s._cmp_key() >= o._cmp_key()) + setter('__eq__', + lambda s, o: + (s is o) or (o is not None and s._cmp_key() == o._cmp_key())) + setter('__lt__', + lambda s, o: o is not None and s._cmp_key() < o._cmp_key()) + setter('__le__', + lambda s, o: o is not None and s._cmp_key() <= o._cmp_key()) + + setter('__ne__', + lambda s, o: + (s is not o) and (o is None or s._cmp_key() != o._cmp_key())) + setter('__gt__', + lambda s, o: o is None or s._cmp_key() > o._cmp_key()) + setter('__ge__', + lambda s, o: o is None or s._cmp_key() >= o._cmp_key()) setter('__hash__', lambda self: hash(self._cmp_key())) @@ -254,10 +260,10 @@ def key_ordering(cls): class HashableMap(dict): """This is a hashable, comparable dictionary. Hash is performed on a tuple of the values in the dictionary.""" + def _cmp_key(self): return tuple(sorted(self.values())) - def copy(self): """Type-agnostic clone method. Preserves subclass type.""" # Construct a new dict of my type @@ -336,24 +342,39 @@ def match_predicate(*args): return match - def DictWrapper(dictionary): """Returns a class that wraps a dictionary and enables it to be used like an object.""" class wrapper(object): - def __getattr__(self, name): return dictionary[name] - def __setattr__(self, name, value): dictionary[name] = value - def setdefault(self, *args): return dictionary.setdefault(*args) - def get(self, *args): return dictionary.get(*args) - def keys(self): return dictionary.keys() - def values(self): return dictionary.values() - def items(self): return dictionary.items() - def __iter__(self): return iter(dictionary) + def __getattr__(self, name): + return dictionary[name] + + def __setattr__(self, name, value): + dictionary[name] = value + + def setdefault(self, *args): + return dictionary.setdefault(*args) + + def get(self, *args): + return dictionary.get(*args) + + def keys(self): + return dictionary.keys() + + def values(self): + return dictionary.values() + + def items(self): + return dictionary.items() + + def __iter__(self): + return iter(dictionary) return wrapper() class RequiredAttributeError(ValueError): + def __init__(self, message): super(RequiredAttributeError, self).__init__(message) diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py index b6d8796084..d6547e933a 100644 --- a/lib/spack/llnl/util/link_tree.py +++ b/lib/spack/llnl/util/link_tree.py @@ -23,12 +23,13 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## """LinkTree class for setting up trees of symbolic links.""" -__all__ = ['LinkTree'] import os import shutil from llnl.util.filesystem import * +__all__ = ['LinkTree'] + empty_file_name = '.spack-empty' @@ -43,13 +44,13 @@ class LinkTree(object): modified. """ + def __init__(self, source_root): if not os.path.exists(source_root): raise IOError("No such file or directory: '%s'", source_root) self._root = source_root - def find_conflict(self, dest_root, **kwargs): """Returns the first file in dest that conflicts with src""" kwargs['follow_nonexisting'] = False @@ -61,9 +62,9 @@ class LinkTree(object): return dest return None - def merge(self, dest_root, **kwargs): - """Link all files in src into dest, creating directories if necessary.""" + """Link all files in src into dest, creating directories + if necessary.""" kwargs['order'] = 'pre' for src, dest in traverse_tree(self._root, dest_root, **kwargs): if os.path.isdir(src): @@ -83,7 +84,6 @@ class LinkTree(object): assert(not os.path.exists(dest)) os.symlink(src, dest) - def unmerge(self, dest_root, **kwargs): """Unlink all files in dest that exist in src. diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py index 479a1b0167..aa8272d5fe 100644 --- a/lib/spack/llnl/util/lock.py +++ b/lib/spack/llnl/util/lock.py @@ -28,6 +28,9 @@ import errno import time import socket +__all__ = ['Lock', 'LockTransaction', 'WriteTransaction', 'ReadTransaction', + 'LockError'] + # Default timeout in seconds, after which locks will raise exceptions. _default_timeout = 60 @@ -36,13 +39,21 @@ _sleep_time = 1e-5 class Lock(object): - def __init__(self,file_path): + """This is an implementation of a filesystem lock using Python's lockf. + + In Python, `lockf` actually calls `fcntl`, so this should work with any + filesystem implementation that supports locking through the fcntl calls. + This includes distributed filesystems like Lustre (when flock is enabled) + and recent NFS versions. + + """ + + def __init__(self, file_path): self._file_path = file_path self._fd = None self._reads = 0 self._writes = 0 - def _lock(self, op, timeout): """This takes a lock using POSIX locks (``fnctl.lockf``). @@ -63,7 +74,9 @@ class Lock(object): fcntl.lockf(self._fd, op | fcntl.LOCK_NB) if op == fcntl.LOCK_EX: - os.write(self._fd, "pid=%s,host=%s" % (os.getpid(), socket.getfqdn())) + os.write( + self._fd, + "pid=%s,host=%s" % (os.getpid(), socket.getfqdn())) return except IOError as error: @@ -75,7 +88,6 @@ class Lock(object): raise LockError("Timed out waiting for lock.") - def _unlock(self): """Releases a lock using POSIX locks (``fcntl.lockf``) @@ -83,11 +95,10 @@ class Lock(object): be masquerading as write locks, but this removes either. """ - fcntl.lockf(self._fd,fcntl.LOCK_UN) + fcntl.lockf(self._fd, fcntl.LOCK_UN) os.close(self._fd) self._fd = None - def acquire_read(self, timeout=_default_timeout): """Acquires a recursive, shared lock for reading. @@ -107,7 +118,6 @@ class Lock(object): self._reads += 1 return False - def acquire_write(self, timeout=_default_timeout): """Acquires a recursive, exclusive lock for writing. @@ -127,7 +137,6 @@ class Lock(object): self._writes += 1 return False - def release_read(self): """Releases a read lock. @@ -148,7 +157,6 @@ class Lock(object): self._reads -= 1 return False - def release_write(self): """Releases a write lock. @@ -170,6 +178,70 @@ class Lock(object): return False +class LockTransaction(object): + """Simple nested transaction context manager that uses a file lock. + + This class can trigger actions when the lock is acquired for the + first time and released for the last. + + If the acquire_fn returns a value, it is used as the return value for + __enter__, allowing it to be passed as the `as` argument of a `with` + statement. + + If acquire_fn returns a context manager, *its* `__enter__` function will be + called in `__enter__` after acquire_fn, and its `__exit__` funciton will be + called before `release_fn` in `__exit__`, allowing you to nest a context + manager to be used along with the lock. + + Timeout for lock is customizable. + + """ + + def __init__(self, lock, acquire_fn=None, release_fn=None, + timeout=_default_timeout): + self._lock = lock + self._timeout = timeout + self._acquire_fn = acquire_fn + self._release_fn = release_fn + self._as = None + + def __enter__(self): + if self._enter() and self._acquire_fn: + self._as = self._acquire_fn() + if hasattr(self._as, '__enter__'): + return self._as.__enter__() + else: + return self._as + + def __exit__(self, type, value, traceback): + suppress = False + if self._exit(): + if self._as and hasattr(self._as, '__exit__'): + if self._as.__exit__(type, value, traceback): + suppress = True + if self._release_fn: + if self._release_fn(type, value, traceback): + suppress = True + return suppress + + +class ReadTransaction(LockTransaction): + + def _enter(self): + return self._lock.acquire_read(self._timeout) + + def _exit(self): + return self._lock.release_read() + + +class WriteTransaction(LockTransaction): + + def _enter(self): + return self._lock.acquire_write(self._timeout) + + def _exit(self): + return self._lock.release_write() + + class LockError(Exception): """Raised when an attempt to acquire a lock times out.""" - pass diff --git a/lib/spack/llnl/util/tty/__init__.py b/lib/spack/llnl/util/tty/__init__.py index ee81e11a20..db74aaba6b 100644 --- a/lib/spack/llnl/util/tty/__init__.py +++ b/lib/spack/llnl/util/tty/__init__.py @@ -36,6 +36,7 @@ _debug = False _verbose = False indent = " " + def is_verbose(): return _verbose @@ -148,7 +149,8 @@ def get_yes_or_no(prompt, **kwargs): elif default_value is False: prompt += ' [y/N] ' else: - raise ValueError("default for get_yes_no() must be True, False, or None.") + raise ValueError( + "default for get_yes_no() must be True, False, or None.") result = None while result is None: @@ -174,8 +176,9 @@ def hline(label=None, **kwargs): char = kwargs.pop('char', '-') max_width = kwargs.pop('max_width', 64) if kwargs: - raise TypeError("'%s' is an invalid keyword argument for this function." - % next(kwargs.iterkeys())) + raise TypeError( + "'%s' is an invalid keyword argument for this function." + % next(kwargs.iterkeys())) rows, cols = terminal_size() if not cols: @@ -200,7 +203,8 @@ def terminal_size(): """Gets the dimensions of the console: (rows, cols).""" def ioctl_GWINSZ(fd): try: - rc = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ, '1234')) + rc = struct.unpack('hh', fcntl.ioctl( + fd, termios.TIOCGWINSZ, '1234')) except: return return rc diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py index 81a83691d7..67acdfa517 100644 --- a/lib/spack/llnl/util/tty/colify.py +++ b/lib/spack/llnl/util/tty/colify.py @@ -27,15 +27,14 @@ Routines for printing columnar output. See colify() for more information. """ import os import sys -import fcntl -import termios -import struct from StringIO import StringIO from llnl.util.tty import terminal_size from llnl.util.tty.color import clen, cextra + class ColumnConfig: + def __init__(self, cols): self.cols = cols self.line_length = 0 @@ -43,7 +42,8 @@ class ColumnConfig: self.widths = [0] * cols # does not include ansi colors def __repr__(self): - attrs = [(a,getattr(self, a)) for a in dir(self) if not a.startswith("__")] + attrs = [(a, getattr(self, a)) + for a in dir(self) if not a.startswith("__")] return "<Config: %s>" % ", ".join("%s: %r" % a for a in attrs) @@ -68,7 +68,7 @@ def config_variable_cols(elts, console_width, padding, cols=0): max_cols = min(len(elts), max_cols) # Range of column counts to try. If forced, use the supplied value. - col_range = [cols] if cols else xrange(1, max_cols+1) + col_range = [cols] if cols else xrange(1, max_cols + 1) # Determine the most columns possible for the console width. configs = [ColumnConfig(c) for c in col_range] @@ -106,7 +106,6 @@ def config_uniform_cols(elts, console_width, padding, cols=0): # 'clen' ignores length of ansi color sequences. max_len = max(clen(e) for e in elts) + padding - max_clen = max(len(e) for e in elts) + padding if cols == 0: cols = max(1, console_width / max_len) cols = min(len(elts), cols) @@ -130,17 +129,19 @@ def colify(elts, **options): output=<stream> A file object to write to. Default is sys.stdout. indent=<int> Optionally indent all columns by some number of spaces. padding=<int> Spaces between columns. Default is 2. - width=<int> Width of the output. Default is 80 if tty is not detected. + width=<int> Width of the output. Default is 80 if tty not detected. cols=<int> Force number of columns. Default is to size to terminal, or single-column if no tty tty=<bool> Whether to attempt to write to a tty. Default is to - autodetect a tty. Set to False to force single-column output. + autodetect a tty. Set to False to force + single-column output. - method=<string> Method to use to fit columns. Options are variable or uniform. - Variable-width columns are tighter, uniform columns are all the - same width and fit less data on the screen. + method=<string> Method to use to fit columns. Options are variable or + uniform. Variable-width columns are tighter, uniform + columns are all the same width and fit less data on + the screen. """ # Get keyword arguments or set defaults cols = options.pop("cols", 0) @@ -152,8 +153,9 @@ def colify(elts, **options): console_cols = options.pop("width", None) if options: - raise TypeError("'%s' is an invalid keyword argument for this function." - % next(options.iterkeys())) + raise TypeError( + "'%s' is an invalid keyword argument for this function." + % next(options.iterkeys())) # elts needs to be an array of strings so we can count the elements elts = [str(elt) for elt in elts] @@ -167,7 +169,8 @@ def colify(elts, **options): r, c = env_size.split('x') console_rows, console_cols = int(r), int(c) tty = True - except: pass + except: + pass # Use only one column if not a tty. if not tty: @@ -228,6 +231,7 @@ def colify_table(table, **options): raise ValueError("Table is empty in colify_table!") columns = len(table[0]) + def transpose(): for i in xrange(columns): for row in table: diff --git a/lib/spack/llnl/util/tty/color.py b/lib/spack/llnl/util/tty/color.py index 0abcb09b97..b0c00f1502 100644 --- a/lib/spack/llnl/util/tty/color.py +++ b/lib/spack/llnl/util/tty/color.py @@ -75,25 +75,27 @@ To output an @, use '@@'. To output a } inside braces, use '}}'. import re import sys + class ColorParseError(Exception): """Raised when a color format fails to parse.""" + def __init__(self, message): super(ColorParseError, self).__init__(message) # Text styles for ansi codes -styles = {'*' : '1', # bold - '_' : '4', # underline - None : '0' } # plain +styles = {'*': '1', # bold + '_': '4', # underline + None: '0'} # plain # Dim and bright ansi colors -colors = {'k' : 30, 'K' : 90, # black - 'r' : 31, 'R' : 91, # red - 'g' : 32, 'G' : 92, # green - 'y' : 33, 'Y' : 93, # yellow - 'b' : 34, 'B' : 94, # blue - 'm' : 35, 'M' : 95, # magenta - 'c' : 36, 'C' : 96, # cyan - 'w' : 37, 'W' : 97 } # white +colors = {'k': 30, 'K': 90, # black + 'r': 31, 'R': 91, # red + 'g': 32, 'G': 92, # green + 'y': 33, 'Y': 93, # yellow + 'b': 34, 'B': 94, # blue + 'm': 35, 'M': 95, # magenta + 'c': 36, 'C': 96, # cyan + 'w': 37, 'W': 97} # white # Regex to be used for color formatting color_re = r'@(?:@|\.|([*_])?([a-zA-Z])?(?:{((?:[^}]|}})*)})?)' @@ -104,6 +106,7 @@ _force_color = False class match_to_ansi(object): + def __init__(self, color=True): self.color = color @@ -179,12 +182,14 @@ def cprint(string, stream=sys.stdout, color=None): """Same as cwrite, but writes a trailing newline to the stream.""" cwrite(string + "\n", stream, color) + def cescape(string): """Replace all @ with @@ in the string provided.""" return str(string).replace('@', '@@') class ColorStream(object): + def __init__(self, stream, color=None): self._stream = stream self._color = color @@ -196,7 +201,7 @@ class ColorStream(object): color = self._color if self._color is None: if raw: - color=True + color = True else: color = self._stream.isatty() or _force_color raw_write(colorize(string, color=color)) diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py index ca82da7b17..b67edcf9cc 100644 --- a/lib/spack/llnl/util/tty/log.py +++ b/lib/spack/llnl/util/tty/log.py @@ -36,6 +36,7 @@ import llnl.util.tty.color as color # Use this to strip escape sequences _escape = re.compile(r'\x1b[^m]*m|\x1b\[?1034h') + def _strip(line): """Strip color and control characters from a line.""" return _escape.sub('', line) @@ -58,10 +59,10 @@ class keyboard_input(object): When the with block completes, this will restore settings before canonical and echo were disabled. """ + def __init__(self, stream): self.stream = stream - def __enter__(self): self.old_cfg = None @@ -86,10 +87,9 @@ class keyboard_input(object): # Apply new settings for terminal termios.tcsetattr(fd, termios.TCSADRAIN, self.new_cfg) - except Exception, e: + except Exception: pass # Some OS's do not support termios, so ignore. - def __exit__(self, exc_type, exception, traceback): # If termios was avaialble, restore old settings after the # with block @@ -114,6 +114,7 @@ class log_output(object): Closes the provided stream when done with the block. If echo is True, also prints the output to stdout. """ + def __init__(self, stream, echo=False, force_color=False, debug=False): self.stream = stream @@ -122,7 +123,7 @@ class log_output(object): self.force_color = force_color self.debug = debug - # Default is to try file-descriptor reassignment unless the system + # Default is to try file-descriptor reassignment unless the system # out/err streams do not have an associated file descriptor self.directAssignment = False @@ -130,7 +131,6 @@ class log_output(object): """Jumps to __exit__ on the child process.""" raise _SkipWithBlock() - def __enter__(self): """Redirect output from the with block to a file. @@ -154,7 +154,8 @@ class log_output(object): with self.stream as log_file: with keyboard_input(sys.stdin): while True: - rlist, w, x = select.select([read_file, sys.stdin], [], []) + rlist, w, x = select.select( + [read_file, sys.stdin], [], []) if not rlist: break @@ -211,7 +212,6 @@ class log_output(object): if self.debug: tty._debug = True - def __exit__(self, exc_type, exception, traceback): """Exits on child, handles skipping the with block on parent.""" # Child should just exit here. @@ -235,7 +235,7 @@ class log_output(object): sys.stderr = self._stderr else: os.dup2(self._stdout, sys.stdout.fileno()) - os.dup2(self._stderr, sys.stderr.fileno()) + os.dup2(self._stderr, sys.stderr.fileno()) return False diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index d67585aac4..3d508d0fde 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -1,3 +1,4 @@ +# flake8: noqa ############################################################################## # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. @@ -50,8 +51,15 @@ repos_path = join_path(var_path, "repos") share_path = join_path(spack_root, "share", "spack") cache_path = join_path(var_path, "cache") +# User configuration location +user_config_path = os.path.expanduser('~/.spack') + import spack.fetch_strategy -cache = spack.fetch_strategy.FsCache(cache_path) +fetch_cache = spack.fetch_strategy.FsCache(cache_path) + +from spack.file_cache import FileCache +user_cache_path = join_path(user_config_path, 'cache') +user_cache = FileCache(user_cache_path) prefix = spack_root opt_path = join_path(prefix, "opt") @@ -140,7 +148,7 @@ _tmp_user = getpass.getuser() _tmp_candidates = (_default_tmp, '/nfs/tmp2', '/tmp', '/var/tmp') for path in _tmp_candidates: # don't add a second username if it's already unique by user. - if not _tmp_user in path: + if _tmp_user not in path: tmp_dirs.append(join_path(path, '%u', 'spack-stage')) else: tmp_dirs.append(join_path(path, 'spack-stage')) @@ -172,12 +180,13 @@ sys_type = None # Spack internal code should call 'import spack' and accesses other # variables (spack.repo, paths, etc.) directly. # -# TODO: maybe this should be separated out and should go in build_environment.py? -# TODO: it's not clear where all the stuff that needs to be included in packages -# should live. This file is overloaded for spack core vs. for packages. +# TODO: maybe this should be separated out to build_environment.py? +# TODO: it's not clear where all the stuff that needs to be included in +# packages should live. This file is overloaded for spack core vs. +# for packages. # -__all__ = ['Package', 'StagedPackage', 'CMakePackage', \ - 'Version', 'when', 'ver', 'alldeps', 'nolink'] +__all__ = ['Package', 'StagedPackage', 'CMakePackage', + 'Version', 'when', 'ver', 'alldeps', 'nolink'] from spack.package import Package, ExtensionConflictError from spack.package import StagedPackage, CMakePackage from spack.version import Version, ver @@ -197,8 +206,8 @@ from spack.util.executable import * __all__ += spack.util.executable.__all__ from spack.package import \ - install_dependency_symlinks, flatten_dependencies, DependencyConflictError, \ - InstallError, ExternalPackageError + install_dependency_symlinks, flatten_dependencies, \ + DependencyConflictError, InstallError, ExternalPackageError __all__ += [ - 'install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError', - 'InstallError', 'ExternalPackageError'] + 'install_dependency_symlinks', 'flatten_dependencies', + 'DependencyConflictError', 'InstallError', 'ExternalPackageError'] diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py index 38cff62af4..064abb9782 100644 --- a/lib/spack/spack/abi.py +++ b/lib/spack/spack/abi.py @@ -30,15 +30,15 @@ from spack.spec import CompilerSpec from spack.util.executable import Executable, ProcessError from llnl.util.lang import memoized + class ABI(object): """This class provides methods to test ABI compatibility between specs. The current implementation is rather rough and could be improved.""" def architecture_compatible(self, parent, child): - """Returns true iff the parent and child specs have ABI compatible targets.""" - return not parent.architecture or not child.architecture \ - or parent.architecture == child.architecture - + """Return true if parent and child have ABI compatible targets.""" + return not parent.architecture or not child.architecture or \ + parent.architecture == child.architecture @memoized def _gcc_get_libstdcxx_version(self, version): @@ -61,8 +61,9 @@ class ABI(object): else: return None try: - output = rungcc("--print-file-name=%s" % libname, return_output=True) - except ProcessError, e: + output = rungcc("--print-file-name=%s" % libname, + return_output=True) + except ProcessError: return None if not output: return None @@ -71,7 +72,6 @@ class ABI(object): return None return os.path.basename(libpath) - @memoized def _gcc_compiler_compare(self, pversion, cversion): """Returns true iff the gcc version pversion and cversion @@ -82,7 +82,6 @@ class ABI(object): return False return plib == clib - def _intel_compiler_compare(self, pversion, cversion): """Returns true iff the intel version pversion and cversion are ABI compatible""" @@ -92,9 +91,8 @@ class ABI(object): return False return pversion.version[:2] == cversion.version[:2] - def compiler_compatible(self, parent, child, **kwargs): - """Returns true iff the compilers for parent and child specs are ABI compatible""" + """Return true if compilers for parent and child are ABI compatible.""" if not parent.compiler or not child.compiler: return True @@ -109,8 +107,8 @@ class ABI(object): # TODO: into compiler classes? for pversion in parent.compiler.versions: for cversion in child.compiler.versions: - # For a few compilers use specialized comparisons. Otherwise - # match on version match. + # For a few compilers use specialized comparisons. + # Otherwise match on version match. if pversion.satisfies(cversion): return True elif (parent.compiler.name == "gcc" and @@ -121,9 +119,8 @@ class ABI(object): return True return False - def compatible(self, parent, child, **kwargs): """Returns true iff a parent and child spec are ABI compatible""" loosematch = kwargs.get('loose', False) return self.architecture_compatible(parent, child) and \ - self.compiler_compatible(parent, child, loose=loosematch) + self.compiler_compatible(parent, child, loose=loosematch) diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py index 974505ee3a..0d210f9741 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -91,6 +91,7 @@ import spack.error as serr class NoPlatformError(serr.SpackError): + def __init__(self): super(NoPlatformError, self).__init__( "Could not determine a platform for this machine.") @@ -383,6 +384,13 @@ class Arch(object): def __contains__(self, string): return string in str(self) + # TODO: make this unnecessary: don't include an empty arch on *every* spec. + def __nonzero__(self): + return (self.platform is not None or + self.platform_os is not None or + self.target is not None) + __bool__ = __nonzero__ + def _cmp_key(self): if isinstance(self.platform, Platform): platform = self.platform.name diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 230115df50..f69f434afd 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -240,4 +240,4 @@ def display_specs(specs, **kwargs): else: raise ValueError( "Invalid mode for display_specs: %s. Must be one of (paths," - "deps, short)." % mode) # NOQA: ignore=E501 + "deps, short)." % mode) diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py index 9867fa8835..797cdcb136 100644 --- a/lib/spack/spack/cmd/activate.py +++ b/lib/spack/spack/cmd/activate.py @@ -29,12 +29,14 @@ import spack.cmd description = "Activate a package extension." + def setup_parser(subparser): subparser.add_argument( '-f', '--force', action='store_true', help="Activate without first activating dependencies.") subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="spec of package extension to activate.") + 'spec', nargs=argparse.REMAINDER, + help="spec of package extension to activate.") def activate(parser, args): diff --git a/lib/spack/spack/cmd/arch.py b/lib/spack/spack/cmd/arch.py index cf2f96fd21..1badd40f7f 100644 --- a/lib/spack/spack/cmd/arch.py +++ b/lib/spack/spack/cmd/arch.py @@ -22,10 +22,10 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import spack import spack.architecture as architecture description = "Print the architecture for this machine" + def arch(parser, args): print architecture.sys_type() diff --git a/lib/spack/spack/cmd/cd.py b/lib/spack/spack/cmd/cd.py index aa45f67ae1..cf7232258c 100644 --- a/lib/spack/spack/cmd/cd.py +++ b/lib/spack/spack/cmd/cd.py @@ -25,7 +25,8 @@ import spack.cmd.location import spack.modules -description="cd to spack directories in the shell." +description = "cd to spack directories in the shell." + def setup_parser(subparser): """This is for decoration -- spack cd is used through spack's diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py index 514c5874ef..dc62fbcaf6 100644 --- a/lib/spack/spack/cmd/clean.py +++ b/lib/spack/spack/cmd/clean.py @@ -31,6 +31,7 @@ import spack.cmd description = "Remove build stage and source tarball for packages." + def setup_parser(subparser): subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to clean") diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py index af04170824..afcba33714 100644 --- a/lib/spack/spack/cmd/common/arguments.py +++ b/lib/spack/spack/cmd/common/arguments.py @@ -35,7 +35,7 @@ _arguments = {} def add_common_arguments(parser, list_of_arguments): for argument in list_of_arguments: if argument not in _arguments: - message = 'Trying to add the non existing argument "{0}" to a command' # NOQA: ignore=E501 + message = 'Trying to add non existing argument "{0}" to a command' raise KeyError(message.format(argument)) x = _arguments[argument] parser.add_argument(*x.flags, **x.kwargs) @@ -82,7 +82,7 @@ parms = Bunch( kwargs={ 'action': 'store_true', 'dest': 'yes_to_all', - 'help': 'Assume "yes" is the answer to every confirmation asked to the user.' # NOQA: ignore=E501 + 'help': 'Assume "yes" is the answer to every confirmation request.' }) _arguments['yes_to_all'] = parms diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py index c325628ebf..ea91c71479 100644 --- a/lib/spack/spack/cmd/compiler.py +++ b/lib/spack/spack/cmd/compiler.py @@ -37,6 +37,7 @@ from spack.util.environment import get_path description = "Manage compilers" + def setup_parser(subparser): sp = subparser.add_subparsers( metavar='SUBCOMMAND', dest='compiler_command') @@ -44,48 +45,58 @@ def setup_parser(subparser): scopes = spack.config.config_scopes # Find - find_parser = sp.add_parser('find', aliases=['add'], help='Search the system for compilers to add to the Spack configuration.') + find_parser = sp.add_parser( + 'find', aliases=['add'], + help='Search the system for compilers to add to Spack configuration.') find_parser.add_argument('add_paths', nargs=argparse.REMAINDER) - find_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope, - help="Configuration scope to modify.") + find_parser.add_argument( + '--scope', choices=scopes, default=spack.cmd.default_modify_scope, + help="Configuration scope to modify.") # Remove - remove_parser = sp.add_parser('remove', aliases=['rm'], help='Remove compiler by spec.') + remove_parser = sp.add_parser( + 'remove', aliases=['rm'], help='Remove compiler by spec.') remove_parser.add_argument( - '-a', '--all', action='store_true', help='Remove ALL compilers that match spec.') + '-a', '--all', action='store_true', + help='Remove ALL compilers that match spec.') remove_parser.add_argument('compiler_spec') - remove_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope, - help="Configuration scope to modify.") + remove_parser.add_argument( + '--scope', choices=scopes, default=spack.cmd.default_modify_scope, + help="Configuration scope to modify.") # List list_parser = sp.add_parser('list', help='list available compilers') - list_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_list_scope, - help="Configuration scope to read from.") + list_parser.add_argument( + '--scope', choices=scopes, default=spack.cmd.default_list_scope, + help="Configuration scope to read from.") # Info info_parser = sp.add_parser('info', help='Show compiler paths.') info_parser.add_argument('compiler_spec') - info_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_list_scope, - help="Configuration scope to read from.") + info_parser.add_argument( + '--scope', choices=scopes, default=spack.cmd.default_list_scope, + help="Configuration scope to read from.") def compiler_find(args): - """Search either $PATH or a list of paths OR MODULES for compilers and add them - to Spack's configuration.""" + """Search either $PATH or a list of paths OR MODULES for compilers and + add them to Spack's configuration. + + """ paths = args.add_paths if not paths: paths = get_path('PATH') - # Don't initialize compilers config via compilers.get_compiler_config. - # Just let compiler_find do the + # Don't initialize compilers config via compilers.get_compiler_config. + # Just let compiler_find do the # entire process and return an empty config from all_compilers # Default for any other process is init_config=True compilers = [c for c in spack.compilers.find_compilers(*paths) if c.spec not in spack.compilers.all_compilers( - scope=args.scope, init_config=False)] + scope=args.scope, init_config=False)] if compilers: spack.compilers.add_compilers_to_config(compilers, scope=args.scope, - init_config=False) + init_config=False) n = len(compilers) s = 's' if n > 1 else '' filename = spack.config.get_config_filename(args.scope, 'compilers') @@ -103,11 +114,12 @@ def compiler_remove(args): elif not args.all and len(compilers) > 1: tty.error("Multiple compilers match spec %s. Choose one:" % cspec) colify(reversed(sorted([c.spec for c in compilers])), indent=4) - tty.msg("Or, you can use `spack compiler remove -a` to remove all of them.") + tty.msg("Or, use `spack compiler remove -a` to remove all of them.") sys.exit(1) for compiler in compilers: - spack.compilers.remove_compiler_from_config(compiler.spec, scope=args.scope) + spack.compilers.remove_compiler_from_config( + compiler.spec, scope=args.scope) tty.msg("Removed compiler %s" % compiler.spec) @@ -133,7 +145,8 @@ def compiler_list(args): tty.msg("Available compilers") index = index_by(spack.compilers.all_compilers(scope=args.scope), 'name') for i, (name, compilers) in enumerate(index.items()): - if i >= 1: print + if i >= 1: + print cname = "%s{%s}" % (spack.spec.compiler_color, name) tty.hline(colorize(cname), char='-') @@ -141,10 +154,10 @@ def compiler_list(args): def compiler(parser, args): - action = {'add' : compiler_find, - 'find' : compiler_find, - 'remove' : compiler_remove, - 'rm' : compiler_remove, - 'info' : compiler_info, - 'list' : compiler_list } + action = {'add': compiler_find, + 'find': compiler_find, + 'remove': compiler_remove, + 'rm': compiler_remove, + 'info': compiler_info, + 'list': compiler_list} action[args.compiler_command](args) diff --git a/lib/spack/spack/cmd/compilers.py b/lib/spack/spack/cmd/compilers.py index 9fbc2bb952..b87f977e5a 100644 --- a/lib/spack/spack/cmd/compilers.py +++ b/lib/spack/spack/cmd/compilers.py @@ -22,18 +22,16 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import llnl.util.tty as tty -from llnl.util.tty.colify import colify -from llnl.util.lang import index_by - import spack from spack.cmd.compiler import compiler_list description = "List available compilers. Same as 'spack compiler list'." + def setup_parser(subparser): subparser.add_argument('--scope', choices=spack.config.config_scopes, help="Configuration scope to read/modify.") + def compilers(parser, args): compiler_list(args) diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py index d6f56c270d..c189e37036 100644 --- a/lib/spack/spack/cmd/config.py +++ b/lib/spack/spack/cmd/config.py @@ -22,15 +22,11 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import sys -import argparse - -import llnl.util.tty as tty - import spack.config description = "Get and set configuration options." + def setup_parser(subparser): # User can only choose one scope_group = subparser.add_mutually_exclusive_group() @@ -64,6 +60,6 @@ def config_edit(args): def config(parser, args): - action = { 'get' : config_get, - 'edit' : config_edit } + action = {'get': config_get, + 'edit': config_edit} action[args.config_command](args) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index da74ceb2f6..52a82eb38f 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -165,7 +165,7 @@ install_dict = { 'python': """\ # FIXME: Add logic to build and install here. - python('setup.py', 'install', '--prefix={0}'.format(prefix))""", + setup_py('install', '--prefix={0}'.format(prefix))""", 'R': """\ # FIXME: Add logic to build and install here. @@ -217,6 +217,7 @@ def setup_parser(subparser): class BuildSystemGuesser(object): + def __call__(self, stage, url): """Try to guess the type of build system used by a project based on the contents of its archive or the URL it was downloaded from.""" diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py index 990309ee48..2b15a0331e 100644 --- a/lib/spack/spack/cmd/deactivate.py +++ b/lib/spack/spack/cmd/deactivate.py @@ -31,6 +31,7 @@ from spack.graph import topological_sort description = "Deactivate a package extension." + def setup_parser(subparser): subparser.add_argument( '-f', '--force', action='store_true', @@ -40,7 +41,8 @@ def setup_parser(subparser): help="Deactivate all extensions of an extendable package, or " "deactivate an extension AND its dependencies.") subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="spec of package extension to deactivate.") + 'spec', nargs=argparse.REMAINDER, + help="spec of package extension to deactivate.") def deactivate(parser, args): @@ -65,7 +67,8 @@ def deactivate(parser, args): if not args.force and not spec.package.activated: tty.die("%s is not activated." % pkg.spec.short_spec) - tty.msg("Deactivating %s and all dependencies." % pkg.spec.short_spec) + tty.msg("Deactivating %s and all dependencies." % + pkg.spec.short_spec) topo_order = topological_sort(spec) index = spec.index() @@ -79,7 +82,9 @@ def deactivate(parser, args): epkg.do_deactivate(force=args.force) else: - tty.die("spack deactivate --all requires an extendable package or an extension.") + tty.die( + "spack deactivate --all requires an extendable package " + "or an extension.") else: if not pkg.is_extension: diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py index 78eb6847b8..7729105e62 100644 --- a/lib/spack/spack/cmd/dependents.py +++ b/lib/spack/spack/cmd/dependents.py @@ -31,9 +31,11 @@ import spack.cmd description = "Show installed packages that depend on another." + def setup_parser(subparser): subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="specs to list dependencies of.") + 'spec', nargs=argparse.REMAINDER, + help="specs to list dependencies of.") def dependents(parser, args): @@ -42,5 +44,6 @@ def dependents(parser, args): tty.die("spack dependents takes only one spec.") fmt = '$_$@$%@$+$=$#' - deps = [d.format(fmt, color=True) for d in specs[0].package.installed_dependents] + deps = [d.format(fmt, color=True) + for d in specs[0].package.installed_dependents] tty.msg("Dependents of %s" % specs[0].format(fmt, color=True), *deps) diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py index 643e6374b2..487654d261 100644 --- a/lib/spack/spack/cmd/diy.py +++ b/lib/spack/spack/cmd/diy.py @@ -35,6 +35,7 @@ from spack.stage import DIYStage description = "Do-It-Yourself: build from an existing source directory." + def setup_parser(subparser): subparser.add_argument( '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', @@ -76,14 +77,17 @@ def diy(self, args): return if not spec.versions.concrete: - tty.die("spack diy spec must have a single, concrete version. Did you forget a package version number?") + tty.die( + "spack diy spec must have a single, concrete version. " + "Did you forget a package version number?") spec.concretize() package = spack.repo.get(spec) if package.installed: tty.error("Already installed in %s" % package.prefix) - tty.msg("Uninstall or try adding a version suffix for this DIY build.") + tty.msg("Uninstall or try adding a version suffix for this " + "DIY build.") sys.exit(1) # Forces the build to run out of the current directory. diff --git a/lib/spack/spack/cmd/doc.py b/lib/spack/spack/cmd/doc.py index b3d0737d13..291b17216f 100644 --- a/lib/spack/spack/cmd/doc.py +++ b/lib/spack/spack/cmd/doc.py @@ -25,6 +25,7 @@ description = "Run pydoc from within spack." + def setup_parser(subparser): subparser.add_argument('entity', help="Run pydoc help on entity") diff --git a/lib/spack/spack/cmd/edit.py b/lib/spack/spack/cmd/edit.py index 49ab83867a..286136dd67 100644 --- a/lib/spack/spack/cmd/edit.py +++ b/lib/spack/spack/cmd/edit.py @@ -68,7 +68,7 @@ def edit_package(name, repo_path, namespace, force=False): if os.path.exists(path): if not os.path.isfile(path): tty.die("Something's wrong. '%s' is not a file!" % path) - if not os.access(path, os.R_OK|os.W_OK): + if not os.access(path, os.R_OK | os.W_OK): tty.die("Insufficient permissions on '%s'!" % path) elif not force: tty.die("No package '%s'. Use spack create, or supply -f/--force " @@ -93,19 +93,23 @@ def setup_parser(subparser): # Various filetypes you can edit directly from the cmd line. excl_args.add_argument( '-c', '--command', dest='path', action='store_const', - const=spack.cmd.command_path, help="Edit the command with the supplied name.") + const=spack.cmd.command_path, + help="Edit the command with the supplied name.") excl_args.add_argument( '-t', '--test', dest='path', action='store_const', const=spack.test_path, help="Edit the test with the supplied name.") excl_args.add_argument( '-m', '--module', dest='path', action='store_const', - const=spack.module_path, help="Edit the main spack module with the supplied name.") + const=spack.module_path, + help="Edit the main spack module with the supplied name.") # Options for editing packages excl_args.add_argument( - '-r', '--repo', default=None, help="Path to repo to edit package in.") + '-r', '--repo', default=None, + help="Path to repo to edit package in.") excl_args.add_argument( - '-N', '--namespace', default=None, help="Namespace of package to edit.") + '-N', '--namespace', default=None, + help="Namespace of package to edit.") subparser.add_argument( 'name', nargs='?', default=None, help="name of package to edit") diff --git a/lib/spack/spack/cmd/env.py b/lib/spack/spack/cmd/env.py index 85d111e91e..f3bad039d4 100644 --- a/lib/spack/spack/cmd/env.py +++ b/lib/spack/spack/cmd/env.py @@ -28,11 +28,13 @@ import llnl.util.tty as tty import spack.cmd import spack.build_environment as build_env -description = "Run a command with the environment for a particular spec's install." +description = "Run a command with the install environment for a spec." + def setup_parser(subparser): subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="specs of package environment to emulate.") + 'spec', nargs=argparse.REMAINDER, + help="specs of package environment to emulate.") def env(parser, args): @@ -47,7 +49,7 @@ def env(parser, args): if sep in args.spec: s = args.spec.index(sep) spec = args.spec[:s] - cmd = args.spec[s+1:] + cmd = args.spec[s + 1:] else: spec = args.spec[0] cmd = args.spec[1:] diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py index 11659e0c96..b5c484305f 100644 --- a/lib/spack/spack/cmd/extensions.py +++ b/lib/spack/spack/cmd/extensions.py @@ -22,7 +22,6 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import sys import argparse import llnl.util.tty as tty @@ -34,6 +33,7 @@ import spack.cmd.find description = "List extensions for package." + def setup_parser(subparser): format_group = subparser.add_mutually_exclusive_group() format_group.add_argument( @@ -47,7 +47,8 @@ def setup_parser(subparser): help='Show full dependency DAG of extensions') subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help='Spec of package to list extensions for') + 'spec', nargs=argparse.REMAINDER, + help='Spec of package to list extensions for') def extensions(parser, args): @@ -85,7 +86,8 @@ def extensions(parser, args): # # List specs of installed extensions. # - installed = [s.spec for s in spack.installed_db.installed_extensions_for(spec)] + installed = [ + s.spec for s in spack.installed_db.installed_extensions_for(spec)] print if not installed: tty.msg("None installed.") @@ -102,4 +104,5 @@ def extensions(parser, args): tty.msg("None activated.") return tty.msg("%d currently activated:" % len(activated)) - spack.cmd.find.display_specs(activated.values(), mode=args.mode, long=args.long) + spack.cmd.find.display_specs( + activated.values(), mode=args.mode, long=args.long) diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py index 1afc51d9fa..c1ac2ed48d 100644 --- a/lib/spack/spack/cmd/fetch.py +++ b/lib/spack/spack/cmd/fetch.py @@ -29,16 +29,21 @@ import spack.cmd description = "Fetch archives for packages" + def setup_parser(subparser): subparser.add_argument( '-n', '--no-checksum', action='store_true', dest='no_checksum', help="Do not check packages against checksum") subparser.add_argument( - '-m', '--missing', action='store_true', help="Also fetch all missing dependencies") + '-m', '--missing', action='store_true', + help="Also fetch all missing dependencies") subparser.add_argument( - '-D', '--dependencies', action='store_true', help="Also fetch all dependencies") + '-D', '--dependencies', action='store_true', + help="Also fetch all dependencies") subparser.add_argument( - 'packages', nargs=argparse.REMAINDER, help="specs of packages to fetch") + 'packages', nargs=argparse.REMAINDER, + help="specs of packages to fetch") + def fetch(parser, args): if not args.packages: @@ -50,7 +55,6 @@ def fetch(parser, args): specs = spack.cmd.parse_specs(args.packages, concretize=True) for spec in specs: if args.missing or args.dependencies: - to_fetch = set() for s in spec.traverse(deptype_query=spack.alldeps): package = spack.repo.get(s) if args.missing and package.installed: diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py index da65121836..8faabfbb7b 100644 --- a/lib/spack/spack/cmd/graph.py +++ b/lib/spack/spack/cmd/graph.py @@ -30,6 +30,7 @@ from spack.graph import * description = "Generate graphs of package dependency relationships." + def setup_parser(subparser): setup_parser.parser = subparser @@ -42,10 +43,12 @@ def setup_parser(subparser): help="Generate graph in dot format and print to stdout.") subparser.add_argument( - '--concretize', action='store_true', help="Concretize specs before graphing.") + '--concretize', action='store_true', + help="Concretize specs before graphing.") subparser.add_argument( - 'specs', nargs=argparse.REMAINDER, help="specs of packages to graph.") + 'specs', nargs=argparse.REMAINDER, + help="specs of packages to graph.") def graph(parser, args): @@ -56,11 +59,11 @@ def graph(parser, args): setup_parser.parser.print_help() return 1 - if args.dot: # Dot graph only if asked for. + if args.dot: # Dot graph only if asked for. graph_dot(*specs) - elif specs: # ascii is default: user doesn't need to provide it explicitly + elif specs: # ascii is default: user doesn't need to provide it explicitly graph_ascii(specs[0], debug=spack.debug) for spec in specs[1:]: - print # extra line bt/w independent graphs + print # extra line bt/w independent graphs graph_ascii(spec, debug=spack.debug) diff --git a/lib/spack/spack/cmd/help.py b/lib/spack/spack/cmd/help.py index 1d23161839..5bc8fc3e74 100644 --- a/lib/spack/spack/cmd/help.py +++ b/lib/spack/spack/cmd/help.py @@ -22,14 +22,14 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import sys - description = "Get help on spack and its commands" + def setup_parser(subparser): subparser.add_argument('help_command', nargs='?', default=None, help='command to get help on') + def help(parser, args): if args.help_command: parser.parse_args([args.help_command, '-h']) diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index 4c076322a9..7663a97a28 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -31,6 +31,7 @@ import spack.cmd description = "Build and install packages" + def setup_parser(subparser): subparser.add_argument( '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', @@ -52,18 +53,18 @@ def setup_parser(subparser): help="Display verbose build output while installing.") subparser.add_argument( '--fake', action='store_true', dest='fake', - help="Fake install. Just remove the prefix and touch a fake file in it.") + help="Fake install. Just remove prefix and create a fake file.") subparser.add_argument( '--dirty', action='store_true', dest='dirty', help="Install a package *without* cleaning the environment.") subparser.add_argument( - 'packages', nargs=argparse.REMAINDER, help="specs of packages to install") + 'packages', nargs=argparse.REMAINDER, + help="specs of packages to install") subparser.add_argument( '--run-tests', action='store_true', dest='run_tests', help="Run tests during installation of a package.") - def install(parser, args): if not args.packages: tty.die("install requires at least one package argument") diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py index 205abbb6b3..85190a5d0b 100644 --- a/lib/spack/spack/cmd/load.py +++ b/lib/spack/spack/cmd/load.py @@ -25,13 +25,16 @@ import argparse import spack.modules -description ="Add package to environment using modules." +description = "Add package to environment using modules." + def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="Spec of package to load with modules. (If -, read specs from STDIN)") + 'spec', nargs=argparse.REMAINDER, + help="Spec of package to load with modules. " + "(If -, read specs from STDIN)") def load(parser, args): diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py index b0dbb1a550..b9c8b5c330 100644 --- a/lib/spack/spack/cmd/location.py +++ b/lib/spack/spack/cmd/location.py @@ -22,8 +22,6 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os -import sys import argparse import llnl.util.tty as tty @@ -32,16 +30,19 @@ from llnl.util.filesystem import join_path import spack import spack.cmd -description="Print out locations of various directories used by Spack" +description = "Print out locations of various directories used by Spack" + def setup_parser(subparser): global directories directories = subparser.add_mutually_exclusive_group() directories.add_argument( - '-m', '--module-dir', action='store_true', help="Spack python module directory.") + '-m', '--module-dir', action='store_true', + help="Spack python module directory.") directories.add_argument( - '-r', '--spack-root', action='store_true', help="Spack installation root.") + '-r', '--spack-root', action='store_true', + help="Spack installation root.") directories.add_argument( '-i', '--install-dir', action='store_true', @@ -53,15 +54,19 @@ def setup_parser(subparser): '-P', '--packages', action='store_true', help="Top-level packages directory for Spack.") directories.add_argument( - '-s', '--stage-dir', action='store_true', help="Stage directory for a spec.") + '-s', '--stage-dir', action='store_true', + help="Stage directory for a spec.") directories.add_argument( - '-S', '--stages', action='store_true', help="Top level Stage directory.") + '-S', '--stages', action='store_true', + help="Top level Stage directory.") directories.add_argument( '-b', '--build-dir', action='store_true', - help="Checked out or expanded source directory for a spec (requires it to be staged first).") + help="Checked out or expanded source directory for a spec " + "(requires it to be staged first).") subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help="spec of package to fetch directory for.") + 'spec', nargs=argparse.REMAINDER, + help="spec of package to fetch directory for.") def location(parser, args): @@ -104,9 +109,9 @@ def location(parser, args): if args.stage_dir: print pkg.stage.path - else: # args.build_dir is the default. + else: # args.build_dir is the default. if not pkg.stage.source_path: - tty.die("Build directory does not exist yet. Run this to create it:", + tty.die("Build directory does not exist yet. " + "Run this to create it:", "spack stage " + " ".join(args.spec)) print pkg.stage.source_path - diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py index 0cf682fc4f..585faaf524 100644 --- a/lib/spack/spack/cmd/mirror.py +++ b/lib/spack/spack/cmd/mirror.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import sys from datetime import datetime import argparse @@ -40,6 +39,7 @@ from spack.util.spack_yaml import syaml_dict description = "Manage mirrors." + def setup_parser(subparser): subparser.add_argument( '-n', '--no-checksum', action='store_true', dest='no_checksum', @@ -61,8 +61,9 @@ def setup_parser(subparser): '-D', '--dependencies', action='store_true', help="Also fetch all dependencies") create_parser.add_argument( - '-o', '--one-version-per-spec', action='store_const', const=1, default=0, - help="Only fetch one 'preferred' version per spec, not all known versions.") + '-o', '--one-version-per-spec', action='store_const', + const=1, default=0, + help="Only fetch one 'preferred' version per spec, not all known.") scopes = spack.config.config_scopes @@ -70,7 +71,7 @@ def setup_parser(subparser): add_parser = sp.add_parser('add', help=mirror_add.__doc__) add_parser.add_argument('name', help="Mnemonic name for mirror.") add_parser.add_argument( - 'url', help="URL of mirror directory created by 'spack mirror create'.") + 'url', help="URL of mirror directory from 'spack mirror create'.") add_parser.add_argument( '--scope', choices=scopes, default=spack.cmd.default_modify_scope, help="Configuration scope to modify.") @@ -107,7 +108,7 @@ def mirror_add(args): tty.die("Mirror with url %s already exists." % url) # should only be one item per mirror dict. - items = [(n,u) for n,u in mirrors.items()] + items = [(n, u) for n, u in mirrors.items()] items.insert(0, (args.name, url)) mirrors = syaml_dict(items) spack.config.update_config('mirrors', mirrors, scope=args.scope) @@ -121,7 +122,7 @@ def mirror_remove(args): if not mirrors: mirrors = syaml_dict() - if not name in mirrors: + if name not in mirrors: tty.die("No mirror with name %s" % name) old_value = mirrors.pop(name) @@ -152,7 +153,7 @@ def _read_specs_from_file(filename): s.package specs.append(s) except SpackError, e: - tty.die("Parse error in %s, line %d:" % (args.file, i+1), + tty.die("Parse error in %s, line %d:" % (args.file, i + 1), ">>> " + string, str(e)) return specs @@ -214,10 +215,10 @@ def mirror_create(args): def mirror(parser, args): - action = { 'create' : mirror_create, - 'add' : mirror_add, - 'remove' : mirror_remove, - 'rm' : mirror_remove, - 'list' : mirror_list } + action = {'create': mirror_create, + 'add': mirror_add, + 'remove': mirror_remove, + 'rm': mirror_remove, + 'list': mirror_list} action[args.mirror_command](args) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index a10e36e077..2d0b83fe00 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -118,7 +118,8 @@ def loads(mtype, specs, args): seen_add = seen.add for spec in specs_from_user_constraint: specs.extend( - [item for item in spec.traverse(order='post', cover='nodes') if not (item in seen or seen_add(item))] # NOQA: ignore=E501 + [item for item in spec.traverse(order='post', cover='nodes') + if not (item in seen or seen_add(item))] ) module_cls = module_types[mtype] @@ -178,7 +179,9 @@ def rm(mtype, specs, args): # Ask for confirmation if not args.yes_to_all: - tty.msg('You are about to remove {0} module files the following specs:\n'.format(mtype)) # NOQA: ignore=E501 + tty.msg( + 'You are about to remove {0} module files the following specs:\n' + .format(mtype)) spack.cmd.display_specs(specs_with_modules, long=True) print('') spack.cmd.ask_for_confirmation('Do you want to proceed ? ') @@ -197,7 +200,9 @@ def refresh(mtype, specs, args): return if not args.yes_to_all: - tty.msg('You are about to regenerate {name} module files for the following specs:\n'.format(name=mtype)) # NOQA: ignore=E501 + tty.msg( + 'You are about to regenerate {name} module files for:\n' + .format(name=mtype)) spack.cmd.display_specs(specs, long=True) print('') spack.cmd.ask_for_confirmation('Do you want to proceed ? ') @@ -245,11 +250,13 @@ def module(parser, args): try: callbacks[args.subparser_name](module_type, args.specs, args) except MultipleMatches: - message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context' # NOQA: ignore=E501 + message = ('the constraint \'{query}\' matches multiple packages, ' + 'and this is not allowed in this context') tty.error(message.format(query=constraint)) for s in args.specs: sys.stderr.write(s.format(color=True) + '\n') raise SystemExit(1) except NoMatch: - message = 'the constraint \'{query}\' match no package, and this is not allowed in this context' # NOQA: ignore=E501 + message = ('the constraint \'{query}\' match no package, ' + 'and this is not allowed in this context') tty.die(message.format(query=constraint)) diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index a27502d30e..9ed42de823 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -32,7 +32,7 @@ description = "Print a list of all packages in reStructuredText." def github_url(pkg): """Link to a package file on github.""" - url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" # NOQA: ignore=E501 + url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" return (url % pkg.name) diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py index a5507e42cf..9c72da40b5 100644 --- a/lib/spack/spack/cmd/patch.py +++ b/lib/spack/spack/cmd/patch.py @@ -29,14 +29,16 @@ import spack.cmd import spack -description="Patch expanded archive sources in preparation for install" +description = "Patch expanded archive sources in preparation for install" + def setup_parser(subparser): subparser.add_argument( '-n', '--no-checksum', action='store_true', dest='no_checksum', help="Do not check downloaded packages against checksum") subparser.add_argument( - 'packages', nargs=argparse.REMAINDER, help="specs of packages to stage") + 'packages', nargs=argparse.REMAINDER, + help="specs of packages to stage") def patch(parser, args): diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py index a24c2759fe..7791b93cf5 100644 --- a/lib/spack/spack/cmd/pkg.py +++ b/lib/spack/spack/cmd/pkg.py @@ -33,6 +33,7 @@ from spack.util.executable import * description = "Query packages associated with particular git revisions." + def setup_parser(subparser): sp = subparser.add_subparsers( metavar='SUBCOMMAND', dest='pkg_command') @@ -46,22 +47,28 @@ def setup_parser(subparser): help="Revision to list packages for.") diff_parser = sp.add_parser('diff', help=pkg_diff.__doc__) - diff_parser.add_argument('rev1', nargs='?', default='HEAD^', - help="Revision to compare against.") - diff_parser.add_argument('rev2', nargs='?', default='HEAD', - help="Revision to compare to rev1 (default is HEAD).") + diff_parser.add_argument( + 'rev1', nargs='?', default='HEAD^', + help="Revision to compare against.") + diff_parser.add_argument( + 'rev2', nargs='?', default='HEAD', + help="Revision to compare to rev1 (default is HEAD).") add_parser = sp.add_parser('added', help=pkg_added.__doc__) - add_parser.add_argument('rev1', nargs='?', default='HEAD^', - help="Revision to compare against.") - add_parser.add_argument('rev2', nargs='?', default='HEAD', - help="Revision to compare to rev1 (default is HEAD).") + add_parser.add_argument( + 'rev1', nargs='?', default='HEAD^', + help="Revision to compare against.") + add_parser.add_argument( + 'rev2', nargs='?', default='HEAD', + help="Revision to compare to rev1 (default is HEAD).") rm_parser = sp.add_parser('removed', help=pkg_removed.__doc__) - rm_parser.add_argument('rev1', nargs='?', default='HEAD^', - help="Revision to compare against.") - rm_parser.add_argument('rev2', nargs='?', default='HEAD', - help="Revision to compare to rev1 (default is HEAD).") + rm_parser.add_argument( + 'rev1', nargs='?', default='HEAD^', + help="Revision to compare against.") + rm_parser.add_argument( + 'rev2', nargs='?', default='HEAD', + help="Revision to compare to rev1 (default is HEAD).") def get_git(): @@ -88,7 +95,8 @@ def pkg_add(args): for pkg_name in args.packages: filename = spack.repo.filename_for_package_name(pkg_name) if not os.path.isfile(filename): - tty.die("No such package: %s. Path does not exist:" % pkg_name, filename) + tty.die("No such package: %s. Path does not exist:" % + pkg_name, filename) git = get_git() git('-C', spack.packages_path, 'add', filename) @@ -112,7 +120,8 @@ def pkg_diff(args): if u1: print "%s:" % args.rev1 colify(sorted(u1), indent=4) - if u1: print + if u1: + print if u2: print "%s:" % args.rev2 @@ -122,19 +131,21 @@ def pkg_diff(args): def pkg_removed(args): """Show packages removed since a commit.""" u1, u2 = diff_packages(args.rev1, args.rev2) - if u1: colify(sorted(u1)) + if u1: + colify(sorted(u1)) def pkg_added(args): """Show packages added since a commit.""" u1, u2 = diff_packages(args.rev1, args.rev2) - if u2: colify(sorted(u2)) + if u2: + colify(sorted(u2)) def pkg(parser, args): - action = { 'add' : pkg_add, - 'diff' : pkg_diff, - 'list' : pkg_list, - 'removed' : pkg_removed, - 'added' : pkg_added } + action = {'add': pkg_add, + 'diff': pkg_diff, + 'list': pkg_list, + 'removed': pkg_removed, + 'added': pkg_added} action[args.pkg_command](args) diff --git a/lib/spack/spack/cmd/providers.py b/lib/spack/spack/cmd/providers.py index e9007486d2..0f4a97cc4a 100644 --- a/lib/spack/spack/cmd/providers.py +++ b/lib/spack/spack/cmd/providers.py @@ -22,7 +22,6 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os import argparse from llnl.util.tty.colify import colify @@ -30,11 +29,13 @@ from llnl.util.tty.colify import colify import spack import spack.cmd -description ="List packages that provide a particular virtual package" +description = "List packages that provide a particular virtual package" + def setup_parser(subparser): - subparser.add_argument('vpkg_spec', metavar='VPACKAGE_SPEC', nargs=argparse.REMAINDER, - help='Find packages that provide this virtual package') + subparser.add_argument( + 'vpkg_spec', metavar='VPACKAGE_SPEC', nargs=argparse.REMAINDER, + help='Find packages that provide this virtual package') def providers(parser, args): diff --git a/lib/spack/spack/cmd/purge.py b/lib/spack/spack/cmd/purge.py index f4e27a3969..26d160635c 100644 --- a/lib/spack/spack/cmd/purge.py +++ b/lib/spack/spack/cmd/purge.py @@ -33,7 +33,11 @@ def setup_parser(subparser): '-s', '--stage', action='store_true', default=True, help="Remove all temporary build stages (default).") subparser.add_argument( - '-c', '--cache', action='store_true', help="Remove cached downloads.") + '-d', '--downloads', action='store_true', + help="Remove cached downloads.") + subparser.add_argument( + '-u', '--user-cache', action='store_true', + help="Remove caches in user home directory. Includes virtual indices.") subparser.add_argument( '-a', '--all', action='store_true', help="Remove all of the above.") @@ -41,12 +45,14 @@ def setup_parser(subparser): def purge(parser, args): # Special case: no flags. - if not any((args.stage, args.cache, args.all)): + if not any((args.stage, args.downloads, args.user_cache, args.all)): stage.purge() return # handle other flags with fall through. if args.stage or args.all: stage.purge() - if args.cache or args.all: - spack.cache.destroy() + if args.downloads or args.all: + spack.fetch_cache.destroy() + if args.user_cache or args.all: + spack.user_cache.destroy() diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py index 59423271b9..12727cb599 100644 --- a/lib/spack/spack/cmd/python.py +++ b/lib/spack/spack/cmd/python.py @@ -30,18 +30,22 @@ import platform import spack + def setup_parser(subparser): subparser.add_argument( '-c', dest='python_command', help='Command to execute.') subparser.add_argument( - 'python_args', nargs=argparse.REMAINDER, help="File to run plus arguments.") + 'python_args', nargs=argparse.REMAINDER, + help="File to run plus arguments.") + description = "Launch an interpreter as spack would launch a command" + def python(parser, args): # Fake a main python shell by setting __name__ to __main__. - console = code.InteractiveConsole({'__name__' : '__main__', - 'spack' : spack}) + console = code.InteractiveConsole({'__name__': '__main__', + 'spack': spack}) if "PYTHONSTARTUP" in os.environ: startup_file = os.environ["PYTHONSTARTUP"] diff --git a/lib/spack/spack/cmd/reindex.py b/lib/spack/spack/cmd/reindex.py index 93eba7a0f1..e37eebbd92 100644 --- a/lib/spack/spack/cmd/reindex.py +++ b/lib/spack/spack/cmd/reindex.py @@ -22,10 +22,10 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import argparse import spack description = "Rebuild Spack's package database." + def reindex(parser, args): spack.installed_db.reindex(spack.install_layout) diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py index cbd8f4784e..5ab2ac0833 100644 --- a/lib/spack/spack/cmd/repo.py +++ b/lib/spack/spack/cmd/repo.py @@ -23,20 +23,16 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import re -import shutil -import argparse import llnl.util.tty as tty -from llnl.util.filesystem import join_path, mkdirp import spack.spec import spack.config -from spack.util.environment import get_path from spack.repository import * description = "Manage package source repositories." + def setup_parser(subparser): sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='repo_command') scopes = spack.config.config_scopes @@ -57,13 +53,15 @@ def setup_parser(subparser): # Add add_parser = sp.add_parser('add', help=repo_add.__doc__) - add_parser.add_argument('path', help="Path to a Spack package repository directory.") + add_parser.add_argument( + 'path', help="Path to a Spack package repository directory.") add_parser.add_argument( '--scope', choices=scopes, default=spack.cmd.default_modify_scope, help="Configuration scope to modify.") # Remove - remove_parser = sp.add_parser('remove', help=repo_remove.__doc__, aliases=['rm']) + remove_parser = sp.add_parser( + 'remove', help=repo_remove.__doc__, aliases=['rm']) remove_parser.add_argument( 'path_or_namespace', help="Path or namespace of a Spack package repository.") @@ -100,7 +98,8 @@ def repo_add(args): # If that succeeds, finally add it to the configuration. repos = spack.config.get_config('repos', args.scope) - if not repos: repos = [] + if not repos: + repos = [] if repo.root in repos or path in repos: tty.die("Repository is already registered with Spack: %s" % path) @@ -135,7 +134,7 @@ def repo_remove(args): tty.msg("Removed repository %s with namespace '%s'." % (repo.root, repo.namespace)) return - except RepoError as e: + except RepoError: continue tty.die("No repository with path or namespace: %s" @@ -149,7 +148,7 @@ def repo_list(args): for r in roots: try: repos.append(Repo(r)) - except RepoError as e: + except RepoError: continue msg = "%d package repositor" % len(repos) @@ -166,9 +165,9 @@ def repo_list(args): def repo(parser, args): - action = { 'create' : repo_create, - 'list' : repo_list, - 'add' : repo_add, - 'remove' : repo_remove, - 'rm' : repo_remove} + action = {'create': repo_create, + 'list': repo_list, + 'add': repo_add, + 'remove': repo_remove, + 'rm': repo_remove} action[args.repo_command](args) diff --git a/lib/spack/spack/cmd/restage.py b/lib/spack/spack/cmd/restage.py index 325d30662f..969afe09bd 100644 --- a/lib/spack/spack/cmd/restage.py +++ b/lib/spack/spack/cmd/restage.py @@ -31,6 +31,7 @@ import spack.cmd description = "Revert checked out package source code." + def setup_parser(subparser): subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to restage") diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py index 04f3d663df..b55e102c0e 100644 --- a/lib/spack/spack/cmd/setup.py +++ b/lib/spack/spack/cmd/setup.py @@ -35,6 +35,7 @@ from spack.stage import DIYStage description = "Create a configuration script and module, but don't build." + def setup_parser(subparser): subparser.add_argument( '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', @@ -70,7 +71,9 @@ def setup(self, args): return if not spec.versions.concrete: - tty.die("spack setup spec must have a single, concrete version. Did you forget a package version number?") + tty.die( + "spack setup spec must have a single, concrete version. " + "Did you forget a package version number?") spec.concretize() package = spack.repo.get(spec) @@ -84,8 +87,8 @@ def setup(self, args): spack.do_checksum = False package.do_install( - keep_prefix=True, # Don't remove install directory, even if you think you should + keep_prefix=True, # Don't remove install directory ignore_deps=args.ignore_deps, verbose=args.verbose, keep_stage=True, # don't remove source dir for SETUP. - install_phases = set(['setup', 'provenance'])) + install_phases=set(['setup', 'provenance'])) diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py index 321e3e429b..6e6d1c1277 100644 --- a/lib/spack/spack/cmd/spec.py +++ b/lib/spack/spack/cmd/spec.py @@ -25,23 +25,22 @@ import argparse import spack.cmd -import llnl.util.tty as tty - import spack -import spack.url as url description = "print out abstract and concrete versions of a spec." + def setup_parser(subparser): subparser.add_argument('-i', '--ids', action='store_true', help="show numerical ids for dependencies.") - subparser.add_argument('specs', nargs=argparse.REMAINDER, help="specs of packages") + subparser.add_argument( + 'specs', nargs=argparse.REMAINDER, help="specs of packages") def spec(parser, args): - kwargs = { 'ids' : args.ids, - 'indent' : 2, - 'color' : True } + kwargs = {'ids': args.ids, + 'indent': 2, + 'color': True} for spec in spack.cmd.parse_specs(args.specs): print "Input spec" diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py index 61e9c6d9ff..bfc2e5f456 100644 --- a/lib/spack/spack/cmd/stage.py +++ b/lib/spack/spack/cmd/stage.py @@ -22,14 +22,14 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os import argparse import llnl.util.tty as tty import spack import spack.cmd -description="Expand downloaded archive in preparation for install" +description = "Expand downloaded archive in preparation for install" + def setup_parser(subparser): subparser.add_argument( diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py index 14c06d136d..8e7173e9a2 100644 --- a/lib/spack/spack/cmd/test-install.py +++ b/lib/spack/spack/cmd/test-install.py @@ -36,25 +36,25 @@ from llnl.util.filesystem import * from spack.build_environment import InstallError from spack.fetch_strategy import FetchError -description = "Run package installation as a unit test, output formatted results." +description = "Run package install as a unit test, output formatted results." def setup_parser(subparser): - subparser.add_argument('-j', - '--jobs', - action='store', - type=int, - help="Explicitly set number of make jobs. Default is #cpus.") + subparser.add_argument( + '-j', '--jobs', action='store', type=int, + help="Explicitly set number of make jobs. Default is #cpus.") - subparser.add_argument('-n', - '--no-checksum', - action='store_true', - dest='no_checksum', - help="Do not check packages against checksum") + subparser.add_argument( + '-n', '--no-checksum', action='store_true', dest='no_checksum', + help="Do not check packages against checksum") - subparser.add_argument('-o', '--output', action='store', help="test output goes in this file") + subparser.add_argument( + '-o', '--output', action='store', + help="test output goes in this file") - subparser.add_argument('package', nargs=argparse.REMAINDER, help="spec of package to install") + subparser.add_argument( + 'package', nargs=argparse.REMAINDER, + help="spec of package to install") class TestResult(object): @@ -65,6 +65,7 @@ class TestResult(object): class TestSuite(object): + def __init__(self, filename): self.filename = filename self.root = ET.Element('testsuite') @@ -75,14 +76,17 @@ class TestSuite(object): def append(self, item): if not isinstance(item, TestCase): - raise TypeError('only TestCase instances may be appended to a TestSuite instance') + raise TypeError( + 'only TestCase instances may be appended to TestSuite') self.tests.append(item) # Append the item to the list of tests def __exit__(self, exc_type, exc_val, exc_tb): # Prepare the header for the entire test suite - number_of_errors = sum(x.result_type == TestResult.ERRORED for x in self.tests) + number_of_errors = sum( + x.result_type == TestResult.ERRORED for x in self.tests) self.root.set('errors', str(number_of_errors)) - number_of_failures = sum(x.result_type == TestResult.FAILED for x in self.tests) + number_of_failures = sum( + x.result_type == TestResult.FAILED for x in self.tests) self.root.set('failures', str(number_of_failures)) self.root.set('tests', str(len(self.tests))) @@ -112,7 +116,8 @@ class TestCase(object): self.element.set('time', str(time)) self.result_type = None - def set_result(self, result_type, message=None, error_type=None, text=None): + def set_result(self, result_type, + message=None, error_type=None, text=None): self.result_type = result_type result = TestCase.results[self.result_type] if result is not None and result is not TestResult.PASSED: @@ -155,13 +160,19 @@ def install_single_spec(spec, number_of_jobs): # If it is already installed, skip the test if spack.repo.get(spec).installed: testcase = TestCase(package.name, package.spec.short_spec, time=0.0) - testcase.set_result(TestResult.SKIPPED, message='Skipped [already installed]', error_type='already_installed') + testcase.set_result( + TestResult.SKIPPED, + message='Skipped [already installed]', + error_type='already_installed') return testcase # If it relies on dependencies that did not install, skip if failed_dependencies(spec): testcase = TestCase(package.name, package.spec.short_spec, time=0.0) - testcase.set_result(TestResult.SKIPPED, message='Skipped [failed dependencies]', error_type='dep_failed') + testcase.set_result( + TestResult.SKIPPED, + message='Skipped [failed dependencies]', + error_type='dep_failed') return testcase # Otherwise try to install the spec @@ -177,26 +188,30 @@ def install_single_spec(spec, number_of_jobs): testcase = TestCase(package.name, package.spec.short_spec, duration) testcase.set_result(TestResult.PASSED) except InstallError: - # An InstallError is considered a failure (the recipe didn't work correctly) + # An InstallError is considered a failure (the recipe didn't work + # correctly) duration = time.time() - start_time # Try to get the log lines = fetch_log(package.build_log_path) text = '\n'.join(lines) testcase = TestCase(package.name, package.spec.short_spec, duration) - testcase.set_result(TestResult.FAILED, message='Installation failure', text=text) + testcase.set_result(TestResult.FAILED, + message='Installation failure', text=text) except FetchError: # A FetchError is considered an error (we didn't even start building) duration = time.time() - start_time testcase = TestCase(package.name, package.spec.short_spec, duration) - testcase.set_result(TestResult.ERRORED, message='Unable to fetch package') + testcase.set_result(TestResult.ERRORED, + message='Unable to fetch package') return testcase def get_filename(args, top_spec): if not args.output: - fname = 'test-{x.name}-{x.version}-{hash}.xml'.format(x=top_spec, hash=top_spec.dag_hash()) + fname = 'test-{x.name}-{x.version}-{hash}.xml'.format( + x=top_spec, hash=top_spec.dag_hash()) output_directory = join_path(os.getcwd(), 'test-output') if not os.path.exists(output_directory): os.mkdir(output_directory) diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py index 36810321ef..bf7342f606 100644 --- a/lib/spack/spack/cmd/test.py +++ b/lib/spack/spack/cmd/test.py @@ -23,28 +23,28 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -from pprint import pprint from llnl.util.filesystem import join_path, mkdirp from llnl.util.tty.colify import colify -from llnl.util.lang import list_modules import spack import spack.test from spack.fetch_strategy import FetchError -description ="Run unit tests" +description = "Run unit tests" + def setup_parser(subparser): subparser.add_argument( 'names', nargs='*', help="Names of tests to run.") subparser.add_argument( - '-l', '--list', action='store_true', dest='list', help="Show available tests") + '-l', '--list', action='store_true', dest='list', + help="Show available tests") subparser.add_argument( - '--createXmlOutput', action='store_true', dest='createXmlOutput', + '--createXmlOutput', action='store_true', dest='createXmlOutput', help="Create JUnit XML from test results") subparser.add_argument( - '--xmlOutputDir', dest='xmlOutputDir', + '--xmlOutputDir', dest='xmlOutputDir', help="Nose creates XML files in this directory") subparser.add_argument( '-v', '--verbose', action='store_true', dest='verbose', @@ -52,6 +52,7 @@ def setup_parser(subparser): class MockCache(object): + def store(self, copyCmd, relativeDst): pass @@ -60,15 +61,17 @@ class MockCache(object): class MockCacheFetcher(object): + def set_stage(self, stage): pass - + def fetch(self): raise FetchError("Mock cache always fails for tests") def __str__(self): return "[mock fetcher]" + def test(parser, args): if args.list: print "Available tests:" @@ -82,8 +85,8 @@ def test(parser, args): outputDir = join_path(os.getcwd(), "test-output") else: outputDir = os.path.abspath(args.xmlOutputDir) - + if not os.path.exists(outputDir): mkdirp(outputDir) - spack.cache = MockCache() + spack.fetch_cache = MockCache() spack.test.run(args.names, outputDir, args.verbose) diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index a17b7c685c..8957d1c908 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -50,25 +50,27 @@ def setup_parser(subparser): subparser.add_argument( '-f', '--force', action='store_true', dest='force', help="Remove regardless of whether other packages depend on this one.") + subparser.add_argument( '-a', '--all', action='store_true', dest='all', - help="USE CAREFULLY. Remove ALL installed packages that match each " + - "supplied spec. i.e., if you say uninstall libelf, ALL versions of " + # NOQA: ignore=E501 - "libelf are uninstalled. This is both useful and dangerous, like rm -r.") # NOQA: ignore=E501 + help="USE CAREFULLY. Remove ALL installed packages that match each " + "supplied spec. i.e., if you say uninstall libelf, ALL versions " + "of libelf are uninstalled. This is both useful and dangerous, " + "like rm -r.") + subparser.add_argument( '-d', '--dependents', action='store_true', dest='dependents', - help='Also uninstall any packages that depend on the ones given via command line.' # NOQA: ignore=E501 - ) + help='Also uninstall any packages that depend on the ones given ' + 'via command line.') + subparser.add_argument( '-y', '--yes-to-all', action='store_true', dest='yes_to_all', - help='Assume "yes" is the answer to every confirmation asked to the user.' # NOQA: ignore=E501 + help='Assume "yes" is the answer to every confirmation requested') - ) subparser.add_argument( 'packages', nargs=argparse.REMAINDER, - help="specs of packages to uninstall" - ) + help="specs of packages to uninstall") def concretize_specs(specs, allow_multiple_matches=False, force=False): @@ -184,7 +186,8 @@ def uninstall(parser, args): uninstall_list = list(set(uninstall_list)) if has_error: - tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well') # NOQA: ignore=E501 + tty.die('You can use spack uninstall --dependents ' + 'to uninstall these dependencies as well') if not args.yes_to_all: tty.msg("The following packages will be uninstalled : ") diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py index 7bd15750ed..b52bedb7b4 100644 --- a/lib/spack/spack/cmd/unload.py +++ b/lib/spack/spack/cmd/unload.py @@ -25,13 +25,15 @@ import argparse import spack.modules -description ="Remove package from environment using module." +description = "Remove package from environment using module." + def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help='Spec of package to unload with modules.') + 'spec', nargs=argparse.REMAINDER, + help='Spec of package to unload with modules.') def unload(parser, args): diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py index 789a690e9c..6403cf6162 100644 --- a/lib/spack/spack/cmd/unuse.py +++ b/lib/spack/spack/cmd/unuse.py @@ -25,13 +25,15 @@ import argparse import spack.modules -description ="Remove package from environment using dotkit." +description = "Remove package from environment using dotkit." + def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help='Spec of package to unuse with dotkit.') + 'spec', nargs=argparse.REMAINDER, + help='Spec of package to unuse with dotkit.') def unuse(parser, args): diff --git a/lib/spack/spack/cmd/url-parse.py b/lib/spack/spack/cmd/url-parse.py index ce12a17d13..b8c7c95040 100644 --- a/lib/spack/spack/cmd/url-parse.py +++ b/lib/spack/spack/cmd/url-parse.py @@ -22,28 +22,28 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import sys - import llnl.util.tty as tty import spack import spack.url from spack.util.web import find_versions_of_archive -description = "Show parsing of a URL, optionally spider web for other versions." +description = "Show parsing of a URL, optionally spider web for versions." + def setup_parser(subparser): subparser.add_argument('url', help="url of a package archive") subparser.add_argument( - '-s', '--spider', action='store_true', help="Spider the source page for versions.") + '-s', '--spider', action='store_true', + help="Spider the source page for versions.") def print_name_and_version(url): name, ns, nl, ntup, ver, vs, vl, vtup = spack.url.substitution_offsets(url) - underlines = [" "] * max(ns+nl, vs+vl) - for i in range(ns, ns+nl): + underlines = [" "] * max(ns + nl, vs + vl) + for i in range(ns, ns + nl): underlines[i] = '-' - for i in range(vs, vs+vl): + for i in range(vs, vs + vl): underlines[i] = '~' print " %s" % url diff --git a/lib/spack/spack/cmd/urls.py b/lib/spack/spack/cmd/urls.py index 2fe2019a22..f151581d7d 100644 --- a/lib/spack/spack/cmd/urls.py +++ b/lib/spack/spack/cmd/urls.py @@ -22,12 +22,12 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import sys import spack import spack.url description = "Inspect urls used by packages in spack." + def setup_parser(subparser): subparser.add_argument( '-c', '--color', action='store_true', @@ -53,6 +53,7 @@ def urls(parser, args): for url in sorted(urls): if args.color or args.extrapolation: - print spack.url.color_url(url, subs=args.extrapolation, errors=True) + print spack.url.color_url( + url, subs=args.extrapolation, errors=True) else: print url diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py index bbb90fde1b..e3612ace48 100644 --- a/lib/spack/spack/cmd/use.py +++ b/lib/spack/spack/cmd/use.py @@ -25,13 +25,15 @@ import argparse import spack.modules -description ="Add package to environment using dotkit." +description = "Add package to environment using dotkit." + def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help='Spec of package to use with dotkit.') + 'spec', nargs=argparse.REMAINDER, + help='Spec of package to use with dotkit.') def use(parser, args): diff --git a/lib/spack/spack/cmd/versions.py b/lib/spack/spack/cmd/versions.py index ec3a4b2e34..1e95225ab8 100644 --- a/lib/spack/spack/cmd/versions.py +++ b/lib/spack/spack/cmd/versions.py @@ -22,15 +22,16 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from llnl.util.tty.colify import colify import llnl.util.tty as tty import spack -description ="List available versions of a package" +description = "List available versions of a package" + def setup_parser(subparser): - subparser.add_argument('package', metavar='PACKAGE', help='Package to list versions for') + subparser.add_argument('package', metavar='PACKAGE', + help='Package to list versions for') def versions(parser, args): diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py index ce4555bc56..a77991e4dc 100644 --- a/lib/spack/spack/compiler.py +++ b/lib/spack/spack/compiler.py @@ -25,10 +25,8 @@ import os import re import itertools -from datetime import datetime import llnl.util.tty as tty -from llnl.util.lang import memoized from llnl.util.filesystem import join_path import spack.error @@ -37,10 +35,10 @@ import spack.architecture from spack.util.multiproc import parmap from spack.util.executable import * from spack.util.environment import get_path -from spack.version import Version __all__ = ['Compiler', 'get_compiler_version'] + def _verify_executables(*paths): for path in paths: if not os.path.isfile(path) and os.access(path, os.X_OK): @@ -49,8 +47,9 @@ def _verify_executables(*paths): _version_cache = {} + def get_compiler_version(compiler_path, version_arg, regex='(.*)'): - if not compiler_path in _version_cache: + if compiler_path not in _version_cache: compiler = Executable(compiler_path) output = compiler(version_arg, output=str, error=str) @@ -113,7 +112,7 @@ class Compiler(object): # Name of module used to switch versions of this compiler PrgEnv_compiler = None - def __init__(self, cspec, operating_system, + def __init__(self, cspec, operating_system, paths, modules=[], alias=None, **kwargs): def check(exe): if exe is None: @@ -130,11 +129,6 @@ class Compiler(object): else: self.fc = check(paths[3]) - #self.cc = check(cc) - #self.cxx = check(cxx) - #self.f77 = check(f77) - #self.fc = check(fc) - # Unfortunately have to make sure these params are accepted # in the same order they are returned by sorted(flags) # in compilers/__init__.py @@ -158,31 +152,30 @@ class Compiler(object): @property def openmp_flag(self): # If it is not overridden, assume it is not supported and warn the user - tty.die("The compiler you have chosen does not currently support OpenMP.", - "If you think it should, please edit the compiler subclass and", - "submit a pull request or issue.") - + tty.die( + "The compiler you have chosen does not currently support OpenMP.", + "If you think it should, please edit the compiler subclass and", + "submit a pull request or issue.") # This property should be overridden in the compiler subclass if # C++11 is supported by that compiler @property def cxx11_flag(self): # If it is not overridden, assume it is not supported and warn the user - tty.die("The compiler you have chosen does not currently support C++11.", - "If you think it should, please edit the compiler subclass and", - "submit a pull request or issue.") - + tty.die( + "The compiler you have chosen does not currently support C++11.", + "If you think it should, please edit the compiler subclass and", + "submit a pull request or issue.") # This property should be overridden in the compiler subclass if # C++14 is supported by that compiler @property def cxx14_flag(self): # If it is not overridden, assume it is not supported and warn the user - tty.die("The compiler you have chosen does not currently support C++14.", - "If you think it should, please edit the compiler subclass and", - "submit a pull request or issue.") - - + tty.die( + "The compiler you have chosen does not currently support C++14.", + "If you think it should, please edit the compiler subclass and", + "submit a pull request or issue.") # # Compiler classes have methods for querying the version of @@ -191,7 +184,6 @@ class Compiler(object): # Compiler *instances* are just data objects, and can only be # constructed from an actual set of executables. # - @classmethod def default_version(cls, cc): """Override just this to override all compiler version functions.""" @@ -258,16 +250,19 @@ class Compiler(object): version = detect_version(full_path) return (version, prefix, suffix, full_path) except ProcessError, e: - tty.debug("Couldn't get version for compiler %s" % full_path, e) + tty.debug( + "Couldn't get version for compiler %s" % full_path, e) return None except Exception, e: # Catching "Exception" here is fine because it just # means something went wrong running a candidate executable. - tty.debug("Error while executing candidate compiler %s" % full_path, - "%s: %s" %(e.__class__.__name__, e)) + tty.debug("Error while executing candidate compiler %s" + % full_path, + "%s: %s" % (e.__class__.__name__, e)) return None - successful = [key for key in parmap(check, checks) if key is not None] + successful = [k for k in parmap(check, checks) if k is not None] + # The 'successful' list is ordered like the input paths. # Reverse it here so that the dict creation (last insert wins) # does not spoil the intented precedence. @@ -278,20 +273,23 @@ class Compiler(object): """Return a string representation of the compiler toolchain.""" return self.__str__() - def __str__(self): """Return a string representation of the compiler toolchain.""" return "%s(%s)" % ( - self.name, '\n '.join((str(s) for s in (self.cc, self.cxx, self.f77, self.fc, self.modules, str(self.operating_system))))) + self.name, '\n '.join((str(s) for s in ( + self.cc, self.cxx, self.f77, self.fc, self.modules, + str(self.operating_system))))) class CompilerAccessError(spack.error.SpackError): + def __init__(self, path): super(CompilerAccessError, self).__init__( "'%s' is not a valid compiler." % path) class InvalidCompilerError(spack.error.SpackError): + def __init__(self): super(InvalidCompilerError, self).__init__( "Compiler has no executables.") diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py index 0ba94741da..eb866c8bbb 100644 --- a/lib/spack/spack/compilers/__init__.py +++ b/lib/spack/spack/compilers/__init__.py @@ -26,15 +26,9 @@ system and configuring Spack to use multiple compilers. """ import imp -import os import platform -import copy -import hashlib -import base64 -import yaml -import sys -from llnl.util.lang import memoized, list_modules +from llnl.util.lang import list_modules from llnl.util.filesystem import join_path import spack @@ -43,11 +37,7 @@ import spack.spec import spack.config import spack.architecture -from spack.util.multiproc import parmap -from spack.compiler import Compiler -from spack.util.executable import which from spack.util.naming import mod_to_class -from spack.util.environment import get_path _imported_compilers_module = 'spack.compilers' _path_instance_vars = ['cc', 'cxx', 'f77', 'fc'] @@ -73,7 +63,8 @@ def _to_dict(compiler): """Return a dict version of compiler suitable to insert in YAML.""" d = {} d['spec'] = str(compiler.spec) - d['paths'] = dict( (attr, getattr(compiler, attr, None)) for attr in _path_instance_vars ) + d['paths'] = dict((attr, getattr(compiler, attr, None)) + for attr in _path_instance_vars) d['operating_system'] = str(compiler.operating_system) d['modules'] = compiler.modules if compiler.modules else [] @@ -140,15 +131,19 @@ def remove_compiler_from_config(compiler_spec, scope=None): - compiler_specs: a list of CompilerSpec objects. - scope: configuration scope to modify. """ + # Need a better way for this + global _cache_config_file + compiler_config = get_compiler_config(scope) config_length = len(compiler_config) - filtered_compiler_config = [comp for comp in compiler_config - if spack.spec.CompilerSpec(comp['compiler']['spec']) != compiler_spec] - # Need a better way for this - global _cache_config_file - _cache_config_file = filtered_compiler_config # Update the cache for changes - if len(filtered_compiler_config) == config_length: # No items removed + filtered_compiler_config = [ + comp for comp in compiler_config + if spack.spec.CompilerSpec(comp['compiler']['spec']) != compiler_spec] + + # Update the cache for changes + _cache_config_file = filtered_compiler_config + if len(filtered_compiler_config) == config_length: # No items removed CompilerSpecInsufficientlySpecificError(compiler_spec) spack.config.update_config('compilers', filtered_compiler_config, scope) @@ -158,7 +153,8 @@ def all_compilers_config(scope=None, init_config=True): available to build with. These are instances of CompilerSpec. """ # Get compilers for this architecture. - global _cache_config_file #Create a cache of the config file so we don't load all the time. + # Create a cache of the config file so we don't load all the time. + global _cache_config_file if not _cache_config_file: _cache_config_file = get_compiler_config(scope, init_config) return _cache_config_file @@ -236,7 +232,8 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs): continue items = items['compiler'] - if not ('paths' in items and all(n in items['paths'] for n in _path_instance_vars)): + if not ('paths' in items and + all(n in items['paths'] for n in _path_instance_vars)): raise InvalidCompilerConfigurationError(cspec) cls = class_for_compiler_name(cspec.name) @@ -254,10 +251,10 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs): mods = [] if 'operating_system' in items: - operating_system = spack.architecture._operating_system_from_dict(items['operating_system'], platform) + os = spack.architecture._operating_system_from_dict( + items['operating_system'], platform) else: - operating_system = None - + os = None alias = items['alias'] if 'alias' in items else None @@ -266,7 +263,8 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs): if f in items: flags[f] = items[f] - compilers.append(cls(cspec, operating_system, compiler_paths, mods, alias, **flags)) + compilers.append( + cls(cspec, os, compiler_paths, mods, alias, **flags)) return compilers @@ -275,7 +273,6 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs): for cspec in matches: compilers.extend(get_compilers(cspec)) return compilers -# return [get_compilers(cspec) for cspec in matches] @_auto_compiler_spec @@ -285,8 +282,9 @@ def compiler_for_spec(compiler_spec, arch): operating_system = arch.platform_os assert(compiler_spec.concrete) - compilers = [c for c in compilers_for_spec(compiler_spec, platform=arch.platform) - if c.operating_system == operating_system] + compilers = [ + c for c in compilers_for_spec(compiler_spec, platform=arch.platform) + if c.operating_system == operating_system] if len(compilers) < 1: raise NoCompilerForSpecError(compiler_spec, operating_system) if len(compilers) > 1: @@ -321,11 +319,13 @@ def all_os_classes(): return classes + def all_compiler_types(): return [class_for_compiler_name(c) for c in supported_compilers()] class InvalidCompilerConfigurationError(spack.error.SpackError): + def __init__(self, compiler_spec): super(InvalidCompilerConfigurationError, self).__init__( "Invalid configuration for [compiler \"%s\"]: " % compiler_spec, @@ -335,14 +335,18 @@ class InvalidCompilerConfigurationError(spack.error.SpackError): class NoCompilersError(spack.error.SpackError): def __init__(self): - super(NoCompilersError, self).__init__("Spack could not find any compilers!") + super(NoCompilersError, self).__init__( + "Spack could not find any compilers!") + class NoCompilerForSpecError(spack.error.SpackError): def __init__(self, compiler_spec, target): - super(NoCompilerForSpecError, self).__init__("No compilers for operating system %s satisfy spec %s" % ( - target, compiler_spec)) + super(NoCompilerForSpecError, self).__init__( + "No compilers for operating system %s satisfy spec %s" + % (target, compiler_spec)) + class CompilerSpecInsufficientlySpecificError(spack.error.SpackError): def __init__(self, compiler_spec): - super(CompilerSpecInsufficientlySpecificError, self).__init__("Multiple compilers satisfy spec %s", - compiler_spec) + super(CompilerSpecInsufficientlySpecificError, self).__init__( + "Multiple compilers satisfy spec %s" % compiler_spec) diff --git a/lib/spack/spack/compilers/craype.py b/lib/spack/spack/compilers/cce.py index 4ba8b110ec..43d000dd69 100644 --- a/lib/spack/spack/compilers/craype.py +++ b/lib/spack/spack/compilers/cce.py @@ -1,34 +1,32 @@ -##############################################################################} -# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. # # This file is part of Spack. -# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. # LLNL-CODE-647188 # -# For details, see https://scalability-llnl.github.io/spack +# For details, see https://github.com/llnl/spack # Please also see the LICENSE file for our notice and the LGPL. # # This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License (as published by -# the Free Software Foundation) version 2.1 dated February 1999. +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU General Public License for more details. +# conditions of the GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU Lesser General Public License -# along with this program; if not, write to the Free Software Foundation, -# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import llnl.util.tty as tty - -#from spack.build_environment import load_module from spack.compiler import * -#from spack.version import ver -class Craype(Compiler): + +class Cce(Compiler): + """Cray compiler environment compiler.""" # Subclasses use possible names of C compiler cc_names = ['cc'] @@ -45,14 +43,13 @@ class Craype(Compiler): suffixes = [r'-mp-\d\.\d'] PrgEnv = 'PrgEnv-cray' - PrgEnv_compiler = 'craype' + PrgEnv_compiler = 'cce' + + link_paths = {'cc': 'cc', + 'cxx': 'c++', + 'f77': 'f77', + 'fc': 'fc'} - link_paths = { 'cc' : 'cc', - 'cxx' : 'c++', - 'f77' : 'f77', - 'fc' : 'fc'} - @classmethod def default_version(cls, comp): - return get_compiler_version(comp, r'([Vv]ersion).*(\d+(\.\d+)+)') - + return get_compiler_version(comp, '-V', r'[Vv]ersion.*(\d+(\.\d+)+)') diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py index 00b406d820..4cf65222ae 100644 --- a/lib/spack/spack/compilers/clang.py +++ b/lib/spack/spack/compilers/clang.py @@ -29,6 +29,7 @@ from spack.util.executable import * import llnl.util.tty as tty from spack.version import ver + class Clang(Compiler): # Subclasses use possible names of C compiler cc_names = ['clang'] @@ -43,11 +44,12 @@ class Clang(Compiler): fc_names = [] # Named wrapper links within spack.build_env_path - link_paths = { 'cc' : 'clang/clang', - 'cxx' : 'clang/clang++', - # Use default wrappers for fortran, in case provided in compilers.yaml - 'f77' : 'f77', - 'fc' : 'f90' } + link_paths = {'cc': 'clang/clang', + 'cxx': 'clang/clang++', + # Use default wrappers for fortran, in case provided in + # compilers.yaml + 'f77': 'f77', + 'fc': 'f90'} @property def is_apple(self): diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py index 2fae6688db..a556f346d7 100644 --- a/lib/spack/spack/compilers/gcc.py +++ b/lib/spack/spack/compilers/gcc.py @@ -26,6 +26,7 @@ import llnl.util.tty as tty from spack.compiler import * from spack.version import ver + class Gcc(Compiler): # Subclasses use possible names of C compiler cc_names = ['gcc'] @@ -44,10 +45,10 @@ class Gcc(Compiler): suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d'] # Named wrapper links within spack.build_env_path - link_paths = {'cc' : 'gcc/gcc', - 'cxx' : 'gcc/g++', - 'f77' : 'gcc/gfortran', - 'fc' : 'gcc/gfortran' } + link_paths = {'cc': 'gcc/gcc', + 'cxx': 'gcc/g++', + 'f77': 'gcc/gfortran', + 'fc': 'gcc/gfortran'} PrgEnv = 'PrgEnv-gnu' PrgEnv_compiler = 'gcc' @@ -79,7 +80,6 @@ class Gcc(Compiler): # older gfortran versions don't have simple dumpversion output. r'(?:GNU Fortran \(GCC\))?(\d+\.\d+(?:\.\d+)?)') - @classmethod def f77_version(cls, f77): return cls.fc_version(f77) diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py index 6cad03ff47..8531ecd19a 100644 --- a/lib/spack/spack/compilers/intel.py +++ b/lib/spack/spack/compilers/intel.py @@ -26,6 +26,7 @@ from spack.compiler import * import llnl.util.tty as tty from spack.version import ver + class Intel(Compiler): # Subclasses use possible names of C compiler cc_names = ['icc'] @@ -40,10 +41,10 @@ class Intel(Compiler): fc_names = ['ifort'] # Named wrapper links within spack.build_env_path - link_paths = { 'cc' : 'intel/icc', - 'cxx' : 'intel/icpc', - 'f77' : 'intel/ifort', - 'fc' : 'intel/ifort' } + link_paths = {'cc': 'intel/icc', + 'cxx': 'intel/icpc', + 'f77': 'intel/ifort', + 'fc': 'intel/ifort'} PrgEnv = 'PrgEnv-intel' PrgEnv_compiler = 'intel' @@ -64,7 +65,6 @@ class Intel(Compiler): else: return "-std=c++11" - @classmethod def default_version(cls, comp): """The '--version' option seems to be the most consistent one diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py index cee11bc97a..fdfc078b5e 100644 --- a/lib/spack/spack/compilers/nag.py +++ b/lib/spack/spack/compilers/nag.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack.compiler import * -import llnl.util.tty as tty + class Nag(Compiler): # Subclasses use possible names of C compiler @@ -39,11 +39,12 @@ class Nag(Compiler): fc_names = ['nagfor'] # Named wrapper links within spack.build_env_path - link_paths = { # Use default wrappers for C and C++, in case provided in compilers.yaml - 'cc' : 'cc', - 'cxx' : 'c++', - 'f77' : 'nag/nagfor', - 'fc' : 'nag/nagfor' } + # Use default wrappers for C and C++, in case provided in compilers.yaml + link_paths = { + 'cc': 'cc', + 'cxx': 'c++', + 'f77': 'nag/nagfor', + 'fc': 'nag/nagfor'} @property def openmp_flag(self): @@ -71,9 +72,8 @@ class Nag(Compiler): """The '-V' option works for nag compilers. Output looks like this:: - NAG Fortran Compiler Release 6.0(Hibiya) Build 1037 - Product NPL6A60NA for x86-64 Linux - Copyright 1990-2015 The Numerical Algorithms Group Ltd., Oxford, U.K. + NAG Fortran Compiler Release 6.0(Hibiya) Build 1037 + Product NPL6A60NA for x86-64 Linux """ return get_compiler_version( comp, '-V', r'NAG Fortran Compiler Release ([0-9.]+)') diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py index 6d36d8bfa6..0e4be6e9ba 100644 --- a/lib/spack/spack/compilers/pgi.py +++ b/lib/spack/spack/compilers/pgi.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack.compiler import * -import llnl.util.tty as tty + class Pgi(Compiler): # Subclasses use possible names of C compiler @@ -39,17 +39,14 @@ class Pgi(Compiler): fc_names = ['pgfortran', 'pgf95', 'pgf90'] # Named wrapper links within spack.build_env_path - link_paths = { 'cc' : 'pgi/pgcc', - 'cxx' : 'pgi/pgc++', - 'f77' : 'pgi/pgfortran', - 'fc' : 'pgi/pgfortran' } - - + link_paths = {'cc': 'pgi/pgcc', + 'cxx': 'pgi/pgc++', + 'f77': 'pgi/pgfortran', + 'fc': 'pgi/pgfortran'} PrgEnv = 'PrgEnv-pgi' PrgEnv_compiler = 'pgi' - @property def openmp_flag(self): return "-mp" diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py index b1431436ad..5c83209781 100644 --- a/lib/spack/spack/compilers/xl.py +++ b/lib/spack/spack/compilers/xl.py @@ -26,24 +26,26 @@ from spack.compiler import * import llnl.util.tty as tty from spack.version import ver + class Xl(Compiler): # Subclasses use possible names of C compiler - cc_names = ['xlc','xlc_r'] + cc_names = ['xlc', 'xlc_r'] # Subclasses use possible names of C++ compiler - cxx_names = ['xlC','xlC_r','xlc++','xlc++_r'] + cxx_names = ['xlC', 'xlC_r', 'xlc++', 'xlc++_r'] # Subclasses use possible names of Fortran 77 compiler - f77_names = ['xlf','xlf_r'] + f77_names = ['xlf', 'xlf_r'] # Subclasses use possible names of Fortran 90 compiler - fc_names = ['xlf90','xlf90_r','xlf95','xlf95_r','xlf2003','xlf2003_r','xlf2008','xlf2008_r'] + fc_names = ['xlf90', 'xlf90_r', 'xlf95', 'xlf95_r', + 'xlf2003', 'xlf2003_r', 'xlf2008', 'xlf2008_r'] # Named wrapper links within spack.build_env_path - link_paths = { 'cc' : 'xl/xlc', - 'cxx' : 'xl/xlc++', - 'f77' : 'xl/xlf', - 'fc' : 'xl/xlf90' } + link_paths = {'cc': 'xl/xlc', + 'cxx': 'xl/xlc++', + 'f77': 'xl/xlf', + 'fc': 'xl/xlf90'} @property def openmp_flag(self): @@ -56,7 +58,6 @@ class Xl(Compiler): else: return "-qlanglvl=extended0x" - @classmethod def default_version(cls, comp): """The '-qversion' is the standard option fo XL compilers. @@ -82,29 +83,28 @@ class Xl(Compiler): """ return get_compiler_version( - comp, '-qversion',r'([0-9]?[0-9]\.[0-9])') - + comp, '-qversion', r'([0-9]?[0-9]\.[0-9])') @classmethod def fc_version(cls, fc): - """The fortran and C/C++ versions of the XL compiler are always two units apart. - By this we mean that the fortran release that goes with XL C/C++ 11.1 is 13.1. - Having such a difference in version number is confusing spack quite a lot. - Most notably if you keep the versions as is the default xl compiler will only - have fortran and no C/C++. - So we associate the Fortran compiler with the version associated to the C/C++ - compiler. - One last stumble. Version numbers over 10 have at least a .1 those under 10 - a .0. There is no xlf 9.x or under currently available. BG/P and BG/L can - such a compiler mix and possibly older version of AIX and linux on power. + """The fortran and C/C++ versions of the XL compiler are always + two units apart. By this we mean that the fortran release that + goes with XL C/C++ 11.1 is 13.1. Having such a difference in + version number is confusing spack quite a lot. Most notably + if you keep the versions as is the default xl compiler will + only have fortran and no C/C++. So we associate the Fortran + compiler with the version associated to the C/C++ compiler. + One last stumble. Version numbers over 10 have at least a .1 + those under 10 a .0. There is no xlf 9.x or under currently + available. BG/P and BG/L can such a compiler mix and possibly + older version of AIX and linux on power. """ - fver = get_compiler_version(fc, '-qversion',r'([0-9]?[0-9]\.[0-9])') + fver = get_compiler_version(fc, '-qversion', r'([0-9]?[0-9]\.[0-9])') cver = float(fver) - 2 - if cver < 10 : - cver = cver - 0.1 + if cver < 10: + cver = cver - 0.1 return str(cver) - @classmethod def f77_version(cls, f77): return cls.fc_version(f77) diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py index 5180f3cf04..726dee62e3 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -61,7 +61,9 @@ class DefaultConcretizer(object): if not providers: raise UnsatisfiableProviderSpecError(providers[0], spec) spec_w_preferred_providers = find_spec( - spec, lambda x: spack.pkgsort.spec_has_preferred_provider(x.name, spec.name)) # NOQA: ignore=E501 + spec, + lambda x: spack.pkgsort.spec_has_preferred_provider( + x.name, spec.name)) if not spec_w_preferred_providers: spec_w_preferred_providers = spec provider_cmp = partial(spack.pkgsort.provider_compare, @@ -336,14 +338,18 @@ class DefaultConcretizer(object): spack.pkgsort.compiler_compare, other_spec.name) matches = sorted(compiler_list, cmp=cmp_compilers) if not matches: - raise UnavailableCompilerVersionError(other_compiler) + arch = spec.architecture + raise UnavailableCompilerVersionError(other_compiler, + arch.platform_os) # copy concrete version into other_compiler index = 0 while not _proper_compiler_style(matches[index], spec.architecture): index += 1 if index == len(matches) - 1: - raise NoValidVersionError(spec) + arch = spec.architecture + raise UnavailableCompilerVersionError(spec.compiler, + arch.platform_os) spec.compiler = matches[index].copy() assert(spec.compiler.concrete) return True # things changed. @@ -489,9 +495,10 @@ class UnavailableCompilerVersionError(spack.error.SpackError): """Raised when there is no available compiler that satisfies a compiler spec.""" - def __init__(self, compiler_spec): + def __init__(self, compiler_spec, operating_system): super(UnavailableCompilerVersionError, self).__init__( - "No available compiler version matches '%s'" % compiler_spec, + "No available compiler version matches '%s' on operating_system %s" + % (compiler_spec, operating_system), "Run 'spack compilers' to see available compiler Options.") @@ -502,14 +509,15 @@ class NoValidVersionError(spack.error.SpackError): def __init__(self, spec): super(NoValidVersionError, self).__init__( - "There are no valid versions for %s that match '%s'" % (spec.name, spec.versions)) # NOQA: ignore=E501 + "There are no valid versions for %s that match '%s'" + % (spec.name, spec.versions)) class NoBuildError(spack.error.SpackError): - """Raised when a package is configured with the buildable option False, but no satisfactory external versions can be found""" def __init__(self, spec): - super(NoBuildError, self).__init__( - "The spec '%s' is configured as not buildable,and no matching external installs were found" % spec.name) # NOQA: ignore=E501 + msg = ("The spec '%s' is configured as not buildable, " + "and no matching external installs were found") + super(NoBuildError, self).__init__(msg % spec.name) diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index e2e7dbc0ee..c90eff4229 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -1,4 +1,3 @@ -# flake8: noqa ############################################################################## # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. @@ -123,15 +122,18 @@ import os import re import sys -import jsonschema -import llnl.util.tty as tty -import spack import yaml +import jsonschema +from yaml.error import MarkedYAMLError from jsonschema import Draft4Validator, validators -from llnl.util.filesystem import mkdirp from ordereddict_backport import OrderedDict + +import llnl.util.tty as tty +from llnl.util.filesystem import mkdirp + +import spack from spack.error import SpackError -from yaml.error import MarkedYAMLError +import spack.schema # Hacked yaml for configuration files preserves line numbers. import spack.util.spack_yaml as syaml @@ -139,257 +141,12 @@ from spack.build_environment import get_path_from_module """Dict from section names -> schema for that section.""" section_schemas = { - 'compilers': { - '$schema': 'http://json-schema.org/schema#', - 'title': 'Spack compiler configuration file schema', - 'type': 'object', - 'additionalProperties': False, - 'patternProperties': { - 'compilers:?': { # optional colon for overriding site config. - 'type': 'array', - 'items': { - 'compiler': { - 'type': 'object', - 'additionalProperties': False, - 'required': ['paths', 'spec', 'modules', 'operating_system'], - 'properties': { - 'paths': { - 'type': 'object', - 'required': ['cc', 'cxx', 'f77', 'fc'], - 'additionalProperties': False, - 'properties': { - 'cc': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'cxx': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'f77': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'fc': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'cflags': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'cxxflags': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'fflags': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'cppflags': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'ldflags': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}, - 'ldlibs': { 'anyOf': [ {'type' : 'string' }, - {'type' : 'null' }]}}}, - 'spec': { 'type': 'string'}, - 'operating_system': { 'type': 'string'}, - 'alias': { 'anyOf': [ {'type' : 'string'}, - {'type' : 'null' }]}, - 'modules': { 'anyOf': [ {'type' : 'string'}, - {'type' : 'null' }, - {'type': 'array'}, - ]} - },},},},},}, - 'mirrors': { - '$schema': 'http://json-schema.org/schema#', - 'title': 'Spack mirror configuration file schema', - 'type': 'object', - 'additionalProperties': False, - 'patternProperties': { - r'mirrors:?': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'patternProperties': { - r'\w[\w-]*': { - 'type': 'string'},},},},}, - - 'repos': { - '$schema': 'http://json-schema.org/schema#', - 'title': 'Spack repository configuration file schema', - 'type': 'object', - 'additionalProperties': False, - 'patternProperties': { - r'repos:?': { - 'type': 'array', - 'default': [], - 'items': { - 'type': 'string'},},},}, - 'packages': { - '$schema': 'http://json-schema.org/schema#', - 'title': 'Spack package configuration file schema', - 'type': 'object', - 'additionalProperties': False, - 'patternProperties': { - r'packages:?': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'patternProperties': { - r'\w[\w-]*': { # package name - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'version': { - 'type' : 'array', - 'default' : [], - 'items' : { 'anyOf' : [ { 'type' : 'string' }, - { 'type' : 'number'}]}}, #version strings - 'compiler': { - 'type' : 'array', - 'default' : [], - 'items' : { 'type' : 'string' } }, #compiler specs - 'buildable': { - 'type': 'boolean', - 'default': True, - }, - 'modules': { - 'type' : 'object', - 'default' : {}, - }, - 'providers': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'patternProperties': { - r'\w[\w-]*': { - 'type' : 'array', - 'default' : [], - 'items' : { 'type' : 'string' },},},}, - 'paths': { - 'type' : 'object', - 'default' : {}, - }, - 'variants': { - 'oneOf' : [ - { 'type' : 'string' }, - { 'type' : 'array', - 'items' : { 'type' : 'string' } }, - ], }, - },},},},},}, - - 'modules': { - '$schema': 'http://json-schema.org/schema#', - 'title': 'Spack module file configuration file schema', - 'type': 'object', - 'additionalProperties': False, - 'definitions': { - 'array_of_strings': { - 'type': 'array', - 'default': [], - 'items': { - 'type': 'string' - } - }, - 'dictionary_of_strings': { - 'type': 'object', - 'patternProperties': { - r'\w[\w-]*': { # key - 'type': 'string' - } - } - }, - 'dependency_selection': { - 'type': 'string', - 'enum': ['none', 'direct', 'all'] - }, - 'module_file_configuration': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'filter': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'environment_blacklist': { - 'type': 'array', - 'default': [], - 'items': { - 'type': 'string' - } - } - } - }, - 'autoload': {'$ref': '#/definitions/dependency_selection'}, - 'prerequisites': {'$ref': '#/definitions/dependency_selection'}, - 'conflict': {'$ref': '#/definitions/array_of_strings'}, - 'load': {'$ref': '#/definitions/array_of_strings'}, - 'suffixes': {'$ref': '#/definitions/dictionary_of_strings'}, - 'environment': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'set': {'$ref': '#/definitions/dictionary_of_strings'}, - 'unset': {'$ref': '#/definitions/array_of_strings'}, - 'prepend_path': {'$ref': '#/definitions/dictionary_of_strings'}, - 'append_path': {'$ref': '#/definitions/dictionary_of_strings'} - } - } - } - }, - 'module_type_configuration': { - 'type': 'object', - 'default': {}, - 'anyOf': [ - { - 'properties': { - 'hash_length': { - 'type': 'integer', - 'minimum': 0, - 'default': 7 - }, - 'whitelist': {'$ref': '#/definitions/array_of_strings'}, - 'blacklist': {'$ref': '#/definitions/array_of_strings'}, - 'naming_scheme': { - 'type': 'string' # Can we be more specific here? - } - } - }, - { - 'patternProperties': {r'\w[\w-]*': {'$ref': '#/definitions/module_file_configuration'}} - } - ] - } - }, - 'patternProperties': { - r'modules:?': { - 'type': 'object', - 'default': {}, - 'additionalProperties': False, - 'properties': { - 'prefix_inspections': { - 'type': 'object', - 'patternProperties': { - r'\w[\w-]*': { # path to be inspected for existence (relative to prefix) - '$ref': '#/definitions/array_of_strings' - } - } - }, - 'enable': { - 'type': 'array', - 'default': [], - 'items': { - 'type': 'string', - 'enum': ['tcl', 'dotkit'] - } - }, - 'tcl': { - 'allOf': [ - {'$ref': '#/definitions/module_type_configuration'}, # Base configuration - {} # Specific tcl extensions - ] - }, - 'dotkit': { - 'allOf': [ - {'$ref': '#/definitions/module_type_configuration'}, # Base configuration - {} # Specific dotkit extensions - ] - }, - } - }, - }, - }, + 'compilers': spack.schema.compilers.schema, + 'mirrors': spack.schema.mirrors.schema, + 'repos': spack.schema.repos.schema, + 'packages': spack.schema.packages.schema, + 'targets': spack.schema.targets.schema, + 'modules': spack.schema.modules.schema, } """OrderedDict of config scopes keyed by name. @@ -406,7 +163,7 @@ def validate_section_name(section): def extend_with_default(validator_class): - """Add support for the 'default' attribute for properties and patternProperties. + """Add support for the 'default' attr for properties and patternProperties. jsonschema does not handle this out of the box -- it only validates. This allows us to set default values for configs @@ -415,13 +172,15 @@ def extend_with_default(validator_class): """ validate_properties = validator_class.VALIDATORS["properties"] - validate_pattern_properties = validator_class.VALIDATORS["patternProperties"] + validate_pattern_properties = validator_class.VALIDATORS[ + "patternProperties"] def set_defaults(validator, properties, instance, schema): for property, subschema in properties.iteritems(): if "default" in subschema: instance.setdefault(property, subschema["default"]) - for err in validate_properties(validator, properties, instance, schema): + for err in validate_properties( + validator, properties, instance, schema): yield err def set_pp_defaults(validator, properties, instance, schema): @@ -432,7 +191,8 @@ def extend_with_default(validator_class): if re.match(property, key) and val is None: instance[key] = subschema["default"] - for err in validate_pattern_properties(validator, properties, instance, schema): + for err in validate_pattern_properties( + validator, properties, instance, schema): yield err return validators.extend(validator_class, { @@ -497,7 +257,8 @@ class ConfigScope(object): except jsonschema.ValidationError as e: raise ConfigSanityError(e, data) except (yaml.YAMLError, IOError) as e: - raise ConfigFileError("Error writing to config file: '%s'" % str(e)) + raise ConfigFileError( + "Error writing to config file: '%s'" % str(e)) def clear(self): """Empty cached config information.""" @@ -512,7 +273,7 @@ ConfigScope('defaults', os.path.join(spack.etc_path, 'spack', 'defaults')) ConfigScope('site', os.path.join(spack.etc_path, 'spack')) """User configuration can override both spack defaults and site config.""" -ConfigScope('user', os.path.expanduser('~/.spack')) +ConfigScope('user', spack.user_config_path) def highest_precedence_scope(): @@ -695,7 +456,7 @@ def print_section(section): data = syaml.syaml_dict() data[section] = get_config(section) syaml.dump(data, stream=sys.stdout, default_flow_style=False) - except (yaml.YAMLError, IOError) as e: + except (yaml.YAMLError, IOError): raise ConfigError("Error reading configuration: %s" % section) @@ -726,7 +487,8 @@ def spec_externals(spec): path = get_path_from_module(module) - external_spec = spack.spec.Spec(external_spec, external=path, external_module=module) + external_spec = spack.spec.Spec( + external_spec, external=path, external_module=module) if external_spec.satisfies(spec): external_specs.append(external_spec) @@ -760,6 +522,7 @@ def get_path(path, data): class ConfigFormatError(ConfigError): """Raised when a configuration format does not match its schema.""" + def __init__(self, validation_error, data): # Try to get line number from erroneous instance and its parent instance_mark = getattr(validation_error.instance, '_start_mark', None) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 317b0d5784..f3dcdef0a9 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -119,6 +119,7 @@ class InstallRecord(object): class Database(object): + def __init__(self, root, db_dir=None): """Create a Database for Spack installations under ``root``. @@ -165,11 +166,11 @@ class Database(object): def write_transaction(self, timeout=_db_lock_timeout): """Get a write lock context manager for use in a `with` block.""" - return WriteTransaction(self, self._read, self._write, timeout) + return WriteTransaction(self.lock, self._read, self._write, timeout) def read_transaction(self, timeout=_db_lock_timeout): """Get a read lock context manager for use in a `with` block.""" - return ReadTransaction(self, self._read, None, timeout) + return ReadTransaction(self.lock, self._read, timeout=timeout) def _write_to_yaml(self, stream): """Write out the databsae to a YAML file. @@ -352,12 +353,22 @@ class Database(object): "Invalid ref_count: %s: %d (expected %d), in DB %s" % (key, found, expected, self._index_path)) - def _write(self): + def _write(self, type, value, traceback): """Write the in-memory database index to its file path. - Does no locking. + This is a helper function called by the WriteTransaction context + manager. If there is an exception while the write lock is active, + nothing will be written to the database file, but the in-memory + database *may* be left in an inconsistent state. It will be consistent + after the start of the next transaction, when it read from disk again. + + This routine does no locking. """ + # Do not write if exceptions were raised + if type is not None: + return + temp_file = self._index_path + ( '.%s.%s.temp' % (socket.getfqdn(), os.getpid())) @@ -589,50 +600,8 @@ class Database(object): return key in self._data and not self._data[key].installed -class _Transaction(object): - """Simple nested transaction context manager that uses a file lock. - - This class can trigger actions when the lock is acquired for the - first time and released for the last. - - Timeout for lock is customizable. - """ - - def __init__(self, db, - acquire_fn=None, - release_fn=None, - timeout=_db_lock_timeout): - self._db = db - self._timeout = timeout - self._acquire_fn = acquire_fn - self._release_fn = release_fn - - def __enter__(self): - if self._enter() and self._acquire_fn: - self._acquire_fn() - - def __exit__(self, type, value, traceback): - if self._exit() and self._release_fn: - self._release_fn() - - -class ReadTransaction(_Transaction): - def _enter(self): - return self._db.lock.acquire_read(self._timeout) - - def _exit(self): - return self._db.lock.release_read() - - -class WriteTransaction(_Transaction): - def _enter(self): - return self._db.lock.acquire_write(self._timeout) - - def _exit(self): - return self._db.lock.release_write() - - class CorruptDatabaseError(SpackError): + def __init__(self, path, msg=''): super(CorruptDatabaseError, self).__init__( "Spack database is corrupt: %s. %s." % (path, msg), @@ -640,6 +609,7 @@ class CorruptDatabaseError(SpackError): class InvalidDatabaseVersionError(SpackError): + def __init__(self, expected, found): super(InvalidDatabaseVersionError, self).__init__( "Expected database version %s but found version %s." diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py index e92dd6fb67..313bf48f0d 100644 --- a/lib/spack/spack/directives.py +++ b/lib/spack/spack/directives.py @@ -349,9 +349,10 @@ class CircularReferenceError(DirectiveError): class UnknownDependencyTypeError(DirectiveError): """This is raised when a dependency is of an unknown type.""" + def __init__(self, directive, package, deptype): super(UnknownDependencyTypeError, self).__init__( directive, - "Package '%s' cannot depend on a package via %s." % - (package, deptype)) + "Package '%s' cannot depend on a package via %s." + % (package, deptype)) self.package = package diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index 8150a6da2b..0ae6f765f4 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -22,16 +22,13 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import re import os import exceptions -import hashlib import shutil import glob import tempfile import yaml -import llnl.util.tty as tty from llnl.util.filesystem import join_path, mkdirp import spack @@ -51,10 +48,10 @@ class DirectoryLayout(object): install, and they can use this to customize the nesting structure of spack installs. """ + def __init__(self, root): self.root = root - @property def hidden_file_paths(self): """Return a list of hidden files used by the directory layout. @@ -67,25 +64,21 @@ class DirectoryLayout(object): """ raise NotImplementedError() - def all_specs(self): """To be implemented by subclasses to traverse all specs for which there is a directory within the root. """ raise NotImplementedError() - def relative_path_for_spec(self, spec): """Implemented by subclasses to return a relative path from the install root to a unique location for the provided spec.""" raise NotImplementedError() - def create_install_directory(self, spec): """Creates the installation directory for a spec.""" raise NotImplementedError() - def check_installed(self, spec): """Checks whether a spec is installed. @@ -95,7 +88,6 @@ class DirectoryLayout(object): """ raise NotImplementedError() - def extension_map(self, spec): """Get a dict of currently installed extension packages for a spec. @@ -104,7 +96,6 @@ class DirectoryLayout(object): """ raise NotImplementedError() - def check_extension_conflict(self, spec, ext_spec): """Ensure that ext_spec can be activated in spec. @@ -113,7 +104,6 @@ class DirectoryLayout(object): """ raise NotImplementedError() - def check_activated(self, spec, ext_spec): """Ensure that ext_spec can be removed from spec. @@ -121,26 +111,22 @@ class DirectoryLayout(object): """ raise NotImplementedError() - def add_extension(self, spec, ext_spec): """Add to the list of currently installed extensions.""" raise NotImplementedError() - def remove_extension(self, spec, ext_spec): """Remove from the list of currently installed extensions.""" raise NotImplementedError() - def path_for_spec(self, spec): - """Return an absolute path from the root to a directory for the spec.""" + """Return absolute path from the root to a directory for the spec.""" _check_concrete(spec) path = self.relative_path_for_spec(spec) assert(not path.startswith(self.root)) return os.path.join(self.root, path) - def remove_install_directory(self, spec): """Removes a prefix and any empty parent directories from the root. Raised RemoveFailedError if something goes wrong. @@ -177,6 +163,7 @@ class YamlDirectoryLayout(DirectoryLayout): only enabled variants are included in the install path. Disabled variants are omitted. """ + def __init__(self, root, **kwargs): super(YamlDirectoryLayout, self).__init__(root) self.metadata_dir = kwargs.get('metadata_dir', '.spack') @@ -191,12 +178,10 @@ class YamlDirectoryLayout(DirectoryLayout): # Cache of already written/read extension maps. self._extension_maps = {} - @property def hidden_file_paths(self): return (self.metadata_dir,) - def relative_path_for_spec(self, spec): _check_concrete(spec) @@ -208,20 +193,19 @@ class YamlDirectoryLayout(DirectoryLayout): spec.version, spec.dag_hash(self.hash_len)) - path = join_path(spec.architecture, + path = join_path( + spec.architecture, "%s-%s" % (spec.compiler.name, spec.compiler.version), dir_name) return path - def write_spec(self, spec, path): """Write a spec out to a file.""" _check_concrete(spec) with open(path, 'w') as f: spec.to_yaml(f) - def read_spec(self, path): """Read the contents of a file and parse them as a spec""" try: @@ -237,32 +221,26 @@ class YamlDirectoryLayout(DirectoryLayout): spec._mark_concrete() return spec - def spec_file_path(self, spec): """Gets full path to spec file""" _check_concrete(spec) return join_path(self.metadata_path(spec), self.spec_file_name) - def metadata_path(self, spec): return join_path(self.path_for_spec(spec), self.metadata_dir) - def build_log_path(self, spec): return join_path(self.path_for_spec(spec), self.metadata_dir, self.build_log_name) - def build_env_path(self, spec): return join_path(self.path_for_spec(spec), self.metadata_dir, self.build_env_name) - def build_packages_path(self, spec): return join_path(self.path_for_spec(spec), self.metadata_dir, self.packages_dir) - def create_install_directory(self, spec): _check_concrete(spec) @@ -273,7 +251,6 @@ class YamlDirectoryLayout(DirectoryLayout): mkdirp(self.metadata_path(spec)) self.write_spec(spec, self.spec_file_path(spec)) - def check_installed(self, spec): _check_concrete(spec) path = self.path_for_spec(spec) @@ -284,7 +261,7 @@ class YamlDirectoryLayout(DirectoryLayout): if not os.path.isfile(spec_file_path): raise InconsistentInstallDirectoryError( - 'Inconsistent state: install prefix exists but contains no spec.yaml:', + 'Install prefix exists but contains no spec.yaml:', " " + path) installed_spec = self.read_spec(spec_file_path) @@ -297,7 +274,6 @@ class YamlDirectoryLayout(DirectoryLayout): raise InconsistentInstallDirectoryError( 'Spec file in %s does not match hash!' % spec_file_path) - def all_specs(self): if not os.path.isdir(self.root): return [] @@ -307,20 +283,17 @@ class YamlDirectoryLayout(DirectoryLayout): spec_files = glob.glob(pattern) return [self.read_spec(s) for s in spec_files] - def specs_by_hash(self): by_hash = {} for spec in self.all_specs(): by_hash[spec.dag_hash()] = spec return by_hash - def extension_file_path(self, spec): """Gets full path to an installed package's extension file""" _check_concrete(spec) return join_path(self.metadata_path(spec), self.extension_file_name) - def _write_extensions(self, spec, extensions): path = self.extension_file_path(spec) @@ -332,23 +305,22 @@ class YamlDirectoryLayout(DirectoryLayout): # write tmp file with tmp: yaml.dump({ - 'extensions' : [ - { ext.name : { - 'hash' : ext.dag_hash(), - 'path' : str(ext.prefix) + 'extensions': [ + {ext.name: { + 'hash': ext.dag_hash(), + 'path': str(ext.prefix) }} for ext in sorted(extensions.values())] }, tmp, default_flow_style=False) # Atomic update by moving tmpfile on top of old one. os.rename(tmp.name, path) - def _extension_map(self, spec): """Get a dict<name -> spec> for all extensions currently installed for this package.""" _check_concrete(spec) - if not spec in self._extension_maps: + if spec not in self._extension_maps: path = self.extension_file_path(spec) if not os.path.exists(path): self._extension_maps[spec] = {} @@ -363,14 +335,14 @@ class YamlDirectoryLayout(DirectoryLayout): dag_hash = entry[name]['hash'] prefix = entry[name]['path'] - if not dag_hash in by_hash: + if dag_hash not in by_hash: raise InvalidExtensionSpecError( "Spec %s not found in %s" % (dag_hash, prefix)) ext_spec = by_hash[dag_hash] - if not prefix == ext_spec.prefix: + if prefix != ext_spec.prefix: raise InvalidExtensionSpecError( - "Prefix %s does not match spec with hash %s: %s" + "Prefix %s does not match spec hash %s: %s" % (prefix, dag_hash, ext_spec)) exts[ext_spec.name] = ext_spec @@ -378,13 +350,11 @@ class YamlDirectoryLayout(DirectoryLayout): return self._extension_maps[spec] - def extension_map(self, spec): """Defensive copying version of _extension_map() for external API.""" _check_concrete(spec) return self._extension_map(spec).copy() - def check_extension_conflict(self, spec, ext_spec): exts = self._extension_map(spec) if ext_spec.name in exts: @@ -394,13 +364,11 @@ class YamlDirectoryLayout(DirectoryLayout): else: raise ExtensionConflictError(spec, ext_spec, installed_spec) - def check_activated(self, spec, ext_spec): exts = self._extension_map(spec) - if (not ext_spec.name in exts) or (ext_spec != exts[ext_spec.name]): + if (ext_spec.name not in exts) or (ext_spec != exts[ext_spec.name]): raise NoSuchExtensionError(spec, ext_spec) - def add_extension(self, spec, ext_spec): _check_concrete(spec) _check_concrete(ext_spec) @@ -413,7 +381,6 @@ class YamlDirectoryLayout(DirectoryLayout): exts[ext_spec.name] = ext_spec self._write_extensions(spec, exts) - def remove_extension(self, spec, ext_spec): _check_concrete(spec) _check_concrete(ext_spec) @@ -429,12 +396,14 @@ class YamlDirectoryLayout(DirectoryLayout): class DirectoryLayoutError(SpackError): """Superclass for directory layout errors.""" + def __init__(self, message, long_msg=None): super(DirectoryLayoutError, self).__init__(message, long_msg) class SpecHashCollisionError(DirectoryLayoutError): """Raised when there is a hash collision in an install layout.""" + def __init__(self, installed_spec, new_spec): super(SpecHashCollisionError, self).__init__( 'Specs %s and %s have the same SHA-1 prefix!' @@ -443,6 +412,7 @@ class SpecHashCollisionError(DirectoryLayoutError): class RemoveFailedError(DirectoryLayoutError): """Raised when a DirectoryLayout cannot remove an install prefix.""" + def __init__(self, installed_spec, prefix, error): super(RemoveFailedError, self).__init__( 'Could not remove prefix %s for %s : %s' @@ -452,12 +422,15 @@ class RemoveFailedError(DirectoryLayoutError): class InconsistentInstallDirectoryError(DirectoryLayoutError): """Raised when a package seems to be installed to the wrong place.""" + def __init__(self, message, long_msg=None): - super(InconsistentInstallDirectoryError, self).__init__(message, long_msg) + super(InconsistentInstallDirectoryError, self).__init__( + message, long_msg) class InstallDirectoryAlreadyExistsError(DirectoryLayoutError): """Raised when create_install_directory is called unnecessarily.""" + def __init__(self, path): super(InstallDirectoryAlreadyExistsError, self).__init__( "Install path %s already exists!") @@ -473,22 +446,26 @@ class InvalidExtensionSpecError(DirectoryLayoutError): class ExtensionAlreadyInstalledError(DirectoryLayoutError): """Raised when an extension is added to a package that already has it.""" + def __init__(self, spec, ext_spec): super(ExtensionAlreadyInstalledError, self).__init__( - "%s is already installed in %s" % (ext_spec.short_spec, spec.short_spec)) + "%s is already installed in %s" + % (ext_spec.short_spec, spec.short_spec)) class ExtensionConflictError(DirectoryLayoutError): """Raised when an extension is added to a package that already has it.""" + def __init__(self, spec, ext_spec, conflict): super(ExtensionConflictError, self).__init__( - "%s cannot be installed in %s because it conflicts with %s"% ( - ext_spec.short_spec, spec.short_spec, conflict.short_spec)) + "%s cannot be installed in %s because it conflicts with %s" + % (ext_spec.short_spec, spec.short_spec, conflict.short_spec)) class NoSuchExtensionError(DirectoryLayoutError): """Raised when an extension isn't there on deactivate.""" + def __init__(self, spec, ext_spec): super(NoSuchExtensionError, self).__init__( - "%s cannot be removed from %s because it's not activated."% ( - ext_spec.short_spec, spec.short_spec)) + "%s cannot be removed from %s because it's not activated." + % (ext_spec.short_spec, spec.short_spec)) diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 30c6228ca4..613ece2f45 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -1,4 +1,4 @@ -# +############################################################################## # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. # @@ -21,7 +21,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -# +############################################################################## import collections import inspect import json @@ -37,6 +37,10 @@ class NameModifier(object): self.args = {'name': name} self.args.update(kwargs) + def update_args(self, **kwargs): + self.__dict__.update(kwargs) + self.args.update(kwargs) + class NameValueModifier(object): @@ -44,7 +48,11 @@ class NameValueModifier(object): self.name = name self.value = value self.separator = kwargs.get('separator', ':') - self.args = {'name': name, 'value': value, 'delim': self.separator} + self.args = {'name': name, 'value': value, 'separator': self.separator} + self.args.update(kwargs) + + def update_args(self, **kwargs): + self.__dict__.update(kwargs) self.args.update(kwargs) @@ -279,7 +287,10 @@ class EnvironmentModifications(object): shell = '{shell}'.format(**info) shell_options = '{shell_options}'.format(**info) source_file = '{source_command} {file} {concatenate_on_success}' - dump_environment = 'python -c "import os, json; print json.dumps(dict(os.environ))"' # NOQA: ignore=E501 + + dump_cmd = "import os, json; print json.dumps(dict(os.environ))" + dump_environment = 'python -c "%s"' % dump_cmd + # Construct the command that will be executed command = [source_file.format(file=file, **info) for file in args] command.append(dump_environment) @@ -318,8 +329,10 @@ class EnvironmentModifications(object): for x in unset_variables: env.unset(x) # Variables that have been modified - common_variables = set(this_environment).intersection(set(after_source_env)) # NOQA: ignore=E501 - modified_variables = [x for x in common_variables if this_environment[x] != after_source_env[x]] # NOQA: ignore=E501 + common_variables = set( + this_environment).intersection(set(after_source_env)) + modified_variables = [x for x in common_variables + if this_environment[x] != after_source_env[x]] def return_separator_if_any(first_value, second_value): separators = ':', ';' @@ -397,7 +410,7 @@ def set_or_unset_not_first(variable, changes, errstream): if indexes: good = '\t \t{context} at {filename}:{lineno}' nogood = '\t--->\t{context} at {filename}:{lineno}' - message = 'Suspicious requests to set or unset the variable \'{var}\' found' # NOQA: ignore=E501 + message = "Suspicious requests to set or unset '{var}' found" errstream(message.format(var=variable)) for ii, item in enumerate(changes): print_format = nogood if ii in indexes else good diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py index 85ad2fe249..c94875e91a 100644 --- a/lib/spack/spack/error.py +++ b/lib/spack/spack/error.py @@ -27,21 +27,21 @@ import sys import llnl.util.tty as tty import spack + class SpackError(Exception): """This is the superclass for all Spack errors. Subclasses can be found in the modules they have to do with. """ + def __init__(self, message, long_message=None): super(SpackError, self).__init__() self.message = message self._long_message = long_message - @property def long_message(self): return self._long_message - def die(self): if spack.debug: sys.excepthook(*sys.exc_info()) @@ -52,21 +52,23 @@ class SpackError(Exception): print self.long_message os._exit(1) - def __str__(self): msg = self.message if self._long_message: msg += "\n %s" % self._long_message return msg + class UnsupportedPlatformError(SpackError): """Raised by packages when a platform is not supported""" + def __init__(self, message): super(UnsupportedPlatformError, self).__init__(message) class NoNetworkConnectionError(SpackError): """Raised when an operation needs an internet connection.""" + def __init__(self, message, url): super(NoNetworkConnectionError, self).__init__( "No network connection: " + str(message), diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index bcb33bd0e6..c69a23033c 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -356,6 +356,7 @@ class URLFetchStrategy(FetchStrategy): class CacheURLFetchStrategy(URLFetchStrategy): """The resource associated with a cache URL may be out of date.""" + def __init__(self, *args, **kwargs): super(CacheURLFetchStrategy, self).__init__(*args, **kwargs) @@ -836,6 +837,7 @@ def for_package_version(pkg, version): class FsCache(object): + def __init__(self, root): self.root = os.path.abspath(root) diff --git a/lib/spack/spack/file_cache.py b/lib/spack/spack/file_cache.py new file mode 100644 index 0000000000..0a66166fd8 --- /dev/null +++ b/lib/spack/spack/file_cache.py @@ -0,0 +1,185 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import os +import shutil + +from llnl.util.filesystem import * +from llnl.util.lock import * + +from spack.error import SpackError + + +class FileCache(object): + """This class manages cached data in the filesystem. + + - Cache files are fetched and stored by unique keys. Keys can be relative + paths, so that thre can be some hierarchy in the cache. + + - The FileCache handles locking cache files for reading and writing, so + client code need not manage locks for cache entries. + + """ + + def __init__(self, root): + """Create a file cache object. + + This will create the cache directory if it does not exist yet. + + """ + self.root = root.rstrip(os.path.sep) + if not os.path.exists(self.root): + mkdirp(self.root) + + self._locks = {} + + def destroy(self): + """Remove all files under the cache root.""" + for f in os.listdir(self.root): + path = join_path(self.root, f) + if os.path.isdir(path): + shutil.rmtree(path, True) + else: + os.remove(path) + + def cache_path(self, key): + """Path to the file in the cache for a particular key.""" + return join_path(self.root, key) + + def _lock_path(self, key): + """Path to the file in the cache for a particular key.""" + keyfile = os.path.basename(key) + keydir = os.path.dirname(key) + + return join_path(self.root, keydir, '.' + keyfile + '.lock') + + def _get_lock(self, key): + """Create a lock for a key, if necessary, and return a lock object.""" + if key not in self._locks: + lock_file = self._lock_path(key) + if not os.path.exists(lock_file): + touch(lock_file) + self._locks[key] = Lock(lock_file) + return self._locks[key] + + def init_entry(self, key): + """Ensure we can access a cache file. Create a lock for it if needed. + + Return whether the cache file exists yet or not. + """ + cache_path = self.cache_path(key) + + exists = os.path.exists(cache_path) + if exists: + if not os.path.isfile(cache_path): + raise CacheError("Cache file is not a file: %s" % cache_path) + + if not os.access(cache_path, os.R_OK | os.W_OK): + raise CacheError("Cannot access cache file: %s" % cache_path) + else: + # if the file is hierarchical, make parent directories + parent = os.path.dirname(cache_path) + if parent.rstrip(os.path.sep) != self.root: + mkdirp(parent) + + if not os.access(parent, os.R_OK | os.W_OK): + raise CacheError("Cannot access cache directory: %s" % parent) + + # ensure lock is created for this key + self._get_lock(key) + return exists + + def read_transaction(self, key): + """Get a read transaction on a file cache item. + + Returns a ReadTransaction context manager and opens the cache file for + reading. You can use it like this: + + with spack.user_cache.read_transaction(key) as cache_file: + cache_file.read() + + """ + return ReadTransaction( + self._get_lock(key), lambda: open(self.cache_path(key))) + + def write_transaction(self, key): + """Get a write transaction on a file cache item. + + Returns a WriteTransaction context manager that opens a temporary file + for writing. Once the context manager finishes, if nothing went wrong, + moves the file into place on top of the old file atomically. + + """ + class WriteContextManager(object): + + def __enter__(cm): + cm.orig_filename = self.cache_path(key) + cm.orig_file = None + if os.path.exists(cm.orig_filename): + cm.orig_file = open(cm.orig_filename, 'r') + + cm.tmp_filename = self.cache_path(key) + '.tmp' + cm.tmp_file = open(cm.tmp_filename, 'w') + + return cm.orig_file, cm.tmp_file + + def __exit__(cm, type, value, traceback): + if cm.orig_file: + cm.orig_file.close() + cm.tmp_file.close() + + if value: + # remove tmp on exception & raise it + shutil.rmtree(cm.tmp_filename, True) + raise value + else: + os.rename(cm.tmp_filename, cm.orig_filename) + + return WriteTransaction(self._get_lock(key), WriteContextManager) + + def mtime(self, key): + """Return modification time of cache file, or 0 if it does not exist. + + Time is in units returned by os.stat in the mtime field, which is + platform-dependent. + + """ + if not self.init_entry(key): + return 0 + else: + sinfo = os.stat(self.cache_path(key)) + return sinfo.st_mtime + + def remove(self, key): + lock = self._get_lock(key) + try: + lock.acquire_write() + os.unlink(self.cache_path(key)) + finally: + lock.release_write() + os.unlink(self._lock_path(key)) + + +class CacheError(SpackError): + pass diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py index 063e4647b6..b875e9da99 100644 --- a/lib/spack/spack/graph.py +++ b/lib/spack/spack/graph.py @@ -61,7 +61,6 @@ Note that ``graph_ascii`` assumes a single spec while ``graph_dot`` can take a number of specs as input. """ -__all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot'] from heapq import * @@ -71,6 +70,8 @@ from llnl.util.tty.color import * import spack from spack.spec import Spec +__all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot'] + def topological_sort(spec, **kwargs): """Topological sort for specs. @@ -94,6 +95,7 @@ def topological_sort(spec, **kwargs): nodes = spec.index() topo_order = [] + par = dict((name, parents(nodes[name])) for name in nodes.keys()) remaining = [name for name in nodes.keys() if not parents(nodes[name])] heapify(remaining) @@ -102,12 +104,12 @@ def topological_sort(spec, **kwargs): topo_order.append(name) node = nodes[name] - for dep in children(node).values(): - del parents(dep)[node.name] - if not parents(dep): + for dep in children(node): + par[dep.name].remove(node) + if not par[dep.name]: heappush(remaining, dep.name) - if any(parents(s) for s in spec.traverse()): + if any(par.get(s.name, []) for s in spec.traverse()): raise ValueError("Spec has cycles!") else: return topo_order @@ -132,7 +134,9 @@ def find(seq, predicate): states = ('node', 'collapse', 'merge-right', 'expand-right', 'back-edge') NODE, COLLAPSE, MERGE_RIGHT, EXPAND_RIGHT, BACK_EDGE = states + class AsciiGraph(object): + def __init__(self): # These can be set after initialization or after a call to # graph() to change behavior. @@ -153,18 +157,15 @@ class AsciiGraph(object): self._prev_state = None # State of previous line self._prev_index = None # Index of expansion point of prev line - def _indent(self): self._out.write(self.indent * ' ') - def _write_edge(self, string, index, sub=0): """Write a colored edge to the output stream.""" name = self._frontier[index][sub] edge = "@%s{%s}" % (self._name_to_color[name], string) self._out.write(edge) - def _connect_deps(self, i, deps, label=None): """Connect dependencies to existing edges in the frontier. @@ -199,7 +200,8 @@ class AsciiGraph(object): collapse = True if self._prev_state == EXPAND_RIGHT: # Special case where previous line expanded and i is off by 1. - self._back_edge_line([], j, i+1, True, label + "-1.5 " + str((i+1,j))) + self._back_edge_line([], j, i + 1, True, + label + "-1.5 " + str((i + 1, j))) collapse = False else: @@ -207,19 +209,20 @@ class AsciiGraph(object): if self._prev_state == NODE and self._prev_index < i: i += 1 - if i-j > 1: + if i - j > 1: # We need two lines to connect if distance > 1 - self._back_edge_line([], j, i, True, label + "-1 " + str((i,j))) + self._back_edge_line([], j, i, True, + label + "-1 " + str((i, j))) collapse = False - self._back_edge_line([j], -1, -1, collapse, label + "-2 " + str((i,j))) + self._back_edge_line([j], -1, -1, collapse, + label + "-2 " + str((i, j))) return True elif deps: self._frontier.insert(i, deps) return False - def _set_state(self, state, index, label=None): if state not in states: raise ValueError("Invalid graph state!") @@ -233,7 +236,6 @@ class AsciiGraph(object): self._out.write("%-20s" % (str(label) if label else '')) self._out.write("%s" % self._frontier) - def _back_edge_line(self, prev_ends, end, start, collapse, label=None): """Write part of a backwards edge in the graph. @@ -287,27 +289,26 @@ class AsciiGraph(object): self._indent() for p in prev_ends: - advance(p, lambda: [("| ", self._pos)] ) - advance(p+1, lambda: [("|/", self._pos)] ) + advance(p, lambda: [("| ", self._pos)]) + advance(p + 1, lambda: [("|/", self._pos)]) if end >= 0: - advance(end + 1, lambda: [("| ", self._pos)] ) - advance(start - 1, lambda: [("|", self._pos), ("_", end)] ) + advance(end + 1, lambda: [("| ", self._pos)]) + advance(start - 1, lambda: [("|", self._pos), ("_", end)]) else: - advance(start - 1, lambda: [("| ", self._pos)] ) + advance(start - 1, lambda: [("| ", self._pos)]) if start >= 0: - advance(start, lambda: [("|", self._pos), ("/", end)] ) + advance(start, lambda: [("|", self._pos), ("/", end)]) if collapse: - advance(flen, lambda: [(" /", self._pos)] ) + advance(flen, lambda: [(" /", self._pos)]) else: - advance(flen, lambda: [("| ", self._pos)] ) + advance(flen, lambda: [("| ", self._pos)]) self._set_state(BACK_EDGE, end, label) self._out.write("\n") - def _node_line(self, index, name): """Writes a line with a node at index.""" self._indent() @@ -316,14 +317,13 @@ class AsciiGraph(object): self._out.write("%s " % self.node_character) - for c in range(index+1, len(self._frontier)): + for c in range(index + 1, len(self._frontier)): self._write_edge("| ", c) self._out.write(" %s" % name) self._set_state(NODE, index) self._out.write("\n") - def _collapse_line(self, index): """Write a collapsing line after a node was added at index.""" self._indent() @@ -335,36 +335,33 @@ class AsciiGraph(object): self._set_state(COLLAPSE, index) self._out.write("\n") - def _merge_right_line(self, index): """Edge at index is same as edge to right. Merge directly with '\'""" self._indent() for c in range(index): self._write_edge("| ", c) self._write_edge("|", index) - self._write_edge("\\", index+1) - for c in range(index+1, len(self._frontier)): - self._write_edge("| ", c ) + self._write_edge("\\", index + 1) + for c in range(index + 1, len(self._frontier)): + self._write_edge("| ", c) self._set_state(MERGE_RIGHT, index) self._out.write("\n") - def _expand_right_line(self, index): self._indent() for c in range(index): self._write_edge("| ", c) self._write_edge("|", index) - self._write_edge("\\", index+1) + self._write_edge("\\", index + 1) - for c in range(index+2, len(self._frontier)): + for c in range(index + 2, len(self._frontier)): self._write_edge(" \\", c) self._set_state(EXPAND_RIGHT, index) self._out.write("\n") - def write(self, spec, **kwargs): """Write out an ascii graph of the provided spec. @@ -398,7 +395,7 @@ class AsciiGraph(object): # Colors associated with each node in the DAG. # Edges are colored by the node they point to. self._name_to_color = dict((name, self.colors[i % len(self.colors)]) - for i, name in enumerate(topo_order)) + for i, name in enumerate(topo_order)) # Frontier tracks open edges of the graph as it's written out. self._frontier = [[spec.name]] @@ -407,7 +404,8 @@ class AsciiGraph(object): i = find(self._frontier, lambda f: len(f) > 1) if i >= 0: - # Expand frontier until there are enough columns for all children. + # Expand frontier until there are enough columns for all + # children. # Figure out how many back connections there are and # sort them so we do them in order @@ -424,8 +422,9 @@ class AsciiGraph(object): prev_ends = [] for j, (b, d) in enumerate(back): self._frontier[i].remove(d) - if i-b > 1: - self._back_edge_line(prev_ends, b, i, False, 'left-1') + if i - b > 1: + self._back_edge_line(prev_ends, b, i, False, + 'left-1') del prev_ends[:] prev_ends.append(b) @@ -439,12 +438,13 @@ class AsciiGraph(object): elif len(self._frontier[i]) > 1: # Expand forward after doing all back connections - if (i+1 < len(self._frontier) and len(self._frontier[i+1]) == 1 - and self._frontier[i+1][0] in self._frontier[i]): + if (i + 1 < len(self._frontier) and + len(self._frontier[i + 1]) == 1 and + self._frontier[i + 1][0] in self._frontier[i]): # We need to connect to the element to the right. # Keep lines straight by connecting directly and # avoiding unnecessary expand/contract. - name = self._frontier[i+1][0] + name = self._frontier[i + 1][0] self._frontier[i].remove(name) self._merge_right_line(i) @@ -458,9 +458,8 @@ class AsciiGraph(object): self._frontier.pop(i) self._connect_deps(i, deps, "post-expand") - # Handle any remaining back edges to the right - j = i+1 + j = i + 1 while j < len(self._frontier): deps = self._frontier.pop(j) if not self._connect_deps(j, deps, "back-from-right"): @@ -477,9 +476,10 @@ class AsciiGraph(object): # Replace node with its dependencies self._frontier.pop(i) - if node.dependencies: - deps = sorted((d for d in node.dependencies), reverse=True) - self._connect_deps(i, deps, "new-deps") # anywhere. + if node.dependencies(): + deps = sorted((d.name for d in node.dependencies()), + reverse=True) + self._connect_deps(i, deps, "new-deps") # anywhere. elif self._frontier: self._collapse_line(i) @@ -501,7 +501,6 @@ def graph_ascii(spec, **kwargs): graph.write(spec, color=color, out=out) - def graph_dot(*specs, **kwargs): """Generate a graph in dot format of all provided specs. diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py index 902e488eca..c7c84defa0 100644 --- a/lib/spack/spack/hooks/__init__.py +++ b/lib/spack/spack/hooks/__init__.py @@ -45,6 +45,7 @@ from llnl.util.lang import memoized, list_modules from llnl.util.filesystem import join_path import spack + @memoized def all_hook_modules(): modules = [] @@ -58,6 +59,7 @@ def all_hook_modules(): class HookRunner(object): + def __init__(self, hook_name): self.hook_name = hook_name diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py index bcbd68dfa0..070b309a43 100644 --- a/lib/spack/spack/hooks/extensions.py +++ b/lib/spack/spack/hooks/extensions.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import spack - def pre_uninstall(pkg): assert(pkg.spec.concrete) diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py index 3a957c6e0e..02c1ce3816 100644 --- a/lib/spack/spack/hooks/sbang.py +++ b/lib/spack/spack/hooks/sbang.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os +import stat import re import llnl.util.tty as tty @@ -62,10 +63,21 @@ def filter_shebang(path): if re.search(r'^#!(/[^/]*)*lua\b', original): original = re.sub(r'^#', '--', original) + # Change non-writable files to be writable if needed. + saved_mode = None + if not os.access(path, os.W_OK): + st = os.stat(path) + saved_mode = st.st_mode + os.chmod(path, saved_mode | stat.S_IWRITE) + with open(path, 'w') as new_file: new_file.write(new_sbang_line) new_file.write(original) + # Restore original permissions. + if saved_mode is not None: + os.chmod(path, saved_mode) + tty.warn("Patched overlong shebang in %s" % path) diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py index 0bbcfba6b4..f053e4405f 100644 --- a/lib/spack/spack/mirror.py +++ b/lib/spack/spack/mirror.py @@ -40,9 +40,8 @@ import spack.error import spack.url as url import spack.fetch_strategy as fs from spack.spec import Spec -from spack.stage import Stage from spack.version import * -from spack.util.compression import extension, allowed_archive +from spack.util.compression import allowed_archive def mirror_archive_filename(spec, fetcher): @@ -52,10 +51,10 @@ def mirror_archive_filename(spec, fetcher): if isinstance(fetcher, fs.URLFetchStrategy): if fetcher.expand_archive: - # If we fetch this version with a URLFetchStrategy, use URL's archive type + # If we fetch with a URLFetchStrategy, use URL's archive type ext = url.downloaded_file_extension(fetcher.url) else: - # If the archive shouldn't be expanded, don't check for its extension. + # If the archive shouldn't be expanded, don't check extension. ext = None else: # Otherwise we'll make a .tar.gz ourselves @@ -106,7 +105,9 @@ def get_matching_versions(specs, **kwargs): def suggest_archive_basename(resource): """ - Return a tentative basename for an archive. Raise an exception if the name is among the allowed archive types. + Return a tentative basename for an archive. + + Raises an exception if the name is not an allowed archive type. :param fetcher: :return: @@ -170,7 +171,7 @@ def create(path, specs, **kwargs): 'error': [] } - # Iterate through packages and download all the safe tarballs for each of them + # Iterate through packages and download all safe tarballs for each for spec in version_specs: add_single_spec(spec, mirror_root, categories, **kwargs) @@ -190,12 +191,15 @@ def add_single_spec(spec, mirror_root, categories, **kwargs): fetcher = stage.fetcher if ii == 0: # create a subdirectory for the current package@version - archive_path = os.path.abspath(join_path(mirror_root, mirror_archive_path(spec, fetcher))) + archive_path = os.path.abspath(join_path( + mirror_root, mirror_archive_path(spec, fetcher))) name = spec.format("$_$@") else: resource = stage.resource - archive_path = join_path(subdir, suggest_archive_basename(resource)) - name = "{resource} ({pkg}).".format(resource=resource.name, pkg=spec.format("$_$@")) + archive_path = join_path( + subdir, suggest_archive_basename(resource)) + name = "{resource} ({pkg}).".format( + resource=resource.name, pkg=spec.format("$_$@")) subdir = os.path.dirname(archive_path) mkdirp(subdir) @@ -217,15 +221,18 @@ def add_single_spec(spec, mirror_root, categories, **kwargs): categories['present'].append(spec) else: categories['mirrored'].append(spec) + except Exception as e: if spack.debug: sys.excepthook(*sys.exc_info()) else: - tty.warn("Error while fetching %s" % spec.format('$_$@'), e.message) + tty.warn("Error while fetching %s" + % spec.format('$_$@'), e.message) categories['error'].append(spec) class MirrorError(spack.error.SpackError): """Superclass of all mirror-creation related errors.""" + def __init__(self, msg, long_msg=None): super(MirrorError, self).__init__(msg, long_msg) diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index db8b20ae42..debc6752b4 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -272,14 +272,26 @@ class EnvModule(object): @property def tokens(self): + """Tokens that can be substituted in environment variable values + and naming schemes + """ tokens = { 'name': self.spec.name, 'version': self.spec.version, - 'compiler': self.spec.compiler + 'compiler': self.spec.compiler, + 'prefix': self.spec.package.prefix } return tokens @property + def upper_tokens(self): + """Tokens that can be substituted in environment variable names""" + upper_tokens = { + 'name': self.spec.name.replace('-', '_').upper() + } + return upper_tokens + + @property def use_name(self): """ Subclasses should implement this to return the name the module command @@ -438,11 +450,17 @@ class EnvModule(object): def process_environment_command(self, env): for command in env: + # Token expansion from configuration file + name = command.args.get('name', '').format(**self.upper_tokens) + value = str(command.args.get('value', '')).format(**self.tokens) + command.update_args(name=name, value=value) + # Format the line int the module file try: yield self.environment_modifications_formats[type( command)].format(**command.args) except KeyError: - message = 'Cannot handle command of type {command} : skipping request' # NOQA: ignore=E501 + message = ('Cannot handle command of type {command}: ' + 'skipping request') details = '{context} at {filename}:{lineno}' tty.warn(message.format(command=type(command))) tty.warn(details.format(**command.args)) @@ -477,7 +495,8 @@ class Dotkit(EnvModule): autoload_format = 'dk_op {module_file}\n' - default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}' # NOQA: ignore=E501 + default_naming_format = \ + '{name}-{version}-{compiler.name}-{compiler.version}' @property def file_name(self): @@ -503,7 +522,8 @@ class Dotkit(EnvModule): def prerequisite(self, spec): tty.warn('prerequisites: not supported by dotkit module files') - tty.warn('\tYou may want to check ~/.spack/modules.yaml') + tty.warn('\tYou may want to check %s/modules.yaml' + % spack.user_config_path) return '' @@ -511,9 +531,9 @@ class TclModule(EnvModule): name = 'tcl' path = join_path(spack.share_path, "modules") environment_modifications_formats = { - PrependPath: 'prepend-path --delim "{delim}" {name} \"{value}\"\n', - AppendPath: 'append-path --delim "{delim}" {name} \"{value}\"\n', - RemovePath: 'remove-path --delim "{delim}" {name} \"{value}\"\n', + PrependPath: 'prepend-path --delim "{separator}" {name} \"{value}\"\n', + AppendPath: 'append-path --delim "{separator}" {name} \"{value}\"\n', + RemovePath: 'remove-path --delim "{separator}" {name} \"{value}\"\n', SetEnv: 'setenv {name} \"{value}\"\n', UnsetEnv: 'unsetenv {name}\n' } @@ -525,7 +545,8 @@ class TclModule(EnvModule): prerequisite_format = 'prereq {module_file}\n' - default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}' # NOQA: ignore=E501 + default_naming_format = \ + '{name}-{version}-{compiler.name}-{compiler.version}' @property def file_name(self): @@ -536,7 +557,7 @@ class TclModule(EnvModule): timestamp = datetime.datetime.now() # TCL Modulefile header header = '#%Module1.0\n' - header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp # NOQA: ignore=E501 + header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp header += '##\n' header += '## %s\n' % self.spec.short_spec header += '##\n' @@ -566,10 +587,12 @@ class TclModule(EnvModule): for naming_dir, conflict_dir in zip( self.naming_scheme.split('/'), item.split('/')): if naming_dir != conflict_dir: - message = 'conflict scheme does not match naming scheme [{spec}]\n\n' # NOQA: ignore=E501 + message = 'conflict scheme does not match naming ' + message += 'scheme [{spec}]\n\n' message += 'naming scheme : "{nformat}"\n' message += 'conflict scheme : "{cformat}"\n\n' - message += '** You may want to check your `modules.yaml` configuration file **\n' # NOQA: ignore=E501 + message += '** You may want to check your ' + message += '`modules.yaml` configuration file **\n' tty.error(message.format(spec=self.spec, nformat=self.naming_scheme, cformat=item)) diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py index 0818f9092f..d1d1f32445 100644 --- a/lib/spack/spack/multimethod.py +++ b/lib/spack/spack/multimethod.py @@ -43,15 +43,13 @@ avoids overly complicated rat nests of if statements. Obviously, depending on the scenario, regular old conditionals might be clearer, so package authors should use their judgement. """ -import sys import functools -import collections from llnl.util.lang import * import spack.architecture import spack.error -from spack.spec import parse_anonymous_spec, Spec +from spack.spec import parse_anonymous_spec class SpecMultiMethod(object): @@ -89,13 +87,13 @@ class SpecMultiMethod(object): See the docs for decorators below for more details. """ + def __init__(self, default=None): self.method_list = [] self.default = default if default: functools.update_wrapper(self, default) - def register(self, spec, method): """Register a version of a method for a particular sys_type.""" self.method_list.append((spec, method)) @@ -105,12 +103,10 @@ class SpecMultiMethod(object): else: assert(self.__name__ == method.__name__) - def __get__(self, obj, objtype): """This makes __call__ support instance methods.""" return functools.partial(self.__call__, obj) - def __call__(self, package_self, *args, **kwargs): """Find the first method with a spec that matches the package's spec. If none is found, call the default @@ -127,7 +123,6 @@ class SpecMultiMethod(object): type(package_self), self.__name__, spec, [m[0] for m in self.method_list]) - def __str__(self): return "SpecMultiMethod {\n\tdefault: %s,\n\tspecs: %s\n}" % ( self.default, self.method_list) @@ -195,11 +190,13 @@ class when(object): platform-specific versions. There's not much we can do to get around this because of the way decorators work. """ + def __init__(self, spec): pkg = get_calling_module_name() if spec is True: spec = pkg - self.spec = parse_anonymous_spec(spec, pkg) if spec is not False else None + self.spec = (parse_anonymous_spec(spec, pkg) + if spec is not False else None) def __call__(self, method): # Get the first definition of the method in the calling scope @@ -218,12 +215,14 @@ class when(object): class MultiMethodError(spack.error.SpackError): """Superclass for multimethod dispatch errors""" + def __init__(self, message): super(MultiMethodError, self).__init__(message) class NoSuchMethodError(spack.error.SpackError): """Raised when we can't find a version of a multi-method.""" + def __init__(self, cls, method_name, spec, possible_specs): super(NoSuchMethodError, self).__init__( "Package %s does not support %s called with %s. Options are: %s" diff --git a/lib/spack/spack/operating_systems/cnl.py b/lib/spack/spack/operating_systems/cnl.py index c160a60be8..78807865b3 100644 --- a/lib/spack/spack/operating_systems/cnl.py +++ b/lib/spack/spack/operating_systems/cnl.py @@ -7,29 +7,33 @@ import spack.spec from spack.util.multiproc import parmap import spack.compilers + class Cnl(OperatingSystem): """ Compute Node Linux (CNL) is the operating system used for the Cray XC series super computers. It is a very stripped down version of GNU/Linux. Any compilers found through this operating system will be used with - modules. If updated, user must make sure that version and name are + modules. If updated, user must make sure that version and name are updated to indicate that OS has been upgraded (or downgraded) """ + def __init__(self): name = 'CNL' version = '10' super(Cnl, self).__init__(name, version) + def __str__(self): + return self.name def find_compilers(self, *paths): types = spack.compilers.all_compiler_types() - compiler_lists = parmap(lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types) + compiler_lists = parmap( + lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types) # ensure all the version calls we made are cached in the parent # process, as well. This speeds up Spack a lot. - clist = reduce(lambda x,y: x+y, compiler_lists) + clist = reduce(lambda x, y: x + y, compiler_lists) return clist - def find_compiler(self, cmp_cls, *paths): compilers = [] if cmp_cls.PrgEnv: @@ -45,13 +49,16 @@ class Cnl(OperatingSystem): if paths: module_paths = ':' + ':'.join(p for p in paths) os.environ['MODULEPATH'] = module_paths - - output = modulecmd('avail', cmp_cls.PrgEnv_compiler, output=str, error=str) - matches = re.findall(r'(%s)/([\d\.]+[\d])' % cmp_cls.PrgEnv_compiler, output) + + output = modulecmd( + 'avail', cmp_cls.PrgEnv_compiler, output=str, error=str) + matches = re.findall( + r'(%s)/([\d\.]+[\d])' % cmp_cls.PrgEnv_compiler, output) for name, version in matches: v = version - comp = cmp_cls(spack.spec.CompilerSpec(name + '@' + v), self, - ['cc', 'CC', 'ftn'], [cmp_cls.PrgEnv, name +'/' + v]) + comp = cmp_cls( + spack.spec.CompilerSpec(name + '@' + v), self, + ['cc', 'CC', 'ftn'], [cmp_cls.PrgEnv, name + '/' + v]) compilers.append(comp) diff --git a/lib/spack/spack/operating_systems/linux_distro.py b/lib/spack/spack/operating_systems/linux_distro.py index 2e3c72719b..6d70ae80b6 100644 --- a/lib/spack/spack/operating_systems/linux_distro.py +++ b/lib/spack/spack/operating_systems/linux_distro.py @@ -2,6 +2,7 @@ import re import platform as py_platform from spack.architecture import OperatingSystem + class LinuxDistro(OperatingSystem): """ This class will represent the autodetected operating system for a Linux System. Since there are many different flavors of @@ -9,6 +10,7 @@ class LinuxDistro(OperatingSystem): autodetection using the python module platform and the method platform.dist() """ + def __init__(self): distname, version, _ = py_platform.linux_distribution( full_distribution_name=False) diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py index f35b3ca577..3e5ab9b2e9 100644 --- a/lib/spack/spack/operating_systems/mac_os.py +++ b/lib/spack/spack/operating_systems/mac_os.py @@ -1,6 +1,7 @@ import platform as py_platform from spack.architecture import OperatingSystem + class MacOs(OperatingSystem): """This class represents the macOS operating system. This will be auto detected using the python platform.mac_ver. The macOS diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index c916bfaaa2..ff8c8e96bc 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -34,6 +34,7 @@ rundown on spack and how it differs from homebrew, look at the README. """ import os +import sys import re import textwrap import time @@ -178,12 +179,10 @@ class Package(object): Most software comes in nicely packaged tarballs, like this one: http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz - Taking a page from homebrew, spack deduces pretty much everything it needs to know from the URL above. If you simply type this: spack create http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz - Spack will download the tarball, generate an md5 hash, figure out the version and the name of the package from the URL, and create a new package file for you with all the names and attributes set correctly. @@ -630,50 +629,12 @@ class Package(object): exts = spack.install_layout.extension_map(self.extendee_spec) return (self.name in exts) and (exts[self.name] == self.spec) - def preorder_traversal(self, visited=None, **kwargs): - """This does a preorder traversal of the package's dependence DAG.""" - virtual = kwargs.get("virtual", False) - - if visited is None: - visited = set() - - if self.name in visited: - return - visited.add(self.name) - - if not virtual: - yield self - - for name in sorted(self.dependencies.keys()): - dep_spec = self.get_dependency(name) - spec = dep_spec.spec - - # Currently, we do not descend into virtual dependencies, as this - # makes doing a sensible traversal much harder. We just assume - # that ANY of the virtual deps will work, which might not be true - # (due to conflicts or unsatisfiable specs). For now this is ok, - # but we might want to reinvestigate if we start using a lot of - # complicated virtual dependencies - # TODO: reinvestigate this. - if spec.virtual: - if virtual: - yield spec - continue - - for pkg in spack.repo.get(name).preorder_traversal(visited, - **kwargs): - yield pkg - def provides(self, vpkg_name): """ True if this package provides a virtual package with the specified name """ return any(s.name == vpkg_name for s in self.provided) - def virtual_dependencies(self, visited=None): - for spec in sorted(set(self.preorder_traversal(virtual=True))): - yield spec - @property def installed(self): return os.path.isdir(self.prefix) @@ -743,13 +704,13 @@ class Package(object): # Ask the user whether to skip the checksum if we're # interactive, but just fail if non-interactive. - checksum_msg = "Add a checksum or use --no-checksum to skip this check." # NOQA: ignore=E501 + ck_msg = "Add a checksum or use --no-checksum to skip this check." ignore_checksum = False if sys.stdout.isatty(): ignore_checksum = tty.get_yes_or_no(" Fetch anyway?", default=False) if ignore_checksum: - tty.msg("Fetching with no checksum.", checksum_msg) + tty.msg("Fetching with no checksum.", ck_msg) if not ignore_checksum: raise FetchError("Will not fetch %s" % @@ -1236,7 +1197,15 @@ class Package(object): def do_uninstall(self, force=False): if not self.installed: - raise InstallError(str(self.spec) + " is not installed.") + # prefix may not exist, but DB may be inconsistent. Try to fix by + # removing, but omit hooks. + specs = spack.installed_db.query(self.spec, installed=True) + if specs: + spack.installed_db.remove(specs[0]) + tty.msg("Removed stale DB entry for %s" % self.spec.short_spec) + return + else: + raise InstallError(str(self.spec) + " is not installed.") if not force: dependents = self.installed_dependents @@ -1335,9 +1304,10 @@ class Package(object): continue for dep in aspec.traverse(deptype='run'): if self.spec == dep: + msg = ("Cannot deactivate %s because %s is activated " + "and depends on it.") raise ActivationError( - "Cannot deactivate %s because %s is activated and depends on it." # NOQA: ignore=E501 - % (self.spec.short_spec, aspec.short_spec)) + msg % (self.spec.short_spec, aspec.short_spec)) self.extendee_spec.package.deactivate(self, **self.extendee_args) @@ -1446,6 +1416,7 @@ def use_cray_compiler_names(): os.environ['FC'] = 'ftn' os.environ['F77'] = 'ftn' + def flatten_dependencies(spec, flat_dir): """Make each dependency of spec present in dir via symlink.""" for dep in spec.traverse(root=False): @@ -1593,6 +1564,7 @@ def make_executable(path): class CMakePackage(StagedPackage): + def make_make(self): import multiprocessing # number of jobs spack will to build with. @@ -1769,12 +1741,14 @@ class ExtensionError(PackageError): class ExtensionConflictError(ExtensionError): + def __init__(self, path): super(ExtensionConflictError, self).__init__( "Extension blocked by file: %s" % path) class ActivationError(ExtensionError): + def __init__(self, msg, long_msg=None): super(ActivationError, self).__init__(msg, long_msg) diff --git a/lib/spack/spack/parse.py b/lib/spack/spack/parse.py index 8adf957e7f..1b88db2d7c 100644 --- a/lib/spack/spack/parse.py +++ b/lib/spack/spack/parse.py @@ -29,6 +29,7 @@ import spack.error class Token: """Represents tokens; generated from input by lexer and fed to parse().""" + def __init__(self, type, value='', start=0, end=0): self.type = type self.value = value @@ -51,11 +52,13 @@ class Token: class Lexer(object): """Base class for Lexers that keep track of line numbers.""" + def __init__(self, lexicon): self.scanner = re.Scanner(lexicon) def token(self, type, value=''): - return Token(type, value, self.scanner.match.start(0), self.scanner.match.end(0)) + return Token(type, value, + self.scanner.match.start(0), self.scanner.match.end(0)) def lex(self, text): tokens, remainder = self.scanner.scan(text) @@ -66,10 +69,11 @@ class Lexer(object): class Parser(object): """Base class for simple recursive descent parsers.""" + def __init__(self, lexer): - self.tokens = iter([]) # iterators over tokens, handled in order. Starts empty. - self.token = Token(None) # last accepted token starts at beginning of file - self.next = None # next token + self.tokens = iter([]) # iterators over tokens, handled in order. + self.token = Token(None) # last accepted token + self.next = None # next token self.lexer = lexer self.text = None @@ -82,11 +86,12 @@ class Parser(object): def push_tokens(self, iterable): """Adds all tokens in some iterable to the token stream.""" - self.tokens = itertools.chain(iter(iterable), iter([self.next]), self.tokens) + self.tokens = itertools.chain( + iter(iterable), iter([self.next]), self.tokens) self.gettok() def accept(self, id): - """Puts the next symbol in self.token if we like it. Then calls gettok()""" + """Put the next symbol in self.token if accepted, then call gettok()""" if self.next and self.next.is_a(id): self.token = self.next self.gettok() @@ -124,9 +129,9 @@ class Parser(object): return self.do_parse() - class ParseError(spack.error.SpackError): """Raised when we don't hit an error while parsing.""" + def __init__(self, message, string, pos): super(ParseError, self).__init__(message) self.string = string @@ -135,5 +140,6 @@ class ParseError(spack.error.SpackError): class LexError(ParseError): """Raised when we don't know how to lex something.""" + def __init__(self, message, string, pos): super(LexError, self).__init__(message, string, pos) diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py index c2e181be2f..0bd9f5d29d 100644 --- a/lib/spack/spack/patch.py +++ b/lib/spack/spack/patch.py @@ -24,7 +24,6 @@ ############################################################################## import os -import llnl.util.tty as tty from llnl.util.filesystem import join_path import spack @@ -59,7 +58,6 @@ class Patch(object): if not os.path.isfile(self.path): raise NoSuchPatchFileError(pkg_name, self.path) - def apply(self, stage): """Fetch this patch, if necessary, and apply it to the source code in the supplied stage. @@ -84,9 +82,9 @@ class Patch(object): patch_stage.destroy() - class NoSuchPatchFileError(spack.error.SpackError): """Raised when user specifies a patch file that doesn't exist.""" + def __init__(self, package, path): super(NoSuchPatchFileError, self).__init__( "No such patch file for package %s: %s" % (package, path)) diff --git a/lib/spack/spack/platforms/bgq.py b/lib/spack/spack/platforms/bgq.py index e0eb76f336..91afdd04db 100644 --- a/lib/spack/spack/platforms/bgq.py +++ b/lib/spack/spack/platforms/bgq.py @@ -1,6 +1,7 @@ import os from spack.architecture import Platform, Target + class Bgq(Platform): priority = 30 front_end = 'power7' @@ -15,4 +16,3 @@ class Bgq(Platform): @classmethod def detect(self): return os.path.exists('/bgsys') - diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py new file mode 100644 index 0000000000..0059b49ff1 --- /dev/null +++ b/lib/spack/spack/platforms/cray.py @@ -0,0 +1,105 @@ +import os +import re +import spack.config +import llnl.util.tty as tty +from spack.util.executable import which +from spack.architecture import Platform, Target, NoPlatformError +from spack.operating_systems.linux_distro import LinuxDistro +from spack.operating_systems.cnl import Cnl +from llnl.util.filesystem import join_path + +# Craype- module prefixes that are not valid CPU targets. +NON_TARGETS = ('hugepages', 'network', 'target', 'accel', 'xtpe') + + +def _target_from_clean_env(name): + '''Return the default back_end target as loaded in a clean login session. + + A bash subshell is launched with a wiped environment and the list of loaded + modules is parsed for the first acceptable CrayPE target. + ''' + # Based on the incantation: + # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')" + targets = [] + if name != 'front_end': + env = which('env') + env.add_default_arg('-') + # CAUTION - $USER is generally needed to initialize the environment. + # There may be other variables needed for general success. + output = env('USER=%s' % os.environ['USER'], + '/bin/bash', '--noprofile', '--norc', '-c', + '. /etc/profile; module list -lt', + output=str, error=str) + default_modules = [i for i in output.splitlines() + if len(i.split()) == 1] + tty.debug("Found default modules:", + *[" " + mod for mod in default_modules]) + pattern = 'craype-(?!{0})(\S*)'.format('|'.join(NON_TARGETS)) + for mod in default_modules: + if 'craype-' in mod: + targets.extend(re.findall(pattern, mod)) + return targets[0] if targets else None + + +class Cray(Platform): + priority = 10 + + def __init__(self): + ''' Create a Cray system platform. + + Target names should use craype target names but not include the + 'craype-' prefix. Uses first viable target from: + self + envars [SPACK_FRONT_END, SPACK_BACK_END] + configuration file "targets.yaml" with keys 'front_end', 'back_end' + scanning /etc/bash/bashrc.local for back_end only + ''' + super(Cray, self).__init__('cray') + + # Get targets from config or make best guess from environment: + conf = spack.config.get_config('targets') + for name in ('front_end', 'back_end'): + _target = getattr(self, name, None) + if _target is None: + _target = os.environ.get('SPACK_' + name.upper()) + if _target is None: + _target = conf.get(name) + if _target is None: + _target = _target_from_clean_env(name) + setattr(self, name, _target) + + if _target is not None: + self.add_target(name, Target(_target, 'craype-' + _target)) + self.add_target(_target, Target(_target, 'craype-' + _target)) + + if self.back_end is not None: + self.default = self.back_end + self.add_target( + 'default', Target(self.default, 'craype-' + self.default)) + else: + raise NoPlatformError() + + front_distro = LinuxDistro() + back_distro = Cnl() + + self.default_os = str(back_distro) + self.back_os = self.default_os + self.front_os = str(front_distro) + + self.add_operating_system(self.back_os, back_distro) + self.add_operating_system(self.front_os, front_distro) + + @classmethod + def setup_platform_environment(self, pkg, env): + """ Change the linker to default dynamic to be more + similar to linux/standard linker behavior + """ + env.set('CRAYPE_LINK_TYPE', 'dynamic') + cray_wrapper_names = join_path(spack.build_env_path, 'cray') + if os.path.isdir(cray_wrapper_names): + env.prepend_path('PATH', cray_wrapper_names) + env.prepend_path('SPACK_ENV_PATH', cray_wrapper_names) + + @classmethod + def detect(self): + return os.environ.get('CRAYPE_VERSION') is not None diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py deleted file mode 100644 index 03d0383cc5..0000000000 --- a/lib/spack/spack/platforms/cray_xc.py +++ /dev/null @@ -1,72 +0,0 @@ -import os -import spack -from spack.architecture import Platform, Target -from spack.operating_systems.linux_distro import LinuxDistro -from spack.operating_systems.cnl import Cnl -from spack.util.executable import which -from llnl.util.filesystem import join_path - - -class CrayXc(Platform): - priority = 20 - front_end = 'sandybridge' - back_end = 'ivybridge' - default = 'ivybridge' - - back_os = "CNL10" - default_os = "CNL10" - - def __init__(self): - ''' Since cori doesn't have ivybridge as a front end it's better - if we use CRAY_CPU_TARGET as the default. This will ensure - that if we're on a XC-40 or XC-30 then we can detect the target - ''' - super(CrayXc, self).__init__('cray_xc') - - # Handle the default here so we can check for a key error - if 'CRAY_CPU_TARGET' in os.environ: - self.default = os.environ['CRAY_CPU_TARGET'] - - # Change the defaults to haswell if we're on an XC40 - if self.default == 'haswell': - self.front_end = self.default - self.back_end = self.default - - # Could switch to use modules and fe targets for front end - # Currently using compilers by path for front end. - self.add_target('sandybridge', Target('sandybridge')) - self.add_target('ivybridge', - Target('ivybridge', 'craype-ivybridge')) - self.add_target('haswell', - Target('haswell', 'craype-haswell')) - - # Front end of the cray platform is a linux distro. - linux_dist = LinuxDistro() - self.front_os = str(linux_dist) - self.add_operating_system(str(linux_dist), linux_dist) - self.add_operating_system('CNL10', Cnl()) - - @classmethod - def setup_platform_environment(self, pkg, env): - """ Change the linker to default dynamic to be more - similar to linux/standard linker behavior - """ - env.set('CRAYPE_LINK_TYPE', 'dynamic') - cray_wrapper_names = join_path(spack.build_env_path, 'cray') - if os.path.isdir(cray_wrapper_names): - env.prepend_path('PATH', cray_wrapper_names) - env.prepend_path('SPACK_ENV_PATHS', cray_wrapper_names) - - @classmethod - def detect(self): - try: - cc_verbose = which('ftn') - text = cc_verbose('-craype-verbose', - output=str, error=str, - ignore_errors=True).split() - if '-D__CRAYXC' in text: - return True - else: - return False - except: - return False diff --git a/lib/spack/spack/platforms/darwin.py b/lib/spack/spack/platforms/darwin.py index d47dd640f9..974ce3a3f9 100644 --- a/lib/spack/spack/platforms/darwin.py +++ b/lib/spack/spack/platforms/darwin.py @@ -2,6 +2,7 @@ import subprocess from spack.architecture import Platform, Target from spack.operating_systems.mac_os import MacOs + class Darwin(Platform): priority = 89 front_end = 'x86_64' @@ -21,6 +22,6 @@ class Darwin(Platform): @classmethod def detect(self): - platform = subprocess.Popen(['uname', '-a'], stdout = subprocess.PIPE) + platform = subprocess.Popen(['uname', '-a'], stdout=subprocess.PIPE) platform, _ = platform.communicate() return 'darwin' in platform.strip().lower() diff --git a/lib/spack/spack/platforms/linux.py b/lib/spack/spack/platforms/linux.py index 4d3f59c320..38d2cdbfec 100644 --- a/lib/spack/spack/platforms/linux.py +++ b/lib/spack/spack/platforms/linux.py @@ -3,6 +3,7 @@ import platform from spack.architecture import Platform, Target from spack.operating_systems.linux_distro import LinuxDistro + class Linux(Platform): priority = 90 @@ -26,6 +27,6 @@ class Linux(Platform): @classmethod def detect(self): - platform = subprocess.Popen(['uname', '-a'], stdout = subprocess.PIPE) + platform = subprocess.Popen(['uname', '-a'], stdout=subprocess.PIPE) platform, _ = platform.communicate() return 'linux' in platform.strip().lower() diff --git a/lib/spack/spack/platforms/test.py b/lib/spack/spack/platforms/test.py index 8fa2585a7a..c918211555 100644 --- a/lib/spack/spack/platforms/test.py +++ b/lib/spack/spack/platforms/test.py @@ -1,4 +1,27 @@ -import subprocess +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## from spack.architecture import Platform, Target from spack.operating_systems.linux_distro import LinuxDistro from spack.operating_systems.cnl import Cnl @@ -9,7 +32,7 @@ class Test(Platform): front_end = 'x86_32' back_end = 'x86_64' default = 'x86_64' - + back_os = 'CNL10' default_os = 'CNL10' diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py index 5f18e212b6..45a41c8e2b 100644 --- a/lib/spack/spack/preferred_packages.py +++ b/lib/spack/spack/preferred_packages.py @@ -156,14 +156,14 @@ class PreferredPackages(object): """Return True iff the named package has a list of preferred providers""" return bool(self._order_for_package(pkgname, 'providers', - provider_str, False)) + provider_str, False)) def spec_preferred_variants(self, pkgname): """Return a VariantMap of preferred variants and their values""" variants = self.preferred.get(pkgname, {}).get('variants', '') if not isinstance(variants, basestring): - variants = "".join(variants) - return spack.spec.Spec(pkgname + variants).variants + variants = " ".join(variants) + return spack.spec.Spec("%s %s" % (pkgname, variants)).variants def version_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if version a of pkgname is diff --git a/lib/spack/spack/virtual.py b/lib/spack/spack/provider_index.py index bb8333f023..3f9cd285e7 100644 --- a/lib/spack/spack/virtual.py +++ b/lib/spack/spack/provider_index.py @@ -25,8 +25,14 @@ """ The ``virtual`` module contains utility classes for virtual dependencies. """ -import spack.spec -import itertools +from itertools import product as iproduct +from pprint import pformat + +import yaml +from yaml.error import MarkedYAMLError + +import spack + class ProviderIndex(object): """This is a dict of dicts used for finding providers of particular @@ -44,13 +50,30 @@ class ProviderIndex(object): Calling providers_for(spec) will find specs that provide a matching implementation of MPI. + """ - def __init__(self, specs, **kwargs): - # TODO: come up with another name for this. This "restricts" values to - # the verbatim impu specs (i.e., it doesn't pre-apply package's constraints, and - # keeps things as broad as possible, so it's really the wrong name) - self.restrict = kwargs.setdefault('restrict', False) + def __init__(self, specs=None, restrict=False): + """Create a new ProviderIndex. + + Optional arguments: + + specs + List (or sequence) of specs. If provided, will call + `update` on this ProviderIndex with each spec in the list. + + restrict + "restricts" values to the verbatim input specs; do not + pre-apply package's constraints. + + TODO: rename this. It is intended to keep things as broad + as possible without overly restricting results, so it is + not the best name. + """ + if specs is None: + specs = [] + + self.restrict = restrict self.providers = {} for spec in specs: @@ -62,9 +85,8 @@ class ProviderIndex(object): self.update(spec) - def update(self, spec): - if type(spec) != spack.spec.Spec: + if not isinstance(spec, spack.spec.Spec): spec = spack.spec.Spec(spec) if not spec.name: @@ -75,12 +97,13 @@ class ProviderIndex(object): pkg = spec.package for provided_spec, provider_spec in pkg.provided.iteritems(): - provider_spec.compiler_flags = spec.compiler_flags.copy()#We want satisfaction other than flags + # We want satisfaction other than flags + provider_spec.compiler_flags = spec.compiler_flags.copy() if provider_spec.satisfies(spec, deps=False): provided_name = provided_spec.name provider_map = self.providers.setdefault(provided_name, {}) - if not provided_spec in provider_map: + if provided_spec not in provider_map: provider_map[provided_spec] = set() if self.restrict: @@ -102,7 +125,6 @@ class ProviderIndex(object): constrained.constrain(provider_spec) provider_map[provided_spec].add(constrained) - def providers_for(self, *vpkg_specs): """Gives specs of all packages that provide virtual packages with the supplied specs.""" @@ -114,26 +136,25 @@ class ProviderIndex(object): # Add all the providers that satisfy the vpkg spec. if vspec.name in self.providers: - for provider_spec, spec_set in self.providers[vspec.name].items(): - if provider_spec.satisfies(vspec, deps=False): + for p_spec, spec_set in self.providers[vspec.name].items(): + if p_spec.satisfies(vspec, deps=False): providers.update(spec_set) # Return providers in order return sorted(providers) - # TODO: this is pretty darned nasty, and inefficient, but there # are not that many vdeps in most specs. def _cross_provider_maps(self, lmap, rmap): result = {} - for lspec, rspec in itertools.product(lmap, rmap): + for lspec, rspec in iproduct(lmap, rmap): try: constrained = lspec.constrained(rspec) except spack.spec.UnsatisfiableSpecError: continue # lp and rp are left and right provider specs. - for lp_spec, rp_spec in itertools.product(lmap[lspec], rmap[rspec]): + for lp_spec, rp_spec in iproduct(lmap[lspec], rmap[rspec]): if lp_spec.name == rp_spec.name: try: const = lp_spec.constrained(rp_spec, deps=False) @@ -142,12 +163,10 @@ class ProviderIndex(object): continue return result - def __contains__(self, name): """Whether a particular vpkg name is in the index.""" return name in self.providers - def satisfies(self, other): """Check that providers of virtual specs are compatible.""" common = set(self.providers) & set(other.providers) @@ -164,3 +183,111 @@ class ProviderIndex(object): result[name] = crossed return all(c in result for c in common) + + def to_yaml(self, stream=None): + provider_list = self._transform( + lambda vpkg, pset: [ + vpkg.to_node_dict(), [p.to_node_dict() for p in pset]], list) + + yaml.dump({'provider_index': {'providers': provider_list}}, + stream=stream) + + @staticmethod + def from_yaml(stream): + try: + yfile = yaml.load(stream) + except MarkedYAMLError, e: + raise spack.spec.SpackYAMLError( + "error parsing YAML ProviderIndex cache:", str(e)) + + if not isinstance(yfile, dict): + raise spack.spec.SpackYAMLError( + "YAML ProviderIndex was not a dict.") + + if 'provider_index' not in yfile: + raise spack.spec.SpackYAMLError( + "YAML ProviderIndex does not start with 'provider_index'") + + index = ProviderIndex() + providers = yfile['provider_index']['providers'] + index.providers = _transform( + providers, + lambda vpkg, plist: ( + spack.spec.Spec.from_node_dict(vpkg), + set(spack.spec.Spec.from_node_dict(p) for p in plist))) + return index + + def merge(self, other): + """Merge `other` ProviderIndex into this one.""" + other = other.copy() # defensive copy. + + for pkg in other.providers: + if pkg not in self.providers: + self.providers[pkg] = other.providers[pkg] + continue + + spdict, opdict = self.providers[pkg], other.providers[pkg] + for provided_spec in opdict: + if provided_spec not in spdict: + spdict[provided_spec] = opdict[provided_spec] + continue + + spdict[provided_spec] += opdict[provided_spec] + + def remove_provider(self, pkg_name): + """Remove a provider from the ProviderIndex.""" + empty_pkg_dict = [] + for pkg, pkg_dict in self.providers.items(): + empty_pset = [] + for provided, pset in pkg_dict.items(): + same_name = set(p for p in pset if p.fullname == pkg_name) + pset.difference_update(same_name) + + if not pset: + empty_pset.append(provided) + + for provided in empty_pset: + del pkg_dict[provided] + + if not pkg_dict: + empty_pkg_dict.append(pkg) + + for pkg in empty_pkg_dict: + del self.providers[pkg] + + def copy(self): + """Deep copy of this ProviderIndex.""" + clone = ProviderIndex() + clone.providers = self._transform( + lambda vpkg, pset: (vpkg, set((p.copy() for p in pset)))) + return clone + + def __eq__(self, other): + return self.providers == other.providers + + def _transform(self, transform_fun, out_mapping_type=dict): + return _transform(self.providers, transform_fun, out_mapping_type) + + def __str__(self): + return pformat( + _transform(self.providers, + lambda k, v: (k, list(v)))) + + +def _transform(providers, transform_fun, out_mapping_type=dict): + """Syntactic sugar for transforming a providers dict. + + transform_fun takes a (vpkg, pset) mapping and runs it on each + pair in nested dicts. + + """ + def mapiter(mappings): + if isinstance(mappings, dict): + return mappings.iteritems() + else: + return iter(mappings) + + return dict( + (name, out_mapping_type([ + transform_fun(vpkg, pset) for vpkg, pset in mapiter(mappings)])) + for name, mappings in providers.items()) diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repository.py index 2c160a5f45..2d8dc39648 100644 --- a/lib/spack/spack/repository.py +++ b/lib/spack/spack/repository.py @@ -23,6 +23,9 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os +import stat +import shutil +import errno import exceptions import sys import inspect @@ -30,15 +33,18 @@ import imp import re import traceback from bisect import bisect_left +from types import ModuleType + import yaml import llnl.util.tty as tty from llnl.util.filesystem import * +import spack import spack.error import spack.config import spack.spec -from spack.virtual import ProviderIndex +from spack.provider_index import ProviderIndex from spack.util.naming import * # @@ -51,6 +57,7 @@ repo_namespace = 'spack.pkg' # These names describe how repos should be laid out in the filesystem. # repo_config_name = 'repo.yaml' # Top-level filename for repo config. +repo_index_name = 'index.yaml' # Top-level filename for repository index. packages_dir_name = 'packages' # Top-level repo directory containing pkgs. package_file_name = 'package.py' # Filename for packages in a repository. @@ -61,6 +68,7 @@ NOT_PROVIDED = object() def _autospec(function): """Decorator that automatically converts the argument of a single-arg function to a Spec.""" + def converter(self, spec_like, *args, **kwargs): if not isinstance(spec_like, spack.spec.Spec): spec_like = spack.spec.Spec(spec_like) @@ -68,12 +76,22 @@ def _autospec(function): return converter -def _make_namespace_module(ns): - module = imp.new_module(ns) - module.__file__ = "(spack namespace)" - module.__path__ = [] - module.__package__ = ns - return module +class SpackNamespace(ModuleType): + """ Allow lazy loading of modules.""" + + def __init__(self, namespace): + super(SpackNamespace, self).__init__(namespace) + self.__file__ = "(spack namespace)" + self.__path__ = [] + self.__name__ = namespace + self.__package__ = namespace + self.__modules = {} + + def __getattr__(self, name): + """Getattr lazily loads modules if they're not already loaded.""" + submodule = self.__package__ + '.' + name + setattr(self, name, __import__(submodule)) + return getattr(self, name) def substitute_spack_prefix(path): @@ -96,6 +114,7 @@ class RepoPath(object): combined results of the Repos in its list instead of on a single package repository. """ + def __init__(self, *repo_dirs, **kwargs): # super-namespace for all packages in the RepoPath self.super_namespace = kwargs.get('namespace', repo_namespace) @@ -104,7 +123,7 @@ class RepoPath(object): self.by_namespace = NamespaceTrie() self.by_path = {} - self._all_package_names = [] + self._all_package_names = None self._provider_index = None # If repo_dirs is empty, just use the configuration @@ -125,7 +144,6 @@ class RepoPath(object): "To remove the bad repository, run this command:", " spack repo rm %s" % root) - def swap(self, other): """Convenience function to make swapping repostiories easier. @@ -143,7 +161,6 @@ class RepoPath(object): setattr(self, attr, getattr(other, attr)) setattr(other, attr, tmp) - def _add(self, repo): """Add a repository to the namespace and path indexes. @@ -157,36 +174,28 @@ class RepoPath(object): if repo.namespace in self.by_namespace: raise DuplicateRepoError( "Package repos '%s' and '%s' both provide namespace %s" - % (repo.root, self.by_namespace[repo.namespace].root, repo.namespace)) + % (repo.root, self.by_namespace[repo.namespace].root, + repo.namespace)) # Add repo to the pkg indexes self.by_namespace[repo.full_namespace] = repo self.by_path[repo.root] = repo - # add names to the cached name list - new_pkgs = set(repo.all_package_names()) - new_pkgs.update(set(self._all_package_names)) - self._all_package_names = sorted(new_pkgs, key=lambda n:n.lower()) - - def put_first(self, repo): """Add repo first in the search path.""" self._add(repo) self.repos.insert(0, repo) - def put_last(self, repo): """Add repo last in the search path.""" self._add(repo) self.repos.append(repo) - def remove(self, repo): """Remove a repo from the search path.""" if repo in self.repos: self.repos.remove(repo) - def get_repo(self, namespace, default=NOT_PROVIDED): """Get a repository by namespace. Arguments @@ -206,38 +215,45 @@ class RepoPath(object): return default return self.by_namespace[fullspace] - def first_repo(self): """Get the first repo in precedence order.""" return self.repos[0] if self.repos else None - def all_package_names(self): """Return all unique package names in all repositories.""" + if self._all_package_names is None: + all_pkgs = set() + for repo in self.repos: + for name in repo.all_package_names(): + all_pkgs.add(name) + self._all_package_names = sorted(all_pkgs, key=lambda n: n.lower()) return self._all_package_names - def all_packages(self): for name in self.all_package_names(): yield self.get(name) + @property + def provider_index(self): + """Merged ProviderIndex from all Repos in the RepoPath.""" + if self._provider_index is None: + self._provider_index = ProviderIndex() + for repo in reversed(self.repos): + self._provider_index.merge(repo.provider_index) + + return self._provider_index @_autospec def providers_for(self, vpkg_spec): - if self._provider_index is None: - self._provider_index = ProviderIndex(self.all_package_names()) - - providers = self._provider_index.providers_for(vpkg_spec) + providers = self.provider_index.providers_for(vpkg_spec) if not providers: raise UnknownPackageError(vpkg_spec.name) return providers - @_autospec def extensions_for(self, extendee_spec): return [p for p in self.all_packages() if p.extends(extendee_spec)] - def find_module(self, fullname, path=None): """Implements precedence for overlaid namespaces. @@ -264,7 +280,6 @@ class RepoPath(object): return None - def load_module(self, fullname): """Handles loading container namespaces when necessary. @@ -273,18 +288,14 @@ class RepoPath(object): if fullname in sys.modules: return sys.modules[fullname] - # partition fullname into prefix and module name. - namespace, dot, module_name = fullname.rpartition('.') - if not self.by_namespace.is_prefix(fullname): raise ImportError("No such Spack repo: %s" % fullname) - module = _make_namespace_module(namespace) + module = SpackNamespace(fullname) module.__loader__ = self sys.modules[fullname] = module return module - @_autospec def repo_for_pkg(self, spec): """Given a spec, get the repository for its package.""" @@ -306,7 +317,6 @@ class RepoPath(object): # that can operate on packages that don't exist yet. return self.first_repo() - @_autospec def get(self, spec, new=False): """Find a repo that contains the supplied spec's package. @@ -315,12 +325,10 @@ class RepoPath(object): """ return self.repo_for_pkg(spec).get(spec) - def get_pkg_class(self, pkg_name): """Find a class for the spec's package and return the class object.""" return self.repo_for_pkg(pkg_name).get_pkg_class(pkg_name) - @_autospec def dump_provenance(self, spec, path): """Dump provenance information for a spec to a particular path. @@ -330,24 +338,19 @@ class RepoPath(object): """ return self.repo_for_pkg(spec).dump_provenance(spec, path) - def dirname_for_package_name(self, pkg_name): return self.repo_for_pkg(pkg_name).dirname_for_package_name(pkg_name) - def filename_for_package_name(self, pkg_name): return self.repo_for_pkg(pkg_name).filename_for_package_name(pkg_name) - def exists(self, pkg_name): return any(repo.exists(pkg_name) for repo in self.repos) - def __contains__(self, pkg_name): return self.exists(pkg_name) - class Repo(object): """Class representing a package repository in the filesystem. @@ -360,6 +363,7 @@ class Repo(object): A Python namespace where the repository's packages should live. """ + def __init__(self, root, namespace=repo_namespace): """Instantiate a package repository from a filesystem path. @@ -381,12 +385,14 @@ class Repo(object): # check and raise BadRepoError on fail. def check(condition, msg): - if not condition: raise BadRepoError(msg) + if not condition: + raise BadRepoError(msg) # Validate repository layout. - self.config_file = join_path(self.root, repo_config_name) + self.config_file = join_path(self.root, repo_config_name) check(os.path.isfile(self.config_file), "No %s found in '%s'" % (repo_config_name, root)) + self.packages_path = join_path(self.root, packages_dir_name) check(os.path.isdir(self.packages_path), "No directory '%s' found in '%s'" % (repo_config_name, root)) @@ -398,12 +404,14 @@ class Repo(object): self.namespace = config['namespace'] check(re.match(r'[a-zA-Z][a-zA-Z0-9_.]+', self.namespace), - ("Invalid namespace '%s' in repo '%s'. " % (self.namespace, self.root)) + + ("Invalid namespace '%s' in repo '%s'. " + % (self.namespace, self.root)) + "Namespaces must be valid python identifiers separated by '.'") # Set up 'full_namespace' to include the super-namespace if self.super_namespace: - self.full_namespace = "%s.%s" % (self.super_namespace, self.namespace) + self.full_namespace = "%s.%s" % ( + self.super_namespace, self.namespace) else: self.full_namespace = self.namespace @@ -414,12 +422,21 @@ class Repo(object): self._modules = {} self._classes = {} self._instances = {} + + # list of packages that are newer than the index. + self._needs_update = [] + + # Index of virtual dependencies self._provider_index = None + + # Cached list of package names. self._all_package_names = None # make sure the namespace for packages in this repo exists. self._create_namespace() + # Unique filename for cache of virtual dependency providers + self._cache_file = 'providers/%s-index.yaml' % self.namespace def _create_namespace(self): """Create this repo's namespace module and insert it into sys.modules. @@ -429,10 +446,11 @@ class Repo(object): """ parent = None - for l in range(1, len(self._names)+1): + for l in range(1, len(self._names) + 1): ns = '.'.join(self._names[:l]) - if not ns in sys.modules: - module = _make_namespace_module(ns) + + if ns not in sys.modules: + module = SpackNamespace(ns) module.__loader__ = self sys.modules[ns] = module @@ -442,14 +460,14 @@ class Repo(object): # This ensures that we can do things like: # import spack.pkg.builtin.mpich as mpich if parent: - modname = self._names[l-1] - if not hasattr(parent, modname): - setattr(parent, modname, module) + modname = self._names[l - 1] + setattr(parent, modname, module) else: - # no need to set up a module, but keep track of the parent. + # no need to set up a module module = sys.modules[ns] - parent = module + # but keep track of the parent in this loop + parent = module def real_name(self, import_name): """Allow users to import Spack packages using Python identifiers. @@ -476,13 +494,11 @@ class Repo(object): return name return None - def is_prefix(self, fullname): """True if fullname is a prefix of this Repo's namespace.""" parts = fullname.split('.') return self._names[:len(parts)] == parts - def find_module(self, fullname, path=None): """Python find_module import hook. @@ -498,7 +514,6 @@ class Repo(object): return None - def load_module(self, fullname): """Python importer load hook. @@ -510,7 +525,7 @@ class Repo(object): namespace, dot, module_name = fullname.rpartition('.') if self.is_prefix(fullname): - module = _make_namespace_module(fullname) + module = SpackNamespace(fullname) elif namespace == self.full_namespace: real_name = self.real_name(module_name) @@ -523,8 +538,12 @@ class Repo(object): module.__loader__ = self sys.modules[fullname] = module - return module + if namespace != fullname: + parent = sys.modules[namespace] + if not hasattr(parent, module_name): + setattr(parent, module_name, module) + return module def _read_config(self): """Check for a YAML config file in this db's root directory.""" @@ -533,40 +552,39 @@ class Repo(object): yaml_data = yaml.load(reponame_file) if (not yaml_data or 'repo' not in yaml_data or - not isinstance(yaml_data['repo'], dict)): - tty.die("Invalid %s in repository %s" - % (repo_config_name, self.root)) + not isinstance(yaml_data['repo'], dict)): + tty.die("Invalid %s in repository %s" % ( + repo_config_name, self.root)) return yaml_data['repo'] - except exceptions.IOError, e: + except exceptions.IOError: tty.die("Error reading %s when opening %s" % (self.config_file, self.root)) - @_autospec def get(self, spec, new=False): if spec.virtual: raise UnknownPackageError(spec.name) if spec.namespace and spec.namespace != self.namespace: - raise UnknownPackageError("Repository %s does not contain package %s" - % (self.namespace, spec.fullname)) + raise UnknownPackageError( + "Repository %s does not contain package %s" + % (self.namespace, spec.fullname)) key = hash(spec) if new or key not in self._instances: package_class = self.get_pkg_class(spec.name) try: - copy = spec.copy() # defensive copy. Package owns its spec. + copy = spec.copy() # defensive copy. Package owns its spec. self._instances[key] = package_class(copy) - except Exception, e: + except Exception: if spack.debug: sys.excepthook(*sys.exc_info()) raise FailedConstructorError(spec.fullname, *sys.exc_info()) return self._instances[key] - @_autospec def dump_provenance(self, spec, path): """Dump provenance information for a spec to a particular path. @@ -579,8 +597,9 @@ class Repo(object): raise UnknownPackageError(spec.name) if spec.namespace and spec.namespace != self.namespace: - raise UnknownPackageError("Repository %s does not contain package %s." - % (self.namespace, spec.fullname)) + raise UnknownPackageError( + "Repository %s does not contain package %s." + % (self.namespace, spec.fullname)) # Install any patch files needed by packages. mkdirp(path) @@ -595,34 +614,61 @@ class Repo(object): # Install the package.py file itself. install(self.filename_for_package_name(spec), path) - def purge(self): """Clear entire package instance cache.""" self._instances.clear() + def _update_provider_index(self): + # Check modification dates of all packages + self._fast_package_check() - @_autospec - def providers_for(self, vpkg_spec): + def read(): + with open(self.index_file) as f: + self._provider_index = ProviderIndex.from_yaml(f) + + # Read the old ProviderIndex, or make a new one. + key = self._cache_file + index_existed = spack.user_cache.init_entry(key) + if index_existed and not self._needs_update: + with spack.user_cache.read_transaction(key) as f: + self._provider_index = ProviderIndex.from_yaml(f) + else: + with spack.user_cache.write_transaction(key) as (old, new): + if old: + self._provider_index = ProviderIndex.from_yaml(old) + else: + self._provider_index = ProviderIndex() + + for pkg_name in self._needs_update: + namespaced_name = '%s.%s' % (self.namespace, pkg_name) + self._provider_index.remove_provider(namespaced_name) + self._provider_index.update(namespaced_name) + + self._provider_index.to_yaml(new) + + @property + def provider_index(self): + """A provider index with names *specific* to this repo.""" if self._provider_index is None: - self._provider_index = ProviderIndex(self.all_package_names()) + self._update_provider_index() + return self._provider_index - providers = self._provider_index.providers_for(vpkg_spec) + @_autospec + def providers_for(self, vpkg_spec): + providers = self.provider_index.providers_for(vpkg_spec) if not providers: raise UnknownPackageError(vpkg_spec.name) return providers - @_autospec def extensions_for(self, extendee_spec): return [p for p in self.all_packages() if p.extends(extendee_spec)] - def _check_namespace(self, spec): """Check that the spec's namespace is the same as this repository's.""" if spec.namespace and spec.namespace != self.namespace: raise UnknownNamespaceError(spec.namespace) - @_autospec def dirname_for_package_name(self, spec): """Get the directory name for a particular package. This is the @@ -630,7 +676,6 @@ class Repo(object): self._check_namespace(spec) return join_path(self.packages_path, spec.name) - @_autospec def filename_for_package_name(self, spec): """Get the filename for the module we should load for a particular @@ -645,48 +690,95 @@ class Repo(object): pkg_dir = self.dirname_for_package_name(spec.name) return join_path(pkg_dir, package_file_name) + def _fast_package_check(self): + """List packages in the repo and check whether index is up to date. - def all_package_names(self): - """Returns a sorted list of all package names in the Repo.""" + Both of these opreations require checking all `package.py` + files so we do them at the same time. We list the repo + directory and look at package.py files, and we compare the + index modification date with the ost recently modified package + file, storing the result. + + The implementation here should try to minimize filesystem + calls. At the moment, it is O(number of packages) and makes + about one stat call per package. This is resonably fast, and + avoids actually importing packages in Spack, which is slow. + + """ if self._all_package_names is None: self._all_package_names = [] + # Get index modification time. + index_mtime = spack.user_cache.mtime(self._cache_file) + for pkg_name in os.listdir(self.packages_path): # Skip non-directories in the package root. pkg_dir = join_path(self.packages_path, pkg_name) - if not os.path.isdir(pkg_dir): - continue - - # Skip directories without a package.py in them. - pkg_file = join_path(self.packages_path, pkg_name, package_file_name) - if not os.path.isfile(pkg_file): - continue # Warn about invalid names that look like packages. if not valid_module_name(pkg_name): - tty.warn("Skipping package at %s. '%s' is not a valid Spack module name." - % (pkg_dir, pkg_name)) + msg = ("Skipping package at %s. " + "'%s' is not a valid Spack module name.") + tty.warn(msg % (pkg_dir, pkg_name)) + continue + + # construct the file name from the directory + pkg_file = join_path( + self.packages_path, pkg_name, package_file_name) + + # Use stat here to avoid lots of calls to the filesystem. + try: + sinfo = os.stat(pkg_file) + except OSError as e: + if e.errno == errno.ENOENT: + # No package.py file here. + continue + elif e.errno == errno.EACCES: + tty.warn("Can't read package file %s." % pkg_file) + continue + raise e + + # if it's not a file, skip it. + if stat.S_ISDIR(sinfo.st_mode): continue # All checks passed. Add it to the list. self._all_package_names.append(pkg_name) + + # record the package if it is newer than the index. + if sinfo.st_mtime > index_mtime: + self._needs_update.append(pkg_name) + self._all_package_names.sort() return self._all_package_names + def all_package_names(self): + """Returns a sorted list of all package names in the Repo.""" + self._fast_package_check() + return self._all_package_names def all_packages(self): + """Iterator over all packages in the repository. + + Use this with care, because loading packages is slow. + + """ for name in self.all_package_names(): yield self.get(name) - def exists(self, pkg_name): """Whether a package with the supplied name exists.""" - # This does a binary search in the sorted list. - idx = bisect_left(self.all_package_names(), pkg_name) - return (idx < len(self._all_package_names) and - self._all_package_names[idx] == pkg_name) + if self._all_package_names: + # This does a binary search in the sorted list. + idx = bisect_left(self.all_package_names(), pkg_name) + return (idx < len(self._all_package_names) and + self._all_package_names[idx] == pkg_name) + # If we haven't generated the full package list, don't. + # Just check whether the file exists. + filename = self.filename_for_package_name(pkg_name) + return os.path.exists(filename) def _get_pkg_module(self, pkg_name): """Create a module for a particular package. @@ -719,7 +811,6 @@ class Repo(object): return self._modules[pkg_name] - def get_pkg_class(self, pkg_name): """Get the class for the package out of its module. @@ -727,6 +818,11 @@ class Repo(object): package. Then extracts the package class from the module according to Spack's naming convention. """ + namespace, _, pkg_name = pkg_name.rpartition('.') + if namespace and (namespace != self.namespace): + raise InvalidNamespaceError('Invalid namespace for %s repo: %s' + % (self.namespace, namespace)) + class_name = mod_to_class(pkg_name) module = self._get_pkg_module(pkg_name) @@ -736,15 +832,12 @@ class Repo(object): return cls - def __str__(self): return "[Repo '%s' at '%s']" % (self.namespace, self.root) - def __repr__(self): return self.__str__() - def __contains__(self, pkg_name): return self.exists(pkg_name) @@ -753,30 +846,37 @@ def create_repo(root, namespace=None): """Create a new repository in root with the specified namespace. If the namespace is not provided, use basename of root. - Return the canonicalized path and the namespace of the created repository. + Return the canonicalized path and namespace of the created repository. """ root = canonicalize_path(root) if not namespace: namespace = os.path.basename(root) if not re.match(r'\w[\.\w-]*', namespace): - raise InvalidNamespaceError("'%s' is not a valid namespace." % namespace) + raise InvalidNamespaceError( + "'%s' is not a valid namespace." % namespace) existed = False if os.path.exists(root): if os.path.isfile(root): - raise BadRepoError('File %s already exists and is not a directory' % root) + raise BadRepoError('File %s already exists and is not a directory' + % root) elif os.path.isdir(root): if not os.access(root, os.R_OK | os.W_OK): - raise BadRepoError('Cannot create new repo in %s: cannot access directory.' % root) + raise BadRepoError( + 'Cannot create new repo in %s: cannot access directory.' + % root) if os.listdir(root): - raise BadRepoError('Cannot create new repo in %s: directory is not empty.' % root) + raise BadRepoError( + 'Cannot create new repo in %s: directory is not empty.' + % root) existed = True full_path = os.path.realpath(root) parent = os.path.dirname(full_path) if not os.access(parent, os.R_OK | os.W_OK): - raise BadRepoError("Cannot create repository in %s: can't access parent!" % root) + raise BadRepoError( + "Cannot create repository in %s: can't access parent!" % root) try: config_path = os.path.join(root, repo_config_name) @@ -827,6 +927,7 @@ class PackageLoadError(spack.error.SpackError): class UnknownPackageError(PackageLoadError): """Raised when we encounter a package spack doesn't have.""" + def __init__(self, name, repo=None): msg = None if repo: @@ -839,6 +940,7 @@ class UnknownPackageError(PackageLoadError): class UnknownNamespaceError(PackageLoadError): """Raised when we encounter an unknown namespace""" + def __init__(self, namespace): super(UnknownNamespaceError, self).__init__( "Unknown namespace: %s" % namespace) @@ -846,6 +948,7 @@ class UnknownNamespaceError(PackageLoadError): class FailedConstructorError(PackageLoadError): """Raised when a package's class constructor fails.""" + def __init__(self, name, exc_type, exc_obj, exc_tb): super(FailedConstructorError, self).__init__( "Class constructor failed for package '%s'." % name, diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py index 24b675f8da..1d4d448298 100644 --- a/lib/spack/spack/resource.py +++ b/lib/spack/spack/resource.py @@ -31,9 +31,11 @@ package to enable optional features. class Resource(object): + """Represents an optional resource to be fetched by a package. + + Aggregates a name, a fetcher, a destination and a placement. """ - Represents an optional resource. Aggregates a name, a fetcher, a destination and a placement - """ + def __init__(self, name, fetcher, destination, placement): self.name = name self.fetcher = fetcher diff --git a/lib/spack/spack/schema/__init__.py b/lib/spack/spack/schema/__init__.py new file mode 100644 index 0000000000..de45ea921f --- /dev/null +++ b/lib/spack/spack/schema/__init__.py @@ -0,0 +1,33 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""This module contains jsonschema files for all of Spack's YAML formats. +""" +from llnl.util.lang import list_modules + +# Automatically bring in all sub-modules +__all__ = [] +for mod in list_modules(__path__[0]): + __import__('%s.%s' % (__name__, mod)) + __all__.append(mod) diff --git a/lib/spack/spack/schema/compilers.py b/lib/spack/spack/schema/compilers.py new file mode 100644 index 0000000000..2ffac03a66 --- /dev/null +++ b/lib/spack/spack/schema/compilers.py @@ -0,0 +1,80 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Schema for compiler configuration files.""" + + +schema = { + '$schema': 'http://json-schema.org/schema#', + 'title': 'Spack compiler configuration file schema', + 'type': 'object', + 'additionalProperties': False, + 'patternProperties': { + 'compilers:?': { # optional colon for overriding site config. + 'type': 'array', + 'items': { + 'compiler': { + 'type': 'object', + 'additionalProperties': False, + 'required': [ + 'paths', 'spec', 'modules', 'operating_system'], + 'properties': { + 'paths': { + 'type': 'object', + 'required': ['cc', 'cxx', 'f77', 'fc'], + 'additionalProperties': False, + 'properties': { + 'cc': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'cxx': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'f77': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'fc': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'cflags': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'cxxflags': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'fflags': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'cppflags': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'ldflags': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'ldlibs': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}}}, + 'spec': {'type': 'string'}, + 'operating_system': {'type': 'string'}, + 'alias': {'anyOf': [{'type': 'string'}, + {'type': 'null'}]}, + 'modules': {'anyOf': [{'type': 'string'}, + {'type': 'null'}, + {'type': 'array'}]} + }, + }, + }, + }, + }, +} diff --git a/lib/spack/spack/schema/mirrors.py b/lib/spack/spack/schema/mirrors.py new file mode 100644 index 0000000000..ff599b9c7d --- /dev/null +++ b/lib/spack/spack/schema/mirrors.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Schema for mirror configuration files.""" + + +schema = { + '$schema': 'http://json-schema.org/schema#', + 'title': 'Spack mirror configuration file schema', + 'type': 'object', + 'additionalProperties': False, + 'patternProperties': { + r'mirrors:?': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'patternProperties': { + r'\w[\w-]*': { + 'type': 'string'}, + }, + }, + }, +} diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py new file mode 100644 index 0000000000..f8066919f1 --- /dev/null +++ b/lib/spack/spack/schema/modules.py @@ -0,0 +1,158 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Schema for mirror configuration files.""" + + +schema = { + '$schema': 'http://json-schema.org/schema#', + 'title': 'Spack module file configuration file schema', + 'type': 'object', + 'additionalProperties': False, + 'definitions': { + 'array_of_strings': { + 'type': 'array', + 'default': [], + 'items': { + 'type': 'string' + } + }, + 'dictionary_of_strings': { + 'type': 'object', + 'patternProperties': { + r'\w[\w-]*': { # key + 'type': 'string' + } + } + }, + 'dependency_selection': { + 'type': 'string', + 'enum': ['none', 'direct', 'all'] + }, + 'module_file_configuration': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'properties': { + 'filter': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'properties': { + 'environment_blacklist': { + 'type': 'array', + 'default': [], + 'items': { + 'type': 'string' + } + } + } + }, + 'autoload': { + '$ref': '#/definitions/dependency_selection'}, + 'prerequisites': { + '$ref': '#/definitions/dependency_selection'}, + 'conflict': { + '$ref': '#/definitions/array_of_strings'}, + 'load': { + '$ref': '#/definitions/array_of_strings'}, + 'suffixes': { + '$ref': '#/definitions/dictionary_of_strings'}, + 'environment': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'properties': { + 'set': { + '$ref': '#/definitions/dictionary_of_strings'}, + 'unset': { + '$ref': '#/definitions/array_of_strings'}, + 'prepend_path': { + '$ref': '#/definitions/dictionary_of_strings'}, + 'append_path': { + '$ref': '#/definitions/dictionary_of_strings'} + } + } + } + }, + 'module_type_configuration': { + 'type': 'object', + 'default': {}, + 'anyOf': [ + {'properties': { + 'hash_length': { + 'type': 'integer', + 'minimum': 0, + 'default': 7 + }, + 'whitelist': { + '$ref': '#/definitions/array_of_strings'}, + 'blacklist': { + '$ref': '#/definitions/array_of_strings'}, + 'naming_scheme': { + 'type': 'string' # Can we be more specific here? + } + }}, + {'patternProperties': { + r'\w[\w-]*': { + '$ref': '#/definitions/module_file_configuration' + } + }} + ] + } + }, + 'patternProperties': { + r'modules:?': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'properties': { + 'prefix_inspections': { + 'type': 'object', + 'patternProperties': { + # prefix-relative path to be inspected for existence + r'\w[\w-]*': { + '$ref': '#/definitions/array_of_strings'}}}, + 'enable': { + 'type': 'array', + 'default': [], + 'items': { + 'type': 'string', + 'enum': ['tcl', 'dotkit']}}, + 'tcl': { + 'allOf': [ + # Base configuration + {'$ref': '#/definitions/module_type_configuration'}, + {} # Specific tcl extensions + ]}, + 'dotkit': { + 'allOf': [ + # Base configuration + {'$ref': '#/definitions/module_type_configuration'}, + {} # Specific dotkit extensions + ]}, + } + }, + }, +} diff --git a/lib/spack/spack/schema/packages.py b/lib/spack/spack/schema/packages.py new file mode 100644 index 0000000000..e19f3f533b --- /dev/null +++ b/lib/spack/spack/schema/packages.py @@ -0,0 +1,86 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Schema for packages.yaml configuration files.""" + + +schema = { + '$schema': 'http://json-schema.org/schema#', + 'title': 'Spack package configuration file schema', + 'type': 'object', + 'additionalProperties': False, + 'patternProperties': { + r'packages:?': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'patternProperties': { + r'\w[\w-]*': { # package name + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'properties': { + 'version': { + 'type': 'array', + 'default': [], + # version strings + 'items': {'anyOf': [{'type': 'string'}, + {'type': 'number'}]}}, + 'compiler': { + 'type': 'array', + 'default': [], + 'items': {'type': 'string'}}, # compiler specs + 'buildable': { + 'type': 'boolean', + 'default': True, + }, + 'modules': { + 'type': 'object', + 'default': {}, + }, + 'providers': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'patternProperties': { + r'\w[\w-]*': { + 'type': 'array', + 'default': [], + 'items': {'type': 'string'}, }, }, }, + 'paths': { + 'type': 'object', + 'default': {}, + }, + 'variants': { + 'oneOf': [ + {'type': 'string'}, + {'type': 'array', + 'items': {'type': 'string'}}], + }, + }, + }, + }, + }, + }, +} diff --git a/lib/spack/spack/schema/repos.py b/lib/spack/spack/schema/repos.py new file mode 100644 index 0000000000..9f01942422 --- /dev/null +++ b/lib/spack/spack/schema/repos.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Schema for repository configuration files.""" + + +schema = { + '$schema': 'http://json-schema.org/schema#', + 'title': 'Spack repository configuration file schema', + 'type': 'object', + 'additionalProperties': False, + 'patternProperties': { + r'repos:?': { + 'type': 'array', + 'default': [], + 'items': { + 'type': 'string'}, + }, + }, +} diff --git a/lib/spack/spack/schema/targets.py b/lib/spack/spack/schema/targets.py new file mode 100644 index 0000000000..312474cab4 --- /dev/null +++ b/lib/spack/spack/schema/targets.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Schema for target configuration files.""" + + +schema = { + '$schema': 'http://json-schema.org/schema#', + 'title': 'Spack target configuration file schema', + 'type': 'object', + 'additionalProperties': False, + 'patternProperties': { + r'targets:?': { + 'type': 'object', + 'default': {}, + 'additionalProperties': False, + 'patternProperties': { + r'\w[\w-]*': { # target name + 'type': 'string', + }, + }, + }, + }, +} diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 8bdae0445e..316b7d6a8c 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -95,32 +95,33 @@ thing. Spack uses ~variant in directory names and in the canonical form of specs to avoid ambiguity. Both are provided because ~ can cause shell expansion when it is the first character in an id typed on the command line. """ -import sys -import hashlib import base64 +import hashlib import imp +import sys from StringIO import StringIO from operator import attrgetter + import yaml from yaml.error import MarkedYAMLError import llnl.util.tty as tty +from llnl.util.filesystem import join_path from llnl.util.lang import * from llnl.util.tty.color import * -from llnl.util.filesystem import join_path import spack import spack.architecture -import spack.parse -import spack.error import spack.compilers as compilers - -from spack.version import * -from spack.util.string import * -from spack.util.prefix import Prefix -from spack.util.naming import mod_to_class -from spack.virtual import ProviderIndex +import spack.error +import spack.parse from spack.build_environment import get_path_from_module, load_module +from spack.util.naming import mod_to_class +from spack.util.prefix import Prefix +from spack.util.string import * +from spack.version import * +from spack.provider_index import ProviderIndex + # Valid pattern for an identifier in Spack identifier_re = r'\w[\w-]*' @@ -161,23 +162,11 @@ special_types = { } -def index_specs(specs): - """Take a list of specs and return a dict of lists. Dict is - keyed by spec name and lists include all specs with the - same name. - """ - spec_dict = {} - for spec in specs: - if spec.name not in spec_dict: - spec_dict[spec.name] = [] - spec_dict[spec.name].append(spec) - return spec_dict - - def colorize_spec(spec): """Returns a spec colorized according to the colors specified in color_formats.""" class insert_color: + def __init__(self): self.last = None @@ -198,6 +187,7 @@ class CompilerSpec(object): """The CompilerSpec field represents the compiler or range of compiler versions that a package should be built with. CompilerSpecs have a name and a version list. """ + def __init__(self, *args): nargs = len(args) if nargs == 1: @@ -308,6 +298,7 @@ class DependencySpec(object): - spec: the spack.spec.Spec description of a dependency. - deptypes: strings representing the type of dependency this is. """ + def __init__(self, spec, deptypes): self.spec = spec self.deptypes = deptypes @@ -329,6 +320,7 @@ class VariantSpec(object): on the particular package being built, and each named variant can be enabled or disabled. """ + def __init__(self, name, value): self.name = name self.value = value @@ -340,11 +332,10 @@ class VariantSpec(object): return VariantSpec(self.name, self.value) def __str__(self): - if self.value in [True, False]: - out = '+' if self.value else '~' - return out + self.name + if type(self.value) == bool: + return '{0}{1}'.format('+' if self.value else '~', self.name) else: - return ' ' + self.name + "=" + self.value + return ' {0}={1}'.format(self.name, self.value) class VariantMap(HashableMap): @@ -453,16 +444,15 @@ class FlagMap(HashableMap): return clone def _cmp_key(self): - return ''.join(str(key) + ' '.join(str(v) for v in value) - for key, value in sorted(self.items())) + return tuple((k, tuple(v)) for k, v in sorted(self.iteritems())) def __str__(self): sorted_keys = filter( lambda flag: self[flag] != [], sorted(self.keys())) cond_symbol = ' ' if len(sorted_keys) > 0 else '' - return cond_symbol + ' '.join(str(key) + '=\"' + ' '.join(str(f) - for f in self[key]) + '\"' - for key in sorted_keys) + return cond_symbol + ' '.join( + str(key) + '=\"' + ' '.join( + str(f) for f in self[key]) + '\"' for key in sorted_keys) class DependencyMap(HashableMap): @@ -475,7 +465,7 @@ class DependencyMap(HashableMap): def __str__(self): return ''.join( - ["^" + str(self[name].spec) for name in sorted(self.keys())]) + ["^" + self[name].format() for name in sorted(self.keys())]) @key_ordering @@ -730,7 +720,7 @@ class Spec(object): """Internal package call gets only the class object for a package. Use this to just get package metadata. """ - return spack.repo.get_pkg_class(self.name) + return spack.repo.get_pkg_class(self.fullname) @property def virtual(self): @@ -876,7 +866,7 @@ class Spec(object): for name in sorted(successors): child = successors[name] children = child.spec.traverse_with_deptype( - visited, d=d + 1, deptype=deptype_query, + visited, d=d + 1, deptype=deptype, deptype_query=deptype_query, _self_deptype=child.deptypes, **kwargs) for elt in children: @@ -919,37 +909,36 @@ class Spec(object): return b32_hash def to_node_dict(self): + d = {} + params = dict((name, v.value) for name, v in self.variants.items()) params.update(dict((name, value) - for name, value in self.compiler_flags.items())) - deps = self.dependencies_dict(deptype=('link', 'run')) - d = { - 'parameters': params, - 'arch': self.architecture, - 'dependencies': dict( + for name, value in self.compiler_flags.items())) + + if params: + d['parameters'] = params + + if self.dependencies(): + deps = self.dependencies_dict(deptype=('link', 'run')) + d['dependencies'] = dict( (name, { 'hash': dspec.spec.dag_hash(), 'type': [str(s) for s in dspec.deptypes]}) for name, dspec in deps.items()) - } - # Older concrete specs do not have a namespace. Omit for - # consistent hashing. - if not self.concrete or self.namespace: + if self.namespace: d['namespace'] = self.namespace if self.architecture: # TODO: Fix the target.to_dict to account for the tuple # Want it to be a dict of dicts d['arch'] = self.architecture.to_dict() - else: - d['arch'] = None if self.compiler: d.update(self.compiler.to_dict()) - else: - d['compiler'] = None - d.update(self.versions.to_dict()) + + if self.versions: + d.update(self.versions.to_dict()) return {self.name: d} @@ -969,17 +958,18 @@ class Spec(object): spec = Spec(name) spec.namespace = node.get('namespace', None) - spec.versions = VersionList.from_dict(node) + spec._hash = node.get('hash', None) - if 'hash' in node: - spec._hash = node['hash'] + if 'version' in node or 'versions' in node: + spec.versions = VersionList.from_dict(node) - spec.architecture = spack.architecture.arch_from_dict(node['arch']) + if 'arch' in node: + spec.architecture = spack.architecture.arch_from_dict(node['arch']) - if node['compiler'] is None: - spec.compiler = None - else: + if 'compiler' in node: spec.compiler = CompilerSpec.from_dict(node) + else: + spec.compiler = None if 'parameters' in node: for name, value in node['parameters'].items(): @@ -987,14 +977,12 @@ class Spec(object): spec.compiler_flags[name] = value else: spec.variants[name] = VariantSpec(name, value) + elif 'variants' in node: for name, value in node['variants'].items(): spec.variants[name] = VariantSpec(name, value) for name in FlagMap.valid_compiler_flags(): spec.compiler_flags[name] = [] - else: - raise SpackRecordError( - "Did not find a valid format for variants in YAML file") # Don't read dependencies here; from_node_dict() is used by # from_yaml() to read the root *and* each dependency spec. @@ -1036,7 +1024,7 @@ class Spec(object): """ try: yfile = yaml.load(stream) - except MarkedYAMLError, e: + except MarkedYAMLError as e: raise SpackYAMLError("error parsing YAML spec:", str(e)) nodes = yfile['spec'] @@ -1052,6 +1040,10 @@ class Spec(object): for node in nodes: # get dependency dict from the node. name = next(iter(node)) + + if 'dependencies' not in node[name]: + continue + yaml_deps = node[name]['dependencies'] for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps): # Fill in dependencies by looking them up by name in deps dict @@ -1350,7 +1342,7 @@ class Spec(object): return flat_deps - except UnsatisfiableSpecError, e: + except UnsatisfiableSpecError as e: # Here, the DAG contains two instances of the same package # with inconsistent constraints. Users cannot produce # inconsistent specs like this on the command line: the @@ -1385,7 +1377,7 @@ class Spec(object): dep = Spec(name) try: dep.constrain(dep_spec) - except UnsatisfiableSpecError, e: + except UnsatisfiableSpecError as e: e.message = ("Conflicting conditional dependencies on" "package %s for spec %s" % (self.name, self)) raise e @@ -1471,7 +1463,7 @@ class Spec(object): try: changed |= spec_deps[dep.name].spec.constrain(dep) - except UnsatisfiableSpecError, e: + except UnsatisfiableSpecError as e: e.message = "Invalid spec: '%s'. " e.message += "Package %s requires %s %s, but spec asked for %s" e.message %= (spec_deps[dep.name].spec, dep.name, @@ -1582,7 +1574,7 @@ class Spec(object): UnsupportedCompilerError. """ for spec in self.traverse(): - # Don't get a package for a virtual name. + # raise an UnknownPackageError if the spec's package isn't real. if (not spec.virtual) and spec.name: spack.repo.get(spec.fullname) @@ -1609,8 +1601,8 @@ class Spec(object): raise UnsatisfiableSpecNameError(self.name, other.name) if (other.namespace is not None and - self.namespace is not None and - other.namespace != self.namespace): + self.namespace is not None and + other.namespace != self.namespace): raise UnsatisfiableSpecNameError(self.fullname, other.fullname) if not self.versions.overlaps(other.versions): @@ -1764,8 +1756,8 @@ class Spec(object): # namespaces either match, or other doesn't require one. if (other.namespace is not None and - self.namespace is not None and - self.namespace != other.namespace): + self.namespace is not None and + self.namespace != other.namespace): return False if self.versions and other.versions: if not self.versions.satisfies(other.versions, strict=strict): @@ -1860,7 +1852,7 @@ class Spec(object): # compatible with mpich2) for spec in self.virtual_dependencies(): if (spec.name in other_index and - not other_index.providers_for(spec)): + not other_index.providers_for(spec)): return False for spec in other.virtual_dependencies(): @@ -2356,6 +2348,7 @@ _lexer = SpecLexer() class SpecParser(spack.parse.Parser): + def __init__(self): super(SpecParser, self).__init__(_lexer) self.previous = None @@ -2405,7 +2398,7 @@ class SpecParser(spack.parse.Parser): # errors now? specs.append(self.spec(None, True)) - except spack.parse.ParseError, e: + except spack.parse.ParseError as e: raise SpecParseError(e) # If the spec has an os or a target and no platform, give it @@ -2839,15 +2832,9 @@ class SpackYAMLError(spack.error.SpackError): super(SpackYAMLError, self).__init__(msg, str(yaml_error)) -class SpackRecordError(spack.error.SpackError): - - def __init__(self, msg): - super(SpackRecordError, self).__init__(msg) - - class AmbiguousHashError(SpecError): def __init__(self, msg, *specs): super(AmbiguousHashError, self).__init__(msg) for spec in specs: - print ' ', spec.format('$.$@$%@+$+$=$#') + print(' ', spec.format('$.$@$%@+$+$=$#')) diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index b08cce43b8..7676cb9ab6 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -37,6 +37,7 @@ import spack import spack.config import spack.fetch_strategy as fs import spack.error +from spack.version import * STAGE_PREFIX = 'spack-stage-' @@ -51,10 +52,12 @@ class Stage(object): lifecycle looks like this: ``` - with Stage() as stage: # Context manager creates and destroys the stage directory + with Stage() as stage: # Context manager creates and destroys the + # stage directory stage.fetch() # Fetch a source archive into the stage. stage.expand_archive() # Expand the source archive. - <install> # Build and install the archive. (handled by user of Stage) + <install> # Build and install the archive. (handled by + # user of Stage) ``` When used as a context manager, the stage is automatically @@ -71,7 +74,8 @@ class Stage(object): stage.create() # Explicitly create the stage directory. stage.fetch() # Fetch a source archive into the stage. stage.expand_archive() # Expand the source archive. - <install> # Build and install the archive. (handled by user of Stage) + <install> # Build and install the archive. (handled by + # user of Stage) finally: stage.destroy() # Explicitly destroy the stage directory. ``` @@ -120,13 +124,17 @@ class Stage(object): elif isinstance(url_or_fetch_strategy, fs.FetchStrategy): self.fetcher = url_or_fetch_strategy else: - raise ValueError("Can't construct Stage without url or fetch strategy") + raise ValueError( + "Can't construct Stage without url or fetch strategy") self.fetcher.set_stage(self) - self.default_fetcher = self.fetcher # self.fetcher can change with mirrors. - self.skip_checksum_for_mirror = True # used for mirrored archives of repositories. + # self.fetcher can change with mirrors. + self.default_fetcher = self.fetcher + # used for mirrored archives of repositories. + self.skip_checksum_for_mirror = True - # TODO : this uses a protected member of tempfile, but seemed the only way to get a temporary name - # TODO : besides, the temporary link name won't be the same as the temporary stage area in tmp_root + # TODO : this uses a protected member of tempfile, but seemed the only + # TODO : way to get a temporary name besides, the temporary link name + # TODO : won't be the same as the temporary stage area in tmp_root self.name = name if name is None: self.name = STAGE_PREFIX + next(tempfile._get_candidate_names()) @@ -143,7 +151,6 @@ class Stage(object): # Flag to decide whether to delete the stage folder on exit or not self.keep = keep - def __enter__(self): """ Entering a stage context will create the stage directory @@ -154,7 +161,6 @@ class Stage(object): self.create() return self - def __exit__(self, exc_type, exc_val, exc_tb): """ Exiting from a stage context will delete the stage directory unless: @@ -173,12 +179,10 @@ class Stage(object): if exc_type is None and not self.keep: self.destroy() - def _need_to_create_path(self): """Makes sure nothing weird has happened since the last time we looked at path. Returns True if path already exists and is ok. - Returns False if path needs to be created. - """ + Returns False if path needs to be created.""" # Path doesn't exist yet. Will need to create it. if not os.path.exists(self.path): return True @@ -196,7 +200,8 @@ class Stage(object): if spack.use_tmp_stage: # If we're using a tmp dir, it's a link, and it points at the # right spot, then keep it. - if (real_path.startswith(real_tmp) and os.path.exists(real_path)): + if (real_path.startswith(real_tmp) and + os.path.exists(real_path)): return False else: # otherwise, just unlink it and start over. @@ -204,7 +209,8 @@ class Stage(object): return True else: - # If we're not tmp mode, then it's a link and we want a directory. + # If we're not tmp mode, then it's a link and we want a + # directory. os.unlink(self.path) return True @@ -215,10 +221,12 @@ class Stage(object): """Possible archive file paths.""" paths = [] if isinstance(self.fetcher, fs.URLFetchStrategy): - paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url))) + paths.append(os.path.join( + self.path, os.path.basename(self.fetcher.url))) if self.mirror_path: - paths.append(os.path.join(self.path, os.path.basename(self.mirror_path))) + paths.append(os.path.join( + self.path, os.path.basename(self.mirror_path))) return paths @@ -227,10 +235,12 @@ class Stage(object): """Path to the source archive within this stage directory.""" paths = [] if isinstance(self.fetcher, fs.URLFetchStrategy): - paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url))) + paths.append(os.path.join( + self.path, os.path.basename(self.fetcher.url))) if self.mirror_path: - paths.append(os.path.join(self.path, os.path.basename(self.mirror_path))) + paths.append(os.path.join( + self.path, os.path.basename(self.mirror_path))) for path in paths: if os.path.exists(path): @@ -262,7 +272,8 @@ class Stage(object): return None def chdir(self): - """Changes directory to the stage path. Or dies if it is not set up.""" + """Changes directory to the stage path. Or dies if it is not set + up.""" if os.path.isdir(self.path): os.chdir(self.path) else: @@ -304,7 +315,26 @@ class Stage(object): # Add URL strategies for all the mirrors with the digest for url in urls: fetchers.insert(0, fs.URLFetchStrategy(url, digest)) - fetchers.insert(0, spack.cache.fetcher(self.mirror_path, digest)) + fetchers.insert(0, spack.fetch_cache.fetcher(self.mirror_path, + digest)) + + # Look for the archive in list_url + package_name = os.path.dirname(self.mirror_path) + pkg = spack.repo.get(package_name) + if pkg.list_url is not None and pkg.url is not None: + try: + archive_version = spack.url.parse_version( + self.default_fetcher.url) + versions = pkg.fetch_remote_versions() + try: + url_from_list = versions[Version(archive_version)] + fetchers.append(fs.URLFetchStrategy( + url_from_list, digest)) + except KeyError: + tty.msg("Can not find version %s in url_list" % + archive_version) + except: + tty.msg("Could not determine url from list_url.") for fetcher in fetchers: try: @@ -321,11 +351,11 @@ class Stage(object): self.fetcher = self.default_fetcher raise fs.FetchError(errMessage, None) - def check(self): """Check the downloaded archive against a checksum digest. No-op if this stage checks code out of a repository.""" - if self.fetcher is not self.default_fetcher and self.skip_checksum_for_mirror: + if self.fetcher is not self.default_fetcher and \ + self.skip_checksum_for_mirror: tty.warn("Fetching from mirror without a checksum!", "This package is normally checked out from a version " "control system, but it has been archived on a spack " @@ -335,16 +365,13 @@ class Stage(object): else: self.fetcher.check() - def cache_local(self): - spack.cache.store(self.fetcher, self.mirror_path) - + spack.fetch_cache.store(self.fetcher, self.mirror_path) def expand_archive(self): """Changes to the stage directory and attempt to expand the downloaded - archive. Fail if the stage is not set up or if the archive is not yet - downloaded. - """ + archive. Fail if the stage is not set up or if the archive is not yet + downloaded.""" archive_dir = self.source_path if not archive_dir: self.fetcher.expand() @@ -386,8 +413,8 @@ class Stage(object): # Create the top-level stage directory mkdirp(spack.stage_path) remove_dead_links(spack.stage_path) - # If a tmp_root exists then create a directory there and then link it in the stage area, - # otherwise create the stage directory in self.path + # If a tmp_root exists then create a directory there and then link it + # in the stage area, otherwise create the stage directory in self.path if self._need_to_create_path(): if self.tmp_root: tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root) @@ -409,6 +436,7 @@ class Stage(object): class ResourceStage(Stage): + def __init__(self, url_or_fetch_strategy, root, resource, **kwargs): super(ResourceStage, self).__init__(url_or_fetch_strategy, **kwargs) self.root_stage = root @@ -418,12 +446,15 @@ class ResourceStage(Stage): super(ResourceStage, self).expand_archive() root_stage = self.root_stage resource = self.resource - placement = os.path.basename(self.source_path) if resource.placement is None else resource.placement + placement = os.path.basename(self.source_path) \ + if resource.placement is None \ + else resource.placement if not isinstance(placement, dict): placement = {'': placement} # Make the paths in the dictionary absolute and link for key, value in placement.iteritems(): - target_path = join_path(root_stage.source_path, resource.destination) + target_path = join_path( + root_stage.source_path, resource.destination) destination_path = join_path(target_path, value) source_path = join_path(self.source_path, key) @@ -437,21 +468,23 @@ class ResourceStage(Stage): if not os.path.exists(destination_path): # Create a symlink - tty.info('Moving resource stage\n\tsource : {stage}\n\tdestination : {destination}'.format( - stage=source_path, destination=destination_path - )) + tty.info('Moving resource stage\n\tsource : ' + '{stage}\n\tdestination : {destination}'.format( + stage=source_path, destination=destination_path + )) shutil.move(source_path, destination_path) -@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive', 'restage', 'destroy', 'cache_local']) +@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive', + 'restage', 'destroy', 'cache_local']) class StageComposite: - """ - Composite for Stage type objects. The first item in this composite is considered to be the root package, and - operations that return a value are forwarded to it. - """ + """Composite for Stage type objects. The first item in this composite is + considered to be the root package, and operations that return a value are + forwarded to it.""" # # __enter__ and __exit__ delegate to all stages in the composite. # + def __enter__(self): for item in self: item.__enter__() @@ -496,8 +529,11 @@ class DIYStage(object): raise ChdirError("Setup failed: no such directory: " + self.path) # DIY stages do nothing as context managers. - def __enter__(self): pass - def __exit__(self, exc_type, exc_val, exc_tb): pass + def __enter__(self): + pass + + def __exit__(self, exc_type, exc_val, exc_tb): + pass def chdir_to_source(self): self.chdir() diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index a849d5f350..db683917b5 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import sys +import os import llnl.util.tty as tty import nose @@ -32,16 +33,53 @@ from llnl.util.tty.colify import colify from spack.test.tally_plugin import Tally """Names of tests to be included in Spack's test suite""" +# All the tests Spack knows about. +# Keep these one per line so that it's easy to see changes in diffs. test_names = [ - 'architecture', 'versions', 'url_parse', 'url_substitution', 'packages', - 'stage', 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize', - 'multimethod', 'install', 'package_sanity', 'config', 'directory_layout', - 'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch', - 'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml', - 'optional_deps', 'make_executable', 'build_system_guess', 'lock', - 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', - 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd', - 'cmd.module' + 'architecture', + 'build_system_guess', + 'cc', + 'cmd.find', + 'cmd.module', + 'cmd.test_install', + 'cmd.uninstall', + 'concretize', + 'concretize_preferences', + 'config', + 'database', + 'directory_layout', + 'environment', + 'file_cache', + 'git_fetch', + 'hg_fetch', + 'install', + 'link_tree', + 'lock', + 'make_executable', + 'mirror', + 'modules', + 'multimethod', + 'namespace_trie', + 'optional_deps', + 'package_sanity', + 'packages', + 'pattern', + 'python_version', + 'sbang', + 'spec_dag', + 'spec_semantics', + 'spec_syntax', + 'spec_yaml', + 'stage', + 'svn_fetch', + 'url_extrapolate', + 'url_parse', + 'url_substitution', + 'versions', + 'provider_index', + 'yaml', + # This test needs to be last until global compiler cache is fixed. + 'cmd.test_compiler_cmd', ] @@ -53,6 +91,10 @@ def list_tests(): def run(names, outputDir, verbose=False): """Run tests with the supplied names. Names should be a list. If it's empty, run ALL of Spack's tests.""" + # Print output to stdout if verbose is 1. + if verbose: + os.environ['NOSE_NOCAPTURE'] = '1' + if not names: names = test_names else: diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index 09bdb021af..22ddd4c97e 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -31,7 +31,7 @@ import platform as py_platform import spack import spack.architecture from spack.spec import * -from spack.platforms.cray_xc import CrayXc +from spack.platforms.cray import Cray from spack.platforms.linux import Linux from spack.platforms.bgq import Bgq from spack.platforms.darwin import Darwin @@ -40,6 +40,7 @@ from spack.test.mock_packages_test import * class ArchitectureTest(MockPackagesTest): + def setUp(self): super(ArchitectureTest, self).setUp() self.platform = spack.architecture.platform() @@ -76,7 +77,7 @@ class ArchitectureTest(MockPackagesTest): def test_platform(self): output_platform_class = spack.architecture.platform() if os.path.exists('/opt/cray/craype'): - my_platform_class = CrayXc() + my_platform_class = Cray() elif os.path.exists('/bgsys'): my_platform_class = Bgq() elif 'Linux' in py_platform.system(): @@ -86,6 +87,29 @@ class ArchitectureTest(MockPackagesTest): self.assertEqual(str(output_platform_class), str(my_platform_class)) + def test_boolness(self): + # Make sure architecture reports that it's False when nothing's set. + arch = spack.architecture.Arch() + self.assertFalse(arch) + + # Dummy architecture parts + plat = spack.architecture.platform() + plat_os = plat.operating_system('default_os') + plat_target = plat.target('default_target') + + # Make sure architecture reports that it's True when anything is set. + arch = spack.architecture.Arch() + arch.platform = plat + self.assertTrue(arch) + + arch = spack.architecture.Arch() + arch.platform_os = plat_os + self.assertTrue(arch) + + arch = spack.architecture.Arch() + arch.target = plat_target + self.assertTrue(arch) + def test_user_front_end_input(self): """Test when user inputs just frontend that both the frontend target and frontend operating system match diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py index ea2b164462..f3e4bb31d2 100644 --- a/lib/spack/spack/test/cc.py +++ b/lib/spack/spack/test/cc.py @@ -45,7 +45,8 @@ test_command = [ '-llib1', '-llib2', 'arg4', '-Wl,--end-group', - '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker', '-rpath', '-Xlinker', '/fourth/rpath', + '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker', + '-rpath', '-Xlinker', '/fourth/rpath', '-llib3', '-llib4', 'arg5', 'arg6'] @@ -67,7 +68,7 @@ class CompilerTest(unittest.TestCase): os.environ['SPACK_FC'] = self.realcc os.environ['SPACK_PREFIX'] = self.prefix - os.environ['SPACK_ENV_PATH']="test" + os.environ['SPACK_ENV_PATH'] = "test" os.environ['SPACK_DEBUG_LOG_DIR'] = "." os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7" os.environ['SPACK_SHORT_SPEC'] = "foo@1.2" @@ -97,16 +98,13 @@ class CompilerTest(unittest.TestCase): if 'SPACK_DEPENDENCIES' in os.environ: del os.environ['SPACK_DEPENDENCIES'] - def tearDown(self): shutil.rmtree(self.tmp_deps, True) - def check_cc(self, command, args, expected): os.environ['SPACK_TEST_COMMAND'] = command self.assertEqual(self.cc(*args, output=str).strip(), expected) - def check_cxx(self, command, args, expected): os.environ['SPACK_TEST_COMMAND'] = command self.assertEqual(self.cxx(*args, output=str).strip(), expected) @@ -115,46 +113,46 @@ class CompilerTest(unittest.TestCase): os.environ['SPACK_TEST_COMMAND'] = command self.assertEqual(self.fc(*args, output=str).strip(), expected) - def check_ld(self, command, args, expected): os.environ['SPACK_TEST_COMMAND'] = command self.assertEqual(self.ld(*args, output=str).strip(), expected) - def check_cpp(self, command, args, expected): os.environ['SPACK_TEST_COMMAND'] = command self.assertEqual(self.cpp(*args, output=str).strip(), expected) - def test_vcheck_mode(self): self.check_cc('dump-mode', ['-I/include', '--version'], "vcheck") self.check_cc('dump-mode', ['-I/include', '-V'], "vcheck") self.check_cc('dump-mode', ['-I/include', '-v'], "vcheck") self.check_cc('dump-mode', ['-I/include', '-dumpversion'], "vcheck") self.check_cc('dump-mode', ['-I/include', '--version', '-c'], "vcheck") - self.check_cc('dump-mode', ['-I/include', '-V', '-o', 'output'], "vcheck") - + self.check_cc('dump-mode', ['-I/include', + '-V', '-o', 'output'], "vcheck") def test_cpp_mode(self): self.check_cc('dump-mode', ['-E'], "cpp") self.check_cpp('dump-mode', [], "cpp") - def test_as_mode(self): self.check_cc('dump-mode', ['-S'], "as") - def test_ccld_mode(self): self.check_cc('dump-mode', [], "ccld") self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld") - self.check_cc('dump-mode', ['foo.c', '-o', 'foo', '-Wl,-rpath,foo'], "ccld") - self.check_cc('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ccld") - + self.check_cc('dump-mode', ['foo.c', '-o', + 'foo', '-Wl,-rpath,foo'], "ccld") + self.check_cc( + 'dump-mode', + ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], + "ccld") def test_ld_mode(self): self.check_ld('dump-mode', [], "ld") - self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld") - + self.check_ld( + 'dump-mode', + ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], + "ld") def test_flags(self): os.environ['SPACK_LDFLAGS'] = '-L foo' @@ -176,10 +174,11 @@ class CompilerTest(unittest.TestCase): # Test cppflags added properly in cpp mode self.check_cpp('dump-args', test_command, "cpp " + - '-g -O1 ' + - ' '.join(test_command)) + '-g -O1 ' + + ' '.join(test_command)) - # Test ldflags, cppflags, and language specific flags are added in proper order + # Test ldflags, cppflags, and language specific flags are added in + # proper order self.check_cc('dump-args', test_command, self.realcc + ' ' + '-Wl,-rpath,' + self.prefix + '/lib ' + @@ -191,14 +190,14 @@ class CompilerTest(unittest.TestCase): '-lfoo') self.check_cxx('dump-args', test_command, - self.realcc + ' ' + - '-Wl,-rpath,' + self.prefix + '/lib ' + - '-Wl,-rpath,' + self.prefix + '/lib64 ' + - '-g -O1 ' + - '-Werror ' + - '-L foo ' + - ' '.join(test_command) + ' ' + - '-lfoo') + self.realcc + ' ' + + '-Wl,-rpath,' + self.prefix + '/lib ' + + '-Wl,-rpath,' + self.prefix + '/lib64 ' + + '-g -O1 ' + + '-Werror ' + + '-L foo ' + + ' '.join(test_command) + ' ' + + '-lfoo') self.check_fc('dump-args', test_command, self.realcc + ' ' + @@ -210,9 +209,8 @@ class CompilerTest(unittest.TestCase): ' '.join(test_command) + ' ' + '-lfoo') - os.environ['SPACK_LDFLAGS']='' - os.environ['SPACK_LDLIBS']='' - + os.environ['SPACK_LDFLAGS'] = '' + os.environ['SPACK_LDLIBS'] = '' def test_dep_rpath(self): """Ensure RPATHs for root package are added.""" @@ -222,7 +220,6 @@ class CompilerTest(unittest.TestCase): '-Wl,-rpath,' + self.prefix + '/lib64 ' + ' '.join(test_command)) - def test_dep_include(self): """Ensure a single dependency include directory is added.""" os.environ['SPACK_DEPENDENCIES'] = self.dep4 @@ -233,7 +230,6 @@ class CompilerTest(unittest.TestCase): '-I' + self.dep4 + '/include ' + ' '.join(test_command)) - def test_dep_lib(self): """Ensure a single dependency RPATH is added.""" os.environ['SPACK_DEPENDENCIES'] = self.dep2 @@ -245,7 +241,6 @@ class CompilerTest(unittest.TestCase): '-Wl,-rpath,' + self.dep2 + '/lib64 ' + ' '.join(test_command)) - def test_all_deps(self): """Ensure includes and RPATHs for all deps are added. """ os.environ['SPACK_DEPENDENCIES'] = ':'.join([ @@ -274,7 +269,6 @@ class CompilerTest(unittest.TestCase): ' '.join(test_command)) - def test_ld_deps(self): """Ensure no (extra) -I args or -Wl, are passed in ld mode.""" os.environ['SPACK_DEPENDENCIES'] = ':'.join([ diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py index 36a4a73fe6..3a0ce32e6c 100644 --- a/lib/spack/spack/test/cmd/module.py +++ b/lib/spack/spack/test/cmd/module.py @@ -33,16 +33,17 @@ import spack.test.mock_database class TestModule(spack.test.mock_database.MockDatabase): def _get_module_files(self, args): - return [ - modules.module_types[args.module_type](spec).file_name for spec in args.specs # NOQA: ignore=E501 - ] + return [modules.module_types[args.module_type](spec).file_name + for spec in args.specs] def test_module_common_operations(self): parser = argparse.ArgumentParser() module.setup_parser(parser) + # Try to remove a non existing module [tcl] args = parser.parse_args(['rm', 'doesnotexist']) self.assertRaises(SystemExit, module.module, parser, args) + # Remove existing modules [tcl] args = parser.parse_args(['rm', '-y', 'mpileaks']) module_files = self._get_module_files(args) @@ -51,22 +52,28 @@ class TestModule(spack.test.mock_database.MockDatabase): module.module(parser, args) for item in module_files: self.assertFalse(os.path.exists(item)) + # Add them back [tcl] args = parser.parse_args(['refresh', '-y', 'mpileaks']) module.module(parser, args) for item in module_files: self.assertTrue(os.path.exists(item)) + # TODO : test the --delete-tree option # TODO : this requires having a separate directory for test modules + # Try to find a module with multiple matches args = parser.parse_args(['find', 'mpileaks']) self.assertRaises(SystemExit, module.module, parser, args) + # Try to find a module with no matches args = parser.parse_args(['find', 'doesnotexist']) self.assertRaises(SystemExit, module.module, parser, args) + # Try to find a module args = parser.parse_args(['find', 'libelf']) module.module(parser, args) + # Remove existing modules [dotkit] args = parser.parse_args(['rm', '-y', '-m', 'dotkit', 'mpileaks']) module_files = self._get_module_files(args) @@ -75,6 +82,7 @@ class TestModule(spack.test.mock_database.MockDatabase): module.module(parser, args) for item in module_files: self.assertFalse(os.path.exists(item)) + # Add them back [dotkit] args = parser.parse_args(['refresh', '-y', '-m', 'dotkit', 'mpileaks']) module.module(parser, args) diff --git a/lib/spack/spack/test/cmd/test_compiler_cmd.py b/lib/spack/spack/test/cmd/test_compiler_cmd.py index d89814154b..fa806ee6f4 100644 --- a/lib/spack/spack/test/cmd/test_compiler_cmd.py +++ b/lib/spack/spack/test/cmd/test_compiler_cmd.py @@ -12,7 +12,9 @@ from spack.test.mock_packages_test import * test_version = '4.5-spacktest' + class MockArgs(object): + def __init__(self, add_paths=[], scope=None, compiler_spec=None, all=None): self.add_paths = add_paths self.scope = scope @@ -52,14 +54,12 @@ done class CompilerCmdTest(MockPackagesTest): """ Test compiler commands for add and remove """ - def test_compiler_remove(self): args = MockArgs(all=True, compiler_spec='gcc@4.5.0') spack.cmd.compiler.compiler_remove(args) compilers = spack.compilers.all_compilers() self.assertTrue(spack.spec.CompilerSpec("gcc@4.5.0") not in compilers) - def test_compiler_add(self): # compilers available by default. old_compilers = set(spack.compilers.all_compilers()) @@ -75,7 +75,8 @@ class CompilerCmdTest(MockPackagesTest): new_compilers = set(spack.compilers.all_compilers()) new_compiler = new_compilers - old_compilers self.assertTrue(new_compiler) - self.assertTrue(new_compiler.pop().version == Version(test_version)) + self.assertTrue(new_compiler.pop().version == + Version(test_version)) finally: shutil.rmtree(compiler_dir, ignore_errors=True) diff --git a/lib/spack/spack/test/cmd/test_install.py b/lib/spack/spack/test/cmd/test_install.py index a94d3c8bba..39287d5d6d 100644 --- a/lib/spack/spack/test/cmd/test_install.py +++ b/lib/spack/spack/test/cmd/test_install.py @@ -22,18 +22,24 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## +import StringIO import collections -from contextlib import contextmanager +import os +import unittest +import contextlib -import StringIO +import spack +import spack.cmd FILE_REGISTRY = collections.defaultdict(StringIO.StringIO) + # Monkey-patch open to write module files to a StringIO instance -@contextmanager +@contextlib.contextmanager def mock_open(filename, mode): if not mode == 'wb': - raise RuntimeError('test.test_install : unexpected opening mode for monkey-patched open') + message = 'test.test_install : unexpected opening mode for mock_open' + raise RuntimeError(message) FILE_REGISTRY[filename] = StringIO.StringIO() @@ -44,19 +50,14 @@ def mock_open(filename, mode): FILE_REGISTRY[filename] = handle.getvalue() handle.close() -import os -import itertools -import unittest - -import spack -import spack.cmd - -# The use of __import__ is necessary to maintain a name with hyphen (which cannot be an identifier in python) +# The use of __import__ is necessary to maintain a name with hyphen (which +# cannot be an identifier in python) test_install = __import__("spack.cmd.test-install", fromlist=['test_install']) class MockSpec(object): + def __init__(self, name, version, hashStr=None): self._dependencies = {} self.name = name @@ -88,10 +89,6 @@ class MockSpec(object): for _, spec in self._dependencies.items(): yield spec.spec yield self - #from_iterable = itertools.chain.from_iterable - #allDeps = from_iterable(i.traverse() - # for i in self.dependencies()) - #return set(itertools.chain([self], allDeps)) def dag_hash(self): return self.hash @@ -102,6 +99,7 @@ class MockSpec(object): class MockPackage(object): + def __init__(self, spec, buildLogPath): self.name = spec.name self.spec = spec @@ -113,6 +111,7 @@ class MockPackage(object): class MockPackageDb(object): + def __init__(self, init=None): self.specToPkg = {} if init: @@ -133,6 +132,7 @@ pkgY = MockPackage(specY, 'logY') class MockArgs(object): + def __init__(self, package): self.package = package self.jobs = None @@ -168,7 +168,7 @@ class TestInstallTest(unittest.TestCase): test_install.open = mock_open # Clean FILE_REGISTRY - FILE_REGISTRY = collections.defaultdict(StringIO.StringIO) + FILE_REGISTRY.clear() pkgX.installed = False pkgY.installed = False @@ -194,7 +194,7 @@ class TestInstallTest(unittest.TestCase): spack.repo = self.saved_db def test_installing_both(self): - test_install.test_install(None, MockArgs('X') ) + test_install.test_install(None, MockArgs('X')) self.assertEqual(len(FILE_REGISTRY), 1) for _, content in FILE_REGISTRY.items(): self.assertTrue('tests="2"' in content) @@ -210,4 +210,5 @@ class TestInstallTest(unittest.TestCase): self.assertTrue('tests="2"' in content) self.assertTrue('failures="0"' in content) self.assertTrue('errors="0"' in content) - self.assertEqual(sum('skipped' in line for line in content.split('\n')), 2) + self.assertEqual( + sum('skipped' in line for line in content.split('\n')), 2) diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py index 9fffaace40..4ccb9ddbf4 100644 --- a/lib/spack/spack/test/cmd/uninstall.py +++ b/lib/spack/spack/test/cmd/uninstall.py @@ -28,6 +28,7 @@ from spack.cmd.uninstall import uninstall class MockArgs(object): + def __init__(self, packages, all=False, force=False, dependents=False): self.packages = packages self.all = all @@ -37,6 +38,7 @@ class MockArgs(object): class TestUninstall(spack.test.mock_database.MockDatabase): + def test_uninstall(self): parser = None # Multiple matches diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index ae3ceecfc8..8ecbddbda2 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -29,6 +29,7 @@ from spack.version import ver from spack.concretize import find_spec from spack.test.mock_packages_test import * + class ConcretizeTest(MockPackagesTest): def check_spec(self, abstract, concrete): @@ -59,7 +60,6 @@ class ConcretizeTest(MockPackagesTest): if abstract.architecture and abstract.architecture.concrete: self.assertEqual(abstract.architecture, concrete.architecture) - def check_concretize(self, abstract_spec): abstract = Spec(abstract_spec) concrete = abstract.concretized() @@ -70,29 +70,24 @@ class ConcretizeTest(MockPackagesTest): return concrete - def test_concretize_no_deps(self): self.check_concretize('libelf') self.check_concretize('libelf@0.8.13') - def test_concretize_dag(self): self.check_concretize('callpath') self.check_concretize('mpileaks') self.check_concretize('libelf') - def test_concretize_variant(self): self.check_concretize('mpich+debug') self.check_concretize('mpich~debug') self.check_concretize('mpich debug=2') self.check_concretize('mpich') - def test_conretize_compiler_flags(self): self.check_concretize('mpich cppflags="-O3"') - def test_concretize_preferred_version(self): spec = self.check_concretize('python') self.assertEqual(spec.versions, ver('2.7.11')) @@ -100,7 +95,6 @@ class ConcretizeTest(MockPackagesTest): spec = self.check_concretize('python@3.5.1') self.assertEqual(spec.versions, ver('3.5.1')) - def test_concretize_with_virtual(self): self.check_concretize('mpileaks ^mpi') self.check_concretize('mpileaks ^mpi@:1.1') @@ -111,7 +105,6 @@ class ConcretizeTest(MockPackagesTest): self.check_concretize('mpileaks ^mpi@:1') self.check_concretize('mpileaks ^mpi@1.2:2') - def test_concretize_with_restricted_virtual(self): self.check_concretize('mpileaks ^mpich2') @@ -142,58 +135,55 @@ class ConcretizeTest(MockPackagesTest): concrete = self.check_concretize('mpileaks ^mpich2@1.3.1:1.4') self.assertTrue(concrete['mpich2'].satisfies('mpich2@1.3.1:1.4')) - def test_concretize_with_provides_when(self): """Make sure insufficient versions of MPI are not in providers list when we ask for some advanced version. """ - self.assertTrue(not any(spec.satisfies('mpich2@:1.0') - for spec in spack.repo.providers_for('mpi@2.1'))) - - self.assertTrue(not any(spec.satisfies('mpich2@:1.1') - for spec in spack.repo.providers_for('mpi@2.2'))) - - self.assertTrue(not any(spec.satisfies('mpich2@:1.1') - for spec in spack.repo.providers_for('mpi@2.2'))) + self.assertTrue( + not any(spec.satisfies('mpich2@:1.0') + for spec in spack.repo.providers_for('mpi@2.1'))) - self.assertTrue(not any(spec.satisfies('mpich@:1') - for spec in spack.repo.providers_for('mpi@2'))) + self.assertTrue( + not any(spec.satisfies('mpich2@:1.1') + for spec in spack.repo.providers_for('mpi@2.2'))) - self.assertTrue(not any(spec.satisfies('mpich@:1') - for spec in spack.repo.providers_for('mpi@3'))) + self.assertTrue( + not any(spec.satisfies('mpich@:1') + for spec in spack.repo.providers_for('mpi@2'))) - self.assertTrue(not any(spec.satisfies('mpich2') - for spec in spack.repo.providers_for('mpi@3'))) + self.assertTrue( + not any(spec.satisfies('mpich@:1') + for spec in spack.repo.providers_for('mpi@3'))) + self.assertTrue( + not any(spec.satisfies('mpich2') + for spec in spack.repo.providers_for('mpi@3'))) def test_concretize_two_virtuals(self): """Test a package with multiple virtual dependencies.""" - s = Spec('hypre').concretize() - + Spec('hypre').concretize() def test_concretize_two_virtuals_with_one_bound(self): """Test a package with multiple virtual dependencies and one preset.""" - s = Spec('hypre ^openblas').concretize() - + Spec('hypre ^openblas').concretize() def test_concretize_two_virtuals_with_two_bound(self): - """Test a package with multiple virtual dependencies and two of them preset.""" - s = Spec('hypre ^openblas ^netlib-lapack').concretize() - + """Test a package with multiple virtual deps and two of them preset.""" + Spec('hypre ^openblas ^netlib-lapack').concretize() def test_concretize_two_virtuals_with_dual_provider(self): """Test a package with multiple virtual dependencies and force a provider that provides both.""" - s = Spec('hypre ^openblas-with-lapack').concretize() - + Spec('hypre ^openblas-with-lapack').concretize() def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self): - """Test a package with multiple virtual dependencies and force a provider - that provides both, and another conflicting package that provides one.""" + """Test a package with multiple virtual dependencies and force a + provider that provides both, and another conflicting package that + provides one. + """ s = Spec('hypre ^openblas-with-lapack ^netlib-lapack') self.assertRaises(spack.spec.MultipleProviderError, s.concretize) - def test_virtual_is_fully_expanded_for_callpath(self): # force dependence on fake "zmpi" by asking for MPI 10.0 spec = Spec('callpath ^mpi@10.0') @@ -210,7 +200,6 @@ class ConcretizeTest(MockPackagesTest): self.assertTrue('fake' in spec._dependencies['zmpi'].spec) - def test_virtual_is_fully_expanded_for_mpileaks(self): spec = Spec('mpileaks ^mpi@10.0') self.assertTrue('mpi' in spec._dependencies) @@ -220,23 +209,24 @@ class ConcretizeTest(MockPackagesTest): self.assertTrue('zmpi' in spec._dependencies) self.assertTrue('callpath' in spec._dependencies) - self.assertTrue('zmpi' in spec._dependencies['callpath']. - spec._dependencies) - self.assertTrue('fake' in spec._dependencies['callpath']. - spec._dependencies['zmpi']. - spec._dependencies) - - self.assertTrue(all(not 'mpi' in d._dependencies for d in spec.traverse())) + self.assertTrue( + 'zmpi' in spec._dependencies['callpath'] + .spec._dependencies) + self.assertTrue( + 'fake' in spec._dependencies['callpath'] + .spec._dependencies['zmpi'] + .spec._dependencies) + + self.assertTrue( + all('mpi' not in d._dependencies for d in spec.traverse())) self.assertTrue('zmpi' in spec) self.assertTrue('mpi' in spec) - def test_my_dep_depends_on_provider_of_my_virtual_dep(self): spec = Spec('indirect_mpich') spec.normalize() spec.concretize() - def test_compiler_inheritance(self): spec = Spec('mpileaks') spec.normalize() @@ -248,26 +238,26 @@ class ConcretizeTest(MockPackagesTest): self.assertTrue(spec['libdwarf'].compiler.satisfies('clang')) self.assertTrue(spec['libelf'].compiler.satisfies('clang')) - def test_external_package(self): spec = Spec('externaltool%gcc') spec.concretize() - self.assertEqual(spec['externaltool'].external, '/path/to/external_tool') + self.assertEqual( + spec['externaltool'].external, '/path/to/external_tool') self.assertFalse('externalprereq' in spec) self.assertTrue(spec['externaltool'].compiler.satisfies('gcc')) - def test_external_package_module(self): # No tcl modules on darwin/linux machines # TODO: improved way to check for this. - if (spack.architecture.platform().name == 'darwin' or - spack.architecture.platform().name == 'linux'): + platform = spack.architecture.platform().name + if (platform == 'darwin' or platform == 'linux'): return spec = Spec('externalmodule') spec.concretize() - self.assertEqual(spec['externalmodule'].external_module, 'external-module') + self.assertEqual( + spec['externalmodule'].external_module, 'external-module') self.assertFalse('externalprereq' in spec) self.assertTrue(spec['externalmodule'].compiler.satisfies('gcc')) @@ -280,16 +270,16 @@ class ConcretizeTest(MockPackagesTest): got_error = True self.assertTrue(got_error) - def test_external_and_virtual(self): spec = Spec('externaltest') spec.concretize() - self.assertEqual(spec['externaltool'].external, '/path/to/external_tool') - self.assertEqual(spec['stuff'].external, '/path/to/external_virtual_gcc') + self.assertEqual( + spec['externaltool'].external, '/path/to/external_tool') + self.assertEqual( + spec['stuff'].external, '/path/to/external_virtual_gcc') self.assertTrue(spec['externaltool'].compiler.satisfies('gcc')) self.assertTrue(spec['stuff'].compiler.satisfies('gcc')) - def test_find_spec_parents(self): """Tests the spec finding logic used by concretization. """ s = Spec('a +foo', @@ -300,7 +290,6 @@ class ConcretizeTest(MockPackagesTest): self.assertEqual('a', find_spec(s['b'], lambda s: '+foo' in s).name) - def test_find_spec_children(self): s = Spec('a', Spec('b +foo', @@ -315,7 +304,6 @@ class ConcretizeTest(MockPackagesTest): Spec('e +foo')) self.assertEqual('c', find_spec(s['b'], lambda s: '+foo' in s).name) - def test_find_spec_sibling(self): s = Spec('a', Spec('b +foo', @@ -333,7 +321,6 @@ class ConcretizeTest(MockPackagesTest): Spec('f +foo'))) self.assertEqual('f', find_spec(s['b'], lambda s: '+foo' in s).name) - def test_find_spec_self(self): s = Spec('a', Spec('b +foo', @@ -342,7 +329,6 @@ class ConcretizeTest(MockPackagesTest): Spec('e')) self.assertEqual('b', find_spec(s['b'], lambda s: '+foo' in s).name) - def test_find_spec_none(self): s = Spec('a', Spec('b', @@ -351,7 +337,6 @@ class ConcretizeTest(MockPackagesTest): Spec('e')) self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s)) - def test_compiler_child(self): s = Spec('mpileaks%clang ^dyninst%gcc') s.concretize() diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py new file mode 100644 index 0000000000..2c8bedc33f --- /dev/null +++ b/lib/spack/spack/test/concretize_preferences.py @@ -0,0 +1,106 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import spack +import spack.architecture +from spack.test.mock_packages_test import * +from tempfile import mkdtemp + + +class ConcretizePreferencesTest(MockPackagesTest): + """Test concretization preferences are being applied correctly. + """ + + def setUp(self): + """Create config section to store concretization preferences + """ + super(ConcretizePreferencesTest, self).setUp() + self.tmp_dir = mkdtemp('.tmp', 'spack-config-test-') + spack.config.ConfigScope('concretize', + os.path.join(self.tmp_dir, 'concretize')) + + def tearDown(self): + super(ConcretizePreferencesTest, self).tearDown() + shutil.rmtree(self.tmp_dir, True) + spack.pkgsort = spack.PreferredPackages() + + def concretize(self, abstract_spec): + return Spec(abstract_spec).concretized() + + def update_packages(self, pkgname, section, value): + """Update config and reread package list""" + conf = {pkgname: {section: value}} + spack.config.update_config('packages', conf, 'concretize') + spack.pkgsort = spack.PreferredPackages() + + def assert_variant_values(self, spec, **variants): + concrete = self.concretize(spec) + for variant, value in variants.items(): + self.assertEqual(concrete.variants[variant].value, value) + + def test_preferred_variants(self): + """Test preferred variants are applied correctly + """ + self.update_packages('mpileaks', 'variants', + '~debug~opt+shared+static') + self.assert_variant_values('mpileaks', debug=False, opt=False, + shared=True, static=True) + + self.update_packages('mpileaks', 'variants', + ['+debug', '+opt', '~shared', '-static']) + self.assert_variant_values('mpileaks', debug=True, opt=True, + shared=False, static=False) + + def test_preferred_compilers(self): + """Test preferred compilers are applied correctly + """ + self.update_packages('mpileaks', 'compiler', ['clang@3.3']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.compiler, spack.spec.CompilerSpec('clang@3.3')) + + self.update_packages('mpileaks', 'compiler', ['gcc@4.5.0']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.compiler, spack.spec.CompilerSpec('gcc@4.5.0')) + + def test_preferred_versions(self): + """Test preferred package versions are applied correctly + """ + self.update_packages('mpileaks', 'version', ['2.3']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.version, spack.spec.Version('2.3')) + + self.update_packages('mpileaks', 'version', ['2.2']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.version, spack.spec.Version('2.2')) + + def test_preferred_providers(self): + """Test preferred providers of virtual packages are applied correctly + """ + self.update_packages('all', 'providers', {'mpi': ['mpich']}) + spec = self.concretize('mpileaks') + self.assertTrue('mpich' in spec) + + self.update_packages('all', 'providers', {'mpi': ['zmpi']}) + spec = self.concretize('mpileaks') + self.assertTrue('zmpi', spec) diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index 252d77e66b..0822e44db8 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -32,79 +32,80 @@ from ordereddict_backport import OrderedDict from spack.test.mock_packages_test import * # Some sample compiler config data -a_comps = [ +a_comps = [ {'compiler': { 'paths': { - "cc" : "/gcc473", + "cc": "/gcc473", "cxx": "/g++473", "f77": None, - "fc" : None - }, + "fc": None + }, 'modules': None, 'spec': 'gcc@4.7.3', 'operating_system': 'CNL10' - }}, + }}, {'compiler': { 'paths': { - "cc" : "/gcc450", + "cc": "/gcc450", "cxx": "/g++450", "f77": 'gfortran', - "fc" : 'gfortran' - }, + "fc": 'gfortran' + }, 'modules': None, 'spec': 'gcc@4.5.0', 'operating_system': 'CNL10' - }}, + }}, {'compiler': { 'paths': { - "cc" : "<overwritten>", + "cc": "<overwritten>", "cxx": "<overwritten>", "f77": '<overwritten>', - "fc" : '<overwritten>' }, + "fc": '<overwritten>'}, 'modules': None, 'spec': 'clang@3.3', 'operating_system': 'CNL10' - }} + }} ] b_comps = [ {'compiler': { 'paths': { - "cc" : "/icc100", + "cc": "/icc100", "cxx": "/icp100", "f77": None, - "fc" : None - }, + "fc": None + }, 'modules': None, 'spec': 'icc@10.0', 'operating_system': 'CNL10' - }}, + }}, {'compiler': { 'paths': { - "cc" : "/icc111", + "cc": "/icc111", "cxx": "/icp111", "f77": 'ifort', - "fc" : 'ifort' - }, + "fc": 'ifort' + }, 'modules': None, 'spec': 'icc@11.1', 'operating_system': 'CNL10' - }}, + }}, {'compiler': { 'paths': { - "cc" : "<overwritten>", + "cc": "<overwritten>", "cxx": "<overwritten>", "f77": '<overwritten>', - "fc" : '<overwritten>' }, + "fc": '<overwritten>'}, 'modules': None, 'spec': 'clang@3.3', 'operating_system': 'CNL10' - }} + }} ] # Some Sample repo data -repos_low = [ "/some/path" ] -repos_high = [ "/some/other/path" ] +repos_low = ["/some/path"] +repos_high = ["/some/other/path"] + class ConfigTest(MockPackagesTest): @@ -112,14 +113,15 @@ class ConfigTest(MockPackagesTest): super(ConfigTest, self).setUp() self.tmp_dir = mkdtemp('.tmp', 'spack-config-test-') spack.config.config_scopes = OrderedDict() - spack.config.ConfigScope('test_low_priority', os.path.join(self.tmp_dir, 'low')) - spack.config.ConfigScope('test_high_priority', os.path.join(self.tmp_dir, 'high')) + spack.config.ConfigScope( + 'test_low_priority', os.path.join(self.tmp_dir, 'low')) + spack.config.ConfigScope('test_high_priority', + os.path.join(self.tmp_dir, 'high')) def tearDown(self): super(ConfigTest, self).tearDown() shutil.rmtree(self.tmp_dir, True) - def check_config(self, comps, *compiler_names): """Check that named compilers in comps match Spack's config.""" config = spack.config.get_config('compilers') @@ -146,7 +148,7 @@ class ConfigTest(MockPackagesTest): spack.config.update_config('repos', repos_low, 'test_low_priority') spack.config.update_config('repos', repos_high, 'test_high_priority') config = spack.config.get_config('repos') - self.assertEqual(config, repos_high+repos_low) + self.assertEqual(config, repos_high + repos_low) def test_write_key_in_memory(self): # Write b_comps "on top of" a_comps. @@ -157,7 +159,6 @@ class ConfigTest(MockPackagesTest): self.check_config(a_comps, 'gcc@4.7.3', 'gcc@4.5.0') self.check_config(b_comps, 'icc@10.0', 'icc@11.1', 'clang@3.3') - def test_write_key_to_disk(self): # Write b_comps "on top of" a_comps. spack.config.update_config('compilers', a_comps, 'test_low_priority') diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index e1322f2081..22b1f17890 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -31,7 +31,6 @@ import multiprocessing import spack from llnl.util.filesystem import join_path -from llnl.util.lock import * from llnl.util.tty.colify import colify from spack.test.mock_database import MockDatabase @@ -72,6 +71,7 @@ def _print_ref_counts(): class DatabaseTest(MockDatabase): + def test_005_db_exists(self): """Make sure db cache file exists after creating.""" index_file = join_path(self.install_path, '.spack-db', 'index.yaml') @@ -88,26 +88,28 @@ class DatabaseTest(MockDatabase): # query specs with multiple configurations mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')] callpath_specs = [s for s in all_specs if s.satisfies('callpath')] - mpi_specs = [s for s in all_specs if s.satisfies('mpi')] + mpi_specs = [s for s in all_specs if s.satisfies('mpi')] self.assertEqual(len(mpileaks_specs), 3) self.assertEqual(len(callpath_specs), 3) self.assertEqual(len(mpi_specs), 3) # query specs with single configurations - dyninst_specs = [s for s in all_specs if s.satisfies('dyninst')] + dyninst_specs = [s for s in all_specs if s.satisfies('dyninst')] libdwarf_specs = [s for s in all_specs if s.satisfies('libdwarf')] - libelf_specs = [s for s in all_specs if s.satisfies('libelf')] + libelf_specs = [s for s in all_specs if s.satisfies('libelf')] self.assertEqual(len(dyninst_specs), 1) self.assertEqual(len(libdwarf_specs), 1) self.assertEqual(len(libelf_specs), 1) # Query by dependency - self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^mpich')]), 1) - self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^mpich2')]), 1) - self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^zmpi')]), 1) - + self.assertEqual( + len([s for s in all_specs if s.satisfies('mpileaks ^mpich')]), 1) + self.assertEqual( + len([s for s in all_specs if s.satisfies('mpileaks ^mpich2')]), 1) + self.assertEqual( + len([s for s in all_specs if s.satisfies('mpileaks ^zmpi')]), 1) def test_015_write_and_read(self): # write and read DB @@ -122,7 +124,6 @@ class DatabaseTest(MockDatabase): self.assertEqual(new_rec.path, rec.path) self.assertEqual(new_rec.installed, rec.installed) - def _check_db_sanity(self): """Utiilty function to check db against install layout.""" expected = sorted(spack.install_layout.all_specs()) @@ -132,12 +133,10 @@ class DatabaseTest(MockDatabase): for e, a in zip(expected, actual): self.assertEqual(e, a) - def test_020_db_sanity(self): """Make sure query() returns what's actually in the db.""" self._check_db_sanity() - def test_030_db_sanity_from_another_process(self): def read_and_modify(): self._check_db_sanity() # check that other process can read DB @@ -152,30 +151,28 @@ class DatabaseTest(MockDatabase): with self.installed_db.read_transaction(): self.assertEqual(len(self.installed_db.query('mpileaks ^zmpi')), 0) - def test_040_ref_counts(self): """Ensure that we got ref counts right when we read the DB.""" self.installed_db._check_ref_counts() - def test_050_basic_query(self): - """Ensure that querying the database is consistent with what is installed.""" + """Ensure querying database is consistent with what is installed.""" # query everything self.assertEqual(len(spack.installed_db.query()), 13) # query specs with multiple configurations mpileaks_specs = self.installed_db.query('mpileaks') callpath_specs = self.installed_db.query('callpath') - mpi_specs = self.installed_db.query('mpi') + mpi_specs = self.installed_db.query('mpi') self.assertEqual(len(mpileaks_specs), 3) self.assertEqual(len(callpath_specs), 3) self.assertEqual(len(mpi_specs), 3) # query specs with single configurations - dyninst_specs = self.installed_db.query('dyninst') + dyninst_specs = self.installed_db.query('dyninst') libdwarf_specs = self.installed_db.query('libdwarf') - libelf_specs = self.installed_db.query('libelf') + libelf_specs = self.installed_db.query('libelf') self.assertEqual(len(dyninst_specs), 1) self.assertEqual(len(libdwarf_specs), 1) @@ -186,7 +183,6 @@ class DatabaseTest(MockDatabase): self.assertEqual(len(self.installed_db.query('mpileaks ^mpich2')), 1) self.assertEqual(len(self.installed_db.query('mpileaks ^zmpi')), 1) - def _check_remove_and_add_package(self, spec): """Remove a spec from the DB, then add it and make sure everything's still ok once it is added. This checks that it was @@ -215,15 +211,12 @@ class DatabaseTest(MockDatabase): self._check_db_sanity() self.installed_db._check_ref_counts() - def test_060_remove_and_add_root_package(self): self._check_remove_and_add_package('mpileaks ^mpich') - def test_070_remove_and_add_dependency_package(self): self._check_remove_and_add_package('dyninst') - def test_080_root_ref_counts(self): rec = self.installed_db.get_record('mpileaks ^mpich') @@ -231,45 +224,89 @@ class DatabaseTest(MockDatabase): self.installed_db.remove('mpileaks ^mpich') # record no longer in DB - self.assertEqual(self.installed_db.query('mpileaks ^mpich', installed=any), []) + self.assertEqual( + self.installed_db.query('mpileaks ^mpich', installed=any), []) # record's deps have updated ref_counts - self.assertEqual(self.installed_db.get_record('callpath ^mpich').ref_count, 0) + self.assertEqual( + self.installed_db.get_record('callpath ^mpich').ref_count, 0) self.assertEqual(self.installed_db.get_record('mpich').ref_count, 1) - # put the spec back + # Put the spec back self.installed_db.add(rec.spec, rec.path) # record is present again - self.assertEqual(len(self.installed_db.query('mpileaks ^mpich', installed=any)), 1) + self.assertEqual( + len(self.installed_db.query('mpileaks ^mpich', installed=any)), 1) # dependencies have ref counts updated - self.assertEqual(self.installed_db.get_record('callpath ^mpich').ref_count, 1) + self.assertEqual( + self.installed_db.get_record('callpath ^mpich').ref_count, 1) self.assertEqual(self.installed_db.get_record('mpich').ref_count, 2) - def test_090_non_root_ref_counts(self): - mpileaks_mpich_rec = self.installed_db.get_record('mpileaks ^mpich') - callpath_mpich_rec = self.installed_db.get_record('callpath ^mpich') + self.installed_db.get_record('mpileaks ^mpich') + self.installed_db.get_record('callpath ^mpich') # "force remove" a non-root spec from the DB self.installed_db.remove('callpath ^mpich') # record still in DB but marked uninstalled - self.assertEqual(self.installed_db.query('callpath ^mpich', installed=True), []) - self.assertEqual(len(self.installed_db.query('callpath ^mpich', installed=any)), 1) + self.assertEqual( + self.installed_db.query('callpath ^mpich', installed=True), []) + self.assertEqual( + len(self.installed_db.query('callpath ^mpich', installed=any)), 1) # record and its deps have same ref_counts - self.assertEqual(self.installed_db.get_record('callpath ^mpich', installed=any).ref_count, 1) + self.assertEqual(self.installed_db.get_record( + 'callpath ^mpich', installed=any).ref_count, 1) self.assertEqual(self.installed_db.get_record('mpich').ref_count, 2) # remove only dependent of uninstalled callpath record self.installed_db.remove('mpileaks ^mpich') # record and parent are completely gone. - self.assertEqual(self.installed_db.query('mpileaks ^mpich', installed=any), []) - self.assertEqual(self.installed_db.query('callpath ^mpich', installed=any), []) + self.assertEqual( + self.installed_db.query('mpileaks ^mpich', installed=any), []) + self.assertEqual( + self.installed_db.query('callpath ^mpich', installed=any), []) # mpich ref count updated properly. mpich_rec = self.installed_db.get_record('mpich') self.assertEqual(mpich_rec.ref_count, 0) + + def test_100_no_write_with_exception_on_remove(self): + def fail_while_writing(): + with self.installed_db.write_transaction(): + self._mock_remove('mpileaks ^zmpi') + raise Exception() + + with self.installed_db.read_transaction(): + self.assertEqual( + len(self.installed_db.query('mpileaks ^zmpi', installed=any)), + 1) + + self.assertRaises(Exception, fail_while_writing) + + # reload DB and make sure zmpi is still there. + with self.installed_db.read_transaction(): + self.assertEqual( + len(self.installed_db.query('mpileaks ^zmpi', installed=any)), + 1) + + def test_110_no_write_with_exception_on_install(self): + def fail_while_writing(): + with self.installed_db.write_transaction(): + self._mock_install('cmake') + raise Exception() + + with self.installed_db.read_transaction(): + self.assertEqual( + self.installed_db.query('cmake', installed=any), []) + + self.assertRaises(Exception, fail_while_writing) + + # reload DB and make sure cmake was not written. + with self.installed_db.read_transaction(): + self.assertEqual( + self.installed_db.query('cmake', installed=any), []) diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py index 74669fe8a2..2d0565acae 100644 --- a/lib/spack/spack/test/directory_layout.py +++ b/lib/spack/spack/test/directory_layout.py @@ -49,13 +49,11 @@ class DirectoryLayoutTest(MockPackagesTest): self.tmpdir = tempfile.mkdtemp() self.layout = YamlDirectoryLayout(self.tmpdir) - def tearDown(self): super(DirectoryLayoutTest, self).tearDown() shutil.rmtree(self.tmpdir, ignore_errors=True) self.layout = None - def test_read_and_write_spec(self): """This goes through each package in spack and creates a directory for it. It then ensures that the spec for the directory's @@ -67,8 +65,8 @@ class DirectoryLayoutTest(MockPackagesTest): for pkg in packages: if pkg.name.startswith('external'): - #External package tests cannot be installed - continue + # External package tests cannot be installed + continue spec = pkg.spec # If a spec fails to concretize, just skip it. If it is a @@ -115,7 +113,6 @@ class DirectoryLayoutTest(MockPackagesTest): self.assertFalse(os.path.isdir(install_dir)) self.assertFalse(os.path.exists(install_dir)) - def test_handle_unknown_package(self): """This test ensures that spack can at least do *some* operations with packages that are installed but that it @@ -166,7 +163,6 @@ class DirectoryLayoutTest(MockPackagesTest): spack.repo.swap(mock_db) - def test_find(self): """Test that finding specs within an install layout works.""" packages = list(spack.repo.all_packages())[:max_packages] @@ -175,13 +171,14 @@ class DirectoryLayoutTest(MockPackagesTest): installed_specs = {} for pkg in packages: if pkg.name.startswith('external'): - #External package tests cannot be installed + # External package tests cannot be installed continue spec = pkg.spec.concretized() installed_specs[spec.name] = spec self.layout.create_install_directory(spec) - # Make sure all the installed specs appear in DirectoryLayout.all_specs() + # Make sure all the installed specs appear in + # DirectoryLayout.all_specs() found_specs = dict((s.name, s) for s in self.layout.all_specs()) for name, spec in found_specs.items(): self.assertTrue(name in found_specs) diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py index 2396961888..9b5d75f273 100644 --- a/lib/spack/spack/test/environment.py +++ b/lib/spack/spack/test/environment.py @@ -38,7 +38,8 @@ class EnvironmentTest(unittest.TestCase): os.environ['UNSET_ME'] = 'foo' os.environ['EMPTY_PATH_LIST'] = '' os.environ['PATH_LIST'] = '/path/second:/path/third' - os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g' # NOQA: ignore=E501 + os.environ['REMOVE_PATH_LIST'] = \ + '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g' def tearDown(self): pass diff --git a/lib/spack/spack/test/file_cache.py b/lib/spack/spack/test/file_cache.py new file mode 100644 index 0000000000..cc66beda2e --- /dev/null +++ b/lib/spack/spack/test/file_cache.py @@ -0,0 +1,83 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +""" +Test Spack's FileCache. +""" +import os +import shutil +import tempfile +import unittest + +from spack.file_cache import FileCache + + +class FileCacheTest(unittest.TestCase): + """Ensure that a file cache can properly write to a file and recover its + contents.""" + + def setUp(self): + self.scratch_dir = tempfile.mkdtemp() + self.cache = FileCache(self.scratch_dir) + + def tearDown(self): + shutil.rmtree(self.scratch_dir) + + def test_write_and_read_cache_file(self): + """Test writing then reading a cached file.""" + with self.cache.write_transaction('test.yaml') as (old, new): + self.assertTrue(old is None) + self.assertTrue(new is not None) + new.write("foobar\n") + + with self.cache.read_transaction('test.yaml') as stream: + text = stream.read() + self.assertEqual("foobar\n", text) + + def test_remove(self): + """Test removing an entry from the cache.""" + self.test_write_and_write_cache_file() + + self.cache.remove('test.yaml') + + self.assertFalse(os.path.exists(self.cache.cache_path('test.yaml'))) + self.assertFalse(os.path.exists(self.cache._lock_path('test.yaml'))) + + def test_write_and_write_cache_file(self): + """Test two write transactions on a cached file.""" + with self.cache.write_transaction('test.yaml') as (old, new): + self.assertTrue(old is None) + self.assertTrue(new is not None) + new.write("foobar\n") + + with self.cache.write_transaction('test.yaml') as (old, new): + self.assertTrue(old is not None) + text = old.read() + self.assertEqual("foobar\n", text) + self.assertTrue(new is not None) + new.write("barbaz\n") + + with self.cache.read_transaction('test.yaml') as stream: + text = stream.read() + self.assertEqual("barbaz\n", text) diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py index 4de65760d7..0d1a8fe949 100644 --- a/lib/spack/spack/test/git_fetch.py +++ b/lib/spack/spack/test/git_fetch.py @@ -87,33 +87,29 @@ class GitFetchTest(MockPackagesTest): self.assert_rev(rev) - def test_fetch_master(self): """Test a default git checkout with no commit or tag specified.""" self.try_fetch('master', self.repo.r0_file, { - 'git' : self.repo.path + 'git': self.repo.path }) - def test_fetch_branch(self): """Test fetching a branch.""" self.try_fetch(self.repo.branch, self.repo.branch_file, { - 'git' : self.repo.path, - 'branch' : self.repo.branch + 'git': self.repo.path, + 'branch': self.repo.branch }) - def test_fetch_tag(self): """Test fetching a tag.""" self.try_fetch(self.repo.tag, self.repo.tag_file, { - 'git' : self.repo.path, - 'tag' : self.repo.tag + 'git': self.repo.path, + 'tag': self.repo.tag }) - def test_fetch_commit(self): """Test fetching a particular commit.""" self.try_fetch(self.repo.r1, self.repo.r1_file, { - 'git' : self.repo.path, - 'commit' : self.repo.r1 + 'git': self.repo.path, + 'commit': self.repo.r1 }) diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py index 292ffba949..44af6730a1 100644 --- a/lib/spack/spack/test/hg_fetch.py +++ b/lib/spack/spack/test/hg_fetch.py @@ -83,17 +83,15 @@ class HgFetchTest(MockPackagesTest): self.assertEqual(self.repo.get_rev(), rev) - def test_fetch_default(self): """Test a default hg checkout with no commit or tag specified.""" self.try_fetch(self.repo.r1, self.repo.r1_file, { - 'hg' : self.repo.path + 'hg': self.repo.path }) - def test_fetch_rev0(self): """Test fetching a branch.""" self.try_fetch(self.repo.r0, self.repo.r0_file, { - 'hg' : self.repo.path, - 'revision' : self.repo.r0 + 'hg': self.repo.path, + 'revision': self.repo.r0 }) diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index 390ec096a9..232d5aeeaf 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -55,7 +55,6 @@ class InstallTest(MockPackagesTest): spack.install_layout = YamlDirectoryLayout(self.tmpdir) spack.installed_db = Database(self.tmpdir) - def tearDown(self): super(InstallTest, self).tearDown() self.repo.destroy() @@ -68,14 +67,12 @@ class InstallTest(MockPackagesTest): spack.installed_db = self.orig_db shutil.rmtree(self.tmpdir, ignore_errors=True) - def fake_fetchify(self, pkg): """Fake the URL for a package so it downloads from a file.""" fetcher = FetchStrategyComposite() fetcher.append(URLFetchStrategy(self.repo.url)) pkg.fetcher = fetcher - def test_install_and_uninstall(self): # Get a basic concrete spec for the trivial install package. spec = Spec('trivial_install_test_package') @@ -90,11 +87,10 @@ class InstallTest(MockPackagesTest): try: pkg.do_install() pkg.do_uninstall() - except Exception, e: + except Exception: pkg.remove_prefix() raise - def test_install_environment(self): spec = Spec('cmake-client').concretized() @@ -104,6 +100,6 @@ class InstallTest(MockPackagesTest): pkg = spec.package try: pkg.do_install() - except Exception, e: + except Exception: pkg.remove_prefix() raise diff --git a/lib/spack/spack/test/link_tree.py b/lib/spack/spack/test/link_tree.py index de40991b57..5d0a7430b6 100644 --- a/lib/spack/spack/test/link_tree.py +++ b/lib/spack/spack/test/link_tree.py @@ -53,16 +53,13 @@ class LinkTreeTest(unittest.TestCase): def tearDown(self): self.stage.destroy() - def check_file_link(self, filename): self.assertTrue(os.path.isfile(filename)) self.assertTrue(os.path.islink(filename)) - def check_dir(self, filename): self.assertTrue(os.path.isdir(filename)) - def test_merge_to_new_directory(self): with working_dir(self.stage.path): self.link_tree.merge('dest') @@ -79,7 +76,6 @@ class LinkTreeTest(unittest.TestCase): self.assertFalse(os.path.exists('dest')) - def test_merge_to_existing_directory(self): with working_dir(self.stage.path): @@ -112,7 +108,6 @@ class LinkTreeTest(unittest.TestCase): self.assertFalse(os.path.isfile('dest/c/d/6')) self.assertFalse(os.path.isfile('dest/c/d/e/7')) - def test_merge_with_empty_directories(self): with working_dir(self.stage.path): mkdirp('dest/f/g') @@ -132,7 +127,6 @@ class LinkTreeTest(unittest.TestCase): self.assertTrue(os.path.isdir('dest/a/b/h')) self.assertTrue(os.path.isdir('dest/f/g')) - def test_ignore(self): with working_dir(self.stage.path): touchp('source/.spec') diff --git a/lib/spack/spack/test/lock.py b/lib/spack/spack/test/lock.py index 0e9f6daf4d..fb96539897 100644 --- a/lib/spack/spack/test/lock.py +++ b/lib/spack/spack/test/lock.py @@ -46,21 +46,21 @@ class LockTest(unittest.TestCase): self.lock_path = join_path(self.tempdir, 'lockfile') touch(self.lock_path) - def tearDown(self): - shutil.rmtree(self.tempdir, ignore_errors=True) - + shutil.rmtree(self.tempdir, ignore_errors=True) def multiproc_test(self, *functions): """Order some processes using simple barrier synchronization.""" b = Barrier(len(functions), timeout=barrier_timeout) procs = [Process(target=f, args=(b,)) for f in functions] - for p in procs: p.start() + + for p in procs: + p.start() + for p in procs: p.join() self.assertEqual(p.exitcode, 0) - # # Process snippets below can be composed into tests. # @@ -68,27 +68,26 @@ class LockTest(unittest.TestCase): lock = Lock(self.lock_path) lock.acquire_write() # grab exclusive lock barrier.wait() - barrier.wait() # hold the lock until exception raises in other procs. + barrier.wait() # hold the lock until exception raises in other procs. def acquire_read(self, barrier): lock = Lock(self.lock_path) lock.acquire_read() # grab shared lock barrier.wait() - barrier.wait() # hold the lock until exception raises in other procs. + barrier.wait() # hold the lock until exception raises in other procs. def timeout_write(self, barrier): lock = Lock(self.lock_path) - barrier.wait() # wait for lock acquire in first process + barrier.wait() # wait for lock acquire in first process self.assertRaises(LockError, lock.acquire_write, 0.1) barrier.wait() def timeout_read(self, barrier): lock = Lock(self.lock_path) - barrier.wait() # wait for lock acquire in first process + barrier.wait() # wait for lock acquire in first process self.assertRaises(LockError, lock.acquire_read, 0.1) barrier.wait() - # # Test that exclusive locks on other processes time out when an # exclusive lock is held. @@ -97,11 +96,13 @@ class LockTest(unittest.TestCase): self.multiproc_test(self.acquire_write, self.timeout_write) def test_write_lock_timeout_on_write_2(self): - self.multiproc_test(self.acquire_write, self.timeout_write, self.timeout_write) + self.multiproc_test( + self.acquire_write, self.timeout_write, self.timeout_write) def test_write_lock_timeout_on_write_3(self): - self.multiproc_test(self.acquire_write, self.timeout_write, self.timeout_write, self.timeout_write) - + self.multiproc_test( + self.acquire_write, self.timeout_write, self.timeout_write, + self.timeout_write) # # Test that shared locks on other processes time out when an @@ -111,11 +112,13 @@ class LockTest(unittest.TestCase): self.multiproc_test(self.acquire_write, self.timeout_read) def test_read_lock_timeout_on_write_2(self): - self.multiproc_test(self.acquire_write, self.timeout_read, self.timeout_read) + self.multiproc_test( + self.acquire_write, self.timeout_read, self.timeout_read) def test_read_lock_timeout_on_write_3(self): - self.multiproc_test(self.acquire_write, self.timeout_read, self.timeout_read, self.timeout_read) - + self.multiproc_test( + self.acquire_write, self.timeout_read, self.timeout_read, + self.timeout_read) # # Test that exclusive locks time out when shared locks are held. @@ -124,27 +127,35 @@ class LockTest(unittest.TestCase): self.multiproc_test(self.acquire_read, self.timeout_write) def test_write_lock_timeout_on_read_2(self): - self.multiproc_test(self.acquire_read, self.timeout_write, self.timeout_write) + self.multiproc_test( + self.acquire_read, self.timeout_write, self.timeout_write) def test_write_lock_timeout_on_read_3(self): - self.multiproc_test(self.acquire_read, self.timeout_write, self.timeout_write, self.timeout_write) - + self.multiproc_test( + self.acquire_read, self.timeout_write, self.timeout_write, + self.timeout_write) # # Test that exclusive locks time while lots of shared locks are held. # def test_write_lock_timeout_with_multiple_readers_2_1(self): - self.multiproc_test(self.acquire_read, self.acquire_read, self.timeout_write) + self.multiproc_test( + self.acquire_read, self.acquire_read, self.timeout_write) def test_write_lock_timeout_with_multiple_readers_2_2(self): - self.multiproc_test(self.acquire_read, self.acquire_read, self.timeout_write, self.timeout_write) + self.multiproc_test( + self.acquire_read, self.acquire_read, self.timeout_write, + self.timeout_write) def test_write_lock_timeout_with_multiple_readers_3_1(self): - self.multiproc_test(self.acquire_read, self.acquire_read, self.acquire_read, self.timeout_write) + self.multiproc_test( + self.acquire_read, self.acquire_read, self.acquire_read, + self.timeout_write) def test_write_lock_timeout_with_multiple_readers_3_2(self): - self.multiproc_test(self.acquire_read, self.acquire_read, self.acquire_read, self.timeout_write, self.timeout_write) - + self.multiproc_test( + self.acquire_read, self.acquire_read, self.acquire_read, + self.timeout_write, self.timeout_write) # # Longer test case that ensures locks are reusable. Ordering is @@ -155,110 +166,283 @@ class LockTest(unittest.TestCase): lock = Lock(self.lock_path) lock.acquire_write() - barrier.wait() # ---------------------------------------- 1 + barrier.wait() # ---------------------------------------- 1 # others test timeout - barrier.wait() # ---------------------------------------- 2 + barrier.wait() # ---------------------------------------- 2 lock.release_write() # release and others acquire read - barrier.wait() # ---------------------------------------- 3 + barrier.wait() # ---------------------------------------- 3 self.assertRaises(LockError, lock.acquire_write, 0.1) lock.acquire_read() - barrier.wait() # ---------------------------------------- 4 + barrier.wait() # ---------------------------------------- 4 lock.release_read() - barrier.wait() # ---------------------------------------- 5 + barrier.wait() # ---------------------------------------- 5 # p2 upgrades read to write - barrier.wait() # ---------------------------------------- 6 + barrier.wait() # ---------------------------------------- 6 self.assertRaises(LockError, lock.acquire_write, 0.1) self.assertRaises(LockError, lock.acquire_read, 0.1) - barrier.wait() # ---------------------------------------- 7 + barrier.wait() # ---------------------------------------- 7 # p2 releases write and read - barrier.wait() # ---------------------------------------- 8 + barrier.wait() # ---------------------------------------- 8 # p3 acquires read - barrier.wait() # ---------------------------------------- 9 + barrier.wait() # ---------------------------------------- 9 # p3 upgrades read to write - barrier.wait() # ---------------------------------------- 10 + barrier.wait() # ---------------------------------------- 10 self.assertRaises(LockError, lock.acquire_write, 0.1) self.assertRaises(LockError, lock.acquire_read, 0.1) - barrier.wait() # ---------------------------------------- 11 + barrier.wait() # ---------------------------------------- 11 # p3 releases locks - barrier.wait() # ---------------------------------------- 12 + barrier.wait() # ---------------------------------------- 12 lock.acquire_read() - barrier.wait() # ---------------------------------------- 13 + barrier.wait() # ---------------------------------------- 13 lock.release_read() - def p2(barrier): lock = Lock(self.lock_path) # p1 acquires write - barrier.wait() # ---------------------------------------- 1 + barrier.wait() # ---------------------------------------- 1 self.assertRaises(LockError, lock.acquire_write, 0.1) self.assertRaises(LockError, lock.acquire_read, 0.1) - barrier.wait() # ---------------------------------------- 2 + barrier.wait() # ---------------------------------------- 2 lock.acquire_read() - barrier.wait() # ---------------------------------------- 3 + barrier.wait() # ---------------------------------------- 3 # p1 tests shared read - barrier.wait() # ---------------------------------------- 4 + barrier.wait() # ---------------------------------------- 4 # others release reads - barrier.wait() # ---------------------------------------- 5 + barrier.wait() # ---------------------------------------- 5 - lock.acquire_write() # upgrade read to write - barrier.wait() # ---------------------------------------- 6 + lock.acquire_write() # upgrade read to write + barrier.wait() # ---------------------------------------- 6 # others test timeout - barrier.wait() # ---------------------------------------- 7 + barrier.wait() # ---------------------------------------- 7 lock.release_write() # release read AND write (need both) lock.release_read() - barrier.wait() # ---------------------------------------- 8 + barrier.wait() # ---------------------------------------- 8 # p3 acquires read - barrier.wait() # ---------------------------------------- 9 + barrier.wait() # ---------------------------------------- 9 # p3 upgrades read to write - barrier.wait() # ---------------------------------------- 10 + barrier.wait() # ---------------------------------------- 10 self.assertRaises(LockError, lock.acquire_write, 0.1) self.assertRaises(LockError, lock.acquire_read, 0.1) - barrier.wait() # ---------------------------------------- 11 + barrier.wait() # ---------------------------------------- 11 # p3 releases locks - barrier.wait() # ---------------------------------------- 12 + barrier.wait() # ---------------------------------------- 12 lock.acquire_read() - barrier.wait() # ---------------------------------------- 13 + barrier.wait() # ---------------------------------------- 13 lock.release_read() - def p3(barrier): lock = Lock(self.lock_path) # p1 acquires write - barrier.wait() # ---------------------------------------- 1 + barrier.wait() # ---------------------------------------- 1 self.assertRaises(LockError, lock.acquire_write, 0.1) self.assertRaises(LockError, lock.acquire_read, 0.1) - barrier.wait() # ---------------------------------------- 2 + barrier.wait() # ---------------------------------------- 2 lock.acquire_read() - barrier.wait() # ---------------------------------------- 3 + barrier.wait() # ---------------------------------------- 3 # p1 tests shared read - barrier.wait() # ---------------------------------------- 4 + barrier.wait() # ---------------------------------------- 4 lock.release_read() - barrier.wait() # ---------------------------------------- 5 + barrier.wait() # ---------------------------------------- 5 # p2 upgrades read to write - barrier.wait() # ---------------------------------------- 6 + barrier.wait() # ---------------------------------------- 6 self.assertRaises(LockError, lock.acquire_write, 0.1) self.assertRaises(LockError, lock.acquire_read, 0.1) - barrier.wait() # ---------------------------------------- 7 + barrier.wait() # ---------------------------------------- 7 # p2 releases write & read - barrier.wait() # ---------------------------------------- 8 + barrier.wait() # ---------------------------------------- 8 lock.acquire_read() - barrier.wait() # ---------------------------------------- 9 + barrier.wait() # ---------------------------------------- 9 lock.acquire_write() - barrier.wait() # ---------------------------------------- 10 + barrier.wait() # ---------------------------------------- 10 # others test timeout - barrier.wait() # ---------------------------------------- 11 + barrier.wait() # ---------------------------------------- 11 lock.release_read() # release read AND write in opposite lock.release_write() # order from before on p2 - barrier.wait() # ---------------------------------------- 12 + barrier.wait() # ---------------------------------------- 12 lock.acquire_read() - barrier.wait() # ---------------------------------------- 13 + barrier.wait() # ---------------------------------------- 13 lock.release_read() self.multiproc_test(p1, p2, p3) + + def test_transaction(self): + def enter_fn(): + vals['entered'] = True + + def exit_fn(t, v, tb): + vals['exited'] = True + vals['exception'] = (t or v or tb) + + lock = Lock(self.lock_path) + vals = {'entered': False, 'exited': False, 'exception': False} + with ReadTransaction(lock, enter_fn, exit_fn): + pass + + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertFalse(vals['exception']) + + vals = {'entered': False, 'exited': False, 'exception': False} + with WriteTransaction(lock, enter_fn, exit_fn): + pass + + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertFalse(vals['exception']) + + def test_transaction_with_exception(self): + def enter_fn(): + vals['entered'] = True + + def exit_fn(t, v, tb): + vals['exited'] = True + vals['exception'] = (t or v or tb) + + lock = Lock(self.lock_path) + + def do_read_with_exception(): + with ReadTransaction(lock, enter_fn, exit_fn): + raise Exception() + + def do_write_with_exception(): + with WriteTransaction(lock, enter_fn, exit_fn): + raise Exception() + + vals = {'entered': False, 'exited': False, 'exception': False} + self.assertRaises(Exception, do_read_with_exception) + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertTrue(vals['exception']) + + vals = {'entered': False, 'exited': False, 'exception': False} + self.assertRaises(Exception, do_write_with_exception) + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertTrue(vals['exception']) + + def test_transaction_with_context_manager(self): + class TestContextManager(object): + + def __enter__(self): + vals['entered'] = True + + def __exit__(self, t, v, tb): + vals['exited'] = True + vals['exception'] = (t or v or tb) + + def exit_fn(t, v, tb): + vals['exited_fn'] = True + vals['exception_fn'] = (t or v or tb) + + lock = Lock(self.lock_path) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + with ReadTransaction(lock, TestContextManager, exit_fn): + pass + + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertFalse(vals['exception']) + self.assertTrue(vals['exited_fn']) + self.assertFalse(vals['exception_fn']) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + with ReadTransaction(lock, TestContextManager): + pass + + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertFalse(vals['exception']) + self.assertFalse(vals['exited_fn']) + self.assertFalse(vals['exception_fn']) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + with WriteTransaction(lock, TestContextManager, exit_fn): + pass + + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertFalse(vals['exception']) + self.assertTrue(vals['exited_fn']) + self.assertFalse(vals['exception_fn']) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + with WriteTransaction(lock, TestContextManager): + pass + + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertFalse(vals['exception']) + self.assertFalse(vals['exited_fn']) + self.assertFalse(vals['exception_fn']) + + def test_transaction_with_context_manager_and_exception(self): + class TestContextManager(object): + + def __enter__(self): + vals['entered'] = True + + def __exit__(self, t, v, tb): + vals['exited'] = True + vals['exception'] = (t or v or tb) + + def exit_fn(t, v, tb): + vals['exited_fn'] = True + vals['exception_fn'] = (t or v or tb) + + lock = Lock(self.lock_path) + + def do_read_with_exception(exit_fn): + with ReadTransaction(lock, TestContextManager, exit_fn): + raise Exception() + + def do_write_with_exception(exit_fn): + with WriteTransaction(lock, TestContextManager, exit_fn): + raise Exception() + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + self.assertRaises(Exception, do_read_with_exception, exit_fn) + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertTrue(vals['exception']) + self.assertTrue(vals['exited_fn']) + self.assertTrue(vals['exception_fn']) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + self.assertRaises(Exception, do_read_with_exception, None) + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertTrue(vals['exception']) + self.assertFalse(vals['exited_fn']) + self.assertFalse(vals['exception_fn']) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + self.assertRaises(Exception, do_write_with_exception, exit_fn) + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertTrue(vals['exception']) + self.assertTrue(vals['exited_fn']) + self.assertTrue(vals['exception_fn']) + + vals = {'entered': False, 'exited': False, 'exited_fn': False, + 'exception': False, 'exception_fn': False} + self.assertRaises(Exception, do_write_with_exception, None) + self.assertTrue(vals['entered']) + self.assertTrue(vals['exited']) + self.assertTrue(vals['exception']) + self.assertFalse(vals['exited_fn']) + self.assertFalse(vals['exception_fn']) diff --git a/lib/spack/spack/test/make_executable.py b/lib/spack/spack/test/make_executable.py index b7a45a3f72..87a43a529a 100644 --- a/lib/spack/spack/test/make_executable.py +++ b/lib/spack/spack/test/make_executable.py @@ -38,6 +38,7 @@ from spack.util.environment import path_put_first class MakeExecutableTest(unittest.TestCase): + def setUp(self): self.tmpdir = tempfile.mkdtemp() @@ -49,34 +50,30 @@ class MakeExecutableTest(unittest.TestCase): path_put_first('PATH', [self.tmpdir]) - def tearDown(self): shutil.rmtree(self.tmpdir) - def test_make_normal(self): make = MakeExecutable('make', 8) self.assertEqual(make(output=str).strip(), '-j8') self.assertEqual(make('install', output=str).strip(), '-j8 install') - def test_make_explicit(self): make = MakeExecutable('make', 8) self.assertEqual(make(parallel=True, output=str).strip(), '-j8') - self.assertEqual(make('install', parallel=True, output=str).strip(), '-j8 install') - + self.assertEqual(make('install', parallel=True, + output=str).strip(), '-j8 install') def test_make_one_job(self): make = MakeExecutable('make', 1) self.assertEqual(make(output=str).strip(), '') self.assertEqual(make('install', output=str).strip(), 'install') - def test_make_parallel_false(self): make = MakeExecutable('make', 8) self.assertEqual(make(parallel=False, output=str).strip(), '') - self.assertEqual(make('install', parallel=False, output=str).strip(), 'install') - + self.assertEqual(make('install', parallel=False, + output=str).strip(), 'install') def test_make_parallel_disabled(self): make = MakeExecutable('make', 8) @@ -100,26 +97,29 @@ class MakeExecutableTest(unittest.TestCase): del os.environ['SPACK_NO_PARALLEL_MAKE'] - def test_make_parallel_precedence(self): make = MakeExecutable('make', 8) # These should work os.environ['SPACK_NO_PARALLEL_MAKE'] = 'true' self.assertEqual(make(parallel=True, output=str).strip(), '') - self.assertEqual(make('install', parallel=True, output=str).strip(), 'install') + self.assertEqual(make('install', parallel=True, + output=str).strip(), 'install') os.environ['SPACK_NO_PARALLEL_MAKE'] = '1' self.assertEqual(make(parallel=True, output=str).strip(), '') - self.assertEqual(make('install', parallel=True, output=str).strip(), 'install') + self.assertEqual(make('install', parallel=True, + output=str).strip(), 'install') # These don't disable (false and random string) os.environ['SPACK_NO_PARALLEL_MAKE'] = 'false' self.assertEqual(make(parallel=True, output=str).strip(), '-j8') - self.assertEqual(make('install', parallel=True, output=str).strip(), '-j8 install') + self.assertEqual(make('install', parallel=True, + output=str).strip(), '-j8 install') os.environ['SPACK_NO_PARALLEL_MAKE'] = 'foobar' self.assertEqual(make(parallel=True, output=str).strip(), '-j8') - self.assertEqual(make('install', parallel=True, output=str).strip(), '-j8 install') + self.assertEqual(make('install', parallel=True, + output=str).strip(), '-j8 install') del os.environ['SPACK_NO_PARALLEL_MAKE'] diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py index b682d4e097..d6d7b30b7c 100644 --- a/lib/spack/spack/test/mirror.py +++ b/lib/spack/spack/test/mirror.py @@ -35,6 +35,7 @@ exclude = ['.hg', '.git', '.svn'] class MirrorTest(MockPackagesTest): + def setUp(self): """Sets up a mock package and a mock repo for each fetch strategy, to ensure that the mirror can create archives for each of them. @@ -42,7 +43,6 @@ class MirrorTest(MockPackagesTest): super(MirrorTest, self).setUp() self.repos = {} - def tearDown(self): """Destroy all the stages created by the repos in setup.""" super(MirrorTest, self).tearDown() @@ -50,7 +50,6 @@ class MirrorTest(MockPackagesTest): repo.destroy() self.repos.clear() - def set_up_package(self, name, MockRepoClass, url_attr): """Set up a mock package to be mirrored. Each package needs us to: @@ -71,16 +70,14 @@ class MirrorTest(MockPackagesTest): v = next(iter(pkg.versions)) pkg.versions[v][url_attr] = repo.url - def check_mirror(self): with Stage('spack-mirror-test') as stage: mirror_root = join_path(stage.path, 'test-mirror') # register mirror with spack config - mirrors = { 'spack-mirror-test' : 'file://' + mirror_root } + mirrors = {'spack-mirror-test': 'file://' + mirror_root} spack.config.update_config('mirrors', mirrors) - os.chdir(stage.path) spack.mirror.create( mirror_root, self.repos, no_checksum=True) @@ -110,16 +107,18 @@ class MirrorTest(MockPackagesTest): original_path = mock_repo.path if 'svn' in name: # have to check out the svn repo to compare. - original_path = join_path(mock_repo.path, 'checked_out') + original_path = join_path( + mock_repo.path, 'checked_out') svn('checkout', mock_repo.url, original_path) dcmp = dircmp(original_path, pkg.stage.source_path) - # make sure there are no new files in the expanded tarball + # make sure there are no new files in the expanded + # tarball self.assertFalse(dcmp.right_only) # and that all original files are present. - self.assertTrue(all(l in exclude for l in dcmp.left_only)) + self.assertTrue( + all(l in exclude for l in dcmp.left_only)) spack.do_checksum = saved_checksum_setting - def test_git_mirror(self): self.set_up_package('git-test', MockGitRepo, 'git') self.check_mirror() diff --git a/lib/spack/spack/test/mock_database.py b/lib/spack/spack/test/mock_database.py index b1194f2451..d5867f06ec 100644 --- a/lib/spack/spack/test/mock_database.py +++ b/lib/spack/spack/test/mock_database.py @@ -33,6 +33,7 @@ from spack.test.mock_packages_test import MockPackagesTest class MockDatabase(MockPackagesTest): + def _mock_install(self, spec): s = Spec(spec) s.concretize() @@ -95,8 +96,10 @@ class MockDatabase(MockPackagesTest): self._mock_install('mpileaks ^zmpi') def tearDown(self): - for spec in spack.installed_db.query(): - spec.package.do_uninstall(spec) + with spack.installed_db.write_transaction(): + for spec in spack.installed_db.query(): + spec.package.do_uninstall(spec) + super(MockDatabase, self).tearDown() shutil.rmtree(self.install_path) spack.install_path = self.spack_install_path diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py index 9d96622a6e..82c2712b0e 100644 --- a/lib/spack/spack/test/mock_packages_test.py +++ b/lib/spack/spack/test/mock_packages_test.py @@ -155,7 +155,9 @@ packages: externalmodule@1.0%gcc@4.5.0: external-module """ + class MockPackagesTest(unittest.TestCase): + def initmock(self): # Use the mock packages database for these tests. This allows # us to set up contrived packages that don't interfere with @@ -172,7 +174,8 @@ class MockPackagesTest(unittest.TestCase): self.mock_user_config = os.path.join(self.temp_config, 'user') mkdirp(self.mock_site_config) mkdirp(self.mock_user_config) - for confs in [('compilers.yaml', mock_compiler_config), ('packages.yaml', mock_packages_config)]: + for confs in [('compilers.yaml', mock_compiler_config), + ('packages.yaml', mock_packages_config)]: conf_yaml = os.path.join(self.mock_site_config, confs[0]) with open(conf_yaml, 'w') as f: f.write(confs[1]) @@ -209,7 +212,6 @@ class MockPackagesTest(unittest.TestCase): pkg.dependencies[spec.name] = {Spec(pkg_name): spec} pkg._deptypes[spec.name] = set(deptypes) - def cleanmock(self): """Restore the real packages path after any test.""" spack.repo.swap(self.db) @@ -226,10 +228,8 @@ class MockPackagesTest(unittest.TestCase): shutil.rmtree(spack.share_path, ignore_errors=True) spack.share_path = self.real_share_path - def setUp(self): self.initmock() - def tearDown(self): self.cleanmock() diff --git a/lib/spack/spack/test/mock_repo.py b/lib/spack/spack/test/mock_repo.py index 386af282e7..0ae7dbd516 100644 --- a/lib/spack/spack/test/mock_repo.py +++ b/lib/spack/spack/test/mock_repo.py @@ -40,6 +40,7 @@ tar = which('tar', required=True) class MockRepo(object): + def __init__(self, stage_name, repo_name): """This creates a stage where some archive/repo files can be staged for testing spack's fetch strategies.""" @@ -50,7 +51,6 @@ class MockRepo(object): self.path = join_path(self.stage.path, repo_name) mkdirp(self.path) - def destroy(self): """Destroy resources associated with this mock repo.""" if self.stage: @@ -90,6 +90,7 @@ class MockArchive(MockRepo): class MockVCSRepo(MockRepo): + def __init__(self, stage_name, repo_name): """This creates a stage and a repo directory within the stage.""" super(MockVCSRepo, self).__init__(stage_name, repo_name) @@ -100,6 +101,7 @@ class MockVCSRepo(MockRepo): class MockGitRepo(MockVCSRepo): + def __init__(self): super(MockGitRepo, self).__init__('mock-git-stage', 'mock-git-repo') @@ -147,6 +149,7 @@ class MockGitRepo(MockVCSRepo): class MockSvnRepo(MockVCSRepo): + def __init__(self): super(MockSvnRepo, self).__init__('mock-svn-stage', 'mock-svn-repo') @@ -176,6 +179,7 @@ class MockSvnRepo(MockVCSRepo): class MockHgRepo(MockVCSRepo): + def __init__(self): super(MockHgRepo, self).__init__('mock-hg-stage', 'mock-hg-repo') self.url = 'file://' + self.path diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py index 135cd028e3..5e280d8e43 100644 --- a/lib/spack/spack/test/modules.py +++ b/lib/spack/spack/test/modules.py @@ -89,7 +89,10 @@ configuration_alter_environment = { 'enable': ['tcl'], 'tcl': { 'all': { - 'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']} + 'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}, + 'environment': { + 'set': {'{name}_ROOT': '{prefix}'} + } }, 'platform=test target=x86_64': { 'environment': { @@ -248,6 +251,8 @@ class TclTests(MockPackagesTest): self.assertEqual( len([x for x in content if 'setenv FOO "foo"' in x]), 1) self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 1) + self.assertEqual( + len([x for x in content if 'setenv MPILEAKS_ROOT' in x]), 1) spec = spack.spec.Spec('libdwarf %clang platform=test target=x86_32') content = self.get_modulefile_content(spec) @@ -262,6 +267,8 @@ class TclTests(MockPackagesTest): len([x for x in content if 'is-loaded foo/bar' in x]), 1) self.assertEqual( len([x for x in content if 'module load foo/bar' in x]), 1) + self.assertEqual( + len([x for x in content if 'setenv LIBDWARF_ROOT' in x]), 1) def test_blacklist(self): spack.modules.CONFIGURATION = configuration_blacklist diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py index c233ea4fd6..a885374080 100644 --- a/lib/spack/spack/test/multimethod.py +++ b/lib/spack/spack/test/multimethod.py @@ -25,15 +25,10 @@ """ Test for multi_method dispatch. """ -import unittest - import spack from spack.multimethod import * from spack.version import * -from spack.spec import Spec -from spack.multimethod import when from spack.test.mock_packages_test import * -from spack.version import * class MultiMethodTest(MockPackagesTest): @@ -42,7 +37,6 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod@2.0') self.assertRaises(NoSuchMethodError, pkg.no_version_2) - def test_one_version_match(self): pkg = spack.repo.get('multimethod@1.0') self.assertEqual(pkg.no_version_2(), 1) @@ -53,7 +47,6 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod@4.0') self.assertEqual(pkg.no_version_2(), 4) - def test_version_overlap(self): pkg = spack.repo.get('multimethod@2.0') self.assertEqual(pkg.version_overlap(), 1) @@ -61,7 +54,6 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod@5.0') self.assertEqual(pkg.version_overlap(), 2) - def test_mpi_version(self): pkg = spack.repo.get('multimethod^mpich@3.0.4') self.assertEqual(pkg.mpi_version(), 3) @@ -72,7 +64,6 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod^mpich@1.0') self.assertEqual(pkg.mpi_version(), 1) - def test_undefined_mpi_version(self): pkg = spack.repo.get('multimethod^mpich@0.4') self.assertEqual(pkg.mpi_version(), 1) @@ -80,7 +71,6 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod^mpich@1.4') self.assertEqual(pkg.mpi_version(), 1) - def test_default_works(self): pkg = spack.repo.get('multimethod%gcc') self.assertEqual(pkg.has_a_default(), 'gcc') @@ -91,21 +81,19 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod%pgi') self.assertEqual(pkg.has_a_default(), 'default') - def test_target_match(self): platform = spack.architecture.platform() targets = platform.targets.values() for target in targets[:-1]: - pkg = spack.repo.get('multimethod target='+target.name) + pkg = spack.repo.get('multimethod target=' + target.name) self.assertEqual(pkg.different_by_target(), target.name) - pkg = spack.repo.get('multimethod target='+targets[-1].name) + pkg = spack.repo.get('multimethod target=' + targets[-1].name) if len(targets) == 1: self.assertEqual(pkg.different_by_target(), targets[-1].name) else: self.assertRaises(NoSuchMethodError, pkg.different_by_target) - def test_dependency_match(self): pkg = spack.repo.get('multimethod^zmpi') self.assertEqual(pkg.different_by_dep(), 'zmpi') @@ -118,7 +106,6 @@ class MultiMethodTest(MockPackagesTest): pkg = spack.repo.get('multimethod^foobar') self.assertEqual(pkg.different_by_dep(), 'mpich') - def test_virtual_dep_match(self): pkg = spack.repo.get('multimethod^mpich2') self.assertEqual(pkg.different_by_virtual_dep(), 2) diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py index b38ecd6179..7927fc8e60 100644 --- a/lib/spack/spack/test/namespace_trie.py +++ b/lib/spack/spack/test/namespace_trie.py @@ -32,7 +32,6 @@ class NamespaceTrieTest(unittest.TestCase): def setUp(self): self.trie = NamespaceTrie() - def test_add_single(self): self.trie['foo'] = 'bar' @@ -40,7 +39,6 @@ class NamespaceTrieTest(unittest.TestCase): self.assertTrue(self.trie.has_value('foo')) self.assertEqual(self.trie['foo'], 'bar') - def test_add_multiple(self): self.trie['foo.bar'] = 'baz' @@ -54,7 +52,6 @@ class NamespaceTrieTest(unittest.TestCase): self.assertFalse(self.trie.is_prefix('foo.bar.baz')) self.assertFalse(self.trie.has_value('foo.bar.baz')) - def test_add_three(self): # add a three-level namespace self.trie['foo.bar.baz'] = 'quux' @@ -89,7 +86,6 @@ class NamespaceTrieTest(unittest.TestCase): self.assertFalse(self.trie.is_prefix('foo.bar.baz.quux')) self.assertFalse(self.trie.has_value('foo.bar.baz.quux')) - def test_add_none_single(self): self.trie['foo'] = None self.assertTrue(self.trie.is_prefix('foo')) @@ -99,8 +95,6 @@ class NamespaceTrieTest(unittest.TestCase): self.assertFalse(self.trie.is_prefix('foo.bar')) self.assertFalse(self.trie.has_value('foo.bar')) - - def test_add_none_multiple(self): self.trie['foo.bar'] = None diff --git a/lib/spack/spack/test/operating_system.py b/lib/spack/spack/test/operating_system.py index ed5f6ff8ad..8723f7244d 100644 --- a/lib/spack/spack/test/operating_system.py +++ b/lib/spack/spack/test/operating_system.py @@ -1,18 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## """ Test checks if the operating_system class is created correctly and that the functions are using the correct operating_system. Also checks whether the operating_system correctly uses the compiler_strategy """ - import unittest -import os -import platform from spack.platforms.cray_xc import CrayXc from spack.platforms.linux import Linux from spack.platforms.darwin import Darwin from spack.operating_system.linux_distro import LinuxDistro -from spack.operating_system.mac_os import MacOs from spack.operating_system.cnl import ComputeNodeLinux + class TestOperatingSystem(unittest.TestCase): def setUp(self): @@ -32,7 +53,7 @@ class TestOperatingSystem(unittest.TestCase): self.assertEquals(self.cray_operating_sys.compiler_strategy, "PATH") def test_cray_back_end_operating_system(self): - self.assertIsInstance(self.cray_back_os,ComputeNodeLinux) + self.assertIsInstance(self.cray_back_os, ComputeNodeLinux) def test_cray_back_end_compiler_strategy(self): self.assertEquals(self.cray_back_os.compiler_strategy, "MODULES") @@ -43,7 +64,6 @@ class TestOperatingSystem(unittest.TestCase): def test_linux_compiler_strategy(self): self.assertEquals(self.linux_operating_sys.compiler_strategy, "PATH") - def test_cray_front_end_compiler_list(self): """ Operating systems will now be in charge of finding compilers. So, depending on which operating system you want to build for diff --git a/lib/spack/spack/test/optional_deps.py b/lib/spack/spack/test/optional_deps.py index b5ba0ecf35..a9a2b9abf5 100644 --- a/lib/spack/spack/test/optional_deps.py +++ b/lib/spack/spack/test/optional_deps.py @@ -22,10 +22,10 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## - from spack.spec import Spec from spack.test.mock_packages_test import * + class ConcretizeTest(MockPackagesTest): def check_normalize(self, spec_string, expected): @@ -34,10 +34,10 @@ class ConcretizeTest(MockPackagesTest): self.assertEqual(spec, expected) self.assertTrue(spec.eq_dag(expected)) - def test_normalize_simple_conditionals(self): self.check_normalize('optional-dep-test', Spec('optional-dep-test')) - self.check_normalize('optional-dep-test~a', Spec('optional-dep-test~a')) + self.check_normalize('optional-dep-test~a', + Spec('optional-dep-test~a')) self.check_normalize('optional-dep-test+a', Spec('optional-dep-test+a', Spec('a'))) @@ -45,7 +45,6 @@ class ConcretizeTest(MockPackagesTest): self.check_normalize('optional-dep-test a=true', Spec('optional-dep-test a=true', Spec('a'))) - self.check_normalize('optional-dep-test a=true', Spec('optional-dep-test+a', Spec('a'))) @@ -55,25 +54,29 @@ class ConcretizeTest(MockPackagesTest): self.check_normalize('optional-dep-test%intel', Spec('optional-dep-test%intel', Spec('c'))) - self.check_normalize('optional-dep-test%intel@64.1', - Spec('optional-dep-test%intel@64.1', Spec('c'), Spec('d'))) + self.check_normalize( + 'optional-dep-test%intel@64.1', + Spec('optional-dep-test%intel@64.1', Spec('c'), Spec('d'))) - self.check_normalize('optional-dep-test%intel@64.1.2', - Spec('optional-dep-test%intel@64.1.2', Spec('c'), Spec('d'))) + self.check_normalize( + 'optional-dep-test%intel@64.1.2', + Spec('optional-dep-test%intel@64.1.2', Spec('c'), Spec('d'))) self.check_normalize('optional-dep-test%clang@35', Spec('optional-dep-test%clang@35', Spec('e'))) - def test_multiple_conditionals(self): - self.check_normalize('optional-dep-test+a@1.1', - Spec('optional-dep-test+a@1.1', Spec('a'), Spec('b'))) + self.check_normalize( + 'optional-dep-test+a@1.1', + Spec('optional-dep-test+a@1.1', Spec('a'), Spec('b'))) - self.check_normalize('optional-dep-test+a%intel', - Spec('optional-dep-test+a%intel', Spec('a'), Spec('c'))) + self.check_normalize( + 'optional-dep-test+a%intel', + Spec('optional-dep-test+a%intel', Spec('a'), Spec('c'))) - self.check_normalize('optional-dep-test@1.1%intel', - Spec('optional-dep-test@1.1%intel', Spec('b'), Spec('c'))) + self.check_normalize( + 'optional-dep-test@1.1%intel', + Spec('optional-dep-test@1.1%intel', Spec('b'), Spec('c'))) self.check_normalize('optional-dep-test@1.1%intel@64.1.2+a', Spec('optional-dep-test@1.1%intel@64.1.2+a', @@ -83,14 +86,12 @@ class ConcretizeTest(MockPackagesTest): Spec('optional-dep-test@1.1%clang@36.5+a', Spec('b'), Spec('a'), Spec('e'))) - def test_chained_mpi(self): self.check_normalize('optional-dep-test-2+mpi', Spec('optional-dep-test-2+mpi', Spec('optional-dep-test+mpi', Spec('mpi')))) - def test_default_variant(self): spec = Spec('optional-dep-test-3') spec.concretize() @@ -104,7 +105,6 @@ class ConcretizeTest(MockPackagesTest): spec.concretize() self.assertTrue('b' in spec) - def test_transitive_chain(self): # Each of these dependencies comes from a conditional # dependency on another. This requires iterating to evaluate diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index 9198986f5d..c3c3923855 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -38,12 +38,10 @@ class PackageSanityTest(unittest.TestCase): for name in spack.repo.all_package_names(): spack.repo.get(name) - def test_get_all_packages(self): """Get all packages once and make sure that works.""" self.check_db() - def test_get_all_mock_packages(self): """Get the mock packages once each too.""" db = RepoPath(spack.mock_packages_path) @@ -51,7 +49,6 @@ class PackageSanityTest(unittest.TestCase): self.check_db() spack.repo.swap(db) - def test_url_versions(self): """Check URLs for regular packages, if they are explicitly defined.""" for pkg in spack.repo.all_packages(): diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py index bea42bb33a..fdd079a8f7 100644 --- a/lib/spack/spack/test/packages.py +++ b/lib/spack/spack/test/packages.py @@ -22,7 +22,6 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## - import spack from llnl.util.filesystem import join_path from spack.repository import Repo @@ -33,33 +32,26 @@ from spack.util.naming import mod_to_class class PackagesTest(MockPackagesTest): def test_load_package(self): - pkg = spack.repo.get('mpich') - + spack.repo.get('mpich') def test_package_name(self): pkg = spack.repo.get('mpich') self.assertEqual(pkg.name, 'mpich') - def test_package_filename(self): repo = Repo(spack.mock_packages_path) filename = repo.filename_for_package_name('mpich') self.assertEqual(filename, - join_path(spack.mock_packages_path, 'packages', 'mpich', 'package.py')) - - - def test_package_name(self): - pkg = spack.repo.get('mpich') - self.assertEqual(pkg.name, 'mpich') - + join_path(spack.mock_packages_path, + 'packages', 'mpich', 'package.py')) def test_nonexisting_package_filename(self): repo = Repo(spack.mock_packages_path) filename = repo.filename_for_package_name('some-nonexisting-package') self.assertEqual( filename, - join_path(spack.mock_packages_path, 'packages', 'some-nonexisting-package', 'package.py')) - + join_path(spack.mock_packages_path, + 'packages', 'some-nonexisting-package', 'package.py')) def test_package_class_names(self): self.assertEqual('Mpich', mod_to_class('mpich')) @@ -68,37 +60,32 @@ class PackagesTest(MockPackagesTest): self.assertEqual('Pmgrcollective', mod_to_class('PmgrCollective')) self.assertEqual('_3db', mod_to_class('3db')) - # # Below tests target direct imports of spack packages from the # spack.pkg namespace # def test_import_package(self): - import spack.pkg.builtin.mock.mpich - + import spack.pkg.builtin.mock.mpich # noqa def test_import_package_as(self): - import spack.pkg.builtin.mock.mpich as mp - + import spack.pkg.builtin.mock.mpich as mp # noqa def test_import_class_from_package(self): - from spack.pkg.builtin.mock.mpich import Mpich - + from spack.pkg.builtin.mock.mpich import Mpich # noqa def test_import_module_from_package(self): - from spack.pkg.builtin.mock import mpich - + from spack.pkg.builtin.mock import mpich # noqa def test_import_namespace_container_modules(self): - import spack.pkg - import spack.pkg as p - from spack import pkg + import spack.pkg # noqa + import spack.pkg as p # noqa + from spack import pkg # noqa - import spack.pkg.builtin - import spack.pkg.builtin as b - from spack.pkg import builtin + import spack.pkg.builtin # noqa + import spack.pkg.builtin as b # noqa + from spack.pkg import builtin # noqa - import spack.pkg.builtin.mock - import spack.pkg.builtin.mock as m - from spack.pkg.builtin import mock + import spack.pkg.builtin.mock # noqa + import spack.pkg.builtin.mock as m # noqa + from spack.pkg.builtin import mock # noqa diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py index 3419d600b8..0c772a0d2d 100644 --- a/lib/spack/spack/test/pattern.py +++ b/lib/spack/spack/test/pattern.py @@ -41,6 +41,7 @@ class CompositeTest(unittest.TestCase): raise NotImplemented('subtract not implemented') class One(Base): + def add(self): Base.counter += 1 @@ -48,6 +49,7 @@ class CompositeTest(unittest.TestCase): Base.counter -= 1 class Two(Base): + def add(self): Base.counter += 2 diff --git a/lib/spack/spack/test/provider_index.py b/lib/spack/spack/test/provider_index.py new file mode 100644 index 0000000000..9847dd05a6 --- /dev/null +++ b/lib/spack/spack/test/provider_index.py @@ -0,0 +1,93 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""Tests for provider index cache files. + +Tests assume that mock packages provide this: + + {'blas': { + blas: set([netlib-blas, openblas, openblas-with-lapack])}, + 'lapack': {lapack: set([netlib-lapack, openblas-with-lapack])}, + 'mpi': {mpi@:1: set([mpich@:1]), + mpi@:2.0: set([mpich2]), + mpi@:2.1: set([mpich2@1.1:]), + mpi@:2.2: set([mpich2@1.2:]), + mpi@:3: set([mpich@3:]), + mpi@:10.0: set([zmpi])}, + 'stuff': {stuff: set([externalvirtual])}} +""" +from StringIO import StringIO + +import spack +from spack.spec import Spec +from spack.provider_index import ProviderIndex +from spack.test.mock_packages_test import * + + +class ProviderIndexTest(MockPackagesTest): + + def test_yaml_round_trip(self): + p = ProviderIndex(spack.repo.all_package_names()) + + ostream = StringIO() + p.to_yaml(ostream) + + istream = StringIO(ostream.getvalue()) + q = ProviderIndex.from_yaml(istream) + + self.assertEqual(p, q) + + def test_providers_for_simple(self): + p = ProviderIndex(spack.repo.all_package_names()) + + blas_providers = p.providers_for('blas') + self.assertTrue(Spec('netlib-blas') in blas_providers) + self.assertTrue(Spec('openblas') in blas_providers) + self.assertTrue(Spec('openblas-with-lapack') in blas_providers) + + lapack_providers = p.providers_for('lapack') + self.assertTrue(Spec('netlib-lapack') in lapack_providers) + self.assertTrue(Spec('openblas-with-lapack') in lapack_providers) + + def test_mpi_providers(self): + p = ProviderIndex(spack.repo.all_package_names()) + + mpi_2_providers = p.providers_for('mpi@2') + self.assertTrue(Spec('mpich2') in mpi_2_providers) + self.assertTrue(Spec('mpich@3:') in mpi_2_providers) + + mpi_3_providers = p.providers_for('mpi@3') + self.assertTrue(Spec('mpich2') not in mpi_3_providers) + self.assertTrue(Spec('mpich@3:') in mpi_3_providers) + self.assertTrue(Spec('zmpi') in mpi_3_providers) + + def test_equal(self): + p = ProviderIndex(spack.repo.all_package_names()) + q = ProviderIndex(spack.repo.all_package_names()) + self.assertEqual(p, q) + + def test_copy(self): + p = ProviderIndex(spack.repo.all_package_names()) + q = p.copy() + self.assertEqual(p, q) diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py index 6c09effc56..5af55bdc5f 100644 --- a/lib/spack/spack/test/python_version.py +++ b/lib/spack/spack/test/python_version.py @@ -36,7 +36,8 @@ import llnl.util.tty as tty import pyqver2 import spack -spack_max_version = (2,6) +spack_max_version = (2, 6) + class PythonVersionTest(unittest.TestCase): @@ -51,12 +52,10 @@ class PythonVersionTest(unittest.TestCase): if re.match(r'^[^.#].*\.py$', filename): yield os.path.join(root, filename) - def package_py_files(self): for name in spack.repo.all_package_names(): yield spack.repo.filename_for_package_name(name) - def check_python_versions(self, *files): # dict version -> filename -> reasons all_issues = {} @@ -66,7 +65,7 @@ class PythonVersionTest(unittest.TestCase): versions = pyqver2.get_versions(pyfile.read()) for ver, reasons in versions.items(): if ver > spack_max_version: - if not ver in all_issues: + if ver not in all_issues: all_issues[ver] = {} all_issues[ver][fn] = reasons @@ -87,7 +86,7 @@ class PythonVersionTest(unittest.TestCase): tty.error("These files require version %d.%d:" % v) maxlen = max(len(f) for f, prob in msgs) - fmt = "%%-%ds%%s" % (maxlen+3) + fmt = "%%-%ds%%s" % (maxlen + 3) print fmt % ('File', 'Reason') print fmt % ('-' * (maxlen), '-' * 20) for msg in msgs: @@ -95,10 +94,8 @@ class PythonVersionTest(unittest.TestCase): self.assertTrue(len(all_issues) == 0) - def test_core_module_compatibility(self): self.check_python_versions(*self.pyfiles(spack.lib_path)) - def test_package_module_compatibility(self): self.check_python_versions(*self.pyfiles(spack.packages_path)) diff --git a/lib/spack/spack/test/sbang.py b/lib/spack/spack/test/sbang.py index ed54ff90b0..12abce7b35 100644 --- a/lib/spack/spack/test/sbang.py +++ b/lib/spack/spack/test/sbang.py @@ -26,6 +26,7 @@ Test that Spack's shebang filtering works correctly. """ import os +import stat import unittest import tempfile import shutil @@ -41,7 +42,9 @@ lua_line_patched = "--!/this/" + ('x' * 200) + "/is/lua\n" sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root last_line = "last!\n" + class SbangTest(unittest.TestCase): + def setUp(self): self.tempdir = tempfile.mkdtemp() @@ -74,10 +77,8 @@ class SbangTest(unittest.TestCase): f.write(long_line) f.write(last_line) - def tearDown(self): - shutil.rmtree(self.tempdir, ignore_errors=True) - + shutil.rmtree(self.tempdir, ignore_errors=True) def test_shebang_handling(self): filter_shebangs_in_directory(self.tempdir) @@ -104,3 +105,14 @@ class SbangTest(unittest.TestCase): self.assertEqual(f.readline(), sbang_line) self.assertEqual(f.readline(), long_line) self.assertEqual(f.readline(), last_line) + + def test_shebang_handles_non_writable_files(self): + # make a file non-writable + st = os.stat(self.long_shebang) + not_writable_mode = st.st_mode & ~stat.S_IWRITE + os.chmod(self.long_shebang, not_writable_mode) + + self.test_shebang_handling() + + st = os.stat(self.long_shebang) + self.assertEqual(oct(not_writable_mode), oct(st.st_mode)) diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index 972e79aa20..8f61c7ac76 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -32,8 +32,6 @@ import spack import spack.architecture import spack.package -from llnl.util.lang import list_modules - from spack.spec import Spec from spack.test.mock_packages_test import * @@ -51,21 +49,19 @@ class SpecDagTest(MockPackagesTest): self.assertRaises(spack.spec.UnsatisfiableVersionSpecError, spec.normalize) - def test_preorder_node_traversal(self): dag = Spec('mpileaks ^zmpi') dag.normalize() names = ['mpileaks', 'callpath', 'dyninst', 'libdwarf', 'libelf', 'zmpi', 'fake'] - pairs = zip([0,1,2,3,4,2,3], names) + pairs = zip([0, 1, 2, 3, 4, 2, 3], names) traversal = dag.traverse() self.assertEqual([x.name for x in traversal], names) traversal = dag.traverse(depth=True) - self.assertEqual([(x, y.name) for x,y in traversal], pairs) - + self.assertEqual([(x, y.name) for x, y in traversal], pairs) def test_preorder_edge_traversal(self): dag = Spec('mpileaks ^zmpi') @@ -73,14 +69,13 @@ class SpecDagTest(MockPackagesTest): names = ['mpileaks', 'callpath', 'dyninst', 'libdwarf', 'libelf', 'libelf', 'zmpi', 'fake', 'zmpi'] - pairs = zip([0,1,2,3,4,3,2,3,1], names) + pairs = zip([0, 1, 2, 3, 4, 3, 2, 3, 1], names) traversal = dag.traverse(cover='edges') self.assertEqual([x.name for x in traversal], names) traversal = dag.traverse(cover='edges', depth=True) - self.assertEqual([(x, y.name) for x,y in traversal], pairs) - + self.assertEqual([(x, y.name) for x, y in traversal], pairs) def test_preorder_path_traversal(self): dag = Spec('mpileaks ^zmpi') @@ -88,14 +83,13 @@ class SpecDagTest(MockPackagesTest): names = ['mpileaks', 'callpath', 'dyninst', 'libdwarf', 'libelf', 'libelf', 'zmpi', 'fake', 'zmpi', 'fake'] - pairs = zip([0,1,2,3,4,3,2,3,1,2], names) + pairs = zip([0, 1, 2, 3, 4, 3, 2, 3, 1, 2], names) traversal = dag.traverse(cover='paths') self.assertEqual([x.name for x in traversal], names) traversal = dag.traverse(cover='paths', depth=True) - self.assertEqual([(x, y.name) for x,y in traversal], pairs) - + self.assertEqual([(x, y.name) for x, y in traversal], pairs) def test_postorder_node_traversal(self): dag = Spec('mpileaks ^zmpi') @@ -103,14 +97,13 @@ class SpecDagTest(MockPackagesTest): names = ['libelf', 'libdwarf', 'dyninst', 'fake', 'zmpi', 'callpath', 'mpileaks'] - pairs = zip([4,3,2,3,2,1,0], names) + pairs = zip([4, 3, 2, 3, 2, 1, 0], names) traversal = dag.traverse(order='post') self.assertEqual([x.name for x in traversal], names) traversal = dag.traverse(depth=True, order='post') - self.assertEqual([(x, y.name) for x,y in traversal], pairs) - + self.assertEqual([(x, y.name) for x, y in traversal], pairs) def test_postorder_edge_traversal(self): dag = Spec('mpileaks ^zmpi') @@ -118,14 +111,13 @@ class SpecDagTest(MockPackagesTest): names = ['libelf', 'libdwarf', 'libelf', 'dyninst', 'fake', 'zmpi', 'callpath', 'zmpi', 'mpileaks'] - pairs = zip([4,3,3,2,3,2,1,1,0], names) + pairs = zip([4, 3, 3, 2, 3, 2, 1, 1, 0], names) traversal = dag.traverse(cover='edges', order='post') self.assertEqual([x.name for x in traversal], names) traversal = dag.traverse(cover='edges', depth=True, order='post') - self.assertEqual([(x, y.name) for x,y in traversal], pairs) - + self.assertEqual([(x, y.name) for x, y in traversal], pairs) def test_postorder_path_traversal(self): dag = Spec('mpileaks ^zmpi') @@ -133,14 +125,13 @@ class SpecDagTest(MockPackagesTest): names = ['libelf', 'libdwarf', 'libelf', 'dyninst', 'fake', 'zmpi', 'callpath', 'fake', 'zmpi', 'mpileaks'] - pairs = zip([4,3,3,2,3,2,1,2,1,0], names) + pairs = zip([4, 3, 3, 2, 3, 2, 1, 2, 1, 0], names) traversal = dag.traverse(cover='paths', order='post') self.assertEqual([x.name for x in traversal], names) traversal = dag.traverse(cover='paths', depth=True, order='post') - self.assertEqual([(x, y.name) for x,y in traversal], pairs) - + self.assertEqual([(x, y.name) for x, y in traversal], pairs) def test_conflicting_spec_constraints(self): mpileaks = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf ^libdwarf') @@ -153,8 +144,7 @@ class SpecDagTest(MockPackagesTest): spec._dependencies['mpich'].spec = Spec('mpich@2.0') self.assertRaises(spack.spec.InconsistentSpecError, - lambda: mpileaks.flat_dependencies(copy=False)) - + lambda: mpileaks.flat_dependencies(copy=False)) def test_normalize_twice(self): """Make sure normalize can be run twice on the same spec, @@ -166,7 +156,6 @@ class SpecDagTest(MockPackagesTest): spec.normalize() self.assertEqual(n1, spec) - def test_normalize_a_lot(self): spec = Spec('mpileaks') spec.normalize() @@ -174,7 +163,6 @@ class SpecDagTest(MockPackagesTest): spec.normalize() spec.normalize() - def test_normalize_with_virtual_spec(self): dag = Spec('mpileaks', Spec('callpath', @@ -189,80 +177,80 @@ class SpecDagTest(MockPackagesTest): # make sure nothing with the same name occurs twice counts = {} for spec in dag.traverse(key=id): - if not spec.name in counts: + if spec.name not in counts: counts[spec.name] = 0 counts[spec.name] += 1 for name in counts: self.assertEqual(counts[name], 1, "Count for %s was not 1!" % name) - def check_links(self, spec_to_check): for spec in spec_to_check.traverse(): for dependent in spec.dependents(): self.assertTrue( spec.name in dependent.dependencies_dict(), "%s not in dependencies of %s" % - (spec.name, dependent.name)) + (spec.name, dependent.name)) for dependency in spec.dependencies(): self.assertTrue( spec.name in dependency.dependents_dict(), "%s not in dependents of %s" % - (spec.name, dependency.name)) - + (spec.name, dependency.name)) def test_dependents_and_dependencies_are_correct(self): spec = Spec('mpileaks', - Spec('callpath', - Spec('dyninst', - Spec('libdwarf', - Spec('libelf')), - Spec('libelf')), - Spec('mpi')), - Spec('mpi')) + Spec('callpath', + Spec('dyninst', + Spec('libdwarf', + Spec('libelf')), + Spec('libelf')), + Spec('mpi')), + Spec('mpi')) self.check_links(spec) spec.normalize() self.check_links(spec) - def test_unsatisfiable_version(self): self.set_pkg_dep('mpileaks', 'mpich@1.0') spec = Spec('mpileaks ^mpich@2.0 ^callpath ^dyninst ^libelf ^libdwarf') - self.assertRaises(spack.spec.UnsatisfiableVersionSpecError, spec.normalize) - + self.assertRaises(spack.spec.UnsatisfiableVersionSpecError, + spec.normalize) def test_unsatisfiable_compiler(self): self.set_pkg_dep('mpileaks', 'mpich%gcc') - spec = Spec('mpileaks ^mpich%intel ^callpath ^dyninst ^libelf ^libdwarf') - self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, spec.normalize) - + spec = Spec('mpileaks ^mpich%intel ^callpath ^dyninst ^libelf' + ' ^libdwarf') + self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, + spec.normalize) def test_unsatisfiable_compiler_version(self): self.set_pkg_dep('mpileaks', 'mpich%gcc@4.6') - spec = Spec('mpileaks ^mpich%gcc@4.5 ^callpath ^dyninst ^libelf ^libdwarf') - self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, spec.normalize) - + spec = Spec('mpileaks ^mpich%gcc@4.5 ^callpath ^dyninst ^libelf' + ' ^libdwarf') + self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, + spec.normalize) def test_unsatisfiable_architecture(self): - platform = spack.architecture.platform() - self.set_pkg_dep('mpileaks', 'mpich platform=test target=be') - spec = Spec('mpileaks ^mpich platform=test target=fe ^callpath ^dyninst ^libelf ^libdwarf') - self.assertRaises(spack.spec.UnsatisfiableArchitectureSpecError, spec.normalize) - + spec = Spec('mpileaks ^mpich platform=test target=fe ^callpath' + ' ^dyninst ^libelf ^libdwarf') + self.assertRaises(spack.spec.UnsatisfiableArchitectureSpecError, + spec.normalize) def test_invalid_dep(self): spec = Spec('libelf ^mpich') - self.assertRaises(spack.spec.InvalidDependencyException, spec.normalize) + self.assertRaises(spack.spec.InvalidDependencyException, + spec.normalize) spec = Spec('libelf ^libdwarf') - self.assertRaises(spack.spec.InvalidDependencyException, spec.normalize) + self.assertRaises(spack.spec.InvalidDependencyException, + spec.normalize) spec = Spec('mpich ^dyninst ^libelf') - self.assertRaises(spack.spec.InvalidDependencyException, spec.normalize) - + self.assertRaises(spack.spec.InvalidDependencyException, + spec.normalize) def test_equal(self): # Different spec structures to test for equality @@ -301,10 +289,10 @@ class SpecDagTest(MockPackagesTest): self.assertFalse(flip_flat.eq_dag(flip_dag)) self.assertFalse(dag.eq_dag(flip_dag)) - def test_normalize_mpileaks(self): # Spec parsed in from a string - spec = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf@1.8.11 ^libdwarf') + spec = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf@1.8.11' + ' ^libdwarf') # What that spec should look like after parsing expected_flat = Spec( @@ -367,7 +355,6 @@ class SpecDagTest(MockPackagesTest): self.assertEqual(spec, non_unique_nodes) self.assertFalse(spec.eq_dag(non_unique_nodes)) - def test_normalize_with_virtual_package(self): spec = Spec('mpileaks ^mpi ^libelf@1.8.11 ^libdwarf') spec.normalize() @@ -383,7 +370,6 @@ class SpecDagTest(MockPackagesTest): self.assertEqual(str(spec), str(expected_normalized)) - def test_contains(self): spec = Spec('mpileaks ^mpi ^libelf@1.8.11 ^libdwarf') self.assertTrue(Spec('mpi') in spec) @@ -394,7 +380,6 @@ class SpecDagTest(MockPackagesTest): self.assertFalse(Spec('libgoblin') in spec) self.assertTrue(Spec('mpileaks') in spec) - def test_copy_simple(self): orig = Spec('mpileaks') copy = orig.copy() @@ -411,7 +396,6 @@ class SpecDagTest(MockPackagesTest): copy_ids = set(id(s) for s in copy.traverse()) self.assertFalse(orig_ids.intersection(copy_ids)) - def test_copy_normalized(self): orig = Spec('mpileaks') orig.normalize() @@ -429,7 +413,6 @@ class SpecDagTest(MockPackagesTest): copy_ids = set(id(s) for s in copy.traverse()) self.assertFalse(orig_ids.intersection(copy_ids)) - def test_copy_concretized(self): orig = Spec('mpileaks') orig.concretize() @@ -472,24 +455,25 @@ class SpecDagTest(MockPackagesTest): run3 -b-> build3 """ + def test_deptype_traversal(self): dag = Spec('dtuse') dag.normalize() - names = ['dtuse', 'dttop', 'dtlink1', 'dtlink3', 'dtlink4', - 'dtrun1', 'dtlink5', 'dtrun3'] + names = ['dtuse', 'dttop', 'dtbuild1', 'dtbuild2', 'dtlink2', + 'dtlink1', 'dtlink3', 'dtlink4'] - traversal = dag.traverse() + traversal = dag.traverse(deptype=('build', 'link')) self.assertEqual([x.name for x in traversal], names) def test_deptype_traversal_with_builddeps(self): dag = Spec('dttop') dag.normalize() - names = ['dttop', 'dtbuild1', 'dtlink2', 'dtrun2', 'dtlink1', - 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', 'dtrun3'] + names = ['dttop', 'dtbuild1', 'dtbuild2', 'dtlink2', + 'dtlink1', 'dtlink3', 'dtlink4'] - traversal = dag.traverse() + traversal = dag.traverse(deptype=('build', 'link')) self.assertEqual([x.name for x in traversal], names) def test_deptype_traversal_full(self): @@ -500,15 +484,14 @@ class SpecDagTest(MockPackagesTest): 'dtlink1', 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', 'dtrun3', 'dtbuild3'] - traversal = dag.traverse(deptype_query=spack.alldeps) + traversal = dag.traverse(deptype=spack.alldeps) self.assertEqual([x.name for x in traversal], names) - def test_deptype_traversal_pythonpath(self): + def test_deptype_traversal_run(self): dag = Spec('dttop') dag.normalize() - names = ['dttop', 'dtbuild1', 'dtrun2', 'dtlink1', 'dtrun1', - 'dtrun3'] + names = ['dttop', 'dtrun1', 'dtrun3'] - traversal = dag.traverse(deptype=spack.nolink, deptype_query='run') + traversal = dag.traverse(deptype='run') self.assertEqual([x.name for x in traversal], names) diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py index b174e5305c..79ffc99298 100644 --- a/lib/spack/spack/test/spec_semantics.py +++ b/lib/spack/spack/test/spec_semantics.py @@ -22,18 +22,18 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import unittest import spack.architecture from spack.spec import * from spack.test.mock_packages_test import * + class SpecSematicsTest(MockPackagesTest): """This tests satisfies(), constrain() and other semantic operations on specs.""" - # ================================================================================ + # ======================================================================== # Utility functions to set everything up. - # ================================================================================ + # ======================================================================== def check_satisfies(self, spec, anon_spec, concrete=False): left = Spec(spec, concrete=concrete) try: @@ -49,7 +49,6 @@ class SpecSematicsTest(MockPackagesTest): # right by left. Reverse is not always true. right.copy().constrain(left) - def check_unsatisfiable(self, spec, anon_spec, concrete=False): left = Spec(spec, concrete=concrete) try: @@ -62,7 +61,6 @@ class SpecSematicsTest(MockPackagesTest): self.assertRaises(UnsatisfiableSpecError, right.copy().constrain, left) - def check_constrain(self, expected, spec, constraint): exp = Spec(expected) spec = Spec(spec) @@ -70,53 +68,48 @@ class SpecSematicsTest(MockPackagesTest): spec.constrain(constraint) self.assertEqual(exp, spec) - def check_constrain_changed(self, spec, constraint): spec = Spec(spec) self.assertTrue(spec.constrain(constraint)) - def check_constrain_not_changed(self, spec, constraint): spec = Spec(spec) self.assertFalse(spec.constrain(constraint)) - def check_invalid_constraint(self, spec, constraint): spec = Spec(spec) constraint = Spec(constraint) self.assertRaises(UnsatisfiableSpecError, spec.constrain, constraint) - - # ================================================================================ + # ======================================================================== # Satisfiability - # ================================================================================ + # ======================================================================== def test_satisfies(self): self.check_satisfies('libelf@0.8.13', '@0:1') self.check_satisfies('libdwarf^libelf@0.8.13', '^libelf@0:1') - def test_satisfies_namespace(self): self.check_satisfies('builtin.mpich', 'mpich') self.check_satisfies('builtin.mock.mpich', 'mpich') - # TODO: only works for deps now, but shouldn't we allow this for root spec? + # TODO: only works for deps now, but shouldn't we allow for root spec? # self.check_satisfies('builtin.mock.mpich', 'mpi') self.check_satisfies('builtin.mock.mpich', 'builtin.mock.mpich') self.check_unsatisfiable('builtin.mock.mpich', 'builtin.mpich') - def test_satisfies_namespaced_dep(self): """Ensure spec from same or unspecified namespace satisfies namespace constraint.""" self.check_satisfies('mpileaks ^builtin.mock.mpich', '^mpich') self.check_satisfies('mpileaks ^builtin.mock.mpich', '^mpi') - self.check_satisfies('mpileaks ^builtin.mock.mpich', '^builtin.mock.mpich') - - self.check_unsatisfiable('mpileaks ^builtin.mock.mpich', '^builtin.mpich') + self.check_satisfies( + 'mpileaks ^builtin.mock.mpich', '^builtin.mock.mpich') + self.check_unsatisfiable( + 'mpileaks ^builtin.mock.mpich', '^builtin.mpich') def test_satisfies_compiler(self): self.check_satisfies('foo%gcc', '%gcc') @@ -124,7 +117,6 @@ class SpecSematicsTest(MockPackagesTest): self.check_unsatisfiable('foo%intel', '%gcc') self.check_unsatisfiable('foo%intel', '%pgi') - def test_satisfies_compiler_version(self): self.check_satisfies('foo%gcc', '%gcc@4.7.2') self.check_satisfies('foo%intel', '%intel@4.7.2') @@ -139,7 +131,6 @@ class SpecSematicsTest(MockPackagesTest): self.check_satisfies('foo %gcc@4.7.3', '%gcc@4.7') self.check_unsatisfiable('foo %gcc@4.7', '%gcc@4.7.3') - def test_satisfies_architecture(self): self.check_satisfies( 'foo platform=test target=frontend os=frontend', @@ -151,7 +142,6 @@ class SpecSematicsTest(MockPackagesTest): 'foo platform=test target=default_target os=default_os', 'platform=test target=default_target os=default_os') - def test_satisfies_dependencies(self): self.check_satisfies('mpileaks^mpich', '^mpich') self.check_satisfies('mpileaks^zmpi', '^zmpi') @@ -159,7 +149,6 @@ class SpecSematicsTest(MockPackagesTest): self.check_unsatisfiable('mpileaks^mpich', '^zmpi') self.check_unsatisfiable('mpileaks^zmpi', '^mpich') - def test_satisfies_dependency_versions(self): self.check_satisfies('mpileaks^mpich@2.0', '^mpich@1:3') self.check_unsatisfiable('mpileaks^mpich@1.2', '^mpich@2.0') @@ -173,7 +162,6 @@ class SpecSematicsTest(MockPackagesTest): self.check_unsatisfiable( 'mpileaks^mpich@4.0^callpath@1.7', '^mpich@1:3^callpath@1.4:1.6') - def test_satisfies_virtual_dependencies(self): self.check_satisfies('mpileaks^mpi', '^mpi') self.check_satisfies('mpileaks^mpi', '^mpich') @@ -181,7 +169,6 @@ class SpecSematicsTest(MockPackagesTest): self.check_satisfies('mpileaks^mpi', '^zmpi') self.check_unsatisfiable('mpileaks^mpich', '^zmpi') - def test_satisfies_virtual_dependency_versions(self): self.check_satisfies('mpileaks^mpi@1.5', '^mpi@1.2:1.6') self.check_unsatisfiable('mpileaks^mpi@3', '^mpi@1.2:1.6') @@ -197,26 +184,23 @@ class SpecSematicsTest(MockPackagesTest): self.check_unsatisfiable('mpileaks^mpi@3:', '^mpich2') self.check_unsatisfiable('mpileaks^mpi@3:', '^mpich@1.0') - def test_satisfies_matching_variant(self): self.check_satisfies('mpich+foo', 'mpich+foo') self.check_satisfies('mpich~foo', 'mpich~foo') self.check_satisfies('mpich foo=1', 'mpich foo=1') - #confirm that synonymous syntax works correctly + # confirm that synonymous syntax works correctly self.check_satisfies('mpich+foo', 'mpich foo=True') self.check_satisfies('mpich foo=true', 'mpich+foo') self.check_satisfies('mpich~foo', 'mpich foo=FALSE') self.check_satisfies('mpich foo=False', 'mpich~foo') - def test_satisfies_unconstrained_variant(self): # only asked for mpich, no constraints. Either will do. self.check_satisfies('mpich+foo', 'mpich') self.check_satisfies('mpich~foo', 'mpich') self.check_satisfies('mpich foo=1', 'mpich') - def test_unsatisfiable_variants(self): # This case is different depending on whether the specs are concrete. @@ -230,24 +214,21 @@ class SpecSematicsTest(MockPackagesTest): self.check_unsatisfiable('mpich', 'mpich~foo', True) self.check_unsatisfiable('mpich', 'mpich foo=1', True) - def test_unsatisfiable_variant_mismatch(self): # No matchi in specs self.check_unsatisfiable('mpich~foo', 'mpich+foo') self.check_unsatisfiable('mpich+foo', 'mpich~foo') self.check_unsatisfiable('mpich foo=1', 'mpich foo=2') - def test_satisfies_matching_compiler_flag(self): self.check_satisfies('mpich cppflags="-O3"', 'mpich cppflags="-O3"') - self.check_satisfies('mpich cppflags="-O3 -Wall"', 'mpich cppflags="-O3 -Wall"') - + self.check_satisfies('mpich cppflags="-O3 -Wall"', + 'mpich cppflags="-O3 -Wall"') def test_satisfies_unconstrained_compiler_flag(self): # only asked for mpich, no constraints. Any will do. self.check_satisfies('mpich cppflags="-O3"', 'mpich') - def test_unsatisfiable_compiler_flag(self): # This case is different depending on whether the specs are concrete. @@ -257,11 +238,10 @@ class SpecSematicsTest(MockPackagesTest): # 'mpich' is concrete: self.check_unsatisfiable('mpich', 'mpich cppflags="-O3"', True) - def test_unsatisfiable_compiler_flag_mismatch(self): # No matchi in specs - self.check_unsatisfiable('mpich cppflags="-O3"', 'mpich cppflags="-O2"') - + self.check_unsatisfiable( + 'mpich cppflags="-O3"', 'mpich cppflags="-O2"') def test_satisfies_virtual(self): # Don't use check_satisfies: it checks constrain() too, and @@ -270,25 +250,30 @@ class SpecSematicsTest(MockPackagesTest): self.assertTrue(Spec('mpich2').satisfies(Spec('mpi'))) self.assertTrue(Spec('zmpi').satisfies(Spec('mpi'))) - def test_satisfies_virtual_dep_with_virtual_constraint(self): """Ensure we can satisfy virtual constraints when there are multiple vdep providers in the specs.""" - self.assertTrue(Spec('netlib-lapack ^openblas').satisfies('netlib-lapack ^openblas')) - self.assertFalse(Spec('netlib-lapack ^netlib-blas').satisfies('netlib-lapack ^openblas')) - - self.assertFalse(Spec('netlib-lapack ^openblas').satisfies('netlib-lapack ^netlib-blas')) - self.assertTrue(Spec('netlib-lapack ^netlib-blas').satisfies('netlib-lapack ^netlib-blas')) - - - # ================================================================================ + self.assertTrue( + Spec('netlib-lapack ^openblas').satisfies( + 'netlib-lapack ^openblas')) + self.assertFalse( + Spec('netlib-lapack ^netlib-blas').satisfies( + 'netlib-lapack ^openblas')) + + self.assertFalse( + Spec('netlib-lapack ^openblas').satisfies( + 'netlib-lapack ^netlib-blas')) + self.assertTrue( + Spec('netlib-lapack ^netlib-blas').satisfies( + 'netlib-lapack ^netlib-blas')) + + # ======================================================================== # Indexing specs - # ================================================================================ + # ======================================================================== def test_self_index(self): s = Spec('callpath') self.assertTrue(s['callpath'] == s) - def test_dep_index(self): s = Spec('callpath') s.normalize() @@ -304,7 +289,6 @@ class SpecSematicsTest(MockPackagesTest): self.assertTrue(s['libelf'].name == 'libelf') self.assertTrue(s['mpi'].name == 'mpi') - def test_spec_contains_deps(self): s = Spec('callpath') s.normalize() @@ -313,7 +297,6 @@ class SpecSematicsTest(MockPackagesTest): self.assertTrue('libelf' in s) self.assertTrue('mpi' in s) - def test_virtual_index(self): s = Spec('callpath') s.concretize() @@ -327,7 +310,6 @@ class SpecSematicsTest(MockPackagesTest): s_zmpi = Spec('callpath ^zmpi') s_zmpi.concretize() - self.assertTrue(s['mpi'].name != 'mpi') self.assertTrue(s_mpich['mpi'].name == 'mpich') self.assertTrue(s_mpich2['mpi'].name == 'mpich2') @@ -336,29 +318,34 @@ class SpecSematicsTest(MockPackagesTest): for spec in [s, s_mpich, s_mpich2, s_zmpi]: self.assertTrue('mpi' in spec) - - # ================================================================================ + # ======================================================================== # Constraints - # ================================================================================ + # ======================================================================== def test_constrain_variants(self): self.check_constrain('libelf@2.1:2.5', 'libelf@0:2.5', 'libelf@2.1:3') self.check_constrain('libelf@2.1:2.5%gcc@4.5:4.6', - 'libelf@0:2.5%gcc@2:4.6', 'libelf@2.1:3%gcc@4.5:4.7') + 'libelf@0:2.5%gcc@2:4.6', + 'libelf@2.1:3%gcc@4.5:4.7') self.check_constrain('libelf+debug+foo', 'libelf+debug', 'libelf+foo') - self.check_constrain('libelf+debug+foo', 'libelf+debug', 'libelf+debug+foo') + self.check_constrain('libelf+debug+foo', + 'libelf+debug', 'libelf+debug+foo') - self.check_constrain('libelf debug=2 foo=1', 'libelf debug=2', 'libelf foo=1') - self.check_constrain('libelf debug=2 foo=1', 'libelf debug=2', 'libelf debug=2 foo=1') + self.check_constrain('libelf debug=2 foo=1', + 'libelf debug=2', 'libelf foo=1') + self.check_constrain('libelf debug=2 foo=1', + 'libelf debug=2', 'libelf debug=2 foo=1') self.check_constrain('libelf+debug~foo', 'libelf+debug', 'libelf~foo') - self.check_constrain('libelf+debug~foo', 'libelf+debug', 'libelf+debug~foo') - + self.check_constrain('libelf+debug~foo', + 'libelf+debug', 'libelf+debug~foo') def test_constrain_compiler_flags(self): - self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', 'libelf cflags="-O3"', 'libelf cppflags="-Wall"') - self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', 'libelf cflags="-O3"', 'libelf cflags="-O3" cppflags="-Wall"') - + self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', + 'libelf cflags="-O3"', 'libelf cppflags="-Wall"') + self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', + 'libelf cflags="-O3"', + 'libelf cflags="-O3" cppflags="-Wall"') def test_constrain_architecture(self): self.check_constrain('libelf target=default_target os=default_os', @@ -369,21 +356,24 @@ class SpecSematicsTest(MockPackagesTest): 'libelf target=default_target os=default_os') def test_constrain_compiler(self): - self.check_constrain('libelf %gcc@4.4.7', 'libelf %gcc@4.4.7', 'libelf %gcc@4.4.7') - self.check_constrain('libelf %gcc@4.4.7', 'libelf', 'libelf %gcc@4.4.7') - + self.check_constrain('libelf %gcc@4.4.7', + 'libelf %gcc@4.4.7', 'libelf %gcc@4.4.7') + self.check_constrain('libelf %gcc@4.4.7', + 'libelf', 'libelf %gcc@4.4.7') def test_invalid_constraint(self): self.check_invalid_constraint('libelf@0:2.0', 'libelf@2.1:3') - self.check_invalid_constraint('libelf@0:2.5%gcc@4.8:4.9', 'libelf@2.1:3%gcc@4.5:4.7') + self.check_invalid_constraint( + 'libelf@0:2.5%gcc@4.8:4.9', 'libelf@2.1:3%gcc@4.5:4.7') self.check_invalid_constraint('libelf+debug', 'libelf~debug') self.check_invalid_constraint('libelf+debug~foo', 'libelf+debug+foo') self.check_invalid_constraint('libelf debug=2', 'libelf debug=1') - self.check_invalid_constraint('libelf cppflags="-O3"', 'libelf cppflags="-O2"') + self.check_invalid_constraint( + 'libelf cppflags="-O3"', 'libelf cppflags="-O2"') self.check_invalid_constraint('libelf platform=test target=be os=be', - 'libelf target=fe os=fe') + 'libelf target=fe os=fe') def test_constrain_changed(self): self.check_constrain_changed('libelf', '@1.0') @@ -396,9 +386,10 @@ class SpecSematicsTest(MockPackagesTest): self.check_constrain_changed('libelf', 'cppflags="-O3"') platform = spack.architecture.platform() - self.check_constrain_changed('libelf', 'target='+platform.target('default_target').name) - self.check_constrain_changed('libelf', 'os='+platform.operating_system('default_os').name) - + self.check_constrain_changed( + 'libelf', 'target=' + platform.target('default_target').name) + self.check_constrain_changed( + 'libelf', 'os=' + platform.operating_system('default_os').name) def test_constrain_not_changed(self): self.check_constrain_not_changed('libelf', 'libelf') @@ -409,12 +400,13 @@ class SpecSematicsTest(MockPackagesTest): self.check_constrain_not_changed('libelf+debug', '+debug') self.check_constrain_not_changed('libelf~debug', '~debug') self.check_constrain_not_changed('libelf debug=2', 'debug=2') - self.check_constrain_not_changed('libelf cppflags="-O3"', 'cppflags="-O3"') + self.check_constrain_not_changed( + 'libelf cppflags="-O3"', 'cppflags="-O3"') platform = spack.architecture.platform() default_target = platform.target('default_target').name - self.check_constrain_not_changed('libelf target='+default_target, 'target='+default_target) - + self.check_constrain_not_changed( + 'libelf target=' + default_target, 'target=' + default_target) def test_constrain_dependency_changed(self): self.check_constrain_changed('libelf^foo', 'libelf^foo@1.0') @@ -426,18 +418,25 @@ class SpecSematicsTest(MockPackagesTest): platform = spack.architecture.platform() default_target = platform.target('default_target').name - self.check_constrain_changed('libelf^foo', 'libelf^foo target='+default_target) - + self.check_constrain_changed( + 'libelf^foo', 'libelf^foo target=' + default_target) def test_constrain_dependency_not_changed(self): self.check_constrain_not_changed('libelf^foo@1.0', 'libelf^foo@1.0') - self.check_constrain_not_changed('libelf^foo@1.0:5.0', 'libelf^foo@1.0:5.0') + self.check_constrain_not_changed( + 'libelf^foo@1.0:5.0', 'libelf^foo@1.0:5.0') self.check_constrain_not_changed('libelf^foo%gcc', 'libelf^foo%gcc') - self.check_constrain_not_changed('libelf^foo%gcc@4.5', 'libelf^foo%gcc@4.5') - self.check_constrain_not_changed('libelf^foo+debug', 'libelf^foo+debug') - self.check_constrain_not_changed('libelf^foo~debug', 'libelf^foo~debug') - self.check_constrain_not_changed('libelf^foo cppflags="-O3"', 'libelf^foo cppflags="-O3"') + self.check_constrain_not_changed( + 'libelf^foo%gcc@4.5', 'libelf^foo%gcc@4.5') + self.check_constrain_not_changed( + 'libelf^foo+debug', 'libelf^foo+debug') + self.check_constrain_not_changed( + 'libelf^foo~debug', 'libelf^foo~debug') + self.check_constrain_not_changed( + 'libelf^foo cppflags="-O3"', 'libelf^foo cppflags="-O3"') platform = spack.architecture.platform() default_target = platform.target('default_target').name - self.check_constrain_not_changed('libelf^foo target='+default_target, 'libelf^foo target='+default_target) + self.check_constrain_not_changed( + 'libelf^foo target=' + default_target, + 'libelf^foo target=' + default_target) diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py index 4a534d7b5c..3079288c77 100644 --- a/lib/spack/spack/test/spec_syntax.py +++ b/lib/spack/spack/test/spec_syntax.py @@ -55,17 +55,22 @@ complex_lex = [Token(ID, 'mvapich_foo'), class SpecSyntaxTest(unittest.TestCase): - # ================================================================================ + # ======================================================================== # Parse checks - # ================================================================================ + # ======================================================================== + def check_parse(self, expected, spec=None, remove_arch=True): """Assert that the provided spec is able to be parsed. - If this is called with one argument, it assumes that the string is - canonical (i.e., no spaces and ~ instead of - for variants) and that it - will convert back to the string it came from. - If this is called with two arguments, the first argument is the expected - canonical form and the second is a non-canonical input to be parsed. + If this is called with one argument, it assumes that the + string is canonical (i.e., no spaces and ~ instead of - for + variants) and that it will convert back to the string it came + from. + + If this is called with two arguments, the first argument is + the expected canonical form and the second is a non-canonical + input to be parsed. + """ if spec is None: spec = expected @@ -74,9 +79,8 @@ class SpecSyntaxTest(unittest.TestCase): parsed = (" ".join(str(spec) for spec in output)) self.assertEqual(expected, parsed) - def check_lex(self, tokens, spec): - """Check that the provided spec parses to the provided list of tokens.""" + """Check that the provided spec parses to the provided token list.""" lex_output = SpecLexer().lex(spec) for tok, spec_tok in zip(tokens, lex_output): if tok.type == ID: @@ -85,9 +89,9 @@ class SpecSyntaxTest(unittest.TestCase): # Only check the type for non-identifiers. self.assertEqual(tok.type, spec_tok.type) - # ================================================================================ + # ======================================================================== # Parse checks - # =============================================================================== + # ======================================================================== def test_package_names(self): self.check_parse("mvapich") self.check_parse("mvapich_foo") @@ -104,18 +108,37 @@ class SpecSyntaxTest(unittest.TestCase): self.check_parse("openmpi^hwloc@1.2e6:1.4b7-rc3") def test_full_specs(self): - self.check_parse("mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4^stackwalker@8.1_1e") - self.check_parse("mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2~qt_4^stackwalker@8.1_1e") - self.check_parse('mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3"+debug~qt_4^stackwalker@8.1_1e') + self.check_parse( + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4" + "^stackwalker@8.1_1e") + self.check_parse( + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2~qt_4" + "^stackwalker@8.1_1e") + self.check_parse( + 'mvapich_foo' + '^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3"+debug~qt_4' + '^stackwalker@8.1_1e') def test_canonicalize(self): self.check_parse( - "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4^stackwalker@8.1_1e", - "mvapich_foo ^_openmpi@1.6,1.2:1.4%intel@12.1:12.6+debug~qt_4 ^stackwalker@8.1_1e") + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4" + "^stackwalker@8.1_1e", + + "mvapich_foo " + "^_openmpi@1.6,1.2:1.4%intel@12.1:12.6+debug~qt_4 " + "^stackwalker@8.1_1e") self.check_parse( - "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4^stackwalker@8.1_1e", - "mvapich_foo ^stackwalker@8.1_1e ^_openmpi@1.6,1.2:1.4%intel@12.1:12.6~qt_4+debug") + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4" + "^stackwalker@8.1_1e", + + "mvapich_foo " + "^stackwalker@8.1_1e " + "^_openmpi@1.6,1.2:1.4%intel@12.1:12.6~qt_4+debug") self.check_parse( "x^y@1,2:3,4%intel@1,2,3,4+a~b+c~d+e~f", @@ -130,58 +153,81 @@ class SpecSyntaxTest(unittest.TestCase): self.assertRaises(SpecParseError, self.check_parse, "x::") def test_duplicate_variant(self): - self.assertRaises(DuplicateVariantError, self.check_parse, "x@1.2+debug+debug") - self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2+debug debug=true") - self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2 debug=false debug=true") - self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2 debug=false~debug") - + self.assertRaises(DuplicateVariantError, + self.check_parse, "x@1.2+debug+debug") + self.assertRaises(DuplicateVariantError, + self.check_parse, "x ^y@1.2+debug debug=true") + self.assertRaises(DuplicateVariantError, self.check_parse, + "x ^y@1.2 debug=false debug=true") + self.assertRaises(DuplicateVariantError, + self.check_parse, "x ^y@1.2 debug=false~debug") def test_duplicate_depdendence(self): - self.assertRaises(DuplicateDependencyError, self.check_parse, "x ^y ^y") + self.assertRaises(DuplicateDependencyError, + self.check_parse, "x ^y ^y") def test_duplicate_compiler(self): - self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x%intel%intel") - self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x%intel%gcc") - self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x%gcc%intel") - self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x ^y%intel%intel") - self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x ^y%intel%gcc") - self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x ^y%gcc%intel") - - - # ================================================================================ + self.assertRaises(DuplicateCompilerSpecError, + self.check_parse, "x%intel%intel") + self.assertRaises(DuplicateCompilerSpecError, + self.check_parse, "x%intel%gcc") + self.assertRaises(DuplicateCompilerSpecError, + self.check_parse, "x%gcc%intel") + self.assertRaises(DuplicateCompilerSpecError, + self.check_parse, "x ^y%intel%intel") + self.assertRaises(DuplicateCompilerSpecError, + self.check_parse, "x ^y%intel%gcc") + self.assertRaises(DuplicateCompilerSpecError, + self.check_parse, "x ^y%gcc%intel") + + # ======================================================================== # Lex checks - # ================================================================================ + # ======================================================================== def test_ambiguous(self): # This first one is ambiguous because - can be in an identifier AND # indicate disabling an option. self.assertRaises( AssertionError, self.check_lex, complex_lex, - "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug-qt_4^stackwalker@8.1_1e") + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug-qt_4" + "^stackwalker@8.1_1e") - # The following lexes are non-ambiguous (add a space before -qt_4) and should all - # result in the tokens in complex_lex + # The following lexes are non-ambiguous (add a space before -qt_4) + # and should all result in the tokens in complex_lex def test_minimal_spaces(self): self.check_lex( complex_lex, - "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4^stackwalker@8.1_1e") + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4" + "^stackwalker@8.1_1e") self.check_lex( complex_lex, - "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4^stackwalker@8.1_1e") + "mvapich_foo" + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4" + "^stackwalker@8.1_1e") def test_spaces_between_dependences(self): self.check_lex( complex_lex, - "mvapich_foo ^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4 ^stackwalker @ 8.1_1e") + "mvapich_foo " + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4 " + "^stackwalker @ 8.1_1e") self.check_lex( complex_lex, - "mvapich_foo ^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4 ^stackwalker @ 8.1_1e") + "mvapich_foo " + "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4 " + "^stackwalker @ 8.1_1e") def test_spaces_between_options(self): self.check_lex( complex_lex, - "mvapich_foo ^_openmpi @1.2:1.4,1.6 %intel @12.1:12.6 +debug -qt_4 ^stackwalker @8.1_1e") + "mvapich_foo " + "^_openmpi @1.2:1.4,1.6 %intel @12.1:12.6 +debug -qt_4 " + "^stackwalker @8.1_1e") def test_way_too_many_spaces(self): self.check_lex( complex_lex, - "mvapich_foo ^ _openmpi @ 1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 ^ stackwalker @ 8.1_1e") + "mvapich_foo " + "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 " + "^ stackwalker @ 8.1_1e") diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py index 0230fc203a..964aea9422 100644 --- a/lib/spack/spack/test/spec_yaml.py +++ b/lib/spack/spack/test/spec_yaml.py @@ -30,41 +30,36 @@ YAML format preserves DAG informatoin in the spec. from spack.spec import Spec from spack.test.mock_packages_test import * -class SpecDagTest(MockPackagesTest): + +class SpecYamlTest(MockPackagesTest): def check_yaml_round_trip(self, spec): yaml_text = spec.to_yaml() spec_from_yaml = Spec.from_yaml(yaml_text) self.assertTrue(spec.eq_dag(spec_from_yaml)) - def test_simple_spec(self): spec = Spec('mpileaks') self.check_yaml_round_trip(spec) - def test_normal_spec(self): spec = Spec('mpileaks+debug~opt') spec.normalize() self.check_yaml_round_trip(spec) - def test_ambiguous_version_spec(self): spec = Spec('mpileaks@1.0:5.0,6.1,7.3+debug~opt') spec.normalize() self.check_yaml_round_trip(spec) - def test_concrete_spec(self): spec = Spec('mpileaks+debug~opt') spec.concretize() self.check_yaml_round_trip(spec) - def test_yaml_subdag(self): spec = Spec('mpileaks^mpich+debug') spec.concretize() - yaml_spec = Spec.from_yaml(spec.to_yaml()) for dep in ('callpath', 'mpich', 'dyninst', 'libdwarf', 'libelf'): diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index d3e3bf1383..ec661bfe50 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -62,6 +62,7 @@ def use_tmp(use_tmp): class StageTest(unittest.TestCase): + def setUp(self): """This sets up a mock archive to fetch, and a mock temp space for use by the Stage class. It doesn't actually create the Stage -- that @@ -89,7 +90,6 @@ class StageTest(unittest.TestCase): # be removed. self.working_dir = os.getcwd() - def tearDown(self): """Blows away the test environment directory.""" shutil.rmtree(test_files_dir) @@ -100,7 +100,6 @@ class StageTest(unittest.TestCase): # restore spack's original tmp environment spack.tmp_dirs = self.old_tmp_dirs - def get_stage_path(self, stage, stage_name): """Figure out where a stage should be living. This depends on whether it's named. @@ -114,7 +113,6 @@ class StageTest(unittest.TestCase): self.assertTrue(stage.path.startswith(spack.stage_path)) return stage.path - def check_setup(self, stage, stage_name): """Figure out whether a stage was set up correctly.""" stage_path = self.get_stage_path(stage, stage_name) @@ -139,14 +137,12 @@ class StageTest(unittest.TestCase): # Make sure the stage path is NOT a link for a non-tmp stage self.assertFalse(os.path.islink(stage_path)) - def check_fetch(self, stage, stage_name): stage_path = self.get_stage_path(stage, stage_name) self.assertTrue(archive_name in os.listdir(stage_path)) self.assertEqual(join_path(stage_path, archive_name), stage.fetcher.archive_file) - def check_expand_archive(self, stage, stage_name): stage_path = self.get_stage_path(stage, stage_name) self.assertTrue(archive_name in os.listdir(stage_path)) @@ -162,19 +158,16 @@ class StageTest(unittest.TestCase): with open(readme) as file: self.assertEqual(readme_text, file.read()) - def check_chdir(self, stage, stage_name): stage_path = self.get_stage_path(stage, stage_name) self.assertEqual(os.path.realpath(stage_path), os.getcwd()) - def check_chdir_to_source(self, stage, stage_name): stage_path = self.get_stage_path(stage, stage_name) self.assertEqual( join_path(os.path.realpath(stage_path), archive_dir), os.getcwd()) - def check_destroy(self, stage, stage_name): """Figure out whether a stage was destroyed correctly.""" stage_path = self.get_stage_path(stage, stage_name) @@ -187,35 +180,30 @@ class StageTest(unittest.TestCase): target = os.path.realpath(stage_path) self.assertFalse(os.path.exists(target)) - def test_setup_and_destroy_name_with_tmp(self): with use_tmp(True): with Stage(archive_url, name=stage_name) as stage: self.check_setup(stage, stage_name) self.check_destroy(stage, stage_name) - def test_setup_and_destroy_name_without_tmp(self): with use_tmp(False): with Stage(archive_url, name=stage_name) as stage: self.check_setup(stage, stage_name) self.check_destroy(stage, stage_name) - def test_setup_and_destroy_no_name_with_tmp(self): with use_tmp(True): with Stage(archive_url) as stage: self.check_setup(stage, None) self.check_destroy(stage, None) - def test_setup_and_destroy_no_name_without_tmp(self): with use_tmp(False): with Stage(archive_url) as stage: self.check_setup(stage, None) self.check_destroy(stage, None) - def test_chdir(self): with Stage(archive_url, name=stage_name) as stage: stage.chdir() @@ -223,7 +211,6 @@ class StageTest(unittest.TestCase): self.check_chdir(stage, stage_name) self.check_destroy(stage, stage_name) - def test_fetch(self): with Stage(archive_url, name=stage_name) as stage: stage.fetch() @@ -232,7 +219,6 @@ class StageTest(unittest.TestCase): self.check_fetch(stage, stage_name) self.check_destroy(stage, stage_name) - def test_expand_archive(self): with Stage(archive_url, name=stage_name) as stage: stage.fetch() @@ -242,8 +228,7 @@ class StageTest(unittest.TestCase): self.check_expand_archive(stage, stage_name) self.check_destroy(stage, stage_name) - - def test_expand_archive(self): + def test_expand_archive_with_chdir(self): with Stage(archive_url, name=stage_name) as stage: stage.fetch() self.check_setup(stage, stage_name) @@ -254,7 +239,6 @@ class StageTest(unittest.TestCase): self.check_chdir_to_source(stage, stage_name) self.check_destroy(stage, stage_name) - def test_restage(self): with Stage(archive_url, name=stage_name) as stage: stage.fetch() @@ -278,20 +262,17 @@ class StageTest(unittest.TestCase): self.assertFalse('foobar' in os.listdir(stage.source_path)) self.check_destroy(stage, stage_name) - def test_no_keep_without_exceptions(self): with Stage(archive_url, name=stage_name, keep=False) as stage: pass self.check_destroy(stage, stage_name) - def test_keep_without_exceptions(self): with Stage(archive_url, name=stage_name, keep=True) as stage: pass path = self.get_stage_path(stage, stage_name) self.assertTrue(os.path.isdir(path)) - def test_no_keep_with_exceptions(self): try: with Stage(archive_url, name=stage_name, keep=False) as stage: @@ -300,8 +281,7 @@ class StageTest(unittest.TestCase): path = self.get_stage_path(stage, stage_name) self.assertTrue(os.path.isdir(path)) except: - pass # ignore here. - + pass # ignore here. def test_keep_exceptions(self): try: @@ -311,4 +291,4 @@ class StageTest(unittest.TestCase): path = self.get_stage_path(stage, stage_name) self.assertTrue(os.path.isdir(path)) except: - pass # ignore here. + pass # ignore here. diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py index 0a745a090b..9ef7593ed1 100644 --- a/lib/spack/spack/test/svn_fetch.py +++ b/lib/spack/spack/test/svn_fetch.py @@ -94,17 +94,15 @@ class SvnFetchTest(MockPackagesTest): self.assert_rev(rev) - def test_fetch_default(self): """Test a default checkout and make sure it's on rev 1""" self.try_fetch(self.repo.r1, self.repo.r1_file, { - 'svn' : self.repo.url + 'svn': self.repo.url }) - def test_fetch_r1(self): """Test fetching an older revision (0).""" self.try_fetch(self.repo.r0, self.repo.r0_file, { - 'svn' : self.repo.url, - 'revision' : self.repo.r0 + 'svn': self.repo.url, + 'revision': self.repo.r0 }) diff --git a/lib/spack/spack/test/tally_plugin.py b/lib/spack/spack/test/tally_plugin.py index 96af1c9b21..808694d186 100644 --- a/lib/spack/spack/test/tally_plugin.py +++ b/lib/spack/spack/test/tally_plugin.py @@ -26,6 +26,7 @@ import os from nose.plugins import Plugin + class Tally(Plugin): name = 'tally' diff --git a/lib/spack/spack/test/url_extrapolate.py b/lib/spack/spack/test/url_extrapolate.py index ffd4230f71..ca14dab958 100644 --- a/lib/spack/spack/test/url_extrapolate.py +++ b/lib/spack/spack/test/url_extrapolate.py @@ -34,20 +34,21 @@ class UrlExtrapolateTest(unittest.TestCase): def check_url(self, base, version, new_url): self.assertEqual(url.substitute_version(base, version), new_url) - def test_libelf_version(self): base = "http://www.mr511.de/software/libelf-0.8.13.tar.gz" self.check_url(base, '0.8.13', base) - self.check_url(base, '0.8.12', "http://www.mr511.de/software/libelf-0.8.12.tar.gz") - self.check_url(base, '0.3.1', "http://www.mr511.de/software/libelf-0.3.1.tar.gz") - self.check_url(base, '1.3.1b', "http://www.mr511.de/software/libelf-1.3.1b.tar.gz") - + self.check_url( + base, '0.8.12', "http://www.mr511.de/software/libelf-0.8.12.tar.gz") + self.check_url( + base, '0.3.1', "http://www.mr511.de/software/libelf-0.3.1.tar.gz") + self.check_url( + base, '1.3.1b', "http://www.mr511.de/software/libelf-1.3.1b.tar.gz") def test_libdwarf_version(self): base = "http://www.prevanders.net/libdwarf-20130729.tar.gz" self.check_url(base, '20130729', base) - self.check_url(base, '8.12', "http://www.prevanders.net/libdwarf-8.12.tar.gz") - + self.check_url( + base, '8.12', "http://www.prevanders.net/libdwarf-8.12.tar.gz") def test_dyninst_version(self): # Dyninst has a version twice in the URL. @@ -58,7 +59,6 @@ class UrlExtrapolateTest(unittest.TestCase): self.check_url(base, '8.3.1', "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.3.1/DyninstAPI-8.3.1.tgz") - def test_partial_version_prefix(self): # Test now with a partial prefix earlier in the URL -- this is # hard to figure out so Spack only substitutes the last @@ -72,7 +72,6 @@ class UrlExtrapolateTest(unittest.TestCase): self.check_url(base, '8.3.1', "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1/DyninstAPI-8.3.1.tgz") - def test_scalasca_partial_version(self): # Note that this probably doesn't actually work, but sites are # inconsistent about their directory structure, so it's not @@ -84,19 +83,16 @@ class UrlExtrapolateTest(unittest.TestCase): self.check_url('http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3-TP1.tar.gz', '8.3.1', 'http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-8.3.1.tar.gz') - def test_mpileaks_version(self): self.check_url('https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz', '2.1.3', 'https://github.com/hpc/mpileaks/releases/download/v2.1.3/mpileaks-2.1.3.tar.gz') - def test_gcc(self): self.check_url('http://open-source-box.org/gcc/gcc-4.9.2/gcc-4.9.2.tar.bz2', '4.7', 'http://open-source-box.org/gcc/gcc-4.7/gcc-4.7.tar.bz2') self.check_url('http://open-source-box.org/gcc/gcc-4.4.7/gcc-4.4.7.tar.bz2', '4.4.7', 'http://open-source-box.org/gcc/gcc-4.4.7/gcc-4.4.7.tar.bz2') - def test_github_raw(self): self.check_url('https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7.tgz?raw=true', '2.0.7', 'https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7.tgz?raw=true') diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py index 648996aaaa..6c944a3e7a 100644 --- a/lib/spack/spack/test/url_parse.py +++ b/lib/spack/spack/test/url_parse.py @@ -32,11 +32,11 @@ import spack.url as url class UrlParseTest(unittest.TestCase): + def assert_not_detected(self, string): self.assertRaises( url.UndetectableVersionError, url.parse_name_and_version, string) - def check(self, name, v, string, **kwargs): # Make sure correct name and version are extracted. parsed_name, parsed_v = url.parse_name_and_version(string) @@ -52,7 +52,6 @@ class UrlParseTest(unittest.TestCase): # build one with a specific version. self.assertEqual(string, url.substitute_version(string, v)) - def test_wwwoffle_version(self): self.check( 'wwwoffle', '2.9h', @@ -72,7 +71,7 @@ class UrlParseTest(unittest.TestCase): def test_version_all_dots(self): self.check( - 'foo.bar.la', '1.14','http://example.com/foo.bar.la.1.14.zip') + 'foo.bar.la', '1.14', 'http://example.com/foo.bar.la.1.14.zip') def test_version_underscore_separator(self): self.check( @@ -286,7 +285,7 @@ class UrlParseTest(unittest.TestCase): 'mvapich2', '1.9', 'http://mvapich.cse.ohio-state.edu/download/mvapich2/mv2/mvapich2-1.9.tgz') - def test_mvapich2_19_version(self): + def test_mvapich2_20_version(self): self.check( 'mvapich2', '2.0', 'http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz') diff --git a/lib/spack/spack/test/url_substitution.py b/lib/spack/spack/test/url_substitution.py index 9cc04834b6..ea6374e3d2 100644 --- a/lib/spack/spack/test/url_substitution.py +++ b/lib/spack/spack/test/url_substitution.py @@ -26,37 +26,31 @@ This test does sanity checks on substituting new versions into URLs """ import unittest - import spack.url as url +base = "https://comp.llnl.gov/linear_solvers/download/hypre-2.9.0b.tar.gz" +stem = "https://comp.llnl.gov/linear_solvers/download/hypre-" + + class PackageSanityTest(unittest.TestCase): - def test_hypre_url_substitution(self): - base = "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.9.0b.tar.gz" + def test_hypre_url_substitution(self): self.assertEqual(url.substitute_version(base, '2.9.0b'), base) self.assertEqual( - url.substitute_version(base, '2.8.0b'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.8.0b.tar.gz") + url.substitute_version(base, '2.8.0b'), stem + "2.8.0b.tar.gz") self.assertEqual( - url.substitute_version(base, '2.7.0b'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.7.0b.tar.gz") + url.substitute_version(base, '2.7.0b'), stem + "2.7.0b.tar.gz") self.assertEqual( - url.substitute_version(base, '2.6.0b'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.6.0b.tar.gz") + url.substitute_version(base, '2.6.0b'), stem + "2.6.0b.tar.gz") self.assertEqual( - url.substitute_version(base, '1.14.0b'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-1.14.0b.tar.gz") + url.substitute_version(base, '1.14.0b'), stem + "1.14.0b.tar.gz") self.assertEqual( - url.substitute_version(base, '1.13.0b'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-1.13.0b.tar.gz") + url.substitute_version(base, '1.13.0b'), stem + "1.13.0b.tar.gz") self.assertEqual( - url.substitute_version(base, '2.0.0'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.0.0.tar.gz") + url.substitute_version(base, '2.0.0'), stem + "2.0.0.tar.gz") self.assertEqual( - url.substitute_version(base, '1.6.0'), - "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-1.6.0.tar.gz") - + url.substitute_version(base, '1.6.0'), stem + "1.6.0.tar.gz") def test_otf2_url_substitution(self): base = "http://www.vi-hps.org/upload/packages/otf2/otf2-1.4.tar.gz" diff --git a/lib/spack/spack/test/yaml.py b/lib/spack/spack/test/yaml.py index f1b83e7b71..dedbd15d10 100644 --- a/lib/spack/spack/test/yaml.py +++ b/lib/spack/spack/test/yaml.py @@ -45,26 +45,25 @@ config_file: """ test_data = { - 'config_file' : syaml.syaml_dict([ + 'config_file': syaml.syaml_dict([ ('x86_64', syaml.syaml_dict([ ('foo', '/path/to/foo'), ('bar', '/path/to/bar'), - ('baz', '/path/to/baz' )])), - ('some_list', [ 'item 1', 'item 2', 'item 3' ]), - ('another_list', [ 1, 2, 3 ]), + ('baz', '/path/to/baz')])), + ('some_list', ['item 1', 'item 2', 'item 3']), + ('another_list', [1, 2, 3]), ('some_key', 'some_string') ])} + class YamlTest(unittest.TestCase): def setUp(self): self.data = syaml.load(test_file) - def test_parse(self): self.assertEqual(test_data, self.data) - def test_dict_order(self): self.assertEqual( ['x86_64', 'some_list', 'another_list', 'some_key'], @@ -74,7 +73,6 @@ class YamlTest(unittest.TestCase): ['foo', 'bar', 'baz'], self.data['config_file']['x86_64'].keys()) - def test_line_numbers(self): def check(obj, start_line, end_line): self.assertEqual(obj._start_mark.line, start_line) diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py index f678a2dca9..02c9c04380 100644 --- a/lib/spack/spack/url.py +++ b/lib/spack/spack/url.py @@ -56,12 +56,12 @@ import spack.error import spack.util.compression as comp from spack.version import Version + # # Note: We call the input to most of these functions a "path" but the functions # work on paths and URLs. There's not a good word for both of these, but # "path" seemed like the most generic term. # - def find_list_url(url): """Finds a good list URL for the supplied URL. This depends on the site. By default, just assumes that a good list URL is the @@ -71,8 +71,8 @@ def find_list_url(url): url_types = [ # e.g. https://github.com/llnl/callpath/archive/v1.0.1.tar.gz - (r'^(https://github.com/[^/]+/[^/]+)/archive/', lambda m: m.group(1) + '/releases') - ] + (r'^(https://github.com/[^/]+/[^/]+)/archive/', + lambda m: m.group(1) + '/releases')] for pattern, fun in url_types: match = re.search(pattern, url) @@ -89,8 +89,10 @@ def strip_query_and_fragment(path): query, frag = components[3:5] suffix = '' - if query: suffix += '?' + query - if frag: suffix += '#' + frag + if query: + suffix += '?' + query + if frag: + suffix += '#' + frag return (urlunsplit(stripped), suffix) @@ -152,8 +154,10 @@ def downloaded_file_extension(path): """ match = re.search(r'github.com/.+/(zip|tar)ball/', path) if match: - if match.group(1) == 'zip': return 'zip' - elif match.group(1) == 'tar': return 'tar.gz' + if match.group(1) == 'zip': + return 'zip' + elif match.group(1) == 'tar': + return 'tar.gz' prefix, ext, suffix = split_url_extension(path) if not ext: @@ -193,7 +197,8 @@ def parse_version_offset(path): (r'[-_](R\d+[AB]\d*(-\d+)?)', path), # e.g., https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz - # e.g., https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz + # e.g., + # https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz (r'github.com/[^/]+/[^/]+/releases/download/v?([^/]+)/.*$', path), # e.g. boost_1_39_0 @@ -201,7 +206,7 @@ def parse_version_offset(path): # e.g. foobar-4.5.1-1 # e.g. ruby-1.9.1-p243 - (r'-((\d+\.)*\d\.\d+-(p|rc|RC)?\d+)(?:[-._](?:bin|dist|stable|src|sources))?$', stem), + (r'-((\d+\.)*\d\.\d+-(p|rc|RC)?\d+)(?:[-._](?:bin|dist|stable|src|sources))?$', stem), # noqa # e.g. lame-398-1 (r'-((\d)+-\d)', stem), @@ -275,7 +280,8 @@ def parse_name_offset(path, v=None): name_types = [ (r'/sourceforge/([^/]+)/', path), - (r'github.com/[^/]+/[^/]+/releases/download/%s/(.*)-%s$' % (v, v), path), + (r'github.com/[^/]+/[^/]+/releases/download/%s/(.*)-%s$' % + (v, v), path), (r'/([^/]+)/(tarball|zipball)/', path), (r'/([^/]+)[_.-](bin|dist|stable|src|sources)[_.-]%s' % v, path), (r'github.com/[^/]+/([^/]+)/archive', path), @@ -283,7 +289,8 @@ def parse_name_offset(path, v=None): (r'([^/]+)[_.-]v?%s' % v, stem), # prefer the stem (r'([^/]+)%s' % v, stem), - (r'/([^/]+)[_.-]v?%s' % v, path), # accept the path if name is not in stem. + # accept the path if name is not in stem. + (r'/([^/]+)[_.-]v?%s' % v, path), (r'/([^/]+)%s' % v, path), (r'^([^/]+)[_.-]v?%s' % v, path), @@ -326,7 +333,7 @@ def insensitize(string): return re.sub(r'([a-zA-Z])', to_ins, string) -def cumsum(elts, init=0, fn=lambda x:x): +def cumsum(elts, init=0, fn=lambda x: x): """Return cumulative sum of result of fn on each element in elts.""" sums = [] s = init @@ -337,21 +344,20 @@ def cumsum(elts, init=0, fn=lambda x:x): def substitution_offsets(path): - """This returns offsets for substituting versions and names in the provided path. - It is a helper for substitute_version(). + """This returns offsets for substituting versions and names in the + provided path. It is a helper for substitute_version(). """ # Get name and version offsets try: ver, vs, vl = parse_version_offset(path) name, ns, nl = parse_name_offset(path, ver) - except UndetectableNameError, e: + except UndetectableNameError: return (None, -1, -1, (), ver, vs, vl, (vs,)) - except UndetectableVersionError, e: + except UndetectableVersionError: return (None, -1, -1, (), None, -1, -1, ()) # protect extensions like bz2 from getting inadvertently # considered versions. - ext = comp.extension(path) path = comp.strip_extension(path) # Construct a case-insensitive regular expression for the package name. @@ -449,7 +455,7 @@ def color_url(path, **kwargs): Cyan: The version found by parse_version_offset(). Red: The name found by parse_name_offset(). - Green: Instances of version string substituted by substitute_version(). + Green: Instances of version string from substitute_version(). Magenta: Instances of the name (protected from substitution). Optional args: @@ -469,31 +475,46 @@ def color_url(path, **kwargs): nerr = verr = 0 out = StringIO() for i in range(len(path)): - if i == vs: out.write('@c'); verr += 1 - elif i == ns: out.write('@r'); nerr += 1 + if i == vs: + out.write('@c') + verr += 1 + elif i == ns: + out.write('@r') + nerr += 1 elif subs: - if i in voffs: out.write('@g') - elif i in noffs: out.write('@m') + if i in voffs: + out.write('@g') + elif i in noffs: + out.write('@m') out.write(path[i]) - if i == vs + vl - 1: out.write('@.'); verr += 1 - elif i == ns + nl - 1: out.write('@.'); nerr += 1 + if i == vs + vl - 1: + out.write('@.') + verr += 1 + elif i == ns + nl - 1: + out.write('@.') + nerr += 1 elif subs: if i in vends or i in nends: out.write('@.') if errors: - if nerr == 0: out.write(" @r{[no name]}") - if verr == 0: out.write(" @r{[no version]}") - if nerr == 1: out.write(" @r{[incomplete name]}") - if verr == 1: out.write(" @r{[incomplete version]}") + if nerr == 0: + out.write(" @r{[no name]}") + if verr == 0: + out.write(" @r{[no version]}") + if nerr == 1: + out.write(" @r{[incomplete name]}") + if verr == 1: + out.write(" @r{[incomplete version]}") return colorize(out.getvalue()) class UrlParseError(spack.error.SpackError): """Raised when the URL module can't parse something correctly.""" + def __init__(self, msg, path): super(UrlParseError, self).__init__(msg) self.path = path @@ -501,6 +522,7 @@ class UrlParseError(spack.error.SpackError): class UndetectableVersionError(UrlParseError): """Raised when we can't parse a version from a string.""" + def __init__(self, path): super(UndetectableVersionError, self).__init__( "Couldn't detect version in: " + path, path) @@ -508,6 +530,7 @@ class UndetectableVersionError(UrlParseError): class UndetectableNameError(UrlParseError): """Raised when we can't parse a package name from a string.""" + def __init__(self, path): super(UndetectableNameError, self).__init__( "Couldn't parse package name in: " + path, path) diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py index dc1188eb0f..64554ab2f7 100644 --- a/lib/spack/spack/util/compression.py +++ b/lib/spack/spack/util/compression.py @@ -32,7 +32,9 @@ PRE_EXTS = ["tar"] EXTS = ["gz", "bz2", "xz", "Z", "zip", "tgz"] # Add PRE_EXTS and EXTS last so that .tar.gz is matched *before* .tar or .gz -ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + PRE_EXTS + EXTS +ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product( + PRE_EXTS, EXTS)] + PRE_EXTS + EXTS + def allowed_archive(path): return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES) diff --git a/lib/spack/spack/util/crypto.py b/lib/spack/spack/util/crypto.py index 1ae9793518..22777fdb68 100644 --- a/lib/spack/spack/util/crypto.py +++ b/lib/spack/spack/util/crypto.py @@ -31,7 +31,7 @@ _acceptable_hashes = [ hashlib.sha224, hashlib.sha256, hashlib.sha384, - hashlib.sha512 ] + hashlib.sha512] """Index for looking up hasher for a digest.""" _size_to_hash = dict((h().digest_size, h) for h in _acceptable_hashes) @@ -52,7 +52,6 @@ def checksum(hashlib_algo, filename, **kwargs): return hasher.hexdigest() - class Checker(object): """A checker checks files against one particular hex digest. It will automatically determine what hashing algorithm @@ -74,25 +73,25 @@ class Checker(object): adjusting the block_size optional arg. By default it's a 1MB (2**20 bytes) buffer. """ + def __init__(self, hexdigest, **kwargs): self.block_size = kwargs.get('block_size', 2**20) self.hexdigest = hexdigest self.sum = None bytes = len(hexdigest) / 2 - if not bytes in _size_to_hash: + if bytes not in _size_to_hash: raise ValueError( - 'Spack knows no hash algorithm for this digest: %s' % hexdigest) + 'Spack knows no hash algorithm for this digest: %s' + % hexdigest) self.hash_fun = _size_to_hash[bytes] - @property def hash_name(self): """Get the name of the hash function this Checker is using.""" return self.hash_fun().name - def check(self, filename): """Read the file with the specified name and check its checksum against self.hexdigest. Return True if they match, False diff --git a/lib/spack/spack/util/debug.py b/lib/spack/spack/util/debug.py index e8a0595416..cf485a611d 100644 --- a/lib/spack/spack/util/debug.py +++ b/lib/spack/spack/util/debug.py @@ -33,10 +33,11 @@ import code import traceback import signal + def debug_handler(sig, frame): """Interrupt running process, and provide a python prompt for interactive debugging.""" - d = {'_frame':frame} # Allow access to frame object. + d = {'_frame': frame} # Allow access to frame object. d.update(frame.f_globals) # Unless shadowed by global d.update(frame.f_locals) @@ -48,5 +49,5 @@ def debug_handler(sig, frame): def register_interrupt_handler(): - """Register a handler to print a stack trace and enter an interpreter on Ctrl-C""" + """Print traceback and enter an interpreter on Ctrl-C""" signal.signal(signal.SIGINT, debug_handler) diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py index 14b56e8d6c..5c27b92df5 100644 --- a/lib/spack/spack/util/executable.py +++ b/lib/spack/spack/util/executable.py @@ -165,7 +165,6 @@ class Executable(object): raise ProcessError("Command exited with status %d:" % proc.returncode, cmd_line) - if output is str or error is str: result = '' if output is str: @@ -227,6 +226,7 @@ def which(name, **kwargs): class ProcessError(spack.error.SpackError): + def __init__(self, msg, long_message=None): # These are used for detailed debugging information for # package builds. They're built up gradually as the exception diff --git a/lib/spack/spack/util/multiproc.py b/lib/spack/spack/util/multiproc.py index 038cd90121..6a25c45713 100644 --- a/lib/spack/spack/util/multiproc.py +++ b/lib/spack/spack/util/multiproc.py @@ -32,18 +32,21 @@ from itertools import izip __all__ = ['spawn', 'parmap', 'Barrier'] + def spawn(f): - def fun(pipe,x): + def fun(pipe, x): pipe.send(f(x)) pipe.close() return fun -def parmap(f,X): - pipe=[Pipe() for x in X] - proc=[Process(target=spawn(f),args=(c,x)) for x,(p,c) in izip(X,pipe)] + +def parmap(f, X): + pipe = [Pipe() for x in X] + proc = [Process(target=spawn(f), args=(c, x)) + for x, (p, c) in izip(X, pipe)] [p.start() for p in proc] [p.join() for p in proc] - return [p.recv() for (p,c) in pipe] + return [p.recv() for (p, c) in pipe] class Barrier: @@ -53,6 +56,7 @@ class Barrier: See http://greenteapress.com/semaphores/downey08semaphores.pdf, p. 41. """ + def __init__(self, n, timeout=None): self.n = n self.to = timeout @@ -61,7 +65,6 @@ class Barrier: self.turnstile1 = Semaphore(0) self.turnstile2 = Semaphore(1) - def wait(self): if not self.mutex.acquire(timeout=self.to): raise BarrierTimeoutError() @@ -90,4 +93,5 @@ class Barrier: self.turnstile2.release() -class BarrierTimeoutError: pass +class BarrierTimeoutError: + pass diff --git a/lib/spack/spack/util/naming.py b/lib/spack/spack/util/naming.py index 2d9762942d..9a5cdee411 100644 --- a/lib/spack/spack/util/naming.py +++ b/lib/spack/spack/util/naming.py @@ -31,9 +31,15 @@ from StringIO import StringIO import spack -__all__ = ['mod_to_class', 'spack_module_to_python_module', 'valid_module_name', - 'valid_fully_qualified_module_name', 'validate_fully_qualified_module_name', - 'validate_module_name', 'possible_spack_module_names', 'NamespaceTrie'] +__all__ = [ + 'mod_to_class', + 'spack_module_to_python_module', + 'valid_module_name', + 'valid_fully_qualified_module_name', + 'validate_fully_qualified_module_name', + 'validate_module_name', + 'possible_spack_module_names', + 'NamespaceTrie'] # Valid module names can contain '-' but can't start with it. _valid_module_re = r'^\w[\w-]*$' @@ -67,8 +73,8 @@ def mod_to_class(mod_name): class_name = string.capwords(class_name, '-') class_name = class_name.replace('-', '') - # If a class starts with a number, prefix it with Number_ to make it a valid - # Python class name. + # If a class starts with a number, prefix it with Number_ to make it + # a valid Python class name. if re.match(r'^[0-9]', class_name): class_name = "_%s" % class_name @@ -126,6 +132,7 @@ def validate_fully_qualified_module_name(mod_name): class InvalidModuleNameError(spack.error.SpackError): """Raised when we encounter a bad module name.""" + def __init__(self, name): super(InvalidModuleNameError, self).__init__( "Invalid module name: " + name) @@ -134,6 +141,7 @@ class InvalidModuleNameError(spack.error.SpackError): class InvalidFullyQualifiedModuleNameError(spack.error.SpackError): """Raised when we encounter a bad full package name.""" + def __init__(self, name): super(InvalidFullyQualifiedModuleNameError, self).__init__( "Invalid fully qualified package name: " + name) @@ -141,17 +149,17 @@ class InvalidFullyQualifiedModuleNameError(spack.error.SpackError): class NamespaceTrie(object): + class Element(object): + def __init__(self, value): self.value = value - def __init__(self, separator='.'): self._subspaces = {} self._value = None self._sep = separator - def __setitem__(self, namespace, value): first, sep, rest = namespace.partition(self._sep) @@ -164,7 +172,6 @@ class NamespaceTrie(object): self._subspaces[first][rest] = value - def _get_helper(self, namespace, full_name): first, sep, rest = namespace.partition(self._sep) if not first: @@ -176,13 +183,12 @@ class NamespaceTrie(object): else: return self._subspaces[first]._get_helper(rest, full_name) - def __getitem__(self, namespace): return self._get_helper(namespace, namespace) - def is_prefix(self, namespace): - """True if the namespace has a value, or if it's the prefix of one that does.""" + """True if the namespace has a value, or if it's the prefix of one that + does.""" first, sep, rest = namespace.partition(self._sep) if not first: return True @@ -191,7 +197,6 @@ class NamespaceTrie(object): else: return self._subspaces[first].is_prefix(rest) - def is_leaf(self, namespace): """True if this namespace has no children in the trie.""" first, sep, rest = namespace.partition(self._sep) @@ -202,7 +207,6 @@ class NamespaceTrie(object): else: return self._subspaces[first].is_leaf(rest) - def has_value(self, namespace): """True if there is a value set for the given namespace.""" first, sep, rest = namespace.partition(self._sep) @@ -213,20 +217,17 @@ class NamespaceTrie(object): else: return self._subspaces[first].has_value(rest) - def __contains__(self, namespace): """Returns whether a value has been set for the namespace.""" return self.has_value(namespace) - def _str_helper(self, stream, level=0): indent = (level * ' ') for name in sorted(self._subspaces): stream.write(indent + name + '\n') if self._value: stream.write(indent + ' ' + repr(self._value.value)) - stream.write(self._subspaces[name]._str_helper(stream, level+1)) - + stream.write(self._subspaces[name]._str_helper(stream, level + 1)) def __str__(self): stream = StringIO() diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py index bc5e9d2ffe..c36445193c 100644 --- a/lib/spack/spack/util/pattern.py +++ b/lib/spack/spack/util/pattern.py @@ -53,7 +53,9 @@ def composite(interface=None, method_list=None, container=list): # Check if at least one of the 'interface' or the 'method_list' arguments # are defined if interface is None and method_list is None: - raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite") # NOQA : ignore=E501 + raise TypeError( + "Either 'interface' or 'method_list' must be defined on a call " + "to composite") def cls_decorator(cls): # Retrieve the base class of the composite. Inspect its methods and @@ -102,7 +104,8 @@ def composite(interface=None, method_list=None, container=list): # python@2.7: interface_methods = {name: method for name, method in # inspect.getmembers(interface, predicate=no_special_no_private)} interface_methods = {} - for name, method in inspect.getmembers(interface, predicate=no_special_no_private): # NOQA: ignore=E501 + for name, method in inspect.getmembers( + interface, predicate=no_special_no_private): interface_methods[name] = method ########## # python@2.7: interface_methods_dict = {name: IterateOver(name, @@ -118,7 +121,8 @@ def composite(interface=None, method_list=None, container=list): # python@2.7: cls_method = {name: method for name, method in # inspect.getmembers(cls, predicate=inspect.ismethod)} cls_method = {} - for name, method in inspect.getmembers(cls, predicate=inspect.ismethod): # NOQA: ignore=E501 + for name, method in inspect.getmembers( + cls, predicate=inspect.ismethod): cls_method[name] = method ########## dictionary_for_type_call.update(cls_method) diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py index e1a0f2958b..985d862269 100644 --- a/lib/spack/spack/util/prefix.py +++ b/lib/spack/spack/util/prefix.py @@ -27,6 +27,7 @@ This file contains utilities to help with installing packages. """ from llnl.util.filesystem import join_path + class Prefix(str): """This class represents an installation prefix, but provides useful attributes for referring to directories inside the prefix. diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py index 909f9a57a8..7bcdf2d61f 100644 --- a/lib/spack/spack/util/spack_yaml.py +++ b/lib/spack/spack/util/spack_yaml.py @@ -34,7 +34,6 @@ import yaml from yaml.nodes import * from yaml.constructor import ConstructorError -from yaml.representer import SafeRepresenter from ordereddict_backport import OrderedDict # Only export load and dump @@ -42,15 +41,23 @@ __all__ = ['load', 'dump'] # Make new classes so we can add custom attributes. # Also, use OrderedDict instead of just dict. + + class syaml_dict(OrderedDict): + def __repr__(self): - mappings = ('%r: %r' % (k,v) for k,v in self.items()) + mappings = ('%r: %r' % (k, v) for k, v in self.items()) return '{%s}' % ', '.join(mappings) + + class syaml_list(list): __repr__ = list.__repr__ + + class syaml_str(str): __repr__ = str.__repr__ + def mark(obj, node): """Add start and end markers to an object.""" obj._start_mark = node.start_mark @@ -73,6 +80,7 @@ class OrderedLineLoader(yaml.Loader): # The standard YAML constructors return empty instances and fill # in with mappings later. We preserve this behavior. # + def construct_yaml_str(self, node): value = self.construct_scalar(node) try: @@ -83,14 +91,12 @@ class OrderedLineLoader(yaml.Loader): mark(value, node) return value - def construct_yaml_seq(self, node): data = syaml_list() mark(data, node) yield data data.extend(self.construct_sequence(node)) - def construct_yaml_map(self, node): data = syaml_dict() mark(data, node) @@ -104,22 +110,23 @@ class OrderedLineLoader(yaml.Loader): # def construct_sequence(self, node, deep=False): if not isinstance(node, SequenceNode): - raise ConstructorError(None, None, - "expected a sequence node, but found %s" % node.id, - node.start_mark) - value = syaml_list(self.construct_object(child, deep=deep) - for child in node.value) + raise ConstructorError( + None, None, + "expected a sequence node, but found %s" % node.id, + node.start_mark) + value = syaml_list(self.construct_object(child, deep=deep) + for child in node.value) mark(value, node) return value - def construct_mapping(self, node, deep=False): """Store mappings as OrderedDicts instead of as regular python dictionaries to preserve file ordering.""" if not isinstance(node, MappingNode): - raise ConstructorError(None, None, - "expected a mapping node, but found %s" % node.id, - node.start_mark) + raise ConstructorError( + None, None, + "expected a mapping node, but found %s" % node.id, + node.start_mark) mapping = syaml_dict() for key_node, value_node in node.value: @@ -127,22 +134,26 @@ class OrderedLineLoader(yaml.Loader): try: hash(key) except TypeError, exc: - raise ConstructorError("while constructing a mapping", node.start_mark, - "found unacceptable key (%s)" % exc, key_node.start_mark) + raise ConstructorError( + "while constructing a mapping", node.start_mark, + "found unacceptable key (%s)" % exc, key_node.start_mark) value = self.construct_object(value_node, deep=deep) if key in mapping: - raise ConstructorError("while constructing a mapping", node.start_mark, - "found already in-use key (%s)" % key, key_node.start_mark) + raise ConstructorError( + "while constructing a mapping", node.start_mark, + "found already in-use key (%s)" % key, key_node.start_mark) mapping[key] = value mark(mapping, node) return mapping # register above new constructors -OrderedLineLoader.add_constructor(u'tag:yaml.org,2002:map', OrderedLineLoader.construct_yaml_map) -OrderedLineLoader.add_constructor(u'tag:yaml.org,2002:seq', OrderedLineLoader.construct_yaml_seq) -OrderedLineLoader.add_constructor(u'tag:yaml.org,2002:str', OrderedLineLoader.construct_yaml_str) - +OrderedLineLoader.add_constructor( + u'tag:yaml.org,2002:map', OrderedLineLoader.construct_yaml_map) +OrderedLineLoader.add_constructor( + u'tag:yaml.org,2002:seq', OrderedLineLoader.construct_yaml_seq) +OrderedLineLoader.add_constructor( + u'tag:yaml.org,2002:str', OrderedLineLoader.construct_yaml_str) class OrderedLineDumper(yaml.Dumper): @@ -154,6 +165,7 @@ class OrderedLineDumper(yaml.Dumper): regular Python equivalents, instead of ugly YAML pyobjects. """ + def represent_mapping(self, tag, mapping, flow_style=None): value = [] node = MappingNode(tag, value, flow_style=flow_style) @@ -173,7 +185,8 @@ class OrderedLineDumper(yaml.Dumper): node_value = self.represent_data(item_value) if not (isinstance(node_key, ScalarNode) and not node_key.style): best_style = False - if not (isinstance(node_value, ScalarNode) and not node_value.style): + if not (isinstance(node_value, ScalarNode) and + not node_value.style): best_style = False value.append((node_key, node_value)) if flow_style is None: diff --git a/lib/spack/spack/util/string.py b/lib/spack/spack/util/string.py index ce017b8126..dae7afbf46 100644 --- a/lib/spack/spack/util/string.py +++ b/lib/spack/spack/util/string.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## + def comma_list(sequence, article=''): if type(sequence) != list: sequence = list(sequence) @@ -32,7 +33,7 @@ def comma_list(sequence, article=''): elif len(sequence) == 1: return sequence[0] else: - out = ', '.join(str(s) for s in sequence[:-1]) + out = ', '.join(str(s) for s in sequence[:-1]) if len(sequence) != 2: out += ',' # oxford comma out += ' ' @@ -41,6 +42,7 @@ def comma_list(sequence, article=''): out += str(sequence[-1]) return out + def comma_or(sequence): return comma_list(sequence, 'or') diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py index 47abc507e0..25f1e605d6 100644 --- a/lib/spack/spack/util/web.py +++ b/lib/spack/spack/util/web.py @@ -25,8 +25,7 @@ import re import os import sys -import subprocess -import urllib2, cookielib +import urllib2 import urlparse from multiprocessing import Pool from HTMLParser import HTMLParser, HTMLParseError @@ -44,6 +43,7 @@ TIMEOUT = 10 class LinkParser(HTMLParser): """This parser just takes an HTML page and strips out the hrefs on the links. Good enough for a really simple spider. """ + def __init__(self): HTMLParser.__init__(self) self.links = [] @@ -84,7 +84,7 @@ def _spider(args): req.get_method = lambda: "HEAD" resp = urllib2.urlopen(req, timeout=TIMEOUT) - if not "Content-type" in resp.headers: + if "Content-type" not in resp.headers: tty.debug("ignoring page " + url) return pages, links @@ -125,11 +125,11 @@ def _spider(args): if abs_link in visited: continue - # If we're not at max depth, follow links. - if depth < max_depth: - subcalls.append((abs_link, visited, root, None, - depth+1, max_depth, raise_on_error)) - visited.add(abs_link) + # If we're not at max depth, follow links. + if depth < max_depth: + subcalls.append((abs_link, visited, root, None, + depth + 1, max_depth, raise_on_error)) + visited.add(abs_link) if subcalls: try: @@ -142,22 +142,22 @@ def _spider(args): pool.terminate() pool.join() - except urllib2.URLError, e: + except urllib2.URLError as e: tty.debug(e) if raise_on_error: raise spack.error.NoNetworkConnectionError(str(e), url) - except HTMLParseError, e: + except HTMLParseError as e: # This error indicates that Python's HTML parser sucks. msg = "Got an error parsing HTML." # Pre-2.7.3 Pythons in particular have rather prickly HTML parsing. - if sys.version_info[:3] < (2,7,3): + if sys.version_info[:3] < (2, 7, 3): msg += " Use Python 2.7.3 or newer for better HTML parsing." tty.warn(msg, url, "HTMLParseError: " + str(e)) - except Exception, e: + except Exception as e: # Other types of errors are completely ignored, except in debug mode. tty.debug("Error in _spider: %s" % e) @@ -173,7 +173,8 @@ def spider(root_url, **kwargs): performance over a sequential fetch. """ max_depth = kwargs.setdefault('depth', 1) - pages, links = _spider((root_url, set(), root_url, None, 1, max_depth, False)) + pages, links = _spider((root_url, set(), root_url, None, + 1, max_depth, False)) return pages, links @@ -235,7 +236,7 @@ def find_versions_of_archive(*archive_urls, **kwargs): try: ver = spack.url.parse_version(url) versions[ver] = url - except spack.url.UndetectableVersionError as e: + except spack.url.UndetectableVersionError: continue return versions diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py index ad875f5ef5..b2c1a73489 100644 --- a/lib/spack/spack/variant.py +++ b/lib/spack/spack/variant.py @@ -29,8 +29,10 @@ currently variants are just flags. """ + class Variant(object): """Represents a variant on a build. Can be either on or off.""" + def __init__(self, default, description): self.default = default self.description = str(description) diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py index 6f6c83b3d8..e1311eb0d9 100644 --- a/lib/spack/spack/version.py +++ b/lib/spack/spack/version.py @@ -50,6 +50,8 @@ from functools import wraps from functools_backport import total_ordering +__all__ = ['Version', 'VersionRange', 'VersionList', 'ver'] + # Valid version characters VALID_VERSION = r'[A-Za-z0-9_.-]' @@ -346,8 +348,8 @@ class VersionRange(object): s, o = self, other if s.start != o.start: - return s.start is None or (o.start is not None and s.start < o.start) # NOQA: ignore=E501 - + return s.start is None or ( + o.start is not None and s.start < o.start) return (s.end != o.end and o.end is None or (s.end is not None and s.end < o.end)) diff --git a/lib/spack/spack/yaml_version_check.py b/lib/spack/spack/yaml_version_check.py index c2d084d6c3..2c5b511d7f 100644 --- a/lib/spack/spack/yaml_version_check.py +++ b/lib/spack/spack/yaml_version_check.py @@ -34,6 +34,7 @@ import spack.config def check_yaml_versions(): check_compiler_yaml_version() + def check_compiler_yaml_version(): config_scopes = spack.config.config_scopes for scope in config_scopes.values(): @@ -46,7 +47,8 @@ def check_compiler_yaml_version(): if data: compilers = data['compilers'] if len(compilers) > 0: - if (not isinstance(compilers, list)) or 'operating_system' not in compilers[0]['compiler']: + if (not isinstance(compilers, list) or + 'operating_system' not in compilers[0]['compiler']): new_file = os.path.join(scope.path, '_old_compilers.yaml') tty.warn('%s in out of date compilers format. ' 'Moved to %s. Spack automatically generate ' diff --git a/share/spack/qa/run-flake8 b/share/spack/qa/run-flake8 index 595df417ec..e41cd0d471 100755 --- a/share/spack/qa/run-flake8 +++ b/share/spack/qa/run-flake8 @@ -2,11 +2,6 @@ # # This script runs source code style checks on Spack. # -# It should be executed from the top-level directory of the repo, -# e.g.: -# -# share/spack/qa/run-flake8 -# # To run it, you'll need to have the Python flake8 installed locally. # PYTHONPATH=./lib/spack:$PYTHONPATH @@ -17,14 +12,40 @@ if [[ ! $flake8 ]]; then exit 1 fi -# Check if changed files are flake8 conformant [framework] -changed=$(git diff --name-only --find-renames develop... | grep '.py$') +# Move to Spack root; allows script to be run from anywhere +cd "$(dirname "$0")/../../.." + +# Add changed files that have been committed since branching off of develop +changed=($(git diff --name-only --find-renames develop... -- '*.py')) +# Add changed files that have been staged but not yet committed +changed+=($(git diff --name-only --find-renames --cached -- '*.py')) +# Add changed files that are unstaged +changed+=($(git diff --name-only --find-renames -- '*.py')) + +# Ensure that each file in the array is unique +changed=($(printf '%s\n' "${changed[@]}" | sort -u)) + +function cleanup { + # Restore original package files after modifying them. + for file in "${changed[@]}"; do + if [[ -e "${file}.sbak~" ]]; then + mv "${file}.sbak~" "${file}" + fi + done +} + +# Cleanup temporary files upon exit or when script is killed +trap cleanup EXIT SIGINT SIGTERM # Add approved style exemptions to the changed packages. -for file in $changed; do - if [[ $file = *package.py ]]; then - cp "$file" "$file~" +for file in "${changed[@]}"; do + # Make a backup to restore later + cp "$file" "$file.sbak~" + # + # Exemptions for package.py files + # + if [[ $file = *package.py ]]; then # Exempt lines with urls and descriptions from overlong line errors. perl -i -pe 's/^(\s*homepage\s*=.*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*url\s*=.*)$/\1 # NOQA: ignore=E501/' $file @@ -36,31 +57,28 @@ for file in $changed; do # Exempt '@when' decorated functions from redefinition errors. perl -i -pe 's/^(\s*\@when\(.*\).*)$/\1 # NOQA: ignore=F811/' $file fi + + # + # Exemptions for all files + # + perl -i -pe 's/^(.*(https?|file)\:.*)$/\1 # NOQA: ignore=E501/' $file done -return_code=0 -if [[ $changed ]]; then +if [[ "${changed[@]}" ]]; then echo ======================================================= echo flake8: running flake8 code checks on spack. echo echo Modified files: - echo $changed | perl -pe 's/^/ /;s/ +/\n /g' + echo "${changed[@]}" | perl -pe 's/^/ /;s/ +/\n /g' echo ======================================================= - if flake8 --format pylint $changed; then + if flake8 --format pylint "${changed[@]}"; then echo "Flake8 checks were clean." else echo "Flake8 found errors." - return_code=1 + exit 1 fi else echo No core framework files modified. fi -# Restore original package files after modifying them. -for file in $changed; do - if [[ $file = *package.py ]]; then - mv "${file}~" "${file}" - fi -done - -exit $return_code +exit 0 diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests new file mode 100755 index 0000000000..33fb1bfae2 --- /dev/null +++ b/share/spack/qa/run-unit-tests @@ -0,0 +1,20 @@ +#!/usr/bin/env bash +# +# This script runs Spack unit tests. +# +# It should be executed from the top-level directory of the repo, +# e.g.: +# +# share/spack/qa/run-unit-tests +# +# To run it, you'll need to have the Python coverage installed locally. +# + +# Regular spack setup and tests +. ./share/spack/setup-env.sh +spack compilers +spack config get compilers +spack install -v libdwarf + +# Run unit tests with code coverage +coverage run bin/spack test diff --git a/var/spack/repos/builtin.mock/packages/a/package.py b/var/spack/repos/builtin.mock/packages/a/package.py index 40b92240fc..0d75ee1256 100644 --- a/var/spack/repos/builtin.mock/packages/a/package.py +++ b/var/spack/repos/builtin.mock/packages/a/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class A(Package): """Simple package with no dependencies""" diff --git a/var/spack/repos/builtin.mock/packages/b/package.py b/var/spack/repos/builtin.mock/packages/b/package.py index c447a56b48..5729f24e79 100644 --- a/var/spack/repos/builtin.mock/packages/b/package.py +++ b/var/spack/repos/builtin.mock/packages/b/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class B(Package): """Simple package with no dependencies""" diff --git a/var/spack/repos/builtin.mock/packages/c/package.py b/var/spack/repos/builtin.mock/packages/c/package.py index 5b6079c4e3..80777a05bb 100644 --- a/var/spack/repos/builtin.mock/packages/c/package.py +++ b/var/spack/repos/builtin.mock/packages/c/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class C(Package): """Simple package with no dependencies""" diff --git a/var/spack/repos/builtin.mock/packages/callpath/package.py b/var/spack/repos/builtin.mock/packages/callpath/package.py index c297a123b8..56b969df98 100644 --- a/var/spack/repos/builtin.mock/packages/callpath/package.py +++ b/var/spack/repos/builtin.mock/packages/callpath/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Callpath(Package): homepage = "https://github.com/tgamblin/callpath" url = "http://github.com/tgamblin/callpath-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index c58430317a..0c78f0bf68 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -25,6 +25,7 @@ from spack import * import os + def check(condition, msg): """Raise an install error if condition is False.""" if not condition: @@ -40,15 +41,14 @@ class CmakeClient(Package): depends_on('cmake', type='build') - def setup_environment(self, spack_env, run_env): spack_cc # Ensure spack module-scope variable is avaiabl check(from_cmake == "from_cmake", "setup_environment couldn't read global set by cmake.") check(self.spec['cmake'].link_arg == "test link arg", - "link arg on dependency spec not readable from setup_environment.") - + "link arg on dependency spec not readable from " + "setup_environment.") def setup_dependent_environment(self, spack_env, run_env, dspec): spack_cc # Ensure spack module-scope variable is avaiable @@ -56,8 +56,8 @@ class CmakeClient(Package): "setup_dependent_environment couldn't read global set by cmake.") check(self.spec['cmake'].link_arg == "test link arg", - "link arg on dependency spec not readable from setup_dependent_environment.") - + "link arg on dependency spec not readable from " + "setup_dependent_environment.") def setup_dependent_package(self, module, dspec): spack_cc # Ensure spack module-scope variable is avaiable @@ -65,9 +65,8 @@ class CmakeClient(Package): "setup_dependent_package couldn't read global set by cmake.") check(self.spec['cmake'].link_arg == "test link arg", - "link arg on dependency spec not readable from setup_dependent_package.") - - + "link arg on dependency spec not readable from " + "setup_dependent_package.") def install(self, spec, prefix): # check that cmake is in the global scope. diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py index 0356cf8afb..c8b6464e69 100644 --- a/var/spack/repos/builtin.mock/packages/cmake/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake/package.py @@ -25,6 +25,7 @@ from spack import * import os + def check(condition, msg): """Raise an install error if condition is False.""" if not condition: @@ -39,7 +40,6 @@ class Cmake(Package): version('3.4.3', '4cb3ff35b2472aae70f542116d616e63', url='https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz') - def setup_environment(self, spack_env, run_env): spack_cc # Ensure spack module-scope variable is avaiable spack_env.set('for_install', 'for_install') @@ -48,7 +48,6 @@ class Cmake(Package): spack_cc # Ensure spack module-scope variable is avaiable spack_env.set('from_cmake', 'from_cmake') - def setup_dependent_package(self, module, dspec): spack_cc # Ensure spack module-scope variable is avaiable @@ -57,7 +56,6 @@ class Cmake(Package): self.spec.link_arg = "test link arg" - def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin.mock/packages/direct_mpich/package.py b/var/spack/repos/builtin.mock/packages/direct_mpich/package.py index 663908d56c..f38589ad4d 100644 --- a/var/spack/repos/builtin.mock/packages/direct_mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/direct_mpich/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class DirectMpich(Package): homepage = "http://www.example.com" url = "http://www.example.com/direct_mpich-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/dyninst/package.py b/var/spack/repos/builtin.mock/packages/dyninst/package.py index ad486011e2..daf1b82ec6 100644 --- a/var/spack/repos/builtin.mock/packages/dyninst/package.py +++ b/var/spack/repos/builtin.mock/packages/dyninst/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Dyninst(Package): homepage = "https://paradyn.org" url = "http://www.paradyn.org/release8.1/DyninstAPI-8.1.1.tgz" diff --git a/var/spack/repos/builtin.mock/packages/e/package.py b/var/spack/repos/builtin.mock/packages/e/package.py index b951a3eaa6..c764007563 100644 --- a/var/spack/repos/builtin.mock/packages/e/package.py +++ b/var/spack/repos/builtin.mock/packages/e/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class E(Package): """Simple package with no dependencies""" diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py index f7b0da3fd9..f7c9b056a4 100644 --- a/var/spack/repos/builtin.mock/packages/externalmodule/package.py +++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py @@ -25,6 +25,7 @@ ############################################################################## from spack import * + class Externalmodule(Package): homepage = "http://somewhere.com" url = "http://somewhere.com/module-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/externalprereq/package.py b/var/spack/repos/builtin.mock/packages/externalprereq/package.py index bd3c4348bf..226742f2cb 100644 --- a/var/spack/repos/builtin.mock/packages/externalprereq/package.py +++ b/var/spack/repos/builtin.mock/packages/externalprereq/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Externalprereq(Package): homepage = "http://somewhere.com" url = "http://somewhere.com/prereq-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/externaltest/package.py b/var/spack/repos/builtin.mock/packages/externaltest/package.py index 2318887aec..252c42556e 100644 --- a/var/spack/repos/builtin.mock/packages/externaltest/package.py +++ b/var/spack/repos/builtin.mock/packages/externaltest/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Externaltest(Package): homepage = "http://somewhere.com" url = "http://somewhere.com/test-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/externaltool/package.py b/var/spack/repos/builtin.mock/packages/externaltool/package.py index 9ff2396f36..d2daddd350 100644 --- a/var/spack/repos/builtin.mock/packages/externaltool/package.py +++ b/var/spack/repos/builtin.mock/packages/externaltool/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Externaltool(Package): homepage = "http://somewhere.com" url = "http://somewhere.com/tool-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py index e19ef332f0..1f3553014b 100644 --- a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py +++ b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Externalvirtual(Package): homepage = "http://somewhere.com" url = "http://somewhere.com/stuff-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/fake/package.py b/var/spack/repos/builtin.mock/packages/fake/package.py index 15aabf1101..b83eec7470 100644 --- a/var/spack/repos/builtin.mock/packages/fake/package.py +++ b/var/spack/repos/builtin.mock/packages/fake/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Fake(Package): homepage = "http://www.fake-spack-example.org" url = "http://www.fake-spack-example.org/downloads/fake-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/git-test/package.py b/var/spack/repos/builtin.mock/packages/git-test/package.py index aeea41146f..730e71ac6b 100644 --- a/var/spack/repos/builtin.mock/packages/git-test/package.py +++ b/var/spack/repos/builtin.mock/packages/git-test/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class GitTest(Package): """Mock package that uses git for fetching.""" homepage = "http://www.git-fetch-example.com" diff --git a/var/spack/repos/builtin.mock/packages/hg-test/package.py b/var/spack/repos/builtin.mock/packages/hg-test/package.py index 64719eb53c..70a9b7f2c7 100644 --- a/var/spack/repos/builtin.mock/packages/hg-test/package.py +++ b/var/spack/repos/builtin.mock/packages/hg-test/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class HgTest(Package): """Test package that does fetching with mercurial.""" homepage = "http://www.hg-fetch-example.com" diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py index 3aedea9bf2..b9e31b09dc 100644 --- a/var/spack/repos/builtin.mock/packages/hypre/package.py +++ b/var/spack/repos/builtin.mock/packages/hypre/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Hypre(Package): """Hypre is included here as an example of a package that depends on both LAPACK and BLAS.""" diff --git a/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py index 6ed779889b..bbbf196129 100644 --- a/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class IndirectMpich(Package): """Test case for a package that depends on MPI and one of its dependencies requires a *particular version* of MPI. diff --git a/var/spack/repos/builtin.mock/packages/libdwarf/package.py b/var/spack/repos/builtin.mock/packages/libdwarf/package.py index b53e295e23..0fcbe4a62e 100644 --- a/var/spack/repos/builtin.mock/packages/libdwarf/package.py +++ b/var/spack/repos/builtin.mock/packages/libdwarf/package.py @@ -23,11 +23,11 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os # Only build certain parts of dwarf because the other ones break. dwarf_dirs = ['libdwarf', 'dwarfdump2'] + class Libdwarf(Package): homepage = "http://www.prevanders.net/dwarf.html" url = "http://www.prevanders.net/libdwarf-20130729.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/libelf/package.py b/var/spack/repos/builtin.mock/packages/libelf/package.py index f52d8cefe1..90d00ad339 100644 --- a/var/spack/repos/builtin.mock/packages/libelf/package.py +++ b/var/spack/repos/builtin.mock/packages/libelf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libelf(Package): homepage = "http://www.mr511.de/software/english.html" url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/mpich/package.py b/var/spack/repos/builtin.mock/packages/mpich/package.py index f278f26b8b..936127398c 100644 --- a/var/spack/repos/builtin.mock/packages/mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/mpich/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpich(Package): homepage = "http://www.mpich.org" url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/mpich2/package.py b/var/spack/repos/builtin.mock/packages/mpich2/package.py index e6b68d2490..c92b4ba43a 100644 --- a/var/spack/repos/builtin.mock/packages/mpich2/package.py +++ b/var/spack/repos/builtin.mock/packages/mpich2/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpich2(Package): homepage = "http://www.mpich.org" url = "http://www.mpich.org/static/downloads/1.5/mpich2-1.5.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py index bc26f539ba..10fbf3845e 100644 --- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py +++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpileaks(Package): homepage = "http://www.llnl.gov" url = "http://www.llnl.gov/mpileaks-1.0.tar.gz" @@ -35,6 +36,8 @@ class Mpileaks(Package): variant('debug', default=False, description='Debug variant') variant('opt', default=False, description='Optimized variant') + variant('shared', default=True, description='Build shared library') + variant('static', default=True, description='Build static library') depends_on("mpi") depends_on("callpath") diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py index ca991632dd..fa3f815135 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py @@ -22,12 +22,10 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import imp -from llnl.util.filesystem import join_path -from spack.util.naming import mod_to_class from spack import * import spack.architecture + class Multimethod(Package): """This package is designed for use with Spack's multimethod test. It has a bunch of test cases for the @when decorator that the @@ -52,7 +50,6 @@ class Multimethod(Package): def no_version_2(self): return 4 - # # These functions overlap, so there is ambiguity, but we'll take # the first one. @@ -65,7 +62,6 @@ class Multimethod(Package): def version_overlap(self): return 2 - # # More complicated case with cascading versions. # @@ -84,7 +80,6 @@ class Multimethod(Package): def mpi_version(self): return 1 - # # Use these to test whether the default method is called when no # match is found. This also tests whether we can switch methods @@ -101,8 +96,6 @@ class Multimethod(Package): def has_a_default(self): return 'intel' - - # # Make sure we can switch methods on different target # @@ -112,15 +105,16 @@ class Multimethod(Package): targets = targets[:-1] for target in targets: - @when('target='+target.name) + @when('target=' + target.name) def different_by_target(self): - if isinstance(self.spec.architecture.target,basestring): + if isinstance(self.spec.architecture.target, basestring): return self.spec.architecture.target else: return self.spec.architecture.target.name # # Make sure we can switch methods on different dependencies # + @when('^mpich') def different_by_dep(self): return 'mpich' @@ -129,7 +123,6 @@ class Multimethod(Package): def different_by_dep(self): return 'zmpi' - # # Make sure we can switch on virtual dependencies # diff --git a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py index 9d567f2e9b..0a5b1d0e6a 100644 --- a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py +++ b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class NetlibBlas(Package): homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" diff --git a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py index 46d6ae43dc..755d3001a4 100644 --- a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class NetlibLapack(Package): homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py index b36237c1e2..0f14fbaa61 100644 --- a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py +++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class OpenblasWithLapack(Package): """Dummy version of OpenBLAS that also provides LAPACK, for testing.""" homepage = "http://www.openblas.net" diff --git a/var/spack/repos/builtin.mock/packages/openblas/package.py b/var/spack/repos/builtin.mock/packages/openblas/package.py index 5b39447e83..f6cdeeea49 100644 --- a/var/spack/repos/builtin.mock/packages/openblas/package.py +++ b/var/spack/repos/builtin.mock/packages/openblas/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Openblas(Package): """OpenBLAS: An optimized BLAS library""" homepage = "http://www.openblas.net" diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py index f97959c763..337f54e24e 100644 --- a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py +++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class OptionalDepTest2(Package): """Depends on the optional-dep-test package""" diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py index d8fe33c3da..2904b3782d 100644 --- a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py +++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class OptionalDepTest3(Package): """Depends on the optional-dep-test package""" diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py index 80c1da55f8..2c07e61769 100644 --- a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py +++ b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class OptionalDepTest(Package): """Description""" diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py index dc21b475e5..a5290161ad 100644 --- a/var/spack/repos/builtin.mock/packages/python/package.py +++ b/var/spack/repos/builtin.mock/packages/python/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Python(Package): """Dummy Python package to demonstrate preferred versions.""" homepage = "http://www.python.org" @@ -40,4 +41,3 @@ class Python(Package): def install(self, spec, prefix): pass - diff --git a/var/spack/repos/builtin.mock/packages/svn-test/package.py b/var/spack/repos/builtin.mock/packages/svn-test/package.py index 2f197593e0..01d0929c28 100644 --- a/var/spack/repos/builtin.mock/packages/svn-test/package.py +++ b/var/spack/repos/builtin.mock/packages/svn-test/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class SvnTest(Package): """Mock package that uses svn for fetching.""" url = "http://www.example.com/svn-test-1.0.tar.gz" diff --git a/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py b/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py index 7c65909ad2..2129d9788b 100644 --- a/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py +++ b/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class TrivialInstallTestPackage(Package): """This package is a stub with a trivial install method. It allows us to test the install and uninstall logic of spack.""" diff --git a/var/spack/repos/builtin.mock/packages/zmpi/package.py b/var/spack/repos/builtin.mock/packages/zmpi/package.py index fcd3afe93b..b6a5b33011 100644 --- a/var/spack/repos/builtin.mock/packages/zmpi/package.py +++ b/var/spack/repos/builtin.mock/packages/zmpi/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Zmpi(Package): """This is a fake MPI package used to demonstrate virtual package providers with dependencies.""" diff --git a/var/spack/repos/builtin/packages/LuaJIT/package.py b/var/spack/repos/builtin/packages/LuaJIT/package.py index db6f7d3cad..244c63c8fb 100644 --- a/var/spack/repos/builtin/packages/LuaJIT/package.py +++ b/var/spack/repos/builtin/packages/LuaJIT/package.py @@ -25,6 +25,7 @@ import os from spack import * + class Luajit(Package): """Flast flexible JITed lua""" homepage = "http://www.luajit.org" diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index ad06c2ca48..e880a3aa66 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -22,10 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os - from spack import * from spack.util.environment import * +import shutil class R(Package): @@ -74,6 +73,10 @@ class R(Package): depends_on('pcre') depends_on('jdk') + @property + def etcdir(self): + return join_path(prefix, 'rlib', 'R', 'etc') + def install(self, spec, prefix): rlibdir = join_path(prefix, 'rlib') configure_args = ['--prefix=%s' % prefix, @@ -88,6 +91,12 @@ class R(Package): make() make('install') + # Make a copy of Makeconf because it will be needed to properly build R + # dependencies in Spack. + src_makeconf = join_path(self.etcdir, 'Makeconf') + dst_makeconf = join_path(self.etcdir, 'Makeconf.spack') + shutil.copy(src_makeconf, dst_makeconf) + self.filter_compilers(spec, prefix) def filter_compilers(self, spec, prefix): @@ -98,18 +107,16 @@ class R(Package): cc and c++. We want them to be bound to whatever compiler they were built with.""" - etcdir = join_path(prefix, 'rlib', 'R', 'etc') - kwargs = {'ignore_absent': True, 'backup': False, 'string': True} - filter_file(env['CC'], self.compiler.cc, - join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['CC'], self.compiler.cc, + join_path(self.etcdir, 'Makeconf'), **kwargs) filter_file(env['CXX'], self.compiler.cxx, - join_path(etcdir, 'Makeconf'), **kwargs) + join_path(self.etcdir, 'Makeconf'), **kwargs) filter_file(env['F77'], self.compiler.f77, - join_path(etcdir, 'Makeconf'), **kwargs) + join_path(self.etcdir, 'Makeconf'), **kwargs) filter_file(env['FC'], self.compiler.fc, - join_path(etcdir, 'Makeconf'), **kwargs) + join_path(self.etcdir, 'Makeconf'), **kwargs) # ======================================================================== # Set up environment to make install easy for R extensions. @@ -117,7 +124,7 @@ class R(Package): @property def r_lib_dir(self): - return os.path.join('rlib', 'R', 'library') + return join_path('rlib', 'R', 'library') def setup_dependent_environment(self, spack_env, run_env, extension_spec): # Set R_LIBS to include the library dir for the @@ -125,15 +132,21 @@ class R(Package): r_libs_path = [] for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): if d.package.extends(self.spec): - r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir)) + r_libs_path.append(join_path(d.prefix, self.r_lib_dir)) r_libs_path = ':'.join(r_libs_path) spack_env.set('R_LIBS', r_libs_path) + spack_env.set('R_MAKEVARS_SITE', + join_path(self.etcdir, 'Makeconf.spack')) + + # Use the number of make_jobs set in spack. The make program will + # determine how many jobs can actually be started. + spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) # For run time environment set only the path for extension_spec and # prepend it to R_LIBS if extension_spec.package.extends(self.spec): - run_env.prepend_path('R_LIBS', os.path.join( + run_env.prepend_path('R_LIBS', join_path( extension_spec.prefix, self.r_lib_dir)) def setup_environment(self, spack_env, run_env): @@ -147,13 +160,14 @@ class R(Package): def setup_dependent_package(self, module, ext_spec): """Called before R modules' install() methods. In most cases, extensions will only need to have one line: - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % - self.stage.source_path)""" + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path)""" + # R extension builds can have a global R executable function module.R = Executable(join_path(self.spec.prefix.bin, 'R')) # Add variable for library directry - module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir) + module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir) # Make the site packages directory for extensions, if it does not exist # already. diff --git a/var/spack/repos/builtin/packages/SAMRAI/package.py b/var/spack/repos/builtin/packages/SAMRAI/package.py index 73c51ced23..e0648290d6 100644 --- a/var/spack/repos/builtin/packages/SAMRAI/package.py +++ b/var/spack/repos/builtin/packages/SAMRAI/package.py @@ -24,12 +24,14 @@ ############################################################################## from spack import * + class Samrai(Package): """SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) - is an object-oriented C++ software library enables exploration of numerical, - algorithmic, parallel computing, and software issues associated with applying - structured adaptive mesh refinement (SAMR) technology in large-scale parallel - application development. + is an object-oriented C++ software library enables exploration of + numerical, algorithmic, parallel computing, and software issues + associated with applying structured adaptive mesh refinement + (SAMR) technology in large-scale parallel application development. + """ homepage = "https://computation.llnl.gov/project/SAMRAI/" url = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py new file mode 100644 index 0000000000..70249aebac --- /dev/null +++ b/var/spack/repos/builtin/packages/ack/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Ack(Package): + """ack 2.14 is a tool like grep, optimized for programmers. + + Designed for programmers with large heterogeneous trees of + source code, ack is written purely in portable Perl 5 and takes + advantage of the power of Perl's regular expressions.""" + + homepage = "http://beyondgrep.com/" + url = "http://beyondgrep.com/ack-2.14-single-file" + + version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False) + + depends_on('perl') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + ack = 'ack-{0}-single-file'.format(self.version) + + # rewrite the script's #! line to call the perl dependency + shbang = '#!' + join_path(spec['perl'].prefix.bin, 'perl') + filter_file(r'^#!/usr/bin/env perl', shbang, ack) + + install(ack, join_path(prefix.bin, "ack")) + set_executable(join_path(prefix.bin, "ack")) diff --git a/var/spack/repos/builtin/packages/activeharmony/package.py b/var/spack/repos/builtin/packages/activeharmony/package.py index 9d15bd71d9..6a4e67a1ca 100644 --- a/var/spack/repos/builtin/packages/activeharmony/package.py +++ b/var/spack/repos/builtin/packages/activeharmony/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class Activeharmony(Package): - """Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application).""" + """Active Harmony: a framework for auto-tuning (the automated search for + values to improve the performance of a target application).""" homepage = "http://www.dyninst.org/harmony" url = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz" @@ -34,6 +36,3 @@ class Activeharmony(Package): def install(self, spec, prefix): make("CFLAGS=-O3") make("install", 'PREFIX=%s' % prefix) - -from spack import * - diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py index 592681bb82..1a6998fd96 100644 --- a/var/spack/repos/builtin/packages/adept-utils/package.py +++ b/var/spack/repos/builtin/packages/adept-utils/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class AdeptUtils(Package): """Utility libraries for LLNL performance tools.""" diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py index a6052ad7bd..c5d53de230 100644 --- a/var/spack/repos/builtin/packages/adol-c/package.py +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -23,21 +23,24 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import sys + class AdolC(Package): - """A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.""" + """A package for the automatic differentiation of first and higher + derivatives of vector functions in C and C++ programs by operator + overloading.""" homepage = "https://projects.coin-or.org/ADOL-C" url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz" version('head', svn='https://projects.coin-or.org/svn/ADOL-C/trunk/') version('2.6.1', '1032b28427d6e399af4610e78c0f087b') - + variant('doc', default=True, description='Install documentation') variant('openmp', default=False, description='Enable OpenMP support') variant('sparse', default=False, description='Enable sparse drivers') - variant('tests', default=True, description='Build all included examples as a test case') - + variant('tests', default=True, + description='Build all included examples as a test case') + patch('openmp_exam.patch') def install(self, spec, prefix): @@ -49,10 +52,14 @@ class AdolC(Package): if '+openmp' in spec: if spec.satisfies('%gcc'): make_args.extend([ - '--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path> + # FIXME: Is this required? -I <path to omp.h> -L <LLVM + # OpenMP library path> + '--with-openmp-flag=-fopenmp' ]) else: - raise InstallError("OpenMP flags for compilers other than GCC are not implemented.") + raise InstallError( + "OpenMP flags for compilers other than GCC " + "are not implemented.") if '+sparse' in spec: make_args.extend([ @@ -63,7 +70,7 @@ class AdolC(Package): # whether Adol-C works as expected if '+tests' in spec: make_args.extend([ - '--enable-docexa', # Documeted examples + '--enable-docexa', # Documeted examples '--enable-addexa' # Additional examples ]) if '+openmp' in spec: @@ -74,31 +81,36 @@ class AdolC(Package): configure(*make_args) make() make("install") - + # Copy the config.h file, as some packages might require it source_directory = self.stage.source_path - config_h = join_path(source_directory,'ADOL-C','src','config.h') - install(config_h, join_path(prefix.include,'adolc')) - + config_h = join_path(source_directory, 'ADOL-C', 'src', 'config.h') + install(config_h, join_path(prefix.include, 'adolc')) + # Install documentation to {prefix}/share if '+doc' in spec: - install_tree(join_path('ADOL-C','doc'), - join_path(prefix.share,'doc')) - + install_tree(join_path('ADOL-C', 'doc'), + join_path(prefix.share, 'doc')) + # Install examples to {prefix}/share if '+tests' in spec: - install_tree(join_path('ADOL-C','examples'), - join_path(prefix.share,'examples')) - + install_tree(join_path('ADOL-C', 'examples'), + join_path(prefix.share, 'examples')) + # Run some examples that don't require user input # TODO: Check that bundled examples produce the correct results - with working_dir(join_path(source_directory,'ADOL-C','examples')): + with working_dir(join_path( + source_directory, 'ADOL-C', 'examples')): Executable('./tapeless_scalar')() Executable('./tapeless_vector')() - - with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')): + + with working_dir(join_path( + source_directory, + 'ADOL-C', 'examples', 'additional_examples')): Executable('./checkpointing/checkpointing')() - + if '+openmp' in spec: - with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')): + with working_dir(join_path( + source_directory, + 'ADOL-C', 'examples', 'additional_examples')): Executable('./checkpointing/checkpointing')() diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py index eb67facaf3..891061c62f 100644 --- a/var/spack/repos/builtin/packages/antlr/package.py +++ b/var/spack/repos/builtin/packages/antlr/package.py @@ -24,8 +24,9 @@ ############################################################################## from spack import * + class Antlr(Package): - + homepage = "http://www.antlr.org" url = "https://github.com/antlr/antlr/tarball/v2.7.7" @@ -41,22 +42,23 @@ class Antlr(Package): # CharScanner.hpp must include this line: #include <cstring> or else # ncap2 will not compile (this tarball is already patched). version('2.7.7', '914865e853fe8e1e61a9f23d045cb4ab', - # Patched version as described above - url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz') - # Unpatched version - # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz') + # Patched version as described above + url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz') + # Unpatched version + # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz') variant('cxx', default=False, description='Enable ANTLR for C++') variant('java', default=False, description='Enable ANTLR for Java') variant('python', default=False, description='Enable ANTLR for Python') variant('csharp', default=False, description='Enable ANTLR for Csharp') - def install(self, spec, prefix): # Check for future enabling of variants for v in ('+java', '+python', '+csharp'): if v in spec: - raise Error('Illegal variant %s; for now, Spack only knows how to build antlr or antlr+cxx') + raise Error( + ('Illegal variant %s; ' % v) + 'for now, ' + 'Spack only knows how to build antlr or antlr+cxx') config_args = [ '--prefix=%s' % prefix, diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py index 59fbe50c93..832e10a1ec 100644 --- a/var/spack/repos/builtin/packages/apex/package.py +++ b/var/spack/repos/builtin/packages/apex/package.py @@ -25,6 +25,7 @@ from spack import * from spack.util.environment import * + class Apex(Package): homepage = "http://github.com/khuck/xpress-apex" url = "http://github.com/khuck/xpress-apex/archive/v0.1.tar.gz" @@ -39,17 +40,17 @@ class Apex(Package): def install(self, spec, prefix): - path=get_path("PATH") + path = get_path("PATH") path.remove(spec["binutils"].prefix.bin) path_set("PATH", path) with working_dir("build", create=True): cmake('-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DUSE_BFD=TRUE', - '-DBFD_ROOT=%s' % spec['binutils'].prefix, - '-DUSE_ACTIVEHARMONY=TRUE', - '-DACTIVEHARMONY_ROOT=%s' % spec['activeharmony'].prefix, - '-DUSE_OMPT=TRUE', - '-DOMPT_ROOT=%s' % spec['ompt-openmp'].prefix, - '..', *std_cmake_args) + '-DUSE_BFD=TRUE', + '-DBFD_ROOT=%s' % spec['binutils'].prefix, + '-DUSE_ACTIVEHARMONY=TRUE', + '-DACTIVEHARMONY_ROOT=%s' % spec['activeharmony'].prefix, + '-DUSE_OMPT=TRUE', + '-DOMPT_ROOT=%s' % spec['ompt-openmp'].prefix, + '..', *std_cmake_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py index 05dc670aed..8e01d3bbdd 100644 --- a/var/spack/repos/builtin/packages/apr-util/package.py +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class AprUtil(Package): """Apache Portable Runtime Utility""" homepage = 'https://apr.apache.org/' diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py index 398e1c323d..0cd51f52e3 100644 --- a/var/spack/repos/builtin/packages/apr/package.py +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Apr(Package): """Apache portable runtime.""" homepage = 'https://apr.apache.org/' diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index d5dc703c06..728c2345f2 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -59,7 +59,8 @@ class ArpackNg(Package): version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4') version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') - variant('shared', default=True, description='Enables the build of shared libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') variant('mpi', default=False, description='Activates MPI support') # The function pdlamch10 does not set the return variable. @@ -86,10 +87,19 @@ class ArpackNg(Package): options.extend(std_cmake_args) options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) - # TODO: - # Arpack calls directly find_package(BLAS REQUIRED) and - # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are - # picked up. + # Make sure we use Spack's blas/lapack: + options.extend([ + '-DLAPACK_FOUND=true', + '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include, + '-DLAPACK_LIBRARIES=%s' % ( + spec['lapack'].lapack_shared_lib if '+shared' in spec else + spec['lapack'].lapack_static_lib), + '-DBLAS_FOUND=true', + '-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include, + '-DBLAS_LIBRARIES=%s' % ( + spec['blas'].blas_shared_lib if '+shared' in spec else + spec['blas'].blas_static_lib) + ]) if '+mpi' in spec: options.append('-DMPI=ON') @@ -101,9 +111,8 @@ class ArpackNg(Package): cmake('.', *options) make() - # TODO: make test does not work - # make('test') - + if self.run_tests: + make('test') make('install') @when('@3.3.0') @@ -120,10 +129,23 @@ class ArpackNg(Package): 'F77=%s' % spec['mpi'].mpif77 ]) - if '~shared' in spec: - options.append('--enable-shared=no') + if '+shared' in spec: + options.extend([ + '--with-blas=%s' % to_link_flags( + spec['blas'].blas_shared_lib), + '--with-lapack=%s' % to_link_flags( + spec['lapack'].lapack_shared_lib) + ]) + else: + options.extend([ + '--with-blas=%s' % spec['blas'].blas_static_lib, + '--with-lapack=%s' % spec['lapack'].lapack_static_lib, + '--enable-shared=no' + ]) bootstrap() configure(*options) make() + if self.run_tests: + make('check') make('install') diff --git a/var/spack/repos/builtin/packages/asciidoc/package.py b/var/spack/repos/builtin/packages/asciidoc/package.py index a846e0ba65..be8db684f5 100644 --- a/var/spack/repos/builtin/packages/asciidoc/package.py +++ b/var/spack/repos/builtin/packages/asciidoc/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Asciidoc(Package): """ A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.""" diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py index 1d26145fd1..d5b6933ec3 100644 --- a/var/spack/repos/builtin/packages/atk/package.py +++ b/var/spack/repos/builtin/packages/atk/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Atk(Package): """ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK @@ -32,9 +33,16 @@ class Atk(Package): homepage = "https://developer.gnome.org/atk/" url = "http://ftp.gnome.org/pub/gnome/sources/atk/2.14/atk-2.14.0.tar.xz" + version('2.20.0', '5187b0972f4d3905f285540b31395e20') version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b') - depends_on("glib") + depends_on('glib') + depends_on('pkg-config', type='build') + + def url_for_version(self, version): + """Handle atk's version-based custom URLs.""" + url = 'http://ftp.gnome.org/pub/gnome/sources/atk' + return 'url+/%s/atk-%s.tar.xz' % (version.up_to(2), version) def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index c43d92c34f..f9d5da6166 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -23,20 +23,24 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +from spack.package_test import * from spack.util.executable import Executable import os.path + class Atlas(Package): - """ - Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and - optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear - algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines - in the LAPACK library. + """Automatically Tuned Linear Algebra Software, generic shared ATLAS is an + approach for the automatic generation and optimization of numerical + software. Currently ATLAS supplies optimized versions for the complete set + of linear algebra kernels known as the Basic Linear Algebra Subroutines + (BLAS), and a subset of the linear algebra routines in the LAPACK library. """ homepage = "http://math-atlas.sourceforge.net/" version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', - url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + # not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0 + # Lapack routines. Stick with 3.5.0 until this is fixed. resource(name='lapack', url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', md5='b1d3e3e425b2e44a06760ff173104bdf', @@ -44,7 +48,7 @@ class Atlas(Package): when='@3:') version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', - url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') + url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2') variant('shared', default=True, description='Builds shared library') @@ -66,9 +70,24 @@ class Atlas(Package): options = [] if '+shared' in spec: - options.append('--shared') + options.extend([ + '--shared' + ]) + # TODO: for non GNU add '-Fa', 'alg', '-fPIC' ? + + # configure for 64-bit build + options.extend([ + '-b', '64' + ]) - # Lapack resource + # set compilers: + options.extend([ + '-C', 'ic', spack_cc, + '-C', 'if', spack_f77 + ]) + + # Lapack resource to provide full lapack build. Note that + # ATLAS only provides a few LAPACK routines natively. lapack_stage = self.stage[1] lapack_tarfile = os.path.basename(lapack_stage.fetcher.url) lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile) @@ -81,4 +100,35 @@ class Atlas(Package): make('check') make('ptcheck') make('time') + if '+shared' in spec: + with working_dir('lib'): + make('shared_all') + make("install") + self.install_test() + + def setup_dependent_package(self, module, dspec): + # libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack, + # serial BLAS), and all ATLAS symbols needed to support them. Whereas + # libtatlas.[so,dylib,dll ] is parallel (multithreaded) version. + name = 'libsatlas.%s' % dso_suffix + libdir = find_library_path(name, + self.prefix.lib64, + self.prefix.lib) + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, name) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib + + def install_test(self): + source_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.c') + blessed_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.output') + + include_flags = ["-I%s" % join_path(self.spec.prefix, "include")] + link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"), + "-lsatlas"] + + output = compile_c_and_execute(source_file, include_flags, link_flags) + compare_output_file(output, blessed_file) diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c new file mode 100644 index 0000000000..2cb90fb883 --- /dev/null +++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c @@ -0,0 +1,49 @@ +#include <cblas.h> +#include <stdio.h> + +double m[] = { + 3, 1, 3, + 1, 5, 9, + 2, 6, 5 +}; + +double x[] = { + -1, 3, -3 +}; + +#ifdef __cplusplus +extern "C" { +#endif + + void dgesv_(int *n, int *nrhs, double *a, int *lda, + int *ipivot, double *b, int *ldb, int *info); + +#ifdef __cplusplus +} +#endif + +int main(void) { + int i; + // blas: + double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; + double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; + double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; + cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); + for (i = 0; i < 9; i++) + printf("%f\n", C[i]); + + // lapack: + int ipiv[3]; + int j; + int info; + int n = 1; + int nrhs = 1; + int lda = 3; + int ldb = 3; + dgesv_(&n,&nrhs, &m[0], &lda, ipiv, &x[0], &ldb, &info); + for (i=0; i<3; ++i) + printf("%5.1f\n", x[i]); + + return 0; +} diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output new file mode 100644 index 0000000000..01404462c4 --- /dev/null +++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output @@ -0,0 +1,12 @@ +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 + -0.3 + 3.0 + -3.0 diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py index 9cacafc634..e3a9d464a9 100644 --- a/var/spack/repos/builtin/packages/atop/package.py +++ b/var/spack/repos/builtin/packages/atop/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Atop(Package): """Atop is an ASCII full-screen performance monitor for Linux""" homepage = "http://www.atoptool.nl/index.php" @@ -37,4 +38,4 @@ class Atop(Package): install("atop", join_path(prefix.bin, "atop")) mkdirp(join_path(prefix.man, "man1")) install(join_path("man", "atop.1"), - join_path(prefix.man, "man1", "atop.1")) + join_path(prefix.man, "man1", "atop.1")) diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py index 2b4681778f..7e586b2991 100644 --- a/var/spack/repos/builtin/packages/automaded/package.py +++ b/var/spack/repos/builtin/packages/automaded/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Automaded(Package): """AutomaDeD (Automata-based Debugging for Dissimilar parallel tasks) is a tool for automatic diagnosis of performance and diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py index 5820595be9..e0cd114635 100644 --- a/var/spack/repos/builtin/packages/bash/package.py +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Bash(Package): """The GNU Project's Bourne Again SHell.""" diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py index 09e897f34e..f69ed395a3 100644 --- a/var/spack/repos/builtin/packages/bbcp/package.py +++ b/var/spack/repos/builtin/packages/bbcp/package.py @@ -24,18 +24,22 @@ ############################################################################## from spack import * + class Bbcp(Package): """Securely and quickly copy data from source to target""" homepage = "http://www.slac.stanford.edu/~abh/bbcp/" - version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master") + version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', + branch="master") def install(self, spec, prefix): cd("src") make() - # BBCP wants to build the executable in a directory whose name depends on the system type + # BBCP wants to build the executable in a directory whose name depends + # on the system type makesname = Executable("../MakeSname") - bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n") + bbcp_executable_path = "../bin/%s/bbcp" % makesname( + output=str).rstrip("\n") destination_path = "%s/bin/" % prefix mkdirp(destination_path) install(bbcp_executable_path, destination_path) diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py new file mode 100644 index 0000000000..a1b4a06dbb --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Bcftools(Package): + """BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. All + commands work transparently with both VCFs and BCFs, both + uncompressed and BGZF-compressed.""" + + homepage = "http://samtools.github.io/bcftools/" + url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" + + version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb') + + depends_on('zlib') + + def install(self, spec, prefix): + make("prefix=%s" % prefix, "all") + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py new file mode 100644 index 0000000000..5120266319 --- /dev/null +++ b/var/spack/repos/builtin/packages/bdw-gc/package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class BdwGc(Package): + """The Boehm-Demers-Weiser conservative garbage collector is a garbage + collecting replacement for C malloc or C++ new.""" + + homepage = "http://www.hboehm.info/gc/" + url = "http://www.hboehm.info/gc/gc_source/gc-7.4.4.tar.gz" + + version('7.4.4', '96d18b0448a841c88d56e4ab3d180297') + + variant('libatomic-ops', default=True, + description='Use external libatomic-ops') + + depends_on('libatomic-ops', when='+libatomic-ops') + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--with-libatomic-ops={0}'.format( + 'yes' if '+libatomic-ops' in spec else 'no') + ] + + configure(*config_args) + + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py index a137fded08..f52050d7b9 100644 --- a/var/spack/repos/builtin/packages/bear/package.py +++ b/var/spack/repos/builtin/packages/bear/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class Bear(Package): - """Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.""" + """Bear is a tool that generates a compilation database for clang tooling + from non-cmake build systems.""" homepage = "https://github.com/rizsotto/Bear" url = "https://github.com/rizsotto/Bear/archive/2.0.4.tar.gz" diff --git a/var/spack/repos/builtin/packages/bib2xhtml/package.py b/var/spack/repos/builtin/packages/bib2xhtml/package.py index a9cbd204b6..b356038180 100644 --- a/var/spack/repos/builtin/packages/bib2xhtml/package.py +++ b/var/spack/repos/builtin/packages/bib2xhtml/package.py @@ -25,10 +25,11 @@ from spack import * from glob import glob + class Bib2xhtml(Package): """bib2xhtml is a program that converts BibTeX files into HTML.""" homepage = "http://www.spinellis.gr/sw/textproc/bib2xhtml/" - url='http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz' + url = 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz' version('3.0-15-gf506', 'a26ba02fe0053bbbf2277bdf0acf8645') diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index c7a125df15..70795f05cc 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -24,9 +24,10 @@ ############################################################################## from spack import * + class Bison(Package): - """Bison is a general-purpose parser generator that converts - an annotated context-free grammar into a deterministic LR or + """Bison is a general-purpose parser generator that converts + an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" homepage = "http://www.gnu.org/software/bison/" diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py index acc6ddcd07..c92e49a732 100644 --- a/var/spack/repos/builtin/packages/blitz/package.py +++ b/var/spack/repos/builtin/packages/blitz/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Blitz(Package): """N-dimensional arrays for C++""" homepage = "http://github.com/blitzpp/blitz" diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 67294fb9a1..690a05a150 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -102,13 +102,18 @@ class Boost(Package): for lib in all_libs: variant(lib, default=(lib not in default_noinstall_libs), - description="Compile with {0} library".format(lib)) - - variant('debug', default=False, description='Switch to the debug version of Boost') - variant('shared', default=True, description="Additionally build shared libraries") - variant('multithreaded', default=True, description="Build multi-threaded versions of libraries") - variant('singlethreaded', default=True, description="Build single-threaded versions of libraries") - variant('icu_support', default=False, description="Include ICU support (for regex/locale libraries)") + description="Compile with {0} library".format(lib)) + + variant('debug', default=False, + description='Switch to the debug version of Boost') + variant('shared', default=True, + description="Additionally build shared libraries") + variant('multithreaded', default=True, + description="Build multi-threaded versions of libraries") + variant('singlethreaded', default=True, + description="Build single-threaded versions of libraries") + variant('icu_support', default=False, + description="Include ICU support (for regex/locale libraries)") variant('graph', default=False, description="Build the Boost Graph library") depends_on('icu', when='+icu_support') @@ -128,8 +133,7 @@ class Boost(Package): parts = [str(p) for p in Version(version)] dots = ".".join(parts) underscores = "_".join(parts) - return "http://downloads.sourceforge.net/project/boost" \ - "/boost/%s/boost_%s.tar.bz2" % (dots, underscores) + return "http://downloads.sourceforge.net/project/boost/boost/%s/boost_%s.tar.bz2" % (dots, underscores) def determine_toolset(self, spec): if spec.satisfies("platform=darwin"): @@ -158,7 +162,7 @@ class Boost(Package): with open('user-config.jam', 'w') as f: compiler_wrapper = join_path(spack.build_env_path, 'c++') f.write("using {0} : : {1} ;\n".format(boostToolsetId, - compiler_wrapper)) + compiler_wrapper)) if '+mpi' in spec: f.write('using mpi : %s ;\n' % diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py index 6d641da49b..a8a1a34ed4 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -24,12 +24,15 @@ ############################################################################## from spack import * from glob import glob + + class Bowtie2(Package): """Description""" homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml" - version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip") + version('2.2.5', '51fa97a862d248d7ee660efc1147c75f', + url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip") - patch('bowtie2-2.5.patch',when='@2.2.5', level=0) + patch('bowtie2-2.5.patch', when='@2.2.5', level=0) def install(self, spec, prefix): make() @@ -45,4 +48,3 @@ class Bowtie2(Package): # install('bowtie2-inspect',prefix.bin) # install('bowtie2-inspect-l',prefix.bin) # install('bowtie2-inspect-s',prefix.bin) - diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py index 216ae1ec12..4f41aba6c6 100644 --- a/var/spack/repos/builtin/packages/boxlib/package.py +++ b/var/spack/repos/builtin/packages/boxlib/package.py @@ -24,12 +24,13 @@ ############################################################################## from spack import * + class Boxlib(Package): """BoxLib, a software framework for massively parallel block-structured adaptive mesh refinement (AMR) codes.""" homepage = "https://ccse.lbl.gov/BoxLib/" - url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git"; + url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git" # TODO: figure out how best to version this. No tags in the repo! version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git') @@ -47,4 +48,3 @@ class Boxlib(Package): cmake('.', *args) make() make("install") - diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py new file mode 100644 index 0000000000..40360a03b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class BppCore(Package): + """Bio++ core library.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" + url = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz" + + version('2.2.0', '5789ed2ae8687d13664140cd77203477') + + depends_on('cmake') + + def install(self, spec, prefix): + cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py new file mode 100644 index 0000000000..62db8d5545 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class BppPhyl(Package): + """Bio++ phylogeny library.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" + url = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz" + + version('2.2.0', '5c40667ec0bf37e0ecaba321be932770') + + depends_on('cmake') + depends_on('bpp-core') + depends_on('bpp-seq') + + def install(self, spec, prefix): + cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py new file mode 100644 index 0000000000..7132c668b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class BppSeq(Package): + """Bio++ seq library.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" + url = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz" + + version('2.2.0', '44adef0ff4d5ca4e69ccf258c9270633') + + depends_on('cmake') + depends_on('bpp-core') + + def install(self, spec, prefix): + cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py new file mode 100644 index 0000000000..41e90e375d --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class BppSuite(Package): + """BppSuite is a suite of ready-to-use programs for phylogenetic and + sequence analysis.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite" + url = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz" + + version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4') + + # FIXME: Add dependencies if required. + depends_on('cmake') + depends_on('texinfo') + depends_on('bpp-core') + depends_on('bpp-seq') + depends_on('bpp-phyl') + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py new file mode 100644 index 0000000000..bb6763629b --- /dev/null +++ b/var/spack/repos/builtin/packages/bwa/package.py @@ -0,0 +1,52 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Bwa(Package): + """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.""" + + homepage = "http://github.com/lh3/bwa" + url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2" + + version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554') + + depends_on('zlib') + + def install(self, spec, prefix): + filter_file(r'^INCLUDES=', + "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile') + filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib, + 'Makefile') + make() + + mkdirp(prefix.bin) + install('bwa', join_path(prefix.bin, 'bwa')) + set_executable(join_path(prefix.bin, 'bwa')) + mkdirp(prefix.doc) + install('README.md', prefix.doc) + install('NEWS.md', prefix.doc) + mkdirp(prefix.man1) + install('bwa.1', prefix.man1) diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index 27303293d2..9e5894a6a8 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -51,15 +51,23 @@ class Bzip2(Package): kwargs = {'ignore_absent': False, 'backup': False, 'string': True} mf = FileFilter('Makefile-libbz2_so') - mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3), # NOQA ignore=E501 - '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), **kwargs) # NOQA ignore=E501 + mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)' # noqa + .format(v2, v3), + '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)' # noqa + .format(v1, v2, v3, v3), + **kwargs) - mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), # NOQA ignore=E501 - '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), **kwargs) # NOQA ignore=E501 - mf.filter('rm -f libbz2.so.{0}'.format(v2), - 'rm -f libbz2.{0}.dylib'.format(v2), **kwargs) - mf.filter('ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2), - 'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), **kwargs) # NOQA ignore=E501 + mf.filter( + '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), # noqa + '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib' + .format(v3), **kwargs) + mf.filter( + 'rm -f libbz2.so.{0}'.format(v2), + 'rm -f libbz2.{0}.dylib'.format(v2), **kwargs) + mf.filter( + 'ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2), + 'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), + **kwargs) def install(self, spec, prefix): # Build the dynamic library first @@ -73,10 +81,12 @@ class Bzip2(Package): v1, v2, v3 = (self.spec.version.up_to(i) for i in (1, 2, 3)) if 'darwin' in self.spec.architecture: lib = 'libbz2.dylib' - lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3)) # NOQA ignore=E501 + lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) + for v in (v1, v2, v3)) else: lib = 'libbz2.so' - lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3)) # NOQA ignore=E501 + lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) + for v in (v1, v2, v3)) install(lib3, join_path(prefix.lib, lib3)) with working_dir(prefix.lib): diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py index 49f9861126..4ebf3811a5 100644 --- a/var/spack/repos/builtin/packages/c-blosc/package.py +++ b/var/spack/repos/builtin/packages/c-blosc/package.py @@ -27,6 +27,7 @@ import sys from spack import * + class CBlosc(Package): """Blosc, an extremely fast, multi-threaded, meta-compressor library""" homepage = "http://www.blosc.org" diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py index 4a0fc54acc..e5aed5ed65 100644 --- a/var/spack/repos/builtin/packages/caliper/package.py +++ b/var/spack/repos/builtin/packages/caliper/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Caliper(Package): """ Caliper is a generic context annotation system. It gives programmers the @@ -44,7 +45,7 @@ class Caliper(Package): depends_on('cmake', type='build') def install(self, spec, prefix): - with working_dir('build', create=True): - cmake('..', *std_cmake_args) - make() - make("install") + with working_dir('build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py index 2f171fb9ce..f8227fa49e 100644 --- a/var/spack/repos/builtin/packages/callpath/package.py +++ b/var/spack/repos/builtin/packages/callpath/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Callpath(Package): """Library for representing callpaths consistently in distributed-memory performance tools.""" diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py index 8e4f23046b..9c9c035325 100644 --- a/var/spack/repos/builtin/packages/cantera/package.py +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -35,11 +35,16 @@ class Cantera(Package): version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa') - variant('lapack', default=True, description='Build with external BLAS/LAPACK libraries') - variant('threadsafe', default=True, description='Build threadsafe, requires Boost') - variant('sundials', default=True, description='Build with external Sundials') - variant('python', default=False, description='Build the Cantera Python module') - variant('matlab', default=False, description='Build the Cantera Matlab toolbox') + variant('lapack', default=True, + description='Build with external BLAS/LAPACK libraries') + variant('threadsafe', default=True, + description='Build threadsafe, requires Boost') + variant('sundials', default=True, + description='Build with external Sundials') + variant('python', default=False, + description='Build the Cantera Python module') + variant('matlab', default=False, + description='Build the Cantera Matlab toolbox') # Required dependencies depends_on('scons', type='build') diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py new file mode 100644 index 0000000000..67cc48ab2a --- /dev/null +++ b/var/spack/repos/builtin/packages/cask/package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +# +# Based on Homebrew's formula: +# https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb +# +from spack import * +from glob import glob + + +class Cask(Package): + """Cask is a project management tool for Emacs Lisp to automate the package + development cycle; development, dependencies, testing, building, + packaging and more.""" + homepage = "http://cask.readthedocs.io/en/latest/" + url = "https://github.com/cask/cask/archive/v0.7.4.tar.gz" + + version('0.7.4', 'c973a7db43bc980dd83759a5864a1260') + + depends_on('emacs', type=nolink) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('bin/cask', prefix.bin) + install_tree('templates', join_path(prefix, 'templates')) + for el_file in glob("*.el"): + install(el_file, prefix) + for misc_file in ['COPYING', 'cask.png', 'README.md']: + install(misc_file, prefix) + # disable cask's automatic upgrading feature + touch(join_path(prefix, ".no-upgrade")) diff --git a/var/spack/repos/builtin/packages/cblas/package.py b/var/spack/repos/builtin/packages/cblas/package.py index 0b85c5842a..0828141307 100644 --- a/var/spack/repos/builtin/packages/cblas/package.py +++ b/var/spack/repos/builtin/packages/cblas/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class Cblas(Package): """The BLAS (Basic Linear Algebra Subprograms) are routines that @@ -42,11 +42,11 @@ class Cblas(Package): def patch(self): mf = FileFilter('Makefile.in') - mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' % self.spec['blas'].prefix.lib) + mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' % + self.spec['blas'].prefix.lib) mf.filter('^CC =.*', 'CC = cc') mf.filter('^FC =.*', 'FC = f90') - def install(self, spec, prefix): make('all') mkdirp(prefix.lib) @@ -54,6 +54,5 @@ class Cblas(Package): # Rename the generated lib file to libcblas.a install('./lib/cblas_LINUX.a', '%s/libcblas.a' % prefix.lib) - install('./include/cblas.h','%s' % prefix.include) - install('./include/cblas_f77.h','%s' % prefix.include) - + install('./include/cblas.h', '%s' % prefix.include) + install('./include/cblas_f77.h', '%s' % prefix.include) diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py index 321d02b556..cbf36c3b61 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -################################################################################ +########################################################################## # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # This program is free software; you can redistribute it and/or modify it under @@ -38,20 +38,24 @@ # You should have received a copy of the GNU General Public License along with # this program; if not, write to the Free Software Foundation, Inc., 59 Temple # Place, Suite 330, Boston, MA 02111-1307 USA -################################################################################ +########################################################################## from spack import * + class CbtfArgonavis(Package): - """CBTF Argo Navis project contains the CUDA collector and supporting - libraries that was done as a result of a DOE SBIR grant.""" + """CBTF Argo Navis project contains the CUDA collector and supporting + libraries that was done as a result of a DOE SBIR grant. + + """ homepage = "http://sourceforge.net/p/cbtf/wiki/Home/" # Mirror access template example - #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/cbtf-argonavis-1.6.tar.gz" - #version('1.6', '0fafa0008478405c2c2319450f174ed4') + # url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/cbtf-argonavis-1.6.tar.gz" + # version('1.6', '0fafa0008478405c2c2319450f174ed4') - version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git') + version('1.6', branch='master', + git='https://github.com/OpenSpeedShop/cbtf-argonavis.git') depends_on("cmake@3.0.2", type='build') depends_on("boost@1.50.0:") @@ -60,17 +64,19 @@ class CbtfArgonavis(Package): depends_on("cbtf") depends_on("cbtf-krell") depends_on("cuda@6.0.37") - #depends_on("cuda") + # depends_on("cuda") parallel = False def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): - # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + # Sets build type parameters into cmakeOptions the options that will + # enable the cbtf-krell built type settings - compile_flags="-O2 -g" + compile_flags = "-O2 -g" BuildTypeOptions = [] - # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the + # stdcmakeargs for word in cmakeOptions[:]: if word.startswith('-DCMAKE_BUILD_TYPE'): cmakeOptions.remove(word) @@ -81,50 +87,54 @@ class CbtfArgonavis(Package): if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'): cmakeOptions.remove(word) BuildTypeOptions.extend([ - '-DCMAKE_VERBOSE_MAKEFILE=ON', - '-DCMAKE_BUILD_TYPE=None', - '-DCMAKE_CXX_FLAGS=%s' % compile_flags, - '-DCMAKE_C_FLAGS=%s' % compile_flags + '-DCMAKE_VERBOSE_MAKEFILE=ON', + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags ]) cmakeOptions.extend(BuildTypeOptions) - def install(self, spec, prefix): - # Look for package installation information in the cbtf and cbtf-krell prefixes - cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) - - with working_dir('CUDA'): - with working_dir('build', create=True): - - cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DCUDA_DIR=%s' % spec['cuda'].prefix, - '-DCUDA_INSTALL_PATH=%s' % spec['cuda'].prefix, - '-DCUDA_TOOLKIT_ROOT_DIR=%s' % spec['cuda'].prefix, - '-DCUPTI_DIR=%s' % join_path(spec['cuda'].prefix + '/extras/CUPTI'), - '-DCUPTI_ROOT=%s' % join_path(spec['cuda'].prefix + '/extras/CUPTI'), - '-DPAPI_ROOT=%s' % spec['papi'].prefix, - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DBoost_DIR=%s' % spec['boost'].prefix, - '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DBoost_NO_SYSTEM_PATHS=ON' - ]) - - # Add in the standard cmake arguments - cmakeOptions.extend(std_cmake_args) - - # Adjust the standard cmake arguments to what we want the build type, etc to be - self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) - - # Invoke cmake - cmake('..', *cmakeOptions) - - make("clean") - make() - make("install") + # Look for package installation information in the cbtf and cbtf-krell + # prefixes + cmake_prefix_path = join_path( + spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) + + with working_dir('CUDA'): + with working_dir('build', create=True): + + cmakeOptions = [] + cmakeOptions.extend( + ['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DCUDA_DIR=%s' % spec['cuda'].prefix, + '-DCUDA_INSTALL_PATH=%s' % spec['cuda'].prefix, + '-DCUDA_TOOLKIT_ROOT_DIR=%s' % spec['cuda'].prefix, + '-DCUPTI_DIR=%s' % join_path( + spec['cuda'].prefix + '/extras/CUPTI'), + '-DCUPTI_ROOT=%s' % join_path( + spec['cuda'].prefix + '/extras/CUPTI'), + '-DPAPI_ROOT=%s' % spec['papi'].prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DBoost_DIR=%s' % spec['boost'].prefix, + '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DBoost_NO_SYSTEM_PATHS=ON']) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build + # type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + make("clean") + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py index acb78a7395..6f15c3f835 100644 --- a/var/spack/repos/builtin/packages/cbtf-krell/package.py +++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -################################################################################ +########################################################################## # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # This program is free software; you can redistribute it and/or modify it under @@ -38,30 +38,40 @@ # You should have received a copy of the GNU General Public License along with # this program; if not, write to the Free Software Foundation, Inc., 59 Temple # Place, Suite 330, Boston, MA 02111-1307 USA -################################################################################ +########################################################################## from spack import * + class CbtfKrell(Package): - """CBTF Krell project contains the Krell Institute contributions to the CBTF project. - These contributions include many performance data collectors and support - libraries as well as some example tools that drive the data collection at - HPC levels of scale.""" + """CBTF Krell project contains the Krell Institute contributions to the + CBTF project. These contributions include many performance data + collectors and support libraries as well as some example tools + that drive the data collection at HPC levels of scale. + + """ homepage = "http://sourceforge.net/p/cbtf/wiki/Home/" # optional mirror access template - #url = "file:/home/jeg/cbtf-krell-1.6.tar.gz" - #version('1.6', 'edeb61cd488f16e7b124f77db9ce762d') + # url = "file:/home/jeg/cbtf-krell-1.6.tar.gz" + # version('1.6', 'edeb61cd488f16e7b124f77db9ce762d') - version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-krell.git') + version('1.6', branch='master', + git='https://github.com/OpenSpeedShop/cbtf-krell.git') # MPI variants - variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.") - variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.") - variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.") - variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.") - variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.") - variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") + variant('openmpi', default=False, + description="Build mpi experiment collector for openmpi MPI..") + variant('mpt', default=False, + description="Build mpi experiment collector for SGI MPT MPI.") + variant('mvapich2', default=False, + description="Build mpi experiment collector for mvapich2 MPI.") + variant('mvapich', default=False, + description="Build mpi experiment collector for mvapich MPI.") + variant('mpich2', default=False, + description="Build mpi experiment collector for mpich2 MPI.") + variant('mpich', default=False, + description="Build mpi experiment collector for mpich MPI.") # Dependencies for cbtf-krell depends_on("cmake@3.0.2", type='build') @@ -83,7 +93,8 @@ class CbtfKrell(Package): depends_on("papi") # MPI Installations - # These have not worked either for build or execution, commenting out for now + # These have not worked either for build or execution, commenting out for + # now depends_on("openmpi", when='+openmpi') depends_on("mpich", when='+mpich') depends_on("mpich2", when='+mpich2') @@ -94,11 +105,13 @@ class CbtfKrell(Package): parallel = False def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): - # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings - - compile_flags="-O2 -g" + # Sets build type parameters into cmakeOptions the options that will + # enable the cbtf-krell built type settings + + compile_flags = "-O2 -g" BuildTypeOptions = [] - # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the + # stdcmakeargs for word in cmakeOptions[:]: if word.startswith('-DCMAKE_BUILD_TYPE'): cmakeOptions.remove(word) @@ -109,75 +122,76 @@ class CbtfKrell(Package): if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'): cmakeOptions.remove(word) BuildTypeOptions.extend([ - '-DCMAKE_VERBOSE_MAKEFILE=ON', - '-DCMAKE_BUILD_TYPE=None', - '-DCMAKE_CXX_FLAGS=%s' % compile_flags, - '-DCMAKE_C_FLAGS=%s' % compile_flags + '-DCMAKE_VERBOSE_MAKEFILE=ON', + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags ]) cmakeOptions.extend(BuildTypeOptions) - - def set_mpi_cmakeOptions(self, spec, cmakeOptions): - # Appends to cmakeOptions the options that will enable the appropriate MPI implementations - + # Appends to cmakeOptions the options that will enable the appropriate + # MPI implementations + MPIOptions = [] # openmpi if '+openmpi' in spec: MPIOptions.extend([ - '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix + '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix ]) # mpich if '+mpich' in spec: MPIOptions.extend([ - '-DMPICH_DIR=%s' % spec['mpich'].prefix + '-DMPICH_DIR=%s' % spec['mpich'].prefix ]) # mpich2 if '+mpich2' in spec: MPIOptions.extend([ - '-DMPICH2_DIR=%s' % spec['mpich2'].prefix + '-DMPICH2_DIR=%s' % spec['mpich2'].prefix ]) # mvapich if '+mvapich' in spec: MPIOptions.extend([ - '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix + '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix ]) # mvapich2 if '+mvapich2' in spec: MPIOptions.extend([ - '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix + '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix ]) # mpt if '+mpt' in spec: MPIOptions.extend([ - '-DMPT_DIR=%s' % spec['mpt'].prefix + '-DMPT_DIR=%s' % spec['mpt'].prefix ]) cmakeOptions.extend(MPIOptions) def install(self, spec, prefix): - # Add in paths for finding package config files that tell us where to find these packages - #cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['dyninst'].prefix) - #'-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path + # Add in paths for finding package config files that tell us + # where to find these packages + # cmake_prefix_path = \ + # join_path(spec['cbtf'].prefix) + ':' + \ + # join_path(spec['dyninst'].prefix) + # '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path - # Build cbtf-krell with cmake + # Build cbtf-krell with cmake with working_dir('build_cbtf_krell', create=True): cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, - '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - '-DPAPI_DIR=%s' % spec['papi'].prefix, - '-DBOOST_DIR=%s' % spec['boost'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix - ]) - + cmakeOptions.extend( + ['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, + '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + '-DPAPI_DIR=%s' % spec['papi'].prefix, + '-DBOOST_DIR=%s' % spec['boost'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix]) # Add any MPI implementations coming from variant settings self.set_mpi_cmakeOptions(spec, cmakeOptions) @@ -185,9 +199,10 @@ class CbtfKrell(Package): # Add in the standard cmake arguments cmakeOptions.extend(std_cmake_args) - # Adjust the standard cmake arguments to what we want the build type, etc to be + # Adjust the standard cmake arguments to what we want the build + # type, etc to be self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) - + # Invoke cmake cmake('..', *cmakeOptions) @@ -195,56 +210,54 @@ class CbtfKrell(Package): make() make("install") - - - #if '+cray' in spec: - #if 'cray' in self.spec.architecture: + # if '+cray' in spec: + # if 'cray' in self.spec.architecture: # if '+runtime' in spec: # with working_dir('build_cbtf_cray_runtime', create=True): # python_vers='%d.%d' % spec['python'].version[:2] # cmake .. \ - # -DCMAKE_BUILD_TYPE=Debug \ - # -DTARGET_OS="cray" \ - # -DRUNTIME_ONLY="true" \ - # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \ - # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \ - # -DCBTF_DIR=${CBTF_ROOT} \ - # -DBOOST_ROOT=${BOOST_INSTALL_PREFIX} \ - # -DXERCESC_DIR=${XERCESC_INSTALL_PREFIX} \ - # -DBINUTILS_DIR=${KRELL_ROOT} \ - # -DLIBMONITOR_DIR=${KRELL_ROOT_COMPUTE} \ - # -DLIBUNWIND_DIR=${KRELL_ROOT_COMPUTE} \ - # -DPAPI_DIR=${PAPI_ROOT} \ - # -DDYNINST_DIR=${DYNINST_CN_ROOT} \ - # -DMRNET_DIR=${MRNET_INSTALL_PREFIX} \ - # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48 + # -DCMAKE_BUILD_TYPE=Debug \ + # -DTARGET_OS="cray" \ + # -DRUNTIME_ONLY="true" \ + # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \ + # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \ + # -DCBTF_DIR=${CBTF_ROOT} \ + # -DBOOST_ROOT=${BOOST_INSTALL_PREFIX} \ + # -DXERCESC_DIR=${XERCESC_INSTALL_PREFIX} \ + # -DBINUTILS_DIR=${KRELL_ROOT} \ + # -DLIBMONITOR_DIR=${KRELL_ROOT_COMPUTE} \ + # -DLIBUNWIND_DIR=${KRELL_ROOT_COMPUTE} \ + # -DPAPI_DIR=${PAPI_ROOT} \ + # -DDYNINST_DIR=${DYNINST_CN_ROOT} \ + # -DMRNET_DIR=${MRNET_INSTALL_PREFIX} \ + # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48 # else: # with working_dir('build_cbtf_cray_frontend', create=True): # python_vers='%d.%d' % spec['python'].version[:2] # cmake .. \ - # -DCMAKE_BUILD_TYPE=Debug \ - # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \ - # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \ - # -DCBTF_DIR=${CBTF_ROOT} \ - # -DRUNTIME_TARGET_OS="cray" \ - # -DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_RUNTIME_ROOT} \ - # -DCBTF_CN_RUNTIME_DIR=${CBTF_CN_RUNTIME_ROOT} \ - # -DLIBMONITOR_CN_RUNTIME_DIR=${LIBMONITOR_CN_ROOT} \ - # -DLIBUNWIND_CN_RUNTIME_DIR=${LIBUNWIND_CN_ROOT} \ - # -DPAPI_CN_RUNTIME_DIR=${PAPI_CN_ROOT} \ - # -DXERCESC_CN_RUNTIME_DIR=/${XERCESC_CN_ROOT} \ - # -DMRNET_CN_RUNTIME_DIR=${MRNET_CN_ROOT} \ - # -DBOOST_CN_RUNTIME_DIR=${BOOST_CN_ROOT} \ - # -DDYNINST_CN_RUNTIME_DIR=${DYNINST_CN_ROOT} \ - # -DBOOST_ROOT=/${KRELL_ROOT} \ - # -DXERCESC_DIR=/${KRELL_ROOT} \ - # -DBINUTILS_DIR=/${KRELL_ROOT} \ - # -DLIBMONITOR_DIR=${KRELL_ROOT} \ - # -DLIBUNWIND_DIR=${KRELL_ROOT} \ - # -DPAPI_DIR=${PAPI_ROOT} \ - # -DDYNINST_DIR=${KRELL_ROOT} \ - # -DMRNET_DIR=${KRELL_ROOT} \ - # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48 + # -DCMAKE_BUILD_TYPE=Debug \ + # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \ + # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \ + # -DCBTF_DIR=${CBTF_ROOT} \ + # -DRUNTIME_TARGET_OS="cray" \ + # -DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_RUNTIME_ROOT} \ + # -DCBTF_CN_RUNTIME_DIR=${CBTF_CN_RUNTIME_ROOT} \ + # -DLIBMONITOR_CN_RUNTIME_DIR=${LIBMONITOR_CN_ROOT} \ + # -DLIBUNWIND_CN_RUNTIME_DIR=${LIBUNWIND_CN_ROOT} \ + # -DPAPI_CN_RUNTIME_DIR=${PAPI_CN_ROOT} \ + # -DXERCESC_CN_RUNTIME_DIR=/${XERCESC_CN_ROOT} \ + # -DMRNET_CN_RUNTIME_DIR=${MRNET_CN_ROOT} \ + # -DBOOST_CN_RUNTIME_DIR=${BOOST_CN_ROOT} \ + # -DDYNINST_CN_RUNTIME_DIR=${DYNINST_CN_ROOT} \ + # -DBOOST_ROOT=/${KRELL_ROOT} \ + # -DXERCESC_DIR=/${KRELL_ROOT} \ + # -DBINUTILS_DIR=/${KRELL_ROOT} \ + # -DLIBMONITOR_DIR=${KRELL_ROOT} \ + # -DLIBUNWIND_DIR=${KRELL_ROOT} \ + # -DPAPI_DIR=${PAPI_ROOT} \ + # -DDYNINST_DIR=${KRELL_ROOT} \ + # -DMRNET_DIR=${KRELL_ROOT} \ + # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48 # fi # # make("clean") @@ -264,22 +277,22 @@ class CbtfKrell(Package): # fi # # else: -# # Build cbtf-krell with cmake +# # Build cbtf-krell with cmake # with working_dir('build_cbtf_krell', create=True): # cmake('..', # '-DCMAKE_BUILD_TYPE=Debug', -# '-DCMAKE_INSTALL_PREFIX=%s' % prefix, -# '-DCBTF_DIR=%s' % spec['cbtf'].prefix, -# '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, -# '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, -# '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, -# '-DPAPI_DIR=%s' % spec['papi'].prefix, -# '-DBOOST_DIR=%s' % spec['boost'].prefix, -# '-DMRNET_DIR=%s' % spec['mrnet'].prefix, -# '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, -# '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, -# '-DOPENMPI_DIR=%s' % openmpi_prefix_path, -# '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, +# '-DCMAKE_INSTALL_PREFIX=%s' % prefix, +# '-DCBTF_DIR=%s' % spec['cbtf'].prefix, +# '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, +# '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, +# '-DLIBUNWIND_DIR=%s'% spec['libunwind'].prefix, +# '-DPAPI_DIR=%s' % spec['papi'].prefix, +# '-DBOOST_DIR=%s' % spec['boost'].prefix, +# '-DMRNET_DIR=%s' % spec['mrnet'].prefix, +# '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, +# '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, +# '-DOPENMPI_DIR=%s' % openmpi_prefix_path, +# '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, # *std_cmake_args) # # make("clean") diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py index 5694535fcc..b614a325f9 100644 --- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py +++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -################################################################################ +########################################################################## # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # This program is free software; you can redistribute it and/or modify it under @@ -38,20 +38,22 @@ # You should have received a copy of the GNU General Public License along with # this program; if not, write to the Free Software Foundation, Inc., 59 Temple # Place, Suite 330, Boston, MA 02111-1307 USA -################################################################################ +########################################################################## from spack import * + class CbtfLanl(Package): - """CBTF LANL project contains a memory tool and data center type system command monitoring tool.""" + """CBTF LANL project contains a memory tool and data center type system + command monitoring tool.""" homepage = "http://sourceforge.net/p/cbtf/wiki/Home/" - # Mirror access template example - #url = "file:/g/g24/jeg/cbtf-lanl-1.5.tar.gz" - #version('1.5', 'c3f78f967b0a42c6734ce4be0e602426') + # url = "file:/g/g24/jeg/cbtf-lanl-1.5.tar.gz" + # version('1.5', 'c3f78f967b0a42c6734ce4be0e602426') - version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl') + version('1.6', branch='master', + git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl') depends_on("cmake@3.0.2", type='build') # Dependencies for cbtf-krell @@ -63,11 +65,13 @@ class CbtfLanl(Package): parallel = False def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): - # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + # Sets build type parameters into cmakeOptions the options that will + # enable the cbtf-krell built type settings - compile_flags="-O2 -g" + compile_flags = "-O2 -g" BuildTypeOptions = [] - # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the + # stdcmakeargs for word in cmakeOptions[:]: if word.startswith('-DCMAKE_BUILD_TYPE'): cmakeOptions.remove(word) @@ -78,40 +82,43 @@ class CbtfLanl(Package): if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'): cmakeOptions.remove(word) BuildTypeOptions.extend([ - '-DCMAKE_VERBOSE_MAKEFILE=ON', - '-DCMAKE_BUILD_TYPE=None', - '-DCMAKE_CXX_FLAGS=%s' % compile_flags, - '-DCMAKE_C_FLAGS=%s' % compile_flags + '-DCMAKE_VERBOSE_MAKEFILE=ON', + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags ]) cmakeOptions.extend(BuildTypeOptions) def install(self, spec, prefix): - # Add in paths for finding package config files that tell us where to find these packages - cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) - - with working_dir('build', create=True): - cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake') - ]) - - # Add in the standard cmake arguments - cmakeOptions.extend(std_cmake_args) - - # Adjust the standard cmake arguments to what we want the build type, etc to be - self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) - - # Invoke cmake - cmake('..', *cmakeOptions) - - make("clean") - make() - make("install") - + # Add in paths for finding package config files that tell us where to + # find these packages + cmake_prefix_path = join_path( + spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) + + with working_dir('build', create=True): + cmakeOptions = [] + cmakeOptions.extend( + ['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DCMAKE_MODULE_PATH=%s' % join_path( + prefix.share, 'KrellInstitute', 'cmake')]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build + # type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + make("clean") + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py index 017b897f3c..bc3116bf2a 100644 --- a/var/spack/repos/builtin/packages/cbtf/package.py +++ b/var/spack/repos/builtin/packages/cbtf/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -################################################################################ +########################################################################## # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # This program is free software; you can redistribute it and/or modify it under @@ -38,24 +38,30 @@ # You should have received a copy of the GNU General Public License along with # this program; if not, write to the Free Software Foundation, Inc., 59 Temple # Place, Suite 330, Boston, MA 02111-1307 USA -################################################################################ +########################################################################## from spack import * + class Cbtf(Package): - """CBTF project contains the base code for CBTF that supports creating components, - component networks and the support to connect these components and component - networks into sequential and distributed network tools.""" + """CBTF project contains the base code for CBTF that supports creating + components, component networks and the support to connect these + components and component networks into sequential and distributed + network tools. + + """ homepage = "http://sourceforge.net/p/cbtf/wiki/Home" # Mirror access template example - #url = "file:/home/jeg/cbtf-1.6.tar.gz" - #version('1.6', 'c1ef4e5aa4e470dffb042abdba0b9987') + # url = "file:/home/jeg/cbtf-1.6.tar.gz" + # version('1.6', 'c1ef4e5aa4e470dffb042abdba0b9987') # Use when the git repository is available - version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf.git') + version('1.6', branch='master', + git='https://github.com/OpenSpeedShop/cbtf.git') - variant('runtime', default=False, description="build only the runtime libraries and collectors.") + variant('runtime', default=False, + description="build only the runtime libraries and collectors.") depends_on("cmake@3.0.2", type='build') depends_on("boost@1.50.0:") @@ -67,11 +73,13 @@ class Cbtf(Package): parallel = False def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): - # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings - - compile_flags="-O2 -g" + # Sets build type parameters into cmakeOptions the options that will + # enable the cbtf-krell built type settings + + compile_flags = "-O2 -g" BuildTypeOptions = [] - # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the + # stdcmakeargs for word in cmakeOptions[:]: if word.startswith('-DCMAKE_BUILD_TYPE'): cmakeOptions.remove(word) @@ -80,61 +88,66 @@ class Cbtf(Package): if word.startswith('-DCMAKE_C_FLAGS'): cmakeOptions.remove(word) BuildTypeOptions.extend([ - '-DCMAKE_BUILD_TYPE=None', - '-DCMAKE_CXX_FLAGS=%s' % compile_flags, - '-DCMAKE_C_FLAGS=%s' % compile_flags + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags ]) cmakeOptions.extend(BuildTypeOptions) def install(self, spec, prefix): - with working_dir('build', create=True): - - # Boost_NO_SYSTEM_PATHS Set to TRUE to suppress searching - # in system paths (or other locations outside of BOOST_ROOT - # or BOOST_INCLUDEDIR). Useful when specifying BOOST_ROOT. - # Defaults to OFF. - - if '+runtime' in spec: - # Install message tag include file for use in Intel MIC cbtf-krell build - # FIXME - cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake') - ]) - - # Add in the standard cmake arguments - cmakeOptions.extend(std_cmake_args) - - # Adjust the standard cmake arguments to what we want the build type, etc to be - self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) - - # Invoke cmake - cmake('..', *cmakeOptions) - - else: - cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake') - ]) - - # Add in the standard cmake arguments - cmakeOptions.extend(std_cmake_args) - - # Adjust the standard cmake arguments to what we want the build type, etc to be - self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) - - # Invoke cmake - cmake('..', *cmakeOptions) - - make("clean") - make() - make("install") + with working_dir('build', create=True): + + # Boost_NO_SYSTEM_PATHS Set to TRUE to suppress searching + # in system paths (or other locations outside of BOOST_ROOT + # or BOOST_INCLUDEDIR). Useful when specifying BOOST_ROOT. + # Defaults to OFF. + + if '+runtime' in spec: + # Install message tag include file for use in Intel MIC + # cbtf-krell build + # FIXME + cmakeOptions = [] + cmakeOptions.extend( + ['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DCMAKE_MODULE_PATH=%s' % join_path( + prefix.share, 'KrellInstitute', 'cmake')]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build + # type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + else: + cmakeOptions = [] + cmakeOptions.extend( + ['-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + '-DCMAKE_MODULE_PATH=%s' % join_path( + prefix.share, 'KrellInstitute', 'cmake')]) + + # Add in the standard cmake arguments + cmakeOptions.extend(std_cmake_args) + + # Adjust the standard cmake arguments to what we want the build + # type, etc to be + self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) + + # Invoke cmake + cmake('..', *cmakeOptions) + + make("clean") + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index 41dc9a274b..716e0103d1 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -26,8 +26,16 @@ from spack import * import os import shutil + class Cereal(Package): - """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.""" + """cereal is a header-only C++11 serialization library. cereal takes + arbitrary data types and reversibly turns them into different + representations, such as compact binary encodings, XML, or + JSON. cereal was designed to be fast, light-weight, and easy to + extend - it has no external dependencies and can be easily bundled + with other code or used standalone. + + """ homepage = "http://uscilab.github.io/cereal/" url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz" diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py index ed49ae5808..c68b3ffc0d 100644 --- a/var/spack/repos/builtin/packages/cfitsio/package.py +++ b/var/spack/repos/builtin/packages/cfitsio/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cfitsio(Package): """ CFITSIO is a library of C and Fortran subroutines for reading and writing diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py index 5c87978339..e522b4a5a0 100644 --- a/var/spack/repos/builtin/packages/cgal/package.py +++ b/var/spack/repos/builtin/packages/cgal/package.py @@ -27,10 +27,12 @@ from spack import * class Cgal(Package): - """ - CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of - a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, - computer aided design, molecular biology, medical imaging, computer graphics, and robotics. + """CGAL is a software project that provides easy access to efficient and + reliable geometric algorithms in the form of a C++ library. CGAL + is used in various areas needing geometric computation, such as + geographic information systems, computer aided design, molecular + biology, medical imaging, computer graphics, and robotics. + """ homepage = 'http://www.cgal.org/' url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz' @@ -38,9 +40,12 @@ class Cgal(Package): version('4.7', '4826714810f3b4c65cac96b90fb03b67') version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d') - # Installation instructions : http://doc.cgal.org/latest/Manual/installation.html - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + # Installation instructions : + # http://doc.cgal.org/latest/Manual/installation.html + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds a debug version of the libraries') depends_on('boost') depends_on('mpfr') @@ -55,7 +60,8 @@ class Cgal(Package): options = [] options.extend(std_cmake_args) - # CGAL supports only Release and Debug build type. Any other build type will raise an error at configure time + # CGAL supports only Release and Debug build type. Any other build type + # will raise an error at configure time if '+debug' in spec: options.append('-DCMAKE_BUILD_TYPE:STRING=Debug') else: diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py index c5da72d25a..5a998d471c 100644 --- a/var/spack/repos/builtin/packages/cgm/package.py +++ b/var/spack/repos/builtin/packages/cgm/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cgm(Package): """The Common Geometry Module, Argonne (CGMA) is a code library which provides geometry functionality used for mesh generation and @@ -33,7 +34,7 @@ class Cgm(Package): version('13.1.1', '4e8dbc4ba8f65767b29f985f7a23b01f') version('13.1.0', 'a6c7b22660f164ce893fb974f9cb2028') - version('13.1' , '95f724bda04919fc76818a5b7bc0b4ed') + version('13.1', '95f724bda04919fc76818a5b7bc0b4ed') depends_on("mpi") @@ -42,7 +43,6 @@ class Cgm(Package): '//\1', 'geom/parallel/CGMReadParallel.cpp') - def install(self, spec, prefix): configure("--with-mpi", "--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/cityhash/package.py b/var/spack/repos/builtin/packages/cityhash/package.py index caa15780e3..d6d7f51558 100644 --- a/var/spack/repos/builtin/packages/cityhash/package.py +++ b/var/spack/repos/builtin/packages/cityhash/package.py @@ -25,16 +25,18 @@ from spack import * from spack.util.environment import * + class Cityhash(Package): homepage = "https://github.com/google/cityhash" url = "https://github.com/google/cityhash" - version('2013-07-31', git='https://github.com/google/cityhash.git', commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db') - version('master', branch='master', git='https://github.com/google/cityhash.git') + version('2013-07-31', git='https://github.com/google/cityhash.git', + commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db') + version('master', branch='master', + git='https://github.com/google/cityhash.git') def install(self, spec, prefix): configure('--enable-sse4.2', '--prefix=%s' % prefix) make() make("install") - diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py index c258e89514..61e6dca433 100644 --- a/var/spack/repos/builtin/packages/cleverleaf/package.py +++ b/var/spack/repos/builtin/packages/cleverleaf/package.py @@ -24,18 +24,21 @@ ############################################################################## from spack import * + class Cleverleaf(Package): - """ - CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive - Mesh Refinement using the SAMRAI toolkit from Lawrence Livermore National - Laboratory. The primary goal of CleverLeaf is to evaluate the application of - AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf. + """CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with + Adaptive Mesh Refinement using the SAMRAI toolkit from Lawrence + Livermore National Laboratory. The primary goal of CleverLeaf is + to evaluate the application of AMR to the Lagrangian-Eulerian + hydrodynamics scheme used by CloverLeaf. + """ homepage = "http://uk-mac.github.io/CleverLeaf/" url = "https://github.com/UK-MAC/CleverLeaf/tarball/master" - version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git', branch='develop') + version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git', + branch='develop') depends_on("SAMRAI@3.8.0:") depends_on("hdf5+mpi") diff --git a/var/spack/repos/builtin/packages/cloog/package.py b/var/spack/repos/builtin/packages/cloog/package.py index db3d2ac928..a979ae83fc 100644 --- a/var/spack/repos/builtin/packages/cloog/package.py +++ b/var/spack/repos/builtin/packages/cloog/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cloog(Package): """CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index bfb8764feb..90a7c20d19 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cmake(Package): """A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" @@ -40,10 +41,13 @@ class Cmake(Package): version('3.0.2', 'db4c687a31444a929d2fdc36c4dfb95f') version('2.8.10.2', '097278785da7182ec0aea8769d06860c') - variant('ncurses', default=True, description='Enables the build of the ncurses gui') - variant('openssl', default=True, description="Enables CMake's OpenSSL features") + variant('ncurses', default=True, + description='Enables the build of the ncurses gui') + variant('openssl', default=True, + description="Enables CMake's OpenSSL features") variant('qt', default=False, description='Enables the build of cmake-gui') - variant('doc', default=False, description='Enables the generation of html and man page documentation') + variant('doc', default=False, + description='Enables the generation of html and man page docs') depends_on('ncurses', when='+ncurses') depends_on('openssl', when='+openssl') @@ -53,7 +57,8 @@ class Cmake(Package): def url_for_version(self, version): """Handle CMake's version-based custom URLs.""" - return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version) + return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % ( + version.up_to(2), version) def validate(self, spec): """ diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py index aa2b3cc3bb..274b78379a 100644 --- a/var/spack/repos/builtin/packages/cmocka/package.py +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cmocka(Package): """Unit-testing framework in pure C""" homepage = "https://cmocka.org/" @@ -36,7 +37,7 @@ class Cmocka(Package): def install(self, spec, prefix): with working_dir('spack-build', create=True): - cmake('..', *std_cmake_args) + cmake('..', *std_cmake_args) - make() - make("install") + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py index f4c05f5b5f..0c62023952 100644 --- a/var/spack/repos/builtin/packages/cnmem/package.py +++ b/var/spack/repos/builtin/packages/cnmem/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cnmem(Package): """CNMem mempool for CUDA devices""" homepage = "https://github.com/NVIDIA/cnmem" @@ -31,6 +32,6 @@ class Cnmem(Package): version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master") def install(self, spec, prefix): - cmake('.',*std_cmake_args) - make() - make('install') + cmake('.', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py index cb8f596b41..94cfa11341 100644 --- a/var/spack/repos/builtin/packages/coreutils/package.py +++ b/var/spack/repos/builtin/packages/coreutils/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Coreutils(Package): """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py new file mode 100644 index 0000000000..5f59286323 --- /dev/null +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -0,0 +1,178 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import os +import shutil +import copy + +from spack import * + + +class Cp2k(Package): + """CP2K is a quantum chemistry and solid state physics software package + that can perform atomistic simulations of solid state, liquid, molecular, + periodic, material, crystal, and biological systems + """ + homepage = 'https://www.cp2k.org' + url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2' + + version('3.0', 'c05bc47335f68597a310b1ed75601d35') + + variant('mpi', default=True, description='Enable MPI support') + variant('plumed', default=False, description='Enable PLUMED support') + + depends_on('python') # Build dependency + + depends_on('lapack') + depends_on('blas') + depends_on('fftw') + + depends_on('mpi', when='+mpi') + depends_on('scalapack', when='+mpi') + depends_on('plumed+shared+mpi', when='+plumed+mpi') + depends_on('plumed+shared~mpi', when='+plumed~mpi') + + # TODO : add dependency on libint + # TODO : add dependency on libsmm, libxsmm + # TODO : add dependency on elpa + # TODO : add dependency on CUDA + # TODO : add dependency on PEXSI + # TODO : add dependency on QUIP + # TODO : add dependency on libwannier90 + + parallel = False + + def install(self, spec, prefix): + # Construct a proper filename for the architecture file + cp2k_architecture = '{0.architecture}-{0.compiler.name}'.format(spec) + cp2k_version = 'sopt' if '~mpi' in spec else 'popt' + makefile_basename = '.'.join([cp2k_architecture, cp2k_version]) + makefile = join_path('arch', makefile_basename) + + # Write the custom makefile + with open(makefile, 'w') as mkf: + # Optimization flags + optflags = { + 'gcc': ['-O2', + '-ffast-math', + '-ffree-form', + '-ffree-line-length-none', + '-ftree-vectorize', + '-funroll-loops', + '-mtune=native'], + 'intel': ['-O2', + '-pc64', + '-unroll', + '-heap-arrays 64'] + } + cppflags = [ + '-D__FFTW3', + '-I' + spec['fftw'].prefix.include + ] + fcflags = copy.deepcopy(optflags[self.spec.compiler.name]) + fcflags.extend([ + '-I' + spec['fftw'].prefix.include + ]) + ldflags = ['-L' + spec['fftw'].prefix.lib] + libs = [] + if '+plumed' in self.spec: + # Include Plumed.inc in the Makefile + mkf.write('include {0}\n'.format( + join_path(self.spec['plumed'].prefix.lib, + 'plumed', + 'src', + 'lib', + 'Plumed.inc') + )) + # Add required macro + cppflags.extend(['-D__PLUMED2']) + libs.extend([ + join_path(self.spec['plumed'].prefix.lib, 'libplumed.so') + ]) + + mkf.write('CC = {0.compiler.cc}\n'.format(self)) + if '%intel' in self.spec: + # CPP is a commented command in Intel arch of CP2K + # This is the hack through which cp2k developers avoid doing : + # + # ${CPP} <file>.F > <file>.f90 + # + # and use `-fpp` instead + mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self)) + mkf.write('AR = xiar -r\n') + else: + mkf.write('CPP = {0.compiler.cc} -E\n'.format(self)) + mkf.write('AR = ar -r\n') + fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc + mkf.write('FC = {0}\n'.format(fc)) + mkf.write('LD = {0}\n'.format(fc)) + # Intel + if '%intel' in self.spec: + cppflags.extend([ + '-D__INTEL_COMPILER', + '-D__MKL' + ]) + fcflags.extend([ + '-diag-disable 8290,8291,10010,10212,11060', + '-free', + '-fpp' + ]) + # MPI + if '+mpi' in self.spec: + cppflags.extend([ + '-D__parallel', + '-D__SCALAPACK' + ]) + ldflags.extend([ + '-L' + spec['scalapack'].prefix.lib + ]) + libs.extend(spec['scalapack'].scalapack_shared_libs) + + # LAPACK / BLAS + ldflags.extend([ + '-L' + spec['lapack'].prefix.lib, + '-L' + spec['blas'].prefix.lib + ]) + libs.extend([ + join_path(spec['fftw'].prefix.lib, 'libfftw3.so'), + spec['lapack'].lapack_shared_lib, + spec['blas'].blas_shared_lib + ]) + + # Write compiler flags to file + mkf.write('CPPFLAGS = {0}\n'.format(' '.join(cppflags))) + mkf.write('FCFLAGS = {0}\n'.format(' '.join(fcflags))) + mkf.write('LDFLAGS = {0}\n'.format(' '.join(ldflags))) + mkf.write('LIBS = {0}\n'.format(' '.join(libs))) + + with working_dir('makefiles'): + # Apparently the Makefile bases its paths on PWD + # so we need to set PWD = os.getcwd() + pwd_backup = env['PWD'] + env['PWD'] = os.getcwd() + make('ARCH={0}'.format(cp2k_architecture), + 'VERSION={0}'.format(cp2k_version)) + env['PWD'] = pwd_backup + exe_dir = join_path('exe', cp2k_architecture) + shutil.copytree(exe_dir, self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/cppcheck/package.py b/var/spack/repos/builtin/packages/cppcheck/package.py index 16f052ef2f..fd48fcb7e3 100644 --- a/var/spack/repos/builtin/packages/cppcheck/package.py +++ b/var/spack/repos/builtin/packages/cppcheck/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cppcheck(Package): """A tool for static C/C++ code analysis.""" homepage = "http://cppcheck.sourceforge.net/" diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py index 283bc5adea..bef26cdcbd 100644 --- a/var/spack/repos/builtin/packages/cram/package.py +++ b/var/spack/repos/builtin/packages/cram/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cram(Package): """Cram runs many small MPI jobs inside one large MPI job.""" homepage = "https://github.com/llnl/cram" diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 77895a7331..e9294a14a6 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -25,12 +25,15 @@ import glob from spack import * + class Cryptopp(Package): """Crypto++ is an open-source C++ library of cryptographic schemes. The - library supports a number of different cryptography algorithms, including - authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2), - public-key encryption (RSA, DSA), and a few obsolete/historical encryption - algorithms (MD5, Panama).""" + library supports a number of different cryptography algorithms, + including authenticated encryption schemes (GCM, CCM), hash + functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a + few obsolete/historical encryption algorithms (MD5, Panama). + + """ homepage = "http://www.cryptopp.com" base_url = "http://www.cryptopp.com" diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py index 88d522f486..f21226cce1 100644 --- a/var/spack/repos/builtin/packages/cscope/package.py +++ b/var/spack/repos/builtin/packages/cscope/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Cscope(Package): """Cscope is a developer's tool for browsing source code.""" homepage = "http://http://cscope.sourceforge.net/" diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py index 40c2cc6893..09237f87c3 100644 --- a/var/spack/repos/builtin/packages/cube/package.py +++ b/var/spack/repos/builtin/packages/cube/package.py @@ -28,8 +28,8 @@ from spack import * class Cube(Package): """ - Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space - consisting of the dimensions: + Cube the profile viewer for Score-P and Scalasca profiles. It displays a + multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource @@ -38,14 +38,17 @@ class Cube(Package): homepage = "http://www.scalasca.org/software/cube-4.x/download.html" url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz" + version('4.3.4', '50f73060f55311cb12c5b3cb354d59fa', + url='http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.4.tar.gz') version('4.3.3', '07e109248ed8ffc7bdcce614264a2909', url='http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.3.tar.gz') - version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20', url="http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz") # TODO : add variant that builds GUI on top of Qt + depends_on('zlib') + def install(self, spec, prefix): configure_args = ["--prefix=%s" % prefix, "--without-paraver", diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py index 96694670ad..558535bec6 100644 --- a/var/spack/repos/builtin/packages/cuda/package.py +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -26,22 +26,27 @@ from spack import * from glob import glob import os + class Cuda(Package): - """CUDA is a parallel computing platform and programming model invented by - NVIDIA. It enables dramatic increases in computing performance by harnessing - the power of the graphics processing unit (GPU). + """CUDA is a parallel computing platform and programming model invented + by NVIDIA. It enables dramatic increases in computing performance by + harnessing the power of the graphics processing unit (GPU). + + Note: NVIDIA does not provide a download URL for CUDA so you will + need to download it yourself. Go to + https://developer.nvidia.com/cuda-downloads and select your Operating + System, Architecture, Distribution, and Version. For the Installer + Type, select runfile and click Download. Spack will search your + current directory for this file. Alternatively, add this file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://software.llnl.gov/spack/mirrors.html - Note: NVIDIA does not provide a download URL for CUDA so you will need to - download it yourself. Go to https://developer.nvidia.com/cuda-downloads - and select your Operating System, Architecture, Distribution, and Version. - For the Installer Type, select runfile and click Download. Spack will search - your current directory for this file. Alternatively, add this file to a - mirror so that Spack can find it. For instructions on how to set up a mirror, - see http://software.llnl.gov/spack/mirrors.html + Note: This package does not currently install the drivers necessary + to run CUDA. These will need to be installed manually. See: + http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for + details. - Note: This package does not currently install the drivers necessary to run - CUDA. These will need to be installed manually. See: - http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details.""" + """ homepage = "http://www.nvidia.com/object/cuda_home_new.html" @@ -50,15 +55,15 @@ class Cuda(Package): version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False, url="file://%s/cuda_6.5.14_linux_64.run" % os.getcwd()) - def install(self, spec, prefix): runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0] chmod = which('chmod') chmod('+x', runfile) runfile = which(runfile) - # Note: NVIDIA does not officially support many newer versions of compilers. - # For example, on CentOS 6, you must use GCC 4.4.7 or older. See: + # Note: NVIDIA does not officially support many newer versions of + # compilers. For example, on CentOS 6, you must use GCC 4.4.7 or + # older. See: # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements # for details. @@ -68,4 +73,3 @@ class Cuda(Package): '--toolkit', # install CUDA Toolkit '--toolkitpath=%s' % prefix ) - diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 79570205fa..4954e435c0 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -32,6 +32,7 @@ class Curl(Package): homepage = "http://curl.haxx.se" url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2" + version('7.50.1', '015f6a0217ca6f2c5442ca406476920b') version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab') version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148') diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index a251a94470..ef6374619b 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -25,12 +25,14 @@ from spack import * import os + class Czmq(Package): """ A C interface to the ZMQ library """ homepage = "http://czmq.zeromq.org" url = "https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz" - version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz') + version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', + url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz') depends_on('libtool', type='build') depends_on('automake', type='build') @@ -39,19 +41,21 @@ class Czmq(Package): depends_on('zeromq') def install(self, spec, prefix): - bash = which("bash") # Work around autogen.sh oddities + # bash = which("bash") # bash("./autogen.sh") mkdirp("config") autoreconf = which("autoreconf") autoreconf("--install", "--verbose", "--force", - "-I", "config", - "-I", os.path.join(spec['pkg-config'].prefix, "share", "aclocal"), - "-I", os.path.join(spec['automake'].prefix, "share", "aclocal"), - "-I", os.path.join(spec['libtool'].prefix, "share", "aclocal"), - ) + "-I", "config", + "-I", os.path.join(spec['pkg-config'].prefix, + "share", "aclocal"), + "-I", os.path.join(spec['automake'].prefix, + "share", "aclocal"), + "-I", os.path.join(spec['libtool'].prefix, + "share", "aclocal"), + ) configure("--prefix=%s" % prefix) make() make("install") - diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py index d0d22d9728..e8f7d0889b 100644 --- a/var/spack/repos/builtin/packages/dakota/package.py +++ b/var/spack/repos/builtin/packages/dakota/package.py @@ -26,17 +26,22 @@ from spack import * class Dakota(Package): - """ - The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems - analysis methods. Dakota contains algorithms for: + """The Dakota toolkit provides a flexible, extensible interface between + analysis codes and iterative systems analysis methods. Dakota + contains algorithms for: - optimization with gradient and non gradient-based methods; - - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; + - uncertainty quantification with sampling, reliability, stochastic + - expansion, and epistemic methods; - parameter estimation with nonlinear least squares methods; - - sensitivity/variance analysis with design of experiments and parameter study methods. + - sensitivity/variance analysis with design of experiments and + - parameter study methods. + + These capabilities may be used on their own or as components within + advanced strategies such as hybrid optimization, surrogate-based + optimization, mixed integer nonlinear programming, or optimization + under uncertainty. - These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, - surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. """ homepage = 'https://dakota.sandia.gov/' @@ -45,8 +50,10 @@ class Dakota(Package): version('6.3', '05a58d209fae604af234c894c3f73f6d') - variant('debug', default=False, description='Builds a debug version of the libraries') - variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds a debug version of the libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') variant('mpi', default=True, description='Activates MPI support') depends_on('blas') @@ -64,12 +71,17 @@ class Dakota(Package): options = [] options.extend(std_cmake_args) - options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), - '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF')]) + options.extend([ + '-DCMAKE_BUILD_TYPE:STRING=%s' % ( + 'Debug' if '+debug' in spec else 'Release'), + '-DBUILD_SHARED_LIBS:BOOL=%s' % ( + 'ON' if '+shared' in spec else 'OFF')]) if '+mpi' in spec: - options.extend(['-DDAKOTA_HAVE_MPI:BOOL=ON', - '-DMPI_CXX_COMPILER:STRING=%s' % join_path(spec['mpi'].prefix.bin, 'mpicxx')]) + options.extend([ + '-DDAKOTA_HAVE_MPI:BOOL=ON', + '-DMPI_CXX_COMPILER:STRING=%s' % join_path( + spec['mpi'].prefix.bin, 'mpicxx')]) build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py index 427997072c..a37728c92b 100644 --- a/var/spack/repos/builtin/packages/damselfly/package.py +++ b/var/spack/repos/builtin/packages/damselfly/package.py @@ -24,17 +24,19 @@ ############################################################################## from spack import * + class Damselfly(Package): """Damselfly is a model-based parallel network simulator.""" homepage = "https://github.com/llnl/damselfly" url = "https://github.com/llnl/damselfly" - version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895', git='https://github.com/llnl/damselfly.git', tag='v1.0') + version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895', + git='https://github.com/llnl/damselfly.git', tag='v1.0') depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): - cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args) - make() - make('install') + cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index 130ba2ea1f..fdca68f53f 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Dbus(Package): """D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 54604d351f..939d8fc013 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -40,25 +40,48 @@ class Dealii(Package): version('develop', git='https://github.com/dealii/dealii.git') variant('mpi', default=True, description='Compile with MPI') - variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') - variant('doc', default=False, description='Compile with documentation') + variant('arpack', default=True, + description='Compile with Arpack and PArpack (only with MPI)') + variant('doc', default=False, + description='Compile with documentation') variant('gsl', default=True, description='Compile with GSL') - variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)') + variant('hdf5', default=True, + description='Compile with HDF5 (only with MPI)') variant('metis', default=True, description='Compile with Metis') - variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)') + variant('netcdf', default=True, + description='Compile with Netcdf (only with MPI)') variant('oce', default=True, description='Compile with OCE') - variant('p4est', default=True, description='Compile with P4est (only with MPI)') - variant('petsc', default=True, description='Compile with Petsc (only with MPI)') - variant('slepc', default=True, description='Compile with Slepc (only with Petsc and MPI)') - variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)') + variant('p4est', default=True, + description='Compile with P4est (only with MPI)') + variant('petsc', default=True, + description='Compile with Petsc (only with MPI)') + variant('slepc', default=True, + description='Compile with Slepc (only with Petsc and MPI)') + variant('trilinos', default=True, + description='Compile with Trilinos (only with MPI)') + variant('python', default=True, + description='Compile with Python bindings') # required dependencies, light version depends_on("blas") # Boost 1.58 is blacklisted, see # https://github.com/dealii/dealii/issues/1591 # Require at least 1.59 - depends_on("boost@1.59.0:+thread+system+serialization+iostreams", when='~mpi') # NOQA: ignore=E501 - depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi') # NOQA: ignore=E501 + # +python won't affect @:8.4.1 + depends_on("boost@1.59.0:+thread+system+serialization+iostreams", + when='@:8.4.1~mpi') + depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi", + when='@:8.4.1+mpi') + # since @8.5.0: (and @develop) python bindings are introduced: + depends_on("boost@1.59.0:+thread+system+serialization+iostreams", + when='@8.5.0:~mpi~python') + depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi", + when='@8.5.0:+mpi~python') + depends_on("boost@1.59.0:+thread+system+serialization+iostreams+python", + when='@8.5.0:~mpi+python') + depends_on( + "boost@1.59.0:+thread+system+serialization+iostreams+mpi+python", + when='@8.5.0:+mpi+python') depends_on("bzip2") depends_on("cmake", type='build') depends_on("lapack") @@ -120,6 +143,12 @@ class Dealii(Package): '-DZLIB_DIR=%s' % spec['zlib'].prefix ]) + if spec.satisfies('@8.5.0:'): + options.extend([ + '-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' % + ('ON' if '+python' in spec else 'OFF') + ]) + # Set directory structure: if spec.satisfies('@:8.2.1'): options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF']) @@ -145,7 +174,8 @@ class Dealii(Package): # Optional dependencies for which librariy names are the same as CMake # variables: - for library in ('gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'): # NOQA: ignore=E501 + for library in ( + 'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'): if library in spec: options.extend([ '-D%s_DIR=%s' % (library.upper(), spec[library].prefix), @@ -276,15 +306,20 @@ class Dealii(Package): print('=== Step-40 Trilinos SuperluDist ====') print('=====================================') # change to direct solvers - filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 - filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', - (''), 'step-40.cc') - filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 - (''), 'step-40.cc') - filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 - (''), 'step-40.cc') - filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 - filter_file(r'(preconditioner\);)', (''), 'step-40.cc') + filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # noqa + filter_file( + r'(LA::MPI::PreconditionAMG preconditioner;)', + (''), 'step-40.cc') + filter_file( + r'(LA::MPI::PreconditionAMG::AdditionalData data;)', + (''), 'step-40.cc') + filter_file( + r'(preconditioner.initialize\(system_matrix, data\);)', + (''), 'step-40.cc') + filter_file( + r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # noqa + filter_file( + r'(preconditioner\);)', (''), 'step-40.cc') if '^trilinos+superlu-dist' in spec: make('release') make('run', paralle=False) diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py index 1685f0009f..94cd75656d 100644 --- a/var/spack/repos/builtin/packages/dia/package.py +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Dia(Package): """Dia is a program for drawing structured diagrams.""" homepage = 'https://wiki.gnome.org/Apps/Dia' @@ -34,7 +35,7 @@ class Dia(Package): depends_on('intltool', type='build') depends_on('gtkplus@2.6.0:') depends_on('cairo') - #depends_on('libart') # optional dependency, not yet supported by spack. + # depends_on('libart') # optional dependency, not yet supported by spack. depends_on('libpng') depends_on('libxslt') depends_on('python') diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index 267ba61756..f29110ac1d 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -24,8 +24,6 @@ ############################################################################## from spack import * -import sys - class Doxygen(Package): """Doxygen is the de facto standard tool for generating documentation @@ -41,7 +39,8 @@ class Doxygen(Package): version('1.8.10', '79767ccd986f12a0f949015efb5f058f') # graphviz appears to be a run-time optional dependency - variant('graphviz', default=True, description='Build with dot command support from Graphviz.') # NOQA: ignore=E501 + variant('graphviz', default=True, + description='Build with dot command support from Graphviz.') depends_on("cmake@2.8.12:", type='build') depends_on("flex", type='build') diff --git a/var/spack/repos/builtin/packages/dri2proto/package.py b/var/spack/repos/builtin/packages/dri2proto/package.py index 25ea783c0c..65b86714f1 100644 --- a/var/spack/repos/builtin/packages/dri2proto/package.py +++ b/var/spack/repos/builtin/packages/dri2proto/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Dri2proto(Package): """DRI2 Protocol Headers.""" homepage = "http://http://cgit.freedesktop.org/xorg/proto/dri2proto/" diff --git a/var/spack/repos/builtin/packages/dtcmp/package.py b/var/spack/repos/builtin/packages/dtcmp/package.py index b50b2ae3ae..e59e246d47 100644 --- a/var/spack/repos/builtin/packages/dtcmp/package.py +++ b/var/spack/repos/builtin/packages/dtcmp/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Dtcmp(Package): """The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPI applications.""" diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py index efe4de4abf..90c83bdc3a 100644 --- a/var/spack/repos/builtin/packages/dyninst/package.py +++ b/var/spack/repos/builtin/packages/dyninst/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Dyninst(Package): """API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.""" @@ -55,16 +56,18 @@ class Dyninst(Package): '-DBoost_INCLUDE_DIR=%s' % spec['boost'].prefix.include, '-DBoost_LIBRARY_DIR=%s' % spec['boost'].prefix.lib, '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DLIBELF_INCLUDE_DIR=%s' % join_path(libelf.include, 'libelf'), - '-DLIBELF_LIBRARIES=%s' % join_path(libelf.lib, 'libelf.so'), + '-DLIBELF_INCLUDE_DIR=%s' % join_path( + libelf.include, 'libelf'), + '-DLIBELF_LIBRARIES=%s' % join_path( + libelf.lib, 'libelf.so'), '-DLIBDWARF_INCLUDE_DIR=%s' % libdwarf.include, - '-DLIBDWARF_LIBRARIES=%s' % join_path(libdwarf.lib, 'libdwarf.so'), + '-DLIBDWARF_LIBRARIES=%s' % join_path( + libdwarf.lib, 'libdwarf.so'), *std_cmake_args) make() make("install") - @when('@:8.1') def install(self, spec, prefix): configure("--prefix=" + prefix) diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 97343f499b..36d6850c1a 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -22,7 +22,6 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## - from spack import * @@ -36,15 +35,19 @@ class Eigen(Package): homepage = 'http://eigen.tuxfamily.org/' url = 'http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2' - version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184', url='http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2') + version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184', + url='http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2') - variant('debug', default=False, description='Builds the library in debug mode') + variant('debug', default=False, + description='Builds the library in debug mode') variant('metis', default=True, description='Enables metis backend') variant('scotch', default=True, description='Enables scotch backend') variant('fftw', default=True, description='Enables FFTW backend') - variant('suitesparse', default=True, description='Enables SuiteSparse support') - variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr') + variant('suitesparse', default=True, + description='Enables SuiteSparse support') + variant('mpfr', default=True, + description='Enables support for multi-precisions FP via mpfr') # TODO : dependency on googlehash, superlu, adolc missing depends_on('cmake', type='build') diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py index ecb5759ddc..ef8c2433c9 100644 --- a/var/spack/repos/builtin/packages/elfutils/package.py +++ b/var/spack/repos/builtin/packages/elfutils/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Elfutils(Package): """elfutils is a collection of various binary tools such as eu-objdump, eu-readelf, and other utilities that allow you to @@ -47,4 +48,3 @@ class Elfutils(Package): configure('--prefix=%s' % prefix, '--enable-maintainer-mode') make() make("install") - diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py index ae81422495..f28d63f6c3 100644 --- a/var/spack/repos/builtin/packages/elpa/package.py +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -34,7 +34,8 @@ class Elpa(Package): homepage = 'http://elpa.mpcdf.mpg.de/' url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz' - version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6', url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz') + version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6', + url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz') variant('openmp', default=False, description='Activates OpenMP support') diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py index a9ebd6d42f..94d42a3c9f 100644 --- a/var/spack/repos/builtin/packages/emacs/package.py +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -35,7 +35,8 @@ class Emacs(Package): version('24.5', 'd74b597503a68105e61b5b9f6d065b44') variant('X', default=True, description="Enable a X toolkit (GTK+)") - variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)") + variant('gtkplus', default=False, + description="Enable a GTK+ as X toolkit (ignored if ~X)") depends_on('ncurses') depends_on('libtiff', when='+X') diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py index 5d5bb3be02..85594bab47 100644 --- a/var/spack/repos/builtin/packages/environment-modules/package.py +++ b/var/spack/repos/builtin/packages/environment-modules/package.py @@ -46,17 +46,18 @@ class EnvironmentModules(Package): "--without-tclx", "--with-tclx-ver=0.0", "--prefix=%s" % prefix, - "--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'), # It looks for tclConfig.sh - "--with-tcl-ver=%d.%d" % (tcl_spec.version.version[0], tcl_spec.version.version[1]), + # It looks for tclConfig.sh + "--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'), + "--with-tcl-ver=%d.%d" % (tcl_spec.version.version[ + 0], tcl_spec.version.version[1]), '--disable-debug', '--disable-dependency-tracking', '--disable-silent-rules', - '--disable-versioning', + '--disable-versioning', '--datarootdir=%s' % prefix.share, 'CPPFLAGS=%s' % ' '.join(CPPFLAGS) ] - configure(*config_args) make() make('install') diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py index eb6c23afeb..15fe1e89a6 100644 --- a/var/spack/repos/builtin/packages/exodusii/package.py +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -32,17 +32,22 @@ from spack import * # TODO: Create installation options for NetCDF that support larger page size # TODO: suggested by Exodus (see the repository "README" file). + class Exodusii(Package): - """Exodus II is a C++/Fortran library developed to store and retrieve data for - finite element analyses. It's used for preprocessing (problem definition), - postprocessing (results visualization), and data transfer between codes. - An Exodus II data file is a random access, machine independent, binary - file that is written and read via C, C++, or Fortran API routines.""" + """Exodus II is a C++/Fortran library developed to store and retrieve + data for finite element analyses. It's used for preprocessing + (problem definition), postprocessing (results visualization), and + data transfer between codes. An Exodus II data file is a random + access, machine independent, binary file that is written and read + via C, C++, or Fortran API routines. + + """ homepage = "https://github.com/gsjaardema/seacas" url = "https://github.com/gsjaardema/seacas/archive/master.zip" - version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529') + version('2016-02-08', + git='https://github.com/gsjaardema/seacas.git', commit='dcf3529') depends_on('cmake@2.8.7:', type='build') depends_on('hdf5~shared~mpi') @@ -54,11 +59,14 @@ class Exodusii(Package): ff = FileFilter('cmake-exodus') ff.filter('CMAKE_INSTALL_PREFIX:PATH=${ACCESS}', - 'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix, string=True) + 'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix, + string=True) ff.filter('NetCDF_DIR:PATH=${TPL}', - 'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix, string=True) + 'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix, + string=True) ff.filter('HDF5_ROOT:PATH=${TPL}', - 'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix, string=True) + 'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix, + string=True) def install(self, spec, prefix): mkdirp('build') diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py new file mode 100644 index 0000000000..7921e64058 --- /dev/null +++ b/var/spack/repos/builtin/packages/exonerate/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Exonerate(Package): + """Pairwise sequence alignment of DNA and proteins""" + + homepage = "http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" + url = "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz" + + version('2.4.0', '126fbade003b80b663a1d530c56f1904') + + depends_on('pkg-config', type="build") + depends_on('glib') + + parallel = False + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), '--disable-debug', + '--disable-dependency-tracking') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 2a9ac123f3..7d0fdae1d4 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Expat(Package): """<eXpat/> is an XML parser library written in C""" homepage = "http://expat.sourceforge.net/" @@ -39,4 +40,3 @@ class Expat(Package): cmake('..', *std_cmake_args) make() make('install') - diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py index 84c410e4ba..72bfbe6326 100644 --- a/var/spack/repos/builtin/packages/extrae/package.py +++ b/var/spack/repos/builtin/packages/extrae/package.py @@ -25,7 +25,23 @@ from spack import * # typical working line with extrae 3.0.1 -# ./configure --prefix=/usr/local --with-mpi=/usr/lib64/mpi/gcc/openmpi --with-unwind=/usr/local --with-papi=/usr --with-dwarf=/usr --with-elf=/usr --with-dyninst=/usr --with-binutils=/usr --with-xml-prefix=/usr --enable-openmp --enable-nanos --enable-pthread --disable-parallel-merge LDFLAGS=-pthread +# ./configure +# --prefix=/usr/local +# --with-mpi=/usr/lib64/mpi/gcc/openmpi +# --with-unwind=/usr/local +# --with-papi=/usr +# --with-dwarf=/usr +# --with-elf=/usr +# --with-dyninst=/usr +# --with-binutils=/usr +# --with-xml-prefix=/usr +# --enable-openmp +# --enable-nanos +# --enable-pthread +# --disable-parallel-merge +# +# LDFLAGS=-pthread + class Extrae(Package): """Extrae is the package devoted to generate tracefiles which can @@ -55,16 +71,16 @@ class Extrae(Package): elif 'mvapich2' in spec: mpi = spec['mvapich2'] - configure("--prefix=%s" % prefix, - "--with-mpi=%s" % mpi.prefix, - "--with-unwind=%s" % spec['libunwind'].prefix, - "--with-dyninst=%s" % spec['dyninst'].prefix, - "--with-boost=%s" % spec['boost'].prefix, - "--with-dwarf=%s" % spec['libdwarf'].prefix, - "--with-papi=%s" % spec['papi'].prefix, - "--with-dyninst-headers=%s" % spec['dyninst'].prefix.include, - "--with-dyninst-libs=%s" % spec['dyninst'].prefix.lib) + configure("--prefix=%s" % prefix, + "--with-mpi=%s" % mpi.prefix, + "--with-unwind=%s" % spec['libunwind'].prefix, + "--with-dyninst=%s" % spec['dyninst'].prefix, + "--with-boost=%s" % spec['boost'].prefix, + "--with-dwarf=%s" % spec['libdwarf'].prefix, + "--with-papi=%s" % spec['papi'].prefix, + "--with-dyninst-headers=%s" % spec[ + 'dyninst'].prefix.include, + "--with-dyninst-libs=%s" % spec['dyninst'].prefix.lib) make() make("install", parallel=False) - diff --git a/var/spack/repos/builtin/packages/exuberant-ctags/package.py b/var/spack/repos/builtin/packages/exuberant-ctags/package.py index c49d0624f6..10be30ab8b 100644 --- a/var/spack/repos/builtin/packages/exuberant-ctags/package.py +++ b/var/spack/repos/builtin/packages/exuberant-ctags/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class ExuberantCtags(Package): """The canonical ctags generator""" homepage = "ctags.sourceforge.net" diff --git a/var/spack/repos/builtin/packages/fastx_toolkit/package.py b/var/spack/repos/builtin/packages/fastx_toolkit/package.py new file mode 100644 index 0000000000..04b4d24b39 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastx_toolkit/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class FastxToolkit(Package): + """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + + homepage = "http://hannonlab.cshl.edu/fastx_toolkit/" + url = "https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2" + + version('0.0.14', 'bf1993c898626bb147de3d6695c20b40') + + depends_on('libgtextutils') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py index 465ab651be..eeeefc540d 100644 --- a/var/spack/repos/builtin/packages/fenics/package.py +++ b/var/spack/repos/builtin/packages/fenics/package.py @@ -36,7 +36,7 @@ class Fenics(Package): homepage = "http://fenicsproject.org/" url = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz" - base_url = "https://bitbucket.org/fenics-project/{pkg}/downloads/{pkg}-{version}.tar.gz" # NOQA: ignore E501 + base_url = "https://bitbucket.org/fenics-project/{pkg}/downloads/{pkg}-{version}.tar.gz" variant('hdf5', default=True, description='Compile with HDF5') variant('parmetis', default=True, description='Compile with ParMETIS') @@ -44,13 +44,18 @@ class Fenics(Package): variant('petsc', default=True, description='Compile with PETSc') variant('slepc', default=True, description='Compile with SLEPc') variant('trilinos', default=True, description='Compile with Trilinos') - variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') + variant('suite-sparse', default=True, + description='Compile with SuiteSparse solvers') variant('vtk', default=False, description='Compile with VTK') variant('qt', default=False, description='Compile with QT') - variant('mpi', default=True, description='Enables the distributed memory support') - variant('openmp', default=True, description='Enables the shared memory support') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('mpi', default=True, + description='Enables the distributed memory support') + variant('openmp', default=True, + description='Enables the shared memory support') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds a debug version of the libraries') # not part of spack list for now # variant('petsc4py', default=True, description='Uses PETSc4py') @@ -109,7 +114,8 @@ class Fenics(Package): ] for release in releases: - version(release['version'], release['md5'], url=base_url.format(pkg='dolfin', version=release['version'])) + version(release['version'], release['md5'], url=base_url.format( + pkg='dolfin', version=release['version'])) for name, md5 in release['resources'].items(): resource(name=name, url=base_url.format(pkg=name, **release), diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index 434aeea616..570cd1bbdd 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -28,26 +28,36 @@ from spack import * class Fftw(Package): - """ - FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of - arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine - transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for - most applications. + """FFTW is a C subroutine library for computing the discrete Fourier + transform (DFT) in one or more dimensions, of arbitrary input + size, and of both real and complex data (as well as of even/odd + data, i.e. the discrete cosine/sine transforms or DCT/DST). We + believe that FFTW, which is free software, should become the FFT + library of choice for most applications. + """ homepage = "http://www.fftw.org" url = "http://www.fftw.org/fftw-3.3.4.tar.gz" version('3.3.4', '2edab8c06b24feeb3b82bbb3ebf3e7b3') - variant('float', default=True, description='Produces a single precision version of the library') - variant('long_double', default=True, description='Produces a long double precision version of the library') - variant('quad', default=False, description='Produces a quad precision version of the library (works only with GCC and libquadmath)') + variant( + 'float', default=True, + description='Produces a single precision version of the library') + variant( + 'long_double', default=True, + description='Produces a long double precision version of the library') + variant( + 'quad', default=False, + description='Produces a quad precision version of the library ' + '(works only with GCC and libquadmath)') variant('openmp', default=False, description="Enable OpenMP support.") variant('mpi', default=False, description='Activate MPI support') depends_on('mpi', when='+mpi') - # TODO : add support for architecture specific optimizations as soon as targets are supported + # TODO : add support for architecture specific optimizations as soon as + # targets are supported def install(self, spec, prefix): options = ['--prefix=%s' % prefix, @@ -57,9 +67,9 @@ class Fftw(Package): if '+openmp' in spec: # Note: Apple's Clang does not support OpenMP. if spec.satisfies('%clang'): - ver = str(self.compiler.version) - if ver.endswith('-apple'): - raise InstallError("Apple's clang does not support OpenMP") + ver = str(self.compiler.version) + if ver.endswith('-apple'): + raise InstallError("Apple's clang does not support OpenMP") options.append('--enable-openmp') if not self.compiler.f77 or not self.compiler.fc: options.append("--disable-fortran") diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py index 9d23a3d63d..0e85f410c1 100644 --- a/var/spack/repos/builtin/packages/fish/package.py +++ b/var/spack/repos/builtin/packages/fish/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Fish(Package): """fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family. diff --git a/var/spack/repos/builtin/packages/fltk/package.py b/var/spack/repos/builtin/packages/fltk/package.py index f8ac5bc2a4..f29b64b02b 100644 --- a/var/spack/repos/builtin/packages/fltk/package.py +++ b/var/spack/repos/builtin/packages/fltk/package.py @@ -26,13 +26,16 @@ from spack import * class Fltk(Package): - """ - FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and - MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its - built-in GLUT emulation. + """FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for + UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides + modern GUI functionality without the bloat and supports 3D + graphics via OpenGL and its built-in GLUT emulation. + + FLTK is designed to be small and modular enough to be statically + linked, but works fine as a shared library. FLTK also includes an + excellent UI builder called FLUID that can be used to create + applications in minutes. - FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK - also includes an excellent UI builder called FLUID that can be used to create applications in minutes. """ homepage = 'http://www.fltk.org/' url = 'http://fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz' @@ -41,7 +44,8 @@ class Fltk(Package): patch('font.patch', when='@1.3.3') - variant('shared', default=True, description='Enables the build of shared libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') def install(self, spec, prefix): options = ['--prefix=%s' % prefix, diff --git a/var/spack/repos/builtin/packages/flux/package.py b/var/spack/repos/builtin/packages/flux/package.py index dec339a6af..2fd2392b5e 100644 --- a/var/spack/repos/builtin/packages/flux/package.py +++ b/var/spack/repos/builtin/packages/flux/package.py @@ -25,13 +25,15 @@ from spack import * import os + class Flux(Package): """ A next-generation resource manager (pre-alpha) """ homepage = "https://github.com/flux-framework/flux-core" url = "https://github.com/flux-framework/flux-core" - version('master', branch='master', git='https://github.com/flux-framework/flux-core') + version('master', branch='master', + git='https://github.com/flux-framework/flux-core') # Also needs autotools, but should use the system version if available depends_on("zeromq@4.0.4:") @@ -52,12 +54,11 @@ class Flux(Package): # Bootstrap with autotools bash = which('bash') bash('./autogen.sh') - bash('./autogen.sh') #yes, twice, intentionally + bash('./autogen.sh') # yes, twice, intentionally # Fix asciidoc dependency on xml style sheets and whatnot - os.environ['XML_CATALOG_FILES'] = os.path.join(spec['docbook-xml'].prefix, - 'catalog.xml') + os.environ['XML_CATALOG_FILES'] = os.path.join( + spec['docbook-xml'].prefix, 'catalog.xml') # Configure, compile & install configure("--prefix=" + prefix) make("install", "V=1") - diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py index 0ff5765895..6b3b87a110 100644 --- a/var/spack/repos/builtin/packages/foam-extend/package.py +++ b/var/spack/repos/builtin/packages/foam-extend/package.py @@ -16,12 +16,24 @@ class FoamExtend(Package): version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0') variant('paraview', default=False, description='Enable ParaFOAM') - variant('scotch', default=True, description='Activate Scotch as a possible decomposition library') - variant('ptscotch', default=True, description='Activate PT-Scotch as a possible decomposition library') - variant('metis', default=True, description='Activate Metis as a possible decomposition library') - variant('parmetis', default=True, description='Activate Parmetis as a possible decomposition library') - variant('parmgridgen', default=True, description='Activate Parmgridgen support') - variant('source', default=True, description='Installs also the source folder') + variant( + 'scotch', default=True, + description='Activate Scotch as a possible decomposition library') + variant( + 'ptscotch', default=True, + description='Activate PT-Scotch as a possible decomposition library') + variant( + 'metis', default=True, + description='Activate Metis as a possible decomposition library') + variant( + 'parmetis', default=True, + description='Activate Parmetis as a possible decomposition library') + variant( + 'parmgridgen', default=True, + description='Activate Parmgridgen support') + variant( + 'source', default=True, + description='Installs also the source folder') supported_compilers = {'clang': 'Clang', 'gcc': 'Gcc', 'intel': 'Icc'} @@ -80,7 +92,7 @@ class FoamExtend(Package): filter_file( r'-lMGridGen', r'-lmgrid', - 'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options') # NOQA: ignore=501 + 'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options') # noqa # Get the wmake arch and compiler (arch, foam_compiler) = self.set_arch() diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py index 76e9d8cb3f..0d7e47f228 100644 --- a/var/spack/repos/builtin/packages/fontconfig/package.py +++ b/var/spack/repos/builtin/packages/fontconfig/package.py @@ -24,12 +24,13 @@ ############################################################################## from spack import * + class Fontconfig(Package): """Fontconfig customizing font access""" homepage = "http://www.freedesktop.org/wiki/Software/fontconfig/" url = "http://www.freedesktop.org/software/fontconfig/release/fontconfig-2.11.1.tar.gz" - version('2.11.1' , 'e75e303b4f7756c2b16203a57ac87eba') + version('2.11.1', 'e75e303b4f7756c2b16203a57ac87eba') depends_on('freetype') depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py index b3bd6c25f2..12ecd9fd6f 100644 --- a/var/spack/repos/builtin/packages/gasnet/package.py +++ b/var/spack/repos/builtin/packages/gasnet/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Gasnet(Package): """GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication @@ -36,24 +37,24 @@ class Gasnet(Package): version('1.24.0', 'c8afdf48381e8b5a7340bdb32ca0f41a') - def install(self, spec, prefix): # TODO: don't use paths with @ in them. change_sed_delimiter('@', ';', 'configure') - configure("--prefix=%s" % prefix, - # TODO: factor IB suport out into architecture description. - "--enable-ibv", - "--enable-udp", - "--disable-mpi", - "--enable-par", - "--enable-mpi-compat", - "--enable-segment-fast", - "--disable-aligned-segments", - # TODO: make an option so that Legion can request builds with/without this. - # See the Legion webpage for details on when to/not to use. - "--disable-pshm", - "--with-segment-mmap-max=64MB") + configure( + "--prefix=%s" % prefix, + # TODO: factor IB suport out into architecture description. + "--enable-ibv", + "--enable-udp", + "--disable-mpi", + "--enable-par", + "--enable-mpi-compat", + "--enable-segment-fast", + "--disable-aligned-segments", + # TODO: make option so Legion can request builds with/without this. + # See the Legion webpage for details on when to/not to use. + "--disable-pshm", + "--with-segment-mmap-max=64MB") make() make("install") diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index 9ed83bc3be..4fdfafc992 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Gdal(Package): """ GDAL is a translator library for raster and vector geospatial diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 78ad4b307d..9145009fa4 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -27,9 +27,10 @@ from spack import * class Gdb(Package): - """ - GDB, the GNU Project debugger, allows you to see what is going on `inside' another program while it executes - -- or what another program was doing at the moment it crashed. + """GDB, the GNU Project debugger, allows you to see what is going on + `inside' another program while it executes -- or what another + program was doing at the moment it crashed. + """ homepage = "https://www.gnu.org/software/gdb" url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz" diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py index daf43f3256..d7a0200395 100644 --- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py +++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class GdkPixbuf(Package): """The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index 88438b0a99..324186cfbc 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class Geos(Package): """GEOS (Geometry Engine - Open Source) is a C++ port of the Java diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py index df301aea3c..cf260c3f8a 100644 --- a/var/spack/repos/builtin/packages/gettext/package.py +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -24,31 +24,80 @@ ############################################################################## from spack import * + class Gettext(Package): """GNU internationalization (i18n) and localization (l10n) library.""" homepage = "https://www.gnu.org/software/gettext/" url = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz" - version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590') + version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + + # Recommended variants + variant('curses', default=True, description='Use libncurses') + variant('libxml2', default=True, description='Use libxml2') + variant('git', default=True, description='Enable git support') + variant('tar', default=True, description='Enable tar support') + variant('bzip2', default=True, description='Enable bzip2 support') + variant('xz', default=True, description='Enable xz support') + + # Optional variants + variant('libunistring', default=False, description='Use libunistring') + + # Recommended dependencies + depends_on('ncurses', when='+curses') + depends_on('libxml2', when='+libxml2') + # Java runtime and compiler (e.g. GNU gcj or kaffe) + # C# runtime and compiler (e.g. pnet or mono) + depends_on('tar', when='+tar') + # depends_on('gzip', when='+gzip') + depends_on('bzip2', when='+bzip2') + depends_on('xz', when='+xz') + + # Optional dependencies + # depends_on('glib') # circular dependency? + # depends_on('libcroco@0.6.1:') + depends_on('libunistring', when='+libunistring') + # depends_on('cvs') def install(self, spec, prefix): - options = ['--disable-dependency-tracking', - '--disable-silent-rules', - '--disable-debug', - '--prefix=%s' % prefix, - '--with-included-gettext', - '--with-included-glib', - '--with-included-libcroco', - '--with-included-libunistring', - '--with-emacs', - '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, - '--disable-java', - '--disable-csharp', - '--without-git', # Don't use VCS systems to create these archives - '--without-cvs', - '--without-xz'] - - configure(*options) + config_args = [ + '--prefix={0}'.format(prefix), + '--disable-java', + '--disable-csharp', + '--with-included-glib', + '--with-included-gettext', + '--with-included-libcroco', + '--without-emacs', + '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, + '--without-cvs' + ] + + if '+curses' in spec: + config_args.append('--with-ncurses-prefix={0}'.format( + spec['ncurses'].prefix)) + else: + config_args.append('--disable-curses') + + if '+libxml2' in spec: + config_args.append('--with-libxml2-prefix={0}'.format( + spec['libxml2'].prefix)) + else: + config_args.append('--with-included-libxml') + + if '+bzip2' not in spec: + config_args.append('--without-bzip2') + + if '+xz' not in spec: + config_args.append('--without-xz') + + if '+libunistring' in spec: + config_args.append('--with-libunistring-prefix={0}'.format( + spec['libunistring'].prefix)) + else: + config_args.append('--with-included-libunistring') + + configure(*config_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py index 47bbf369ef..7e04c9b682 100644 --- a/var/spack/repos/builtin/packages/gflags/package.py +++ b/var/spack/repos/builtin/packages/gflags/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Gflags(Package): """The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 4cbbaac342..3cc879088d 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Git(Package): """Git is a free and open source distributed version control system designed to handle everything from small to very large @@ -36,40 +37,36 @@ class Git(Package): version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6') version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060') - # See here for info on vulnerable Git versions: # http://www.theregister.co.uk/2016/03/16/git_server_client_patch_now/ # All the following are vulnerable - #version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') - #version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') - #version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') - #version('2.6.0', 'eb76a07148d94802a1745d759716a57e') - #version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') - #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') - + # version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') + # version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') + # version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') + # version('2.6.0', 'eb76a07148d94802a1745d759716a57e') + # version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') + # version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') depends_on("openssl") depends_on("autoconf", type='build') depends_on("curl") depends_on("expat") - - # Also depends_on gettext: apt-get install gettext (Ubuntu) - - # Use system perl for now. - # depends_on("perl") - # depends_on("pcre") - + depends_on("gettext") depends_on("zlib") + depends_on("pcre") + depends_on("perl") def install(self, spec, prefix): + env['LDFLAGS'] = "-L%s" % spec['gettext'].prefix.lib + " -lintl" configure_args = [ "--prefix=%s" % prefix, - "--without-pcre", + "--with-libpcre=%s" % spec['pcre'].prefix, "--with-openssl=%s" % spec['openssl'].prefix, "--with-zlib=%s" % spec['zlib'].prefix, "--with-curl=%s" % spec['curl'].prefix, "--with-expat=%s" % spec['expat'].prefix, - ] + "--with-perl=%s" % join_path(spec['perl'].prefix.bin, 'perl'), + ] which('autoreconf')('-i') configure(*configure_args) diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py index 25172bd544..d5e7b00027 100644 --- a/var/spack/repos/builtin/packages/gl2ps/package.py +++ b/var/spack/repos/builtin/packages/gl2ps/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Gl2ps(Package): """GL2PS is a C library providing high quality vector output for any OpenGL application.""" diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 0a0a02f464..2720831e4f 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import sys class Glib(Package): @@ -32,17 +31,24 @@ class Glib(Package): and interfaces for such runtime functionality as an event loop, threads, dynamic loading and an object system.""" homepage = "https://developer.gnome.org/glib/" - url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz" + url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz" + version('2.49.4', 'e2c87c03017b0cd02c4c73274b92b148') version('2.42.1', '89c4119e50e767d3532158605ee9121a') - depends_on("libffi") - depends_on("zlib") - depends_on("pkg-config", type='build') - depends_on('gettext', when=sys.platform == 'darwin') + depends_on('libffi') + depends_on('zlib') + depends_on('pkg-config', type='build') + depends_on('gettext') + depends_on('pcre+utf', when='@2.49:') # The following patch is needed for gcc-6.1 - patch('g_date_strftime.patch') + patch('g_date_strftime.patch', when='@2.42.1') + + def url_for_version(self, version): + """Handle glib's version-based custom URLs.""" + url = 'http://ftp.gnome.org/pub/gnome/sources/glib' + return url + '/%s/glib-%s.tar.xz' % (version.up_to(2), version) def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index 442c1cdf40..c565b3cae7 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -26,9 +26,10 @@ from spack import * class Glm(Package): - """ - OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on - the OpenGL Shading Language (GLSL) specification. + """OpenGL Mathematics (GLM) is a header only C++ mathematics library for + graphics software based on the OpenGL Shading Language (GLSL) + specification. + """ homepage = "https://github.com/g-truc/glm" diff --git a/var/spack/repos/builtin/packages/glog/package.py b/var/spack/repos/builtin/packages/glog/package.py index 03ee092429..14f042732b 100644 --- a/var/spack/repos/builtin/packages/glog/package.py +++ b/var/spack/repos/builtin/packages/glog/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Glog(Package): """C++ implementation of the Google logging module.""" diff --git a/var/spack/repos/builtin/packages/glpk/package.py b/var/spack/repos/builtin/packages/glpk/package.py index 2ab3c38150..1b52643e59 100644 --- a/var/spack/repos/builtin/packages/glpk/package.py +++ b/var/spack/repos/builtin/packages/glpk/package.py @@ -22,22 +22,23 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## - from spack import * class Glpk(Package): - """ - The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed - integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in - the form of a callable library + """The GLPK (GNU Linear Programming Kit) package is intended for solving + large-scale linear programming (LP), mixed integer programming + (MIP), and other related problems. It is a set of routines written + in ANSI C and organized in the form of a callable library + """ homepage = "https://www.gnu.org/software/glpk" url = "http://ftp.gnu.org/gnu/glpk/glpk-4.57.tar.gz" version('4.57', '237531a54f73155842f8defe51aedb0f') - variant('gmp', default=False, description='Activates support for GMP library') + variant('gmp', default=False, + description='Activates support for GMP library') depends_on('gmp', when='+gmp') diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index e2c2892f18..d85330dd6e 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -24,16 +24,18 @@ ############################################################################## from spack import * + class Gmp(Package): - """GMP is a free library for arbitrary precision arithmetic, - operating on signed integers, rational numbers, and - floating-point numbers.""" + """GMP is a free library for arbitrary precision arithmetic, operating + on signed integers, rational numbers, and floating-point numbers.""" + homepage = "https://gmplib.org" url = "https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2" - version('6.1.0' , '86ee6e54ebfc4a90b643a65e402c4048') + version('6.1.1', '4c175f86e11eb32d8bf9872ca3a8e11d') + version('6.1.0', '86ee6e54ebfc4a90b643a65e402c4048') version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') - version('6.0.0' , '6ef5869ae735db9995619135bd856b84') + version('6.0.0', '6ef5869ae735db9995619135bd856b84') depends_on("m4", type='build') diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index fe26cb3bf2..72f490e2f4 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -41,15 +41,21 @@ class Gmsh(Package): version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09') version('2.11.0', 'f15b6e7ac9ca649c9a74440e1259d0db') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds the library in debug mode') - variant('mpi', default=False, description='Builds MPI support for parser and solver') - variant('fltk', default=False, description='Enables the build of the FLTK GUI') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds the library in debug mode') + variant('mpi', default=False, + description='Builds MPI support for parser and solver') + variant('fltk', default=False, + description='Enables the build of the FLTK GUI') variant('hdf5', default=False, description='Enables HDF5 support') - variant('compression', default=True, description='Enables IO compression through zlib') + variant('compression', default=True, + description='Enables IO compression through zlib') variant('oce', default=False, description='Build with OCE') variant('petsc', default=False, description='Build with PETSc') - variant('slepc', default=False, description='Build with SLEPc (only when PETSc is enabled)') + variant('slepc', default=False, + description='Build with SLEPc (only when PETSc is enabled)') depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py index f497ed3001..1e0487c654 100644 --- a/var/spack/repos/builtin/packages/gnu-prolog/package.py +++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class GnuProlog(Package): """A free Prolog compiler with constraint solving over finite domains.""" homepage = "http://www.gprolog.org/" diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py index a76677e066..600b6d285f 100644 --- a/var/spack/repos/builtin/packages/gnuplot/package.py +++ b/var/spack/repos/builtin/packages/gnuplot/package.py @@ -27,13 +27,18 @@ from spack import * import os + class Gnuplot(Package): - """ - Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other - platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was - originally created to allow scientists and students to visualize mathematical functions and data interactively, - but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by - third-party applications like Octave. Gnuplot has been supported and under active development since 1986 + """Gnuplot is a portable command-line driven graphing utility for Linux, + OS/2, MS Windows, OSX, VMS, and many other platforms. The source + code is copyrighted but freely distributed (i.e., you don't have + to pay for it). It was originally created to allow scientists and + students to visualize mathematical functions and data + interactively, but has grown to support many non-interactive uses + such as web scripting. It is also used as a plotting engine by + third-party applications like Octave. Gnuplot has been supported + and under active development since 1986 + """ homepage = "http://www.gnuplot.info" url = "http://downloads.sourceforge.net/project/gnuplot/gnuplot/5.0.1/gnuplot-5.0.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/gnutls/package.py b/var/spack/repos/builtin/packages/gnutls/package.py index 71b571bc88..5f7b0daf9b 100644 --- a/var/spack/repos/builtin/packages/gnutls/package.py +++ b/var/spack/repos/builtin/packages/gnutls/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Gnutls(Package): """GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py index 1dc74fbcf4..6f3cafec06 100644 --- a/var/spack/repos/builtin/packages/googletest/package.py +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Googletest(Package): """Google test framework for C++. Also called gtest.""" homepage = "https://github.com/google/googletest" @@ -40,9 +41,8 @@ class Googletest(Package): # Google Test doesn't have a make install # We have to do our own install here. - install_tree('include', prefix.include) + install_tree('include', prefix.include) mkdirp(prefix.lib) - install('./libgtest.a', '%s' % prefix.lib) - install('./libgtest_main.a', '%s' % prefix.lib) - + install('./libgtest.a', '%s' % prefix.lib) + install('./libgtest_main.a', '%s' % prefix.lib) diff --git a/var/spack/repos/builtin/packages/gperf/package.py b/var/spack/repos/builtin/packages/gperf/package.py index af176afcf6..0e54d0e037 100644 --- a/var/spack/repos/builtin/packages/gperf/package.py +++ b/var/spack/repos/builtin/packages/gperf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Gperf(Package): """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in diff --git a/var/spack/repos/builtin/packages/gperftools/package.py b/var/spack/repos/builtin/packages/gperftools/package.py index 1f17ab71a4..c6ca6c8057 100644 --- a/var/spack/repos/builtin/packages/gperftools/package.py +++ b/var/spack/repos/builtin/packages/gperftools/package.py @@ -24,14 +24,20 @@ ############################################################################## from spack import * + class Gperftools(Package): - """Google's fast malloc/free implementation, especially for multi-threaded applications. - Contains tcmalloc, heap-checker, heap-profiler, and cpu-profiler.""" + """Google's fast malloc/free implementation, especially for + multi-threaded applications. Contains tcmalloc, heap-checker, + heap-profiler, and cpu-profiler. + + """ homepage = "https://code.google.com/p/gperftools" url = "https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz" - version('2.4', '2171cea3bbe053036fb5d5d25176a160', url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz") - version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90', url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz") + version('2.4', '2171cea3bbe053036fb5d5d25176a160', + url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz") + version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90', + url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz") depends_on("libunwind") diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py index 087a322acc..0c3cd9b649 100644 --- a/var/spack/repos/builtin/packages/graphlib/package.py +++ b/var/spack/repos/builtin/packages/graphlib/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Graphlib(Package): """Library to create, manipulate, and export graphs Graphlib.""" homepage = "http://https://github.com/lee218llnl/graphlib" diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index e5898a6e59..b37121248c 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -37,7 +37,9 @@ class Graphviz(Package): # related to missing Perl packages. If spack begins support for Perl in the # future, this package can be updated to depend_on('perl') and the # ncecessary devel packages. - variant('perl', default=False, description='Enable if you need the optional Perl language bindings.') # NOQA: ignore=E501 + variant( + 'perl', default=False, + description='Enable if you need the optional Perl language bindings.') parallel = False diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 55eacc8d38..d39c9738ef 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -22,19 +22,21 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## + from spack import * class Gromacs(Package): - """ - GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for - simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry - department of University of Groningen, and is now maintained by contributors in universities and research centers - across the world. - - GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. - It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is - released under the GNU Lesser General Public License. + """GROMACS (GROningen MAchine for Chemical Simulations) is a molecular + dynamics package primarily designed for simulations of proteins, lipids + and nucleic acids. It was originally developed in the Biophysical + Chemistry department of University of Groningen, and is now maintained + by contributors in universities and research centers across the world. + + GROMACS is one of the fastest and most popular software packages + available and can run on CPUs as well as GPUs. It is free, open source + released under the GNU General Public License. Starting from version 4.6, + GROMACS is released under the GNU Lesser General Public License. """ homepage = 'http://www.gromacs.org' @@ -43,17 +45,26 @@ class Gromacs(Package): version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98') variant('mpi', default=True, description='Activate MPI support') - variant('shared', default=True, description='Enables the build of shared libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') variant('debug', default=False, description='Enables debug mode') - variant('double', default=False, description='Produces a double precision version of the executables') + variant( + 'double', default=False, + description='Produces a double precision version of the executables') + variant('plumed', default=False, description='Enable PLUMED support') depends_on('mpi', when='+mpi') - + depends_on('plumed+mpi', when='+plumed+mpi') + depends_on('plumed~mpi', when='+plumed~mpi') depends_on('fftw') depends_on('cmake', type='build') # TODO : add GPU support + def patch(self): + if '+plumed' in self.spec: + self.spec['plumed'].package.apply_patch(self) + def install(self, spec, prefix): options = [] diff --git a/var/spack/repos/builtin/packages/gsl/package.py b/var/spack/repos/builtin/packages/gsl/package.py index c1695a6f02..574d3b9402 100644 --- a/var/spack/repos/builtin/packages/gsl/package.py +++ b/var/spack/repos/builtin/packages/gsl/package.py @@ -27,17 +27,19 @@ from spack import * class Gsl(Package): - """ - The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the - GNU General Public License. The library provides a wide range of mathematical routines such as random number - generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive - test suite. + """The GNU Scientific Library (GSL) is a numerical library for C and C++ + programmers. It is free software under the GNU General Public + License. The library provides a wide range of mathematical + routines such as random number generators, special functions and + least-squares fitting. There are over 1000 functions in total with + an extensive test suite. + """ homepage = "http://www.gnu.org/software/gsl" url = "http://mirror.switch.ch/ftp/mirror/gnu/gsl/gsl-2.1.tar.gz" - version('2.1' , 'd8f70abafd3e9f0bae03c52d1f4e8de5') - version('2.0' , 'ae44cdfed78ece40e73411b63a78c375') + version('2.1', 'd8f70abafd3e9f0bae03c52d1f4e8de5') + version('2.0', 'ae44cdfed78ece40e73411b63a78c375') version('1.16', 'e49a664db13d81c968415cd53f62bc8b') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/gtkplus/package.py b/var/spack/repos/builtin/packages/gtkplus/package.py index c135e89f78..c85bbe4094 100644 --- a/var/spack/repos/builtin/packages/gtkplus/package.py +++ b/var/spack/repos/builtin/packages/gtkplus/package.py @@ -24,12 +24,15 @@ ############################################################################## from spack import * + class Gtkplus(Package): - """The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.""" + """The GTK+ 2 package contains libraries used for creating graphical user + interfaces for applications.""" homepage = "http://www.gtk.org" - version('2.24.25', '612350704dd3aacb95355a4981930c6f', - url="http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.25.tar.xz") + version( + '2.24.25', '612350704dd3aacb95355a4981930c6f', + url="http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.25.tar.xz") depends_on("atk") depends_on("gdk-pixbuf") diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py new file mode 100644 index 0000000000..22aff1bddf --- /dev/null +++ b/var/spack/repos/builtin/packages/guile/package.py @@ -0,0 +1,68 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Guile(Package): + """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + + homepage = "https://www.gnu.org/software/guile/" + url = "ftp://ftp.gnu.org/gnu/guile/guile-2.0.11.tar.gz" + + version('2.0.11', 'e532c68c6f17822561e3001136635ddd') + + variant('readline', default=True, description='Use the readline library') + + depends_on('gmp@4.2:') + depends_on('gettext') + depends_on('libtool@1.5.6:') + depends_on('libunistring@0.9.3:') + depends_on('bdw-gc@7.0:') + depends_on('libffi') + depends_on('readline', when='+readline') + depends_on('pkg-config', type='build') + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--with-libunistring-prefix={0}'.format( + spec['libunistring'].prefix), + '--with-libltdl-prefix={0}'.format(spec['libtool'].prefix), + '--with-libgmp-prefix={0}'.format(spec['gmp'].prefix), + '--with-libintl-prefix={0}'.format(spec['gettext'].prefix) + ] + + if '+readline' in spec: + config_args.append('--with-libreadline-prefix={0}'.format( + spec['readline'].prefix)) + else: + config_args.append('--without-libreadline-prefix') + + configure(*config_args) + + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py new file mode 100644 index 0000000000..184535ebb0 --- /dev/null +++ b/var/spack/repos/builtin/packages/harminv/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Harminv(Package): + """Harminv is a free program (and accompanying library) to solve the + problem of harmonic inversion - given a discrete-time, finite-length + signal that consists of a sum of finitely-many sinusoids (possibly + exponentially decaying) in a given bandwidth, it determines the + frequencies, decay constants, amplitudes, and phases of those sinusoids.""" + + homepage = "http://ab-initio.mit.edu/wiki/index.php/Harminv" + url = "http://ab-initio.mit.edu/harminv/harminv-1.4.tar.gz" + + version('1.4', 'b95e24a9bc7e07d3d2202d1605e9e86f') + + depends_on('blas') + depends_on('lapack') + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--with-blas={0}'.format(spec['blas'].prefix.lib), + '--with-lapack={0}'.format(spec['lapack'].prefix.lib), + '--enable-shared' + ] + + configure(*config_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py index 7ad4df2fde..aafb345be6 100644 --- a/var/spack/repos/builtin/packages/hdf/package.py +++ b/var/spack/repos/builtin/packages/hdf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Hdf(Package): """HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines.""" @@ -41,10 +42,9 @@ class Hdf(Package): depends_on("szip", when='+szip') depends_on("zlib") - def url_for_version(self, version): - return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(version) + "/src/hdf-" + str(version) + ".tar.gz" - + return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str( + version) + "/src/hdf-" + str(version) + ".tar.gz" def install(self, spec, prefix): config_args = [ @@ -52,9 +52,9 @@ class Hdf(Package): '--prefix=%s' % prefix, '--with-jpeg=%s' % spec['jpeg'].prefix, '--with-zlib=%s' % spec['zlib'].prefix, - '--disable-netcdf', # must be disabled to build NetCDF with HDF4 support + '--disable-netcdf', # must be disabled to build NetCDF with HDF4 '--enable-fortran', - '--disable-shared', # fortran and shared libraries are not compatible + '--disable-shared', # fortran and shared libs are not compatible '--enable-static', '--enable-production' ] diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py index 28b65711b0..b9c19dff62 100644 --- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py +++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py @@ -29,6 +29,7 @@ import sys from spack import * + def _install_shlib(name, src, dst): """Install a shared library from directory src to directory dst""" if sys.platform == "darwin": @@ -44,6 +45,7 @@ def _install_shlib(name, src, dst): os.symlink(shlib000, join_path(dst, shlib0)) os.symlink(shlib0, join_path(dst, shlib)) + class Hdf5Blosc(Package): """Blosc filter for HDF5""" homepage = "https://github.com/Blosc/hdf5-blosc" @@ -60,18 +62,21 @@ class Hdf5Blosc(Package): def install(self, spec, prefix): # The included cmake recipe doesn"t work for Darwin # cmake(".", *std_cmake_args) - # + # # make() # make("install") # if sys.platform == "darwin": # fix_darwin_install_name(prefix.lib) libtool = Executable(join_path(spec["libtool"].prefix.bin, "libtool")) - if "+mpi" in spec["hdf5"]: - cc = "mpicc" - else: - cc = "cc" - shlibext = "so" if sys.platform!="darwin" else "dylib" + + # TODO: these vars are not used. + # if "+mpi" in spec["hdf5"]: + # cc = "mpicc" + # else: + # cc = "cc" + # shlibext = "so" if sys.platform != "darwin" else "dylib" + mkdirp(prefix.include) mkdirp(prefix.lib) @@ -118,7 +123,7 @@ class Hdf5Blosc(Package): #include <stdio.h> #include <stdlib.h> -#define FILTER_BLOSC 32001 /* Blosc filter ID registered with the HDF group */ +#define FILTER_BLOSC 32001 /* Blosc filter ID registered with the HDF group */ int main(int argc, char **argv) { herr_t herr; @@ -184,13 +189,13 @@ Done. if not success: print "Produced output does not match expected output." print "Expected output:" - print "-"*80 + print "-" * 80 print expected - print "-"*80 + print "-" * 80 print "Produced output:" - print "-"*80 + print "-" * 80 print output - print "-"*80 + print "-" * 80 print "Environment:" env = which("env") env() diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index d169940c86..aedaf18218 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -44,15 +44,18 @@ class Hdf5(Package): version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') - variant('debug', default=False, description='Builds a debug version of the library') - variant('shared', default=True, description='Builds a shared version of the library') + variant('debug', default=False, + description='Builds a debug version of the library') + variant('shared', default=True, + description='Builds a shared version of the library') variant('cxx', default=True, description='Enable C++ support') variant('fortran', default=True, description='Enable Fortran support') variant('mpi', default=False, description='Enable MPI support') variant('szip', default=False, description='Enable szip support') - variant('threadsafe', default=False, description='Enable thread-safe capabilities') + variant('threadsafe', default=False, + description='Enable thread-safe capabilities') depends_on("mpi", when='+mpi') depends_on("szip", when='+szip') diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py index 060cd0b713..79e99e7b89 100644 --- a/var/spack/repos/builtin/packages/hoomd-blue/package.py +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -25,6 +25,7 @@ from spack import * import os + class HoomdBlue(Package): """HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. @@ -56,7 +57,7 @@ class HoomdBlue(Package): cmake_args = [ '-DPYTHON_EXECUTABLE=%s/python' % spec['python'].prefix.bin, - '-DBOOST_ROOT=%s' % spec['boost' ].prefix + '-DBOOST_ROOT=%s' % spec['boost'].prefix ] # MPI support @@ -73,9 +74,9 @@ class HoomdBlue(Package): cmake_args.append('-DENABLE_CUDA=OFF') # CUDA-aware MPI library support - #if '+cuda' in spec and '+mpi' in spec: + # if '+cuda' in spec and '+mpi' in spec: # cmake_args.append('-DENABLE_MPI_CUDA=ON') - #else: + # else: # cmake_args.append('-DENABLE_MPI_CUDA=OFF') # There may be a bug in the MPI-CUDA code. See: diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py index cd0c0b7a7b..686e959719 100644 --- a/var/spack/repos/builtin/packages/hpx5/package.py +++ b/var/spack/repos/builtin/packages/hpx5/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Hpx5(Package): """The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an open source, portable, performance-oriented runtime developed at diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py new file mode 100644 index 0000000000..1a8b8fd2f5 --- /dev/null +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Htslib(Package): + """C library for high-throughput sequencing data formats.""" + + homepage = "https://github.com/samtools/htslib" + url = "https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2" + + version('1.3.1', '16d78f90b72f29971b042e8da8be6843') + + depends_on('zlib') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index ee0168c38e..c163628840 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Hwloc(Package): """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py index 3d56056022..eee346ba49 100644 --- a/var/spack/repos/builtin/packages/hydra/package.py +++ b/var/spack/repos/builtin/packages/hydra/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Hydra(Package): """Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with existing launcher daemons @@ -37,7 +38,6 @@ class Hydra(Package): version('3.2', '4d670916695bf7e3a869cc336a881b39') - def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 65fef57559..fdc236dcf4 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -39,9 +39,11 @@ class Hypre(Package): version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') # hypre does not know how to build shared libraries on Darwin - variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)") + variant('shared', default=(sys.platform != 'darwin'), + description="Build shared library (disables static library)") # SuperluDist have conflicting headers with those in Hypre - variant('internal-superlu', default=True, description="Use internal Superlu routines") + variant('internal-superlu', default=True, + description="Use internal Superlu routines") depends_on("mpi") depends_on("blas") @@ -62,10 +64,10 @@ class Hypre(Package): '--prefix=%s' % prefix, '--with-lapack-libs=%s' % to_lib_name( spec['lapack'].lapack_shared_lib), - '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix, + '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib, '--with-blas-libs=%s' % to_lib_name( spec['blas'].blas_shared_lib), - '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix + '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib ] if '+shared' in self.spec: diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index ed1e6c6cbf..8e83058e94 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -1,5 +1,6 @@ from spack import * + class Ibmisc(CMakePackage): """Misc. reusable utilities used by IceBin.""" @@ -8,14 +9,22 @@ class Ibmisc(CMakePackage): version('0.1.0', '12f2a32432a11db48e00217df18e59fa') - variant('everytrace', default=False, description='Report errors through Everytrace') - variant('proj', default=True, description='Compile utilities for PROJ.4 library') - variant('blitz', default=True, description='Compile utilities for Blitz library') - variant('netcdf', default=True, description='Compile utilities for NetCDF library') - variant('boost', default=True, description='Compile utilities for Boost library') - variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library') - variant('googletest', default=True, description='Compile utilities for Google Test library') - variant('python', default=True, description='Compile utilities for use with Python/Cython') + variant('everytrace', default=False, + description='Report errors through Everytrace') + variant('proj', default=True, + description='Compile utilities for PROJ.4 library') + variant('blitz', default=True, + description='Compile utilities for Blitz library') + variant('netcdf', default=True, + description='Compile utilities for NetCDF library') + variant('boost', default=True, + description='Compile utilities for Boost library') + variant('udunits2', default=True, + description='Compile utilities for UDUNITS2 library') + variant('googletest', default=True, + description='Compile utilities for Google Test library') + variant('python', default=True, + description='Compile utilities for use with Python/Cython') extends('python') diff --git a/var/spack/repos/builtin/packages/icu/package.py b/var/spack/repos/builtin/packages/icu/package.py index c7cabb5d95..b8d366b905 100644 --- a/var/spack/repos/builtin/packages/icu/package.py +++ b/var/spack/repos/builtin/packages/icu/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Icu(Package): """The International Components for Unicode (ICU) package is a mature, widely used set of C/C++ libraries providing Unicode and @@ -36,12 +37,10 @@ class Icu(Package): version('54.1', 'e844caed8f2ca24c088505b0d6271bc0') - def url_for_version(self, version): return "http://download.icu-project.org/files/icu4c/%s/icu4c-%s-src.tgz" % ( version, str(version).replace('.', '_')) - def install(self, spec, prefix): with working_dir("source"): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py index 6cfec99c3f..2bcf86cd13 100644 --- a/var/spack/repos/builtin/packages/icu4c/package.py +++ b/var/spack/repos/builtin/packages/icu4c/package.py @@ -24,9 +24,12 @@ ############################################################################## from spack import * + class Icu4c(Package): - """ICU is a mature, widely used set of C/C++ and Java libraries - providing Unicode and Globalization support for software applications.""" + """ICU is a mature, widely used set of C/C++ and Java libraries providing + Unicode and Globalization support for software applications. + + """ homepage = "http://site.icu-project.org/" url = "http://downloads.sourceforge.net/project/icu/ICU4C/54.1/icu4c-54_1-src.tgz" diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py index fb98b2473c..65db3351a1 100644 --- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -17,19 +17,19 @@ class IntelParallelStudio(IntelInstaller): # TODO: can also try the online installer (will download files on demand) version('composer.2016.2', '1133fb831312eb519f7da897fec223fa', - url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" % os.getcwd()) version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', - url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', - url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) version('composer.2016.3', '3208eeabee951fc27579177b593cefe9', - url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" % os.getcwd()) version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3', - url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3', - url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) variant('rpath', default=True, description="Add rpath to .cfg files") variant('newdtags', default=False, @@ -50,6 +50,11 @@ class IntelParallelStudio(IntelInstaller): provides('daal', when='+daal') provides('ipp', when='+ipp') + # virtual dependency + provides('blas', when='+mkl') + provides('lapack', when='+mkl') + # TODO: MKL also provides implementation of Scalapack. + def check_variants(self, spec): error_message = '\t{variant} can not be turned off if "+all" is set' @@ -75,7 +80,7 @@ class IntelParallelStudio(IntelInstaller): regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)' base_components = \ filter_pick(all_components, re.compile(regex).search) - regex = '(icsxe|imb|mpi|itac|intel-tc|clck)' + regex = '(icsxe|imb|mpi|itac|intel-ta|intel-tc|clck)' mpi_components = \ filter_pick(all_components, re.compile(regex).search) mkl_components = \ @@ -99,7 +104,7 @@ class IntelParallelStudio(IntelInstaller): if spec.satisfies('+ipp'): components += ipp_components if spec.satisfies('+tools') and (spec.satisfies('@cluster') or - spec.satisfies('@professional')): + spec.satisfies('@professional')): components += tool_components if spec.satisfies('+all'): @@ -108,10 +113,11 @@ class IntelParallelStudio(IntelInstaller): self.intel_components = ';'.join(components) IntelInstaller.install(self, spec, prefix) - absbindir = os.path.dirname(os.path.realpath(os.path.join( - self.prefix.bin, "icc"))) - abslibdir = os.path.dirname(os.path.realpath(os.path.join - (self.prefix.lib, "intel64", "libimf.a"))) + absbindir = os.path.dirname( + os.path.realpath(os.path.join(self.prefix.bin, "icc"))) + abslibdir = os.path.dirname( + os.path.realpath(os.path.join( + self.prefix.lib, "intel64", "libimf.a"))) os.symlink(self.global_license_file, os.path.join(absbindir, "license.lic")) @@ -129,25 +135,31 @@ class IntelParallelStudio(IntelInstaller): if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \ spec.satisfies('@cluster'): - for ifile in os.listdir(os.path.join(self.prefix, "itac")): - if os.path.isdir(os.path.join(self.prefix, "itac", ifile)): - os.symlink(self.global_license_file, - os.path.join(self.prefix, "itac", ifile, - "license.lic")) - if spec.satisfies('~newdtags'): - wrappers = ["mpif77", "mpif77", "mpif90", "mpif90", - "mpigcc", "mpigcc", "mpigxx", "mpigxx", - "mpiicc", "mpiicc", "mpiicpc", "mpiicpc", - "mpiifort", "mpiifort"] - wrapper_paths = [] - for root, dirs, files in os.walk(spec.prefix): - for name in files: - if name in wrappers: - wrapper_paths.append(os.path.join(spec.prefix, - root, name)) - for wrapper in wrapper_paths: - filter_file(r'-Xlinker --enable-new-dtags', r' ', - wrapper) + for ifile in os.listdir(os.path.join(self.prefix, "itac")): + if os.path.isdir(os.path.join(self.prefix, "itac", ifile)): + os.symlink(self.global_license_file, + os.path.join(self.prefix, "itac", ifile, + "license.lic")) + if os.path.isdir(os.path.join(self.prefix, "itac", + ifile, "intel64")): + os.symlink(self.global_license_file, + os.path.join(self.prefix, "itac", + ifile, "intel64", + "license.lic")) + if spec.satisfies('~newdtags'): + wrappers = ["mpif77", "mpif77", "mpif90", "mpif90", + "mpigcc", "mpigcc", "mpigxx", "mpigxx", + "mpiicc", "mpiicc", "mpiicpc", "mpiicpc", + "mpiifort", "mpiifort"] + wrapper_paths = [] + for root, dirs, files in os.walk(spec.prefix): + for name in files: + if name in wrappers: + wrapper_paths.append(os.path.join(spec.prefix, + root, name)) + for wrapper in wrapper_paths: + filter_file(r'-Xlinker --enable-new-dtags', r' ', + wrapper) if spec.satisfies('+rpath'): for compiler_command in ["icc", "icpc", "ifort"]: @@ -159,6 +171,24 @@ class IntelParallelStudio(IntelInstaller): os.symlink(os.path.join(self.prefix.man, "common", "man1"), os.path.join(self.prefix.man, "man1")) + def setup_dependent_package(self, module, dspec): + # For now use Single Dynamic Library: + # To set the threading layer at run time, use the + # mkl_set_threading_layer function or set MKL_THREADING_LAYER + # variable to one of the following values: INTEL, SEQUENTIAL, PGI. + # To set interface layer at run time, use the mkl_set_interface_layer + # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64. + + # Otherwise one would need to specify several libraries + # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect + # different interface and threading layers. + + name = 'libmkl_rt.%s' % dso_suffix + libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib) + + self.spec.blas_shared_lib = join_path(libdir, name) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib + def setup_environment(self, spack_env, run_env): # TODO: Determine variables needed for the professional edition. @@ -227,6 +257,8 @@ class IntelParallelStudio(IntelInstaller): run_env.set('I_MPI_ROOT', join_path(self.prefix, 'impi')) if self.spec.satisfies('+all') or self.spec.satisfies('+mkl'): + spack_env.set('MKLROOT', self.prefix) + run_env.prepend_path('LD_LIBRARY_PATH', join_path(self.prefix, 'mkl', 'lib', 'intel64')) diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index d171411946..26134a12ae 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -83,10 +83,10 @@ class Intel(IntelInstaller): # TODO: can also try the online installer (will download files on demand) version('16.0.2', '1133fb831312eb519f7da897fec223fa', - url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" % os.getcwd()) version('16.0.3', '3208eeabee951fc27579177b593cefe9', - url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501 + url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" % os.getcwd()) variant('rpath', default=True, description="Add rpath to .cfg files") diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py index 48830c474a..e934734691 100644 --- a/var/spack/repos/builtin/packages/intltool/package.py +++ b/var/spack/repos/builtin/packages/intltool/package.py @@ -24,8 +24,12 @@ ############################################################################## from spack import * + class Intltool(Package): - """intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.""" + """intltool is a set of tools to centralize translation of many different + file formats using GNU gettext-compatible PO files. + + """ homepage = 'https://freedesktop.org/wiki/Software/intltool/' version('0.51.0', '12e517cac2b57a0121cda351570f1e63') @@ -37,7 +41,7 @@ class Intltool(Package): def install(self, spec, prefix): # configure, build, install: - options = ['--prefix=%s' % prefix ] + options = ['--prefix=%s' % prefix] configure(*options) make() make('install') diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py index 6aa72e5cc9..b8825c0fe4 100644 --- a/var/spack/repos/builtin/packages/ior/package.py +++ b/var/spack/repos/builtin/packages/ior/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Ior(Package): """The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5 interfaces.""" @@ -41,7 +42,6 @@ class Ior(Package): depends_on('hdf5+mpi', when='+hdf5') depends_on('netcdf+mpi', when='+ncmpi') - def install(self, spec, prefix): os.system('./bootstrap') diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py index 3bd21df89e..d5981e9975 100644 --- a/var/spack/repos/builtin/packages/ipopt/package.py +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Ipopt(Package): """Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.""" @@ -39,8 +40,8 @@ class Ipopt(Package): depends_on("blas") depends_on("lapack") depends_on("pkg-config", type='build') - depends_on("mumps+double~mpi") - + depends_on("mumps+double~mpi") + def install(self, spec, prefix): # Dependency directories blas_dir = spec['blas'].prefix @@ -55,7 +56,7 @@ class Ipopt(Package): # By convention, spack links blas & lapack libs to libblas & liblapack blas_lib = "-L%s" % blas_dir.lib + " -lblas" lapack_lib = "-L%s" % lapack_dir.lib + " -llapack" - + configure_args = [ "--prefix=%s" % prefix, "--with-mumps-incdir=%s" % mumps_dir.include, @@ -65,8 +66,8 @@ class Ipopt(Package): "--with-blas-lib=%s" % blas_lib, "--with-lapack-incdir=%s" % lapack_dir.include, "--with-lapack-lib=%s" % lapack_lib - ] - + ] + configure(*configure_args) # IPOPT does not build correctly in parallel on OS X diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py index f456f62225..259f4881f5 100644 --- a/var/spack/repos/builtin/packages/isl/package.py +++ b/var/spack/repos/builtin/packages/isl/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Isl(Package): """isl is a thread-safe C library for manipulating sets and relations of integer points bounded by affine constraints.""" diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 593a6d8340..63bf6514cb 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -25,7 +25,7 @@ # # Author: Justin Too <too1@llnl.gov> # -import distutils +import distutils.dir_util import spack from spack import * @@ -35,19 +35,19 @@ import llnl.util.tty as tty class Jdk(Package): """The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimed at Java developers.""" - homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html" # noqa: E501 + homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html" version('8u66-linux-x64', '88f31f3d642c3287134297b8c10e61bf', - url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz") + url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz") version('8u92-linux-x64', '65a1cc17ea362453a6e0eb4f13be76e4', - url="http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jdk-8u92-linux-x64.tar.gz") + url="http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jdk-8u92-linux-x64.tar.gz") # Oracle requires that you accept their License Agreement in order # to access the Java packages in download.oracle.com. In order to # automate this process, we need to utilize these additional curl # commandline options. # - # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux # noqa: E501 + # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux curl_options = [ '-j', # junk cookies '-H', # specify required License Agreement cookie diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py index a67754a513..f5a983b7a9 100644 --- a/var/spack/repos/builtin/packages/jemalloc/package.py +++ b/var/spack/repos/builtin/packages/jemalloc/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class Jemalloc(Package): - """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.""" + """jemalloc is a general purpose malloc(3) implementation that emphasizes + fragmentation avoidance and scalable concurrency support.""" homepage = "http://www.canonware.com/jemalloc/" url = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2" @@ -36,7 +38,7 @@ class Jemalloc(Package): variant('prof', default=False, description='Enable heap profiling') def install(self, spec, prefix): - configure_args = ['--prefix=%s' % prefix,] + configure_args = ['--prefix=%s' % prefix, ] if '+stats' in spec: configure_args.append('--enable-stats') diff --git a/var/spack/repos/builtin/packages/jpeg/package.py b/var/spack/repos/builtin/packages/jpeg/package.py index e4a9d8535b..594240d950 100644 --- a/var/spack/repos/builtin/packages/jpeg/package.py +++ b/var/spack/repos/builtin/packages/jpeg/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Jpeg(Package): """libjpeg is a widely used free library with functions for handling the JPEG image data format. It implements a JPEG codec (encoding and decoding) diff --git a/var/spack/repos/builtin/packages/judy/package.py b/var/spack/repos/builtin/packages/judy/package.py index 8d47767ef0..8b8b261e53 100644 --- a/var/spack/repos/builtin/packages/judy/package.py +++ b/var/spack/repos/builtin/packages/judy/package.py @@ -24,8 +24,9 @@ ############################################################################## from spack import * + class Judy(Package): - """A general-purpose dynamic array, associative array and hash-trie - Judy""" + """Judy: General-purpose dynamic array, associative array and hash-trie.""" homepage = "http://judy.sourceforge.net/" url = "http://downloads.sourceforge.net/project/judy/judy/Judy-1.0.5/Judy-1.0.5.tar.gz" diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py new file mode 100644 index 0000000000..48f4b9c379 --- /dev/null +++ b/var/spack/repos/builtin/packages/kdiff3/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Kdiff3(Package): + """Compare and merge 2 or 3 files or directories.""" + homepage = "http://kdiff3.sourceforge.net/" + url = "https://downloads.sourceforge.net/project/kdiff3/kdiff3/0.9.98/kdiff3-0.9.98.tar.gz" + + version('0.9.98', 'b52f99f2cf2ea75ed5719315cbf77446') + + depends_on("qt@5.2.0:") + + def install(self, spec, prefix): + # make is done inside + configure('qt4') + + # there is no make install, bummer... + mkdirp(self.prefix.bin) + install(join_path(self.stage.source_path, 'releaseQt', 'kdiff3'), + self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py index 7c73c4518b..5346fc8cb9 100644 --- a/var/spack/repos/builtin/packages/kealib/package.py +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -24,20 +24,21 @@ ############################################################################## from spack import * + class Kealib(Package): """An HDF5 Based Raster File Format - + KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. - + Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software. - + Development work on this project has been funded by Landcare Research. """ homepage = "http://kealib.org/" @@ -51,7 +52,8 @@ class Kealib(Package): with working_dir('trunk', create=False): cmake_args = [] cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix) - cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include) + cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % + spec['hdf5'].prefix.include) cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib) cmake('.', *cmake_args) diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py index d405e9a51d..cf8d2b7e39 100644 --- a/var/spack/repos/builtin/packages/kripke/package.py +++ b/var/spack/repos/builtin/packages/kripke/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Kripke(Package): """Kripke is a simple, scalable, 3D Sn deterministic particle transport proxy/mini app. diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py index 8aa6d72727..d7c96a03d8 100644 --- a/var/spack/repos/builtin/packages/launchmon/package.py +++ b/var/spack/repos/builtin/packages/launchmon/package.py @@ -29,7 +29,7 @@ class Launchmon(Package): """Software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job.""" homepage = "https://github.com/LLNL/LaunchMON" - url = "https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz" # NOQA: ignore=E501 + url = "https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz" version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a') diff --git a/var/spack/repos/builtin/packages/lcms/package.py b/var/spack/repos/builtin/packages/lcms/package.py index 434d8e6c98..4d3fc59568 100644 --- a/var/spack/repos/builtin/packages/lcms/package.py +++ b/var/spack/repos/builtin/packages/lcms/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Lcms(Package): """Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py index 408f1d31c1..f571baa1ce 100644 --- a/var/spack/repos/builtin/packages/leveldb/package.py +++ b/var/spack/repos/builtin/packages/leveldb/package.py @@ -22,10 +22,10 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os import glob from spack import * + class Leveldb(Package): """LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.""" diff --git a/var/spack/repos/builtin/packages/libNBC/package.py b/var/spack/repos/builtin/packages/libNBC/package.py index ed1d0ce96f..414498a37a 100644 --- a/var/spack/repos/builtin/packages/libNBC/package.py +++ b/var/spack/repos/builtin/packages/libNBC/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libnbc(Package): """LibNBC is a prototypic implementation of a nonblocking interface for MPI collective operations. Based on ANSI C and diff --git a/var/spack/repos/builtin/packages/libarchive/package.py b/var/spack/repos/builtin/packages/libarchive/package.py index f11d732afa..0cf3932957 100644 --- a/var/spack/repos/builtin/packages/libarchive/package.py +++ b/var/spack/repos/builtin/packages/libarchive/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libarchive(Package): """libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats.""" diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py new file mode 100644 index 0000000000..0167fbcb33 --- /dev/null +++ b/var/spack/repos/builtin/packages/libatomic-ops/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class LibatomicOps(Package): + """This package provides semi-portable access to hardware-provided + atomic memory update operations on a number architectures.""" + + homepage = "https://github.com/ivmai/libatomic_ops" + url = "http://www.hboehm.info/gc/gc_source/libatomic_ops-7.4.4.tar.gz" + + version('7.4.4', '426d804baae12c372967a6d183e25af2') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), + '--enable-shared') + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py index b30d76f4e9..7fb47f8dcd 100644 --- a/var/spack/repos/builtin/packages/libcerf/package.py +++ b/var/spack/repos/builtin/packages/libcerf/package.py @@ -27,9 +27,10 @@ from spack import * class Libcerf(Package): - """ - A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function - w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian + """A self-contained C library providing complex error functions, based + on Faddeeva's plasma dispersion function w(z). Also provides Dawson's + integral and Voigt's convolution of a Gaussian and a Lorentzian + """ homepage = "http://sourceforge.net/projects/libcerf" url = "http://downloads.sourceforge.net/project/libcerf/libcerf-1.3.tgz" diff --git a/var/spack/repos/builtin/packages/libcircle/package.py b/var/spack/repos/builtin/packages/libcircle/package.py index 75fdb96125..971c29f5f1 100644 --- a/var/spack/repos/builtin/packages/libcircle/package.py +++ b/var/spack/repos/builtin/packages/libcircle/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Libcircle(Package): """libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing.""" @@ -32,7 +32,7 @@ class Libcircle(Package): homepage = "https://github.com/hpc/libcircle" version('0.2.1-rc.1', '2b1369a5736457239f908abf88143ec2', - url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz') + url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py new file mode 100644 index 0000000000..53d30ce5c3 --- /dev/null +++ b/var/spack/repos/builtin/packages/libctl/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libctl(Package): + """libctl is a free Guile-based library implementing flexible + control files for scientific simulations.""" + + homepage = "http://ab-initio.mit.edu/wiki/index.php/Libctl" + url = "http://ab-initio.mit.edu/libctl/libctl-3.2.2.tar.gz" + + version('3.2.2', '5fd7634dc9ae8e7fa70a68473b9cbb68') + + depends_on('guile') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), + '--enable-shared', + 'GUILE={0}'.format(join_path( + spec['guile'].prefix.bin, 'guile')), + 'GUILE_CONFIG={0}'.format(join_path( + spec['guile'].prefix.bin, 'guile-config'))) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py index b05412e588..543eab11b3 100644 --- a/var/spack/repos/builtin/packages/libdrm/package.py +++ b/var/spack/repos/builtin/packages/libdrm/package.py @@ -24,12 +24,13 @@ ############################################################################## from spack import * + class Libdrm(Package): """A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other operating systems that support the ioctl interface.""" - homepage = "http://dri.freedesktop.org/libdrm/" # no real website... + homepage = "http://dri.freedesktop.org/libdrm/" # no real website... url = "http://dri.freedesktop.org/libdrm/libdrm-2.4.59.tar.gz" version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6') diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py index 4366344679..235e7648bc 100644 --- a/var/spack/repos/builtin/packages/libedit/package.py +++ b/var/spack/repos/builtin/packages/libedit/package.py @@ -24,12 +24,14 @@ ############################################################################## from spack import * + class Libedit(Package): """An autotools compatible port of the NetBSD editline library""" homepage = "http://thrysoee.dk/editline/" url = "http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz" - version('3.1', '43cdb5df3061d78b5e9d59109871b4f6', url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz") + version('3.1', '43cdb5df3061d78b5e9d59109871b4f6', + url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz") depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 1e1deea818..3304d27bdb 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libelf(Package): """libelf lets you read, modify or create ELF object files in an architecture-independent way. The library takes care of size diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py new file mode 100644 index 0000000000..364ea1e30c --- /dev/null +++ b/var/spack/repos/builtin/packages/libepoxy/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libepoxy(Package): + """Epoxy is a library for handling OpenGL function pointer management for + you.""" + homepage = "https://github.com/anholt/libepoxy" + url = "https://github.com/anholt/libepoxy/releases/download/v1.3.1/libepoxy-1.3.1.tar.bz2" + + version('1.3.1', '96f6620a9b005a503e7b44b0b528287d') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py index 3ae427a2eb..65b3a716c0 100644 --- a/var/spack/repos/builtin/packages/libevent/package.py +++ b/var/spack/repos/builtin/packages/libevent/package.py @@ -24,11 +24,13 @@ ############################################################################## from spack import * + class Libevent(Package): """The libevent API provides a mechanism to execute a callback function - when a specific event occurs on a file descriptor or after a timeout has been - reached. Furthermore, libevent also support callbacks due to signals or regular - timeouts. + when a specific event occurs on a file descriptor or after a + timeout has been reached. Furthermore, libevent also support + callbacks due to signals or regular timeouts. + """ homepage = "http://libevent.org" @@ -46,7 +48,8 @@ class Libevent(Package): version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc') version('2.0.12', '42986228baf95e325778ed328a93e070') - variant('openssl', default=True, description="Build with encryption enabled at the libevent level.") + variant('openssl', default=True, + description="Build with encryption enabled at the libevent level.") depends_on('openssl', when='+openssl') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py index 1d3c85c8e0..fa113ee86c 100644 --- a/var/spack/repos/builtin/packages/libffi/package.py +++ b/var/spack/repos/builtin/packages/libffi/package.py @@ -24,18 +24,21 @@ ############################################################################## from spack import * + class Libffi(Package): """The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time.""" homepage = "https://sourceware.org/libffi/" - - version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") - #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc + + version('3.2.1', '83b89587607e3eb65c70d361f13bab43', + url="ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") + # version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = + # "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug + # $(lib64) instead of ${lib64} in libffi.pc def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() make("install") - diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py index b1a316cc1b..b556def4d3 100644 --- a/var/spack/repos/builtin/packages/libgcrypt/package.py +++ b/var/spack/repos/builtin/packages/libgcrypt/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libgcrypt(Package): """Libgcrypt is a general purpose cryptographic library based on the code from GnuPG. It provides functions for all cryptographic diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index 938f4f6f3b..acfdebb972 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -27,11 +27,14 @@ from spack import * class Libgd(Package): - """ - GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and - "wrappers" are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, - among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the - fly. While not restricted to use on the web, the most common applications of GD involve website development. + """GD is an open source code library for the dynamic creation of images + by programmers. GD is written in C, and "wrappers" are available + for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, + WebP, XPM, BMP images, among other formats. GD is commonly used to + generate charts, graphics, thumbnails, and most anything else, on + the fly. While not restricted to use on the web, the most common + applications of GD involve website development. + """ homepage = "https://github.com/libgd/libgd" diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py index 3fe82a69e7..a0e2acd516 100644 --- a/var/spack/repos/builtin/packages/libgpg-error/package.py +++ b/var/spack/repos/builtin/packages/libgpg-error/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class LibgpgError(Package): """Libgpg-error is a small library that defines common error values for all GnuPG components. Among these are GPG, GPGSM, diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py new file mode 100644 index 0000000000..201e031869 --- /dev/null +++ b/var/spack/repos/builtin/packages/libgtextutils/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libgtextutils(Package): + """Gordon's Text utils Library.""" + + homepage = "https://github.com/agordon/libgtextutils" + url = "https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz" + + version('0.7', '593c7c62e3c76ec49f5736eed4f96806') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libhio/package.py b/var/spack/repos/builtin/packages/libhio/package.py new file mode 100644 index 0000000000..17bd86d310 --- /dev/null +++ b/var/spack/repos/builtin/packages/libhio/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libhio(Package): + """ + A library for writing to hierarchical data store systems. + """ + + homepage = "https://github.com/hpc/libhio/" + url = "https://github.com/hpc/libhio/releases/download/hio.1.3.0.1/libhio-1.3.0.1.tar.gz" + + version('1.3.0.1', 'c073541de8dd70aeb8878bd00d6d877f') + + depends_on("libjson-c") + depends_on("bzip2") + depends_on("pkg-config", type="build") + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py new file mode 100644 index 0000000000..f2eeb07b26 --- /dev/null +++ b/var/spack/repos/builtin/packages/libiconv/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libiconv(Package): + """GNU libiconv provides an implementation of the iconv() function + and the iconv program for character set conversion.""" + + homepage = "https://www.gnu.org/software/libiconv/" + url = "http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz" + + version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), + '--enable-extra-encodings') + + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py index d1239ba0d9..6252a88542 100644 --- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py +++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class LibjpegTurbo(Package): """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and diff --git a/var/spack/repos/builtin/packages/libmng/package.py b/var/spack/repos/builtin/packages/libmng/package.py index dd0903c4bd..a77aada79c 100644 --- a/var/spack/repos/builtin/packages/libmng/package.py +++ b/var/spack/repos/builtin/packages/libmng/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libmng(Package): """libmng -THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation @@ -39,7 +40,8 @@ class Libmng(Package): def patch(self): # jpeg requires stdio to beincluded before its headrs. - filter_file(r'^(\#include \<jpeglib\.h\>)', '#include<stdio.h>\n\\1', 'libmng_types.h') + filter_file(r'^(\#include \<jpeglib\.h\>)', + '#include<stdio.h>\n\\1', 'libmng_types.h') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/libmonitor/package.py b/var/spack/repos/builtin/packages/libmonitor/package.py index 883d8af405..f680baa265 100644 --- a/var/spack/repos/builtin/packages/libmonitor/package.py +++ b/var/spack/repos/builtin/packages/libmonitor/package.py @@ -24,19 +24,19 @@ ############################################################################## from spack import * + class Libmonitor(Package): """Libmonitor is a library for process and thread control.""" - homepage = "http://hpctoolkit.org" - - version('20130218', svn='http://libmonitor.googlecode.com/svn/trunk/', revision=146) - variant('krellpatch', default=False, description="build with openspeedshop based patch.") - + homepage = "https://github.com/HPCToolkit/libmonitor" + version('20130218', git='https://github.com/HPCToolkit/libmonitor.git', + commit='4f2311e') + variant('krellpatch', default=False, + description="build with openspeedshop based patch.") patch('libmonitorkrell-0000.patch', when='@20130218+krellpatch') patch('libmonitorkrell-0001.patch', when='@20130218+krellpatch') patch('libmonitorkrell-0002.patch', when='@20130218+krellpatch') - def install(self, spec, prefix): configure("--prefix=" + prefix) make() diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py index 91cef95cec..a65b81b69b 100644 --- a/var/spack/repos/builtin/packages/libpciaccess/package.py +++ b/var/spack/repos/builtin/packages/libpciaccess/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os.path + class Libpciaccess(Package): """Generic PCI access library.""" diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index 951b91eabd..1afe4911e6 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libpng(Package): """libpng graphics file format""" homepage = "http://www.libpng.org/pub/png/libpng.html" diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py index 4bcca43c24..ea36758a83 100644 --- a/var/spack/repos/builtin/packages/libpthread-stubs/package.py +++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class LibpthreadStubs(Package): """The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py index 14acdcbcd2..715d24bcf7 100644 --- a/var/spack/repos/builtin/packages/libsigsegv/package.py +++ b/var/spack/repos/builtin/packages/libsigsegv/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libsigsegv(Package): """GNU libsigsegv is a library for handling page faults in user mode.""" homepage = "https://www.gnu.org/software/libsigsegv/" diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py index 831a75e659..1c930e21dd 100644 --- a/var/spack/repos/builtin/packages/libsodium/package.py +++ b/var/spack/repos/builtin/packages/libsodium/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libsodium(Package): """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py index c7db959a40..64688505c4 100644 --- a/var/spack/repos/builtin/packages/libtermkey/package.py +++ b/var/spack/repos/builtin/packages/libtermkey/package.py @@ -24,17 +24,17 @@ ############################################################################## from spack import * + class Libtermkey(Package): """Easy keyboard entry processing for terminal programs""" homepage = "http://www.leonerd.org.uk/code/libtermkey/" url = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-0.18.tar.gz" - version('0.18' , '3be2e3e5a851a49cc5e8567ac108b520') - version('0.17' , '20edb99e0d95ec1690fe90e6a555ae6d') - version('0.16' , '7a24b675aaeb142d30db28e7554987d4') + version('0.18', '3be2e3e5a851a49cc5e8567ac108b520') + version('0.17', '20edb99e0d95ec1690fe90e6a555ae6d') + version('0.16', '7a24b675aaeb142d30db28e7554987d4') version('0.15b', '27689756e6c86c56ae454f2ac259bc3d') - version('0.14' , 'e08ce30f440f9715c459060e0e048978') - + version('0.14', 'e08ce30f440f9715c459060e0e048978') def install(self, spec, prefix): make() diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py index 4b03e7997b..cef9fcaae5 100644 --- a/var/spack/repos/builtin/packages/libtiff/package.py +++ b/var/spack/repos/builtin/packages/libtiff/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libtiff(Package): """libtiff graphics format library""" homepage = "http://www.remotesensing.org/libtiff/" diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py new file mode 100644 index 0000000000..5b8837e72b --- /dev/null +++ b/var/spack/repos/builtin/packages/libunistring/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libunistring(Package): + """This library provides functions for manipulating Unicode strings + and for manipulating C strings according to the Unicode standard.""" + + homepage = "https://www.gnu.org/software/libunistring/" + url = "http://ftp.gnu.org/gnu/libunistring/libunistring-0.9.6.tar.xz" + + version('0.9.6', 'cb09c398020c27edac10ca590e9e9ef3') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + # make('check') # test-verify fails for me, contacted developers + make('install') diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py index 980b765c02..63ab4aec59 100644 --- a/var/spack/repos/builtin/packages/libunwind/package.py +++ b/var/spack/repos/builtin/packages/libunwind/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libunwind(Package): """A portable and efficient C programming interface (API) to determine the call-chain of a program.""" diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py index 0dd32ec77d..553f0dddb8 100644 --- a/var/spack/repos/builtin/packages/libuuid/package.py +++ b/var/spack/repos/builtin/packages/libuuid/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libuuid(Package): """Portable uuid C library""" # FIXME: add a proper url for your package's homepage here. diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py index 0d29270b38..dae10809f2 100644 --- a/var/spack/repos/builtin/packages/libuv/package.py +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libuv(Package): """Multi-platform library with a focus on asynchronous IO""" homepage = "http://libuv.org" diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py index e57af273ad..2e1ef99b98 100644 --- a/var/spack/repos/builtin/packages/libvterm/package.py +++ b/var/spack/repos/builtin/packages/libvterm/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libvterm(Package): """An abstract library implementation of a terminal emulator""" homepage = "http://www.leonerd.org.uk/code/libvterm/" diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py index 55816ecdbd..b9215bc601 100644 --- a/var/spack/repos/builtin/packages/libxau/package.py +++ b/var/spack/repos/builtin/packages/libxau/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libxau(Package): """The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client @@ -34,11 +35,10 @@ class Libxau(Package): version('1.0.8', '685f8abbffa6d145c0f930f00703b21b') depends_on('xproto') + depends_on('pkg-config', type='build') def install(self, spec, prefix): - # FIXME: Modify the configure line to suit your build system here. configure('--prefix=%s' % prefix) - # FIXME: Add logic to build and install here make() make("install") diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py index 87437373d6..9ea4d1c326 100644 --- a/var/spack/repos/builtin/packages/libxc/package.py +++ b/var/spack/repos/builtin/packages/libxc/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libxc(Package): """Libxc is a library of exchange-correlation functionals for density-functional theory.""" @@ -33,7 +34,6 @@ class Libxc(Package): version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec') - def install(self, spec, prefix): configure('--prefix=%s' % prefix, '--enable-shared') diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index 586eb970d8..82ddb2742e 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libxcb(Package): """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct @@ -43,11 +44,14 @@ class Libxcb(Package): depends_on('libxau') def patch(self): - filter_file('typedef struct xcb_auth_info_t {', 'typedef struct {', 'src/xcb.h') - + filter_file( + 'typedef struct xcb_auth_info_t {', + 'typedef struct {', + 'src/xcb.h') def install(self, spec, prefix): - env['PKG_CONFIG_PATH'] = env['PKG_CONFIG_PATH'] + ':/usr/lib64/pkgconfig' + env['PKG_CONFIG_PATH'] = env[ + 'PKG_CONFIG_PATH'] + ':/usr/lib64/pkgconfig' configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index a6dabd2c05..0f4810fa8a 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -36,7 +36,9 @@ class Libxml2(Package): variant('python', default=False, description='Enable Python support') - extends('python', when='+python', ignore=r'(bin.*$)|(include.*$)|(share.*$)|(lib/libxml2.*$)|(lib/xml2.*$)|(lib/cmake.*$)') + extends('python', when='+python', + ignore=r'(bin.*$)|(include.*$)|(share.*$)|(lib/libxml2.*$)|' + '(lib/xml2.*$)|(lib/cmake.*$)') depends_on('zlib') depends_on('xz') diff --git a/var/spack/repos/builtin/packages/libxshmfence/package.py b/var/spack/repos/builtin/packages/libxshmfence/package.py index 6d63ea6426..fe5d5667e9 100644 --- a/var/spack/repos/builtin/packages/libxshmfence/package.py +++ b/var/spack/repos/builtin/packages/libxshmfence/package.py @@ -24,11 +24,12 @@ ############################################################################## from spack import * + class Libxshmfence(Package): """This is a tiny library that exposes a event API on top of Linux futexes.""" - homepage = "http://keithp.com/blogs/dri3_extension/" # not really... + homepage = "http://keithp.com/blogs/dri3_extension/" # not really... url = "http://xorg.freedesktop.org/archive/individual/lib/libxshmfence-1.2.tar.gz" version('1.2', 'f0b30c0fc568b22ec524859ee28556f1') diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py index c6c439ad09..47d1c170c6 100644 --- a/var/spack/repos/builtin/packages/libxslt/package.py +++ b/var/spack/repos/builtin/packages/libxslt/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libxslt(Package): """Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py new file mode 100644 index 0000000000..a736490600 --- /dev/null +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -0,0 +1,66 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libxsmm(Package): + '''LIBXSMM is a library for small dense and small sparse matrix-matrix + multiplications targeting Intel Architecture (x86).''' + + homepage = 'https://github.com/hfp/libxsmm' + url = 'https://github.com/hfp/libxsmm/archive/1.4.3.tar.gz' + + version('1.4.3', '9839bf0fb8be7badf1e97ce4c817149b') + version('1.4.2', 'ea025761437f3b5c936821b9ca21ec31') + version('1.4.1', '71648500ea4510529845d329091917df') + version('1.4', 'b42f91bf5285e7ad0463446e55ebdc2b') + + def patch(self): + kwargs = {'ignore_absent': False, 'backup': False, 'string': True} + makefile = FileFilter('Makefile.inc') + + # Spack sets CC, CXX, and FC to point to the compiler wrappers + # Don't let Makefile.inc overwrite these + makefile.filter('CC = icc', 'CC ?= icc', **kwargs) + makefile.filter('CC = gcc', 'CC ?= gcc', **kwargs) + makefile.filter('CXX = icpc', 'CXX ?= icpc', **kwargs) + makefile.filter('CXX = g++', 'CXX ?= g++', **kwargs) + makefile.filter('FC = ifort', 'FC ?= ifort', **kwargs) + makefile.filter('FC = gfortran', 'FC ?= gfortran', **kwargs) + + def manual_install(self, prefix): + install_tree('include', prefix.include) + install_tree('lib', prefix.lib) + install_tree('documentation', prefix.share + '/libxsmm/doc') + + def install(self, spec, prefix): + make_args = [ + 'ROW_MAJOR=0', + 'INDICES_M={0}'.format(' '.join(str(i) for i in range(1, 25))), + 'INDICES_N={0}'.format(' '.join(str(i) for i in range(1, 25))), + 'INDICES_K={0}'.format(' '.join(str(i) for i in range(1, 25))) + ] + make(*make_args) + self.manual_install(prefix) diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py index 127fe1204d..1dcf88e3c0 100644 --- a/var/spack/repos/builtin/packages/llvm-lld/package.py +++ b/var/spack/repos/builtin/packages/llvm-lld/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class LlvmLld(Package): """lld - The LLVM Linker lld is a new set of modular code for creating linker tools.""" diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index e79c123a7e..61ea8daac4 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -23,32 +23,51 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os, glob +import os class Llvm(Package): """The LLVM Project is a collection of modular and reusable compiler and - toolchain technologies. Despite its name, LLVM has little to do with - traditional virtual machines, though it does provide helpful libraries - that can be used to build them. The name "LLVM" itself is not an acronym; - it is the full name of the project. + toolchain technologies. Despite its name, LLVM has little to do + with traditional virtual machines, though it does provide helpful + libraries that can be used to build them. The name "LLVM" itself + is not an acronym; it is the full name of the project. + """ homepage = 'http://llvm.org/' url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz' - version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package + # currently required by mesa package + version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', + url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') - variant('debug', default=False, description="Build a debug version of LLVM, this increases binary size by an order of magnitude, make sure you have 20-30gb of space available to build this") - variant('clang', default=True, description="Build the LLVM C/C++/Objective-C compiler frontend") + variant('debug', default=False, + description="Build a debug version of LLVM, this increases " + "binary size by an order of magnitude, make sure you have " + "20-30gb of space available to build this") + variant('clang', default=True, + description="Build the LLVM C/C++/Objective-C compiler frontend") variant('lldb', default=True, description="Build the LLVM debugger") - variant('internal_unwind', default=True, description="Build the libcxxabi libunwind") - variant('polly', default=True, description="Build the LLVM polyhedral optimization plugin, only builds for 3.7.0+") - variant('libcxx', default=True, description="Build the LLVM C++ standard library") - variant('compiler-rt', default=True, description="Build the LLVM compiler runtime, including sanitizers") - variant('gold', default=True, description="Add support for LTO with the gold linker plugin") - variant('shared_libs', default=False, description="Build all components as shared libraries, faster, less memory to build, less stable") - variant('link_dylib', default=False, description="Build and link the libLLVM shared library rather than static") - variant('all_targets', default=True, description="Build all supported targets, default targets <current arch>,NVPTX,AMDGPU,CppBackend") + variant('internal_unwind', default=True, + description="Build the libcxxabi libunwind") + variant('polly', default=True, + description="Build the LLVM polyhedral optimization plugin, " + "only builds for 3.7.0+") + variant('libcxx', default=True, + description="Build the LLVM C++ standard library") + variant('compiler-rt', default=True, + description="Build LLVM compiler runtime, including sanitizers") + variant('gold', default=True, + description="Add support for LTO with the gold linker plugin") + variant('shared_libs', default=False, + description="Build all components as shared libraries, faster, " + "less memory to build, less stable") + variant('link_dylib', default=False, + description="Build and link the libLLVM shared library rather " + "than static") + variant('all_targets', default=True, + description="Build all supported targets, default targets " + "<current arch>,NVPTX,AMDGPU,CppBackend") # Build dependency depends_on('cmake@2.8.12.2:', type='build') @@ -68,147 +87,147 @@ class Llvm(Package): depends_on('gmp', when='@:3.6.999 +polly') depends_on('isl', when='@:3.6.999 +polly') - base_url = 'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz' - llvm_url = base_url % { 'pkg' : 'llvm'} + base_url = 'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz' + llvm_url = base_url % {'pkg': 'llvm'} resources = { - 'compiler-rt' : { - 'url' : base_url % { 'pkg' : 'compiler-rt'}, - 'destination' : 'projects', - 'placement' : 'compiler-rt', - }, - 'openmp' : { - 'url' : base_url % { 'pkg' : 'openmp'}, - 'destination' : 'projects', - 'placement' : 'openmp', - }, - 'libcxx' : { - 'url' : base_url % { 'pkg' : 'libcxx'}, - 'destination' : 'projects', - 'placement' : 'libcxx', - }, - 'libcxxabi' : { - 'url' : base_url % { 'pkg' : 'libcxxabi'}, - 'destination' : 'projects', - 'placement' : 'libcxxabi', - }, - 'clang' : { - 'url' : base_url % { 'pkg' : 'cfe'}, - 'destination' : 'tools', - 'placement' : 'clang', - }, - 'clang-tools-extra' : { - 'url' : base_url % { 'pkg' : 'clang-tools-extra'}, - 'destination' : 'tools/clang/tools', - 'placement' : 'extra', - }, - 'lldb' : { - 'url' : base_url % { 'pkg' : 'lldb'}, - 'destination' : 'tools', - 'placement' : 'lldb', - }, - 'polly' : { - 'url' : base_url % { 'pkg' : 'polly'}, - 'destination' : 'tools', - 'placement' : 'polly', - }, - 'llvm-libunwind' : { - 'url' : base_url % { 'pkg' : 'libunwind'}, - 'destination' : 'projects', - 'placement' : 'libunwind', - }, - } + 'compiler-rt': { + 'url': base_url % {'pkg': 'compiler-rt'}, + 'destination': 'projects', + 'placement': 'compiler-rt', + }, + 'openmp': { + 'url': base_url % {'pkg': 'openmp'}, + 'destination': 'projects', + 'placement': 'openmp', + }, + 'libcxx': { + 'url': base_url % {'pkg': 'libcxx'}, + 'destination': 'projects', + 'placement': 'libcxx', + }, + 'libcxxabi': { + 'url': base_url % {'pkg': 'libcxxabi'}, + 'destination': 'projects', + 'placement': 'libcxxabi', + }, + 'clang': { + 'url': base_url % {'pkg': 'cfe'}, + 'destination': 'tools', + 'placement': 'clang', + }, + 'clang-tools-extra': { + 'url': base_url % {'pkg': 'clang-tools-extra'}, + 'destination': 'tools/clang/tools', + 'placement': 'extra', + }, + 'lldb': { + 'url': base_url % {'pkg': 'lldb'}, + 'destination': 'tools', + 'placement': 'lldb', + }, + 'polly': { + 'url': base_url % {'pkg': 'polly'}, + 'destination': 'tools', + 'placement': 'polly', + }, + 'llvm-libunwind': { + 'url': base_url % {'pkg': 'libunwind'}, + 'destination': 'projects', + 'placement': 'libunwind', + }, + } releases = [ - { - 'version' : 'trunk', - 'repo' : 'http://llvm.org/svn/llvm-project/llvm/trunk', - 'resources' : { - 'compiler-rt' : 'http://llvm.org/svn/llvm-project/compiler-rt/trunk', - 'openmp' : 'http://llvm.org/svn/llvm-project/openmp/trunk', - 'polly' : 'http://llvm.org/svn/llvm-project/polly/trunk', - 'libcxx' : 'http://llvm.org/svn/llvm-project/libcxx/trunk', - 'libcxxabi' : 'http://llvm.org/svn/llvm-project/libcxxabi/trunk', - 'clang' : 'http://llvm.org/svn/llvm-project/cfe/trunk', - 'clang-tools-extra' : 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk', - 'lldb' : 'http://llvm.org/svn/llvm-project/lldb/trunk', - 'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk', - } - }, - { - 'version' : '3.8.0', - 'md5':'07a7a74f3c6bd65de4702bf941b511a0', - 'resources' : { - 'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025', - 'openmp' : '8fd7cc35d48051613cf1e750e9f22e40', - 'polly' : '1b3b20f52d34a4024e21a4ea7112caa7', - 'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a', - 'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7', - 'clang' : 'cc99e7019bb74e6459e80863606250c5', - 'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036', - 'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e', - 'llvm-libunwind' : '162ade468607f153cca12be90b5194fa', - } - }, - { - 'version' : '3.7.1', - 'md5':'bf8b3a2c79e61212c5409041dfdbd319', - 'resources' : { - 'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01', - 'openmp' : 'b4ad08cda4e5c22e42b66062b140438e', - 'polly' : '3a2a7367002740881637f4d47bca4dc3', - 'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140', - 'libcxxabi' : '52d925afac9f97e9dcac90745255c169', - 'clang' : '0acd026b5529164197563d135a8fd83e', - 'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2', - 'lldb' : 'a106d8a0d21fc84d76953822fbaf3398', - 'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c', - } - }, - { - 'version' : '3.7.0', - 'md5':'b98b9495e5655a672d6cb83e1a180f8e', - 'resources' : { - 'compiler-rt' : '383c10affd513026f08936b5525523f5', - 'openmp' : 'f482c86fdead50ba246a1a2b0bbf206f', - 'polly' : '32f93ffc9cc7e042df22089761558f8b', - 'libcxx' : '46aa5175cbe1ad42d6e9c995968e56dd', - 'libcxxabi' : '5aa769e2fca79fa5335cfae8f6258772', - 'clang' : '8f9d27335e7331cf0a4711e952f21f01', - 'clang-tools-extra' : 'd5a87dacb65d981a427a536f6964642e', - 'lldb' : 'e5931740400d1dc3e7db4c7ba2ceff68', - 'llvm-libunwind' : '9a75392eb7eb8ed5c0840007e212baf5', - } - }, - { - 'version' : '3.6.2', - 'md5':'0c1ee3597d75280dee603bae9cbf5cc2', - 'resources' : { - 'compiler-rt' : 'e3bc4eb7ba8c39a6fe90d6c988927f3c', - 'openmp' : '65dd5863b9b270960a96817e9152b123', - 'libcxx' : '22214c90697636ef960a49aef7c1823a', - 'libcxxabi' : '17518e361e4e228f193dd91e8ef54ba2', - 'clang' : 'ff862793682f714bb7862325b9c06e20', - 'clang-tools-extra' : '3ebc1dc41659fcec3db1b47d81575e06', - 'lldb' : '51e5eb552f777b950bb0ff326e60d5f0', - } - }, - { - 'version' : '3.5.1', - 'md5':'2d3d8004f38852aa679e5945b8ce0b14', - 'resources' : { - 'compiler-rt' : 'd626cfb8a9712cb92b820798ab5bc1f8', - 'openmp' : '121ddb10167d7fc38b1f7e4b029cf059', - 'libcxx' : '406f09b1dab529f3f7879f4d548329d2', - 'libcxxabi' : 'b22c707e8d474a99865ad3c521c3d464', - 'clang' : '93f9532f8f7e6f1d8e5c1116907051cb', - 'clang-tools-extra' : 'f13f31ed3038acadc6fa63fef812a246', - 'lldb' : 'cc5ea8a414c62c33e760517f8929a204', - } - }, - ] + { + 'version': 'trunk', + 'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk', + 'resources': { + 'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk', + 'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk', + 'polly': 'http://llvm.org/svn/llvm-project/polly/trunk', + 'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk', + 'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk', + 'clang': 'http://llvm.org/svn/llvm-project/cfe/trunk', + 'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk', + 'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk', + 'llvm-libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk', + } + }, + { + 'version': '3.8.0', + 'md5': '07a7a74f3c6bd65de4702bf941b511a0', + 'resources': { + 'compiler-rt': 'd6fcbe14352ffb708e4d1ac2e48bb025', + 'openmp': '8fd7cc35d48051613cf1e750e9f22e40', + 'polly': '1b3b20f52d34a4024e21a4ea7112caa7', + 'libcxx': 'd6e0bdbbee39f7907ad74fd56d03b88a', + 'libcxxabi': 'bbe6b4d72c7c5978550d370af529bcf7', + 'clang': 'cc99e7019bb74e6459e80863606250c5', + 'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036', + 'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e', + 'llvm-libunwind': '162ade468607f153cca12be90b5194fa', + } + }, + { + 'version': '3.7.1', + 'md5': 'bf8b3a2c79e61212c5409041dfdbd319', + 'resources': { + 'compiler-rt': '1c6975daf30bb3b0473b53c3a1a6ff01', + 'openmp': 'b4ad08cda4e5c22e42b66062b140438e', + 'polly': '3a2a7367002740881637f4d47bca4dc3', + 'libcxx': 'f9c43fa552a10e14ff53b94d04bea140', + 'libcxxabi': '52d925afac9f97e9dcac90745255c169', + 'clang': '0acd026b5529164197563d135a8fd83e', + 'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2', + 'lldb': 'a106d8a0d21fc84d76953822fbaf3398', + 'llvm-libunwind': '814bd52c9247c5d04629658fbcb3ab8c', + } + }, + { + 'version': '3.7.0', + 'md5': 'b98b9495e5655a672d6cb83e1a180f8e', + 'resources': { + 'compiler-rt': '383c10affd513026f08936b5525523f5', + 'openmp': 'f482c86fdead50ba246a1a2b0bbf206f', + 'polly': '32f93ffc9cc7e042df22089761558f8b', + 'libcxx': '46aa5175cbe1ad42d6e9c995968e56dd', + 'libcxxabi': '5aa769e2fca79fa5335cfae8f6258772', + 'clang': '8f9d27335e7331cf0a4711e952f21f01', + 'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e', + 'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68', + 'llvm-libunwind': '9a75392eb7eb8ed5c0840007e212baf5', + } + }, + { + 'version': '3.6.2', + 'md5': '0c1ee3597d75280dee603bae9cbf5cc2', + 'resources': { + 'compiler-rt': 'e3bc4eb7ba8c39a6fe90d6c988927f3c', + 'openmp': '65dd5863b9b270960a96817e9152b123', + 'libcxx': '22214c90697636ef960a49aef7c1823a', + 'libcxxabi': '17518e361e4e228f193dd91e8ef54ba2', + 'clang': 'ff862793682f714bb7862325b9c06e20', + 'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06', + 'lldb': '51e5eb552f777b950bb0ff326e60d5f0', + } + }, + { + 'version': '3.5.1', + 'md5': '2d3d8004f38852aa679e5945b8ce0b14', + 'resources': { + 'compiler-rt': 'd626cfb8a9712cb92b820798ab5bc1f8', + 'openmp': '121ddb10167d7fc38b1f7e4b029cf059', + 'libcxx': '406f09b1dab529f3f7879f4d548329d2', + 'libcxxabi': 'b22c707e8d474a99865ad3c521c3d464', + 'clang': '93f9532f8f7e6f1d8e5c1116907051cb', + 'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246', + 'lldb': 'cc5ea8a414c62c33e760517f8929a204', + } + }, + ] for release in releases: - if release['version'] == 'trunk' : + if release['version'] == 'trunk': version(release['version'], svn=release['repo']) for name, repo in release['resources'].items(): @@ -230,18 +249,19 @@ class Llvm(Package): def install(self, spec, prefix): env['CXXFLAGS'] = self.compiler.cxx11_flag - cmake_args = [ arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg ] + cmake_args = [arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg] build_type = 'RelWithDebInfo' if '+debug' in spec else 'Release' cmake_args.extend([ - '..', - '-DCMAKE_BUILD_TYPE=' + build_type, - '-DLLVM_REQUIRES_RTTI:BOOL=ON', - '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp', - '-DPYTHON_EXECUTABLE:PATH=%s/bin/python' % spec['python'].prefix ]) + '..', + '-DCMAKE_BUILD_TYPE=' + build_type, + '-DLLVM_REQUIRES_RTTI:BOOL=ON', + '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp', + '-DPYTHON_EXECUTABLE:PATH=%s/bin/python' % spec['python'].prefix]) if '+gold' in spec: - cmake_args.append('-DLLVM_BINUTILS_INCDIR=' + os.path.join( spec['binutils'].prefix, 'include')) + cmake_args.append('-DLLVM_BINUTILS_INCDIR=' + + os.path.join(spec['binutils'].prefix, 'include')) if '+polly' in spec: cmake_args.append('-DLINK_POLLY_INTO_TOOLS:Bool=ON') else: @@ -265,7 +285,7 @@ class Llvm(Package): if '+link_dylib' in spec: cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON') - if '+all_targets' not in spec: # all is default on cmake + if '+all_targets' not in spec: # all is default on cmake targets = ['CppBackend', 'NVPTX', 'AMDGPU'] if 'x86' in spec.architecture.target.lower(): targets.append('X86') @@ -279,13 +299,16 @@ class Llvm(Package): 'power' in spec.architecture.target.lower()): targets.append('PowerPC') - cmake_args.append('-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets)) + cmake_args.append( + '-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets)) - if '+clang' not in spec: + if '+clang' not in spec: if '+clang_extra' in spec: - raise SpackException('The clang_extra variant requires the clang variant to be selected') + raise SpackException( + 'The clang_extra variant requires the `+clang` variant.') if '+lldb' in spec: - raise SpackException('The lldb variant requires the clang variant to be selected') + raise SpackException( + 'The lldb variant requires the `+clang` variant') with working_dir('spack-build', create=True): cmake(*cmake_args) diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py index 79c020b2df..8c6c23d8dc 100644 --- a/var/spack/repos/builtin/packages/lmdb/package.py +++ b/var/spack/repos/builtin/packages/lmdb/package.py @@ -25,12 +25,12 @@ import os from spack import * + class Lmdb(Package): """Read-only mirror of official repo on openldap.org. Issues and pull requests here are ignored. Use OpenLDAP ITS for issues. http://www.openldap.org/software/repo.html""" - homepage = "http://www.openldap.org/software/repo.html" url = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.16.tar.gz" diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 01911c1a30..69965bc423 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -35,9 +35,10 @@ class Lmod(Package): variable. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found. """ - homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod' # NOQA: ignore=E501 + homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod' url = 'https://github.com/TACC/Lmod/archive/6.4.1.tar.gz' + version('6.4.5', '14f6c58dbc0a5a75574d795eac2c1e3c') version('6.4.1', '7978ba777c8aa41a4d8c05fec5f780f4') version('6.3.7', '0fa4d5a24c41cae03776f781aa2dedc1') version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9') @@ -55,15 +56,16 @@ class Lmod(Package): spack_env.append_path('LUA_PATH', stage_lua_path.format( version=self.version), separator=';') - patch('fix_tclsh_paths.patch') + patch('fix_tclsh_paths.patch', when='@:6.4.3') def patch(self): """The tcl scripts should use the tclsh that was discovered by the configure script. Touch up their #! lines so that the sed in the Makefile's install step has something to work on. Requires the change in the associated patch file.fg""" - for tclscript in glob('src/*.tcl'): - filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript) + if self.spec.version <= Version('6.4.3'): + for tclscript in glob('src/*.tcl'): + filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript) def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/lwgrp/package.py b/var/spack/repos/builtin/packages/lwgrp/package.py index 471098c873..9322d69b9b 100644 --- a/var/spack/repos/builtin/packages/lwgrp/package.py +++ b/var/spack/repos/builtin/packages/lwgrp/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Lwgrp(Package): """Thie light-weight group library provides process group representations using O(log N) space and time.""" diff --git a/var/spack/repos/builtin/packages/lwm2/package.py b/var/spack/repos/builtin/packages/lwm2/package.py index 340474b47e..063204b84a 100644 --- a/var/spack/repos/builtin/packages/lwm2/package.py +++ b/var/spack/repos/builtin/packages/lwm2/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Lwm2(Package): """LWM2: Light Weight Measurement Module. This is a PMPI module that can collect a number of time-sliced MPI and POSIX I/O diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py index dcb306dcd3..b3bb5e61ce 100644 --- a/var/spack/repos/builtin/packages/m4/package.py +++ b/var/spack/repos/builtin/packages/m4/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class M4(Package): """GNU M4 is an implementation of the traditional Unix macro processor.""" homepage = "https://www.gnu.org/software/m4/m4.html" @@ -33,14 +34,16 @@ class M4(Package): patch('pgi.patch', when='@1.4.17') - variant('sigsegv', default=True, description="Build the libsigsegv dependency") + variant('sigsegv', default=True, + description="Build the libsigsegv dependency") depends_on('libsigsegv', when='+sigsegv') def install(self, spec, prefix): configure_args = [] if 'libsigsegv' in spec: - configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix) + configure_args.append('--with-libsigsegv-prefix=%s' % + spec['libsigsegv'].prefix) else: configure_args.append('--without-libsigsegv-prefix') diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py new file mode 100644 index 0000000000..131b8c58f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/mafft/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Mafft(Package): + """MAFFT is a multiple sequence alignment program for unix-like + operating systems. It offers a range of multiple alignment + methods, L-INS-i (accurate; for alignment of <~200 sequences), + FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.""" + + homepage = "http://mafft.cbrc.jp/alignment/software/index.html" + url = "http://mafft.cbrc.jp/alignment/software/mafft-7.221-with-extensions-src.tgz" + + version('7.221', 'b1aad911e51024d631722a2e061ba215') + + def install(self, spec, prefix): + with working_dir('core'): + make('PREFIX=%s' % prefix) + make('PREFIX=%s' % prefix, 'install') diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py index 13c0ce768f..e1a42c0d9a 100644 --- a/var/spack/repos/builtin/packages/mbedtls/package.py +++ b/var/spack/repos/builtin/packages/mbedtls/package.py @@ -24,17 +24,21 @@ ############################################################################## from spack import * + class Mbedtls(Package): - """ - mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographic and SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal coding footprint. + """mbed TLS (formerly known as PolarSSL) makes it trivially easy for + developers to include cryptographic and SSL/TLS capabilities in + their (embedded) products, facilitating this functionality with a + minimal coding footprint. + """ homepage = "https://tls.mbed.org" url = "https://github.com/ARMmbed/mbedtls/archive/mbedtls-2.2.1.tar.gz" - version('2.2.1' , '73a38f96898d6d03e32f55dd9f9a67be') - version('2.2.0' , 'eaf4586c1ef93ae872e606b6c1203942') - version('2.1.4' , '40cdf67b6c6d92c9cbcfd552d39ea3ae') - version('2.1.3' , '7eb4cf1dfa68578a2c8dbd0b6fa752dd') + version('2.2.1', '73a38f96898d6d03e32f55dd9f9a67be') + version('2.2.0', 'eaf4586c1ef93ae872e606b6c1203942') + version('2.1.4', '40cdf67b6c6d92c9cbcfd552d39ea3ae') + version('2.1.3', '7eb4cf1dfa68578a2c8dbd0b6fa752dd') version('1.3.16', '4144d7320c691f721aeb9e67a1bc38e0') depends_on('cmake', type='build') diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py new file mode 100644 index 0000000000..2c1018e711 --- /dev/null +++ b/var/spack/repos/builtin/packages/meep/package.py @@ -0,0 +1,109 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Meep(Package): + """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation + software package developed at MIT to model electromagnetic systems.""" + + homepage = "http://ab-initio.mit.edu/wiki/index.php/Meep" + + version('1.3', '18a5b9e18008627a0411087e0bb60db5') + version('1.2.1', '9be2e743c3a832ae922de9d955d016c5') + version('1.1.1', '415e0cd312b6caa22b5dd612490e1ccf') + + variant('blas', default=True, description='Enable BLAS support') + variant('lapack', default=True, description='Enable LAPACK support') + variant('harminv', default=True, description='Enable Harminv support') + variant('guile', default=True, description='Enable Guilde support') + variant('libctl', default=True, description='Enable libctl support') + variant('mpi', default=True, description='Enable MPI support') + variant('hdf5', default=True, description='Enable HDF5 support') + variant('gsl', default=True, description='Enable GSL support') + + depends_on('blas', when='+blas') + depends_on('lapack', when='+lapack') + depends_on('harminv', when='+harminv') + depends_on('guile', when='+guile') + depends_on('libctl@3.2:', when='+libctl') + depends_on('mpi', when='+mpi') + depends_on('hdf5~mpi', when='+hdf5~mpi') + depends_on('hdf5+mpi', when='+hdf5+mpi') + depends_on('gsl', when='+gsl') + + def url_for_version(self, version): + base_url = "http://ab-initio.mit.edu/meep" + if version > Version('1.1.1'): + return "{0}/meep-{1}.tar.gz".format(base_url, version) + else: + return "{0}/old/meep-{1}.tar.gz".format(base_url, version) + + def install(self, spec, prefix): + config_args = [ + '--prefix={0}'.format(prefix), + '--enable-shared' + ] + + if '+blas' in spec: + config_args.append('--with-blas={0}'.format( + spec['blas'].prefix.lib)) + else: + config_args.append('--without-blas') + + if '+lapack' in spec: + config_args.append('--with-lapack={0}'.format( + spec['lapack'].prefix.lib)) + else: + config_args.append('--without-lapack') + + if '+libctl' in spec: + config_args.append('--with-libctl={0}'.format( + join_path(spec['libctl'].prefix.share, 'libctl'))) + else: + config_args.append('--without-libctl') + + if '+mpi' in spec: + config_args.append('--with-mpi') + else: + config_args.append('--without-mpi') + + if '+hdf5' in spec: + config_args.append('--with-hdf5') + else: + config_args.append('--without-hdf5') + + configure(*config_args) + + make() + + # aniso_disp test fails unless installed with harminv + # near2far test fails unless installed with gsl + if self.run_tests and '+harminv' in spec and '+gsl' in spec: + # Most tests fail when run in parallel + # 2D_convergence tests still fails to converge for unknown reasons + make('check', parallel=False) + + make('install') diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py index 31672abaec..ffad167788 100644 --- a/var/spack/repos/builtin/packages/memaxes/package.py +++ b/var/spack/repos/builtin/packages/memaxes/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Memaxes(Package): """MemAxes is a visualizer for sampled memory trace data.""" diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py index 3bad17b5cb..299b9a9267 100644 --- a/var/spack/repos/builtin/packages/mesa/package.py +++ b/var/spack/repos/builtin/packages/mesa/package.py @@ -24,13 +24,13 @@ ############################################################################## from spack import * + class Mesa(Package): """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" homepage = "http://www.mesa3d.org" url = "ftp://ftp.freedesktop.org/pub/mesa/older-versions/8.x/8.0.5/MesaLib-8.0.5.tar.gz" - # url = "ftp://ftp.freedesktop.org/pub/mesa/10.4.4/MesaLib-10.4.4.tar.gz" # version('10.4.4', '8d863a3c209bf5116b2babfccccc68ce') version('8.0.5', 'cda5d101f43b8784fa60bdeaca4056f2') @@ -50,7 +50,6 @@ class Mesa(Package): # depends_on("libxcb") # depends_on("libxshmfence") - def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 2180f2cce2..9f8ed5c9e8 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -43,12 +43,16 @@ class Metis(Package): version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5') version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds the library in debug mode') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') - variant('idx64', default=False, description='Use int64_t as default index type') - variant('real64', default=False, description='Use double precision floating point types') + variant('idx64', default=False, + description='Use int64_t as default index type') + variant('real64', default=False, + description='Use double precision floating point types') depends_on('cmake@2.8:', when='@5:', type='build') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index e7a1d96388..fd91f705eb 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -23,7 +23,9 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import glob, string +import glob +import string + class Mfem(Package): """Free, lightweight, scalable C++ library for finite element methods.""" @@ -31,10 +33,12 @@ class Mfem(Package): homepage = 'http://www.mfem.org' url = 'https://github.com/mfem/mfem' - version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', + version('3.2', + '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', url='http://goo.gl/Y9T75B', expand=False, preferred=True) - version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', + version('3.1', + '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', url='http://goo.gl/xrScXn', expand=False) # version('3.1', git='https://github.com/mfem/mfem.git', # commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') @@ -71,8 +75,9 @@ class Mfem(Package): if '+suite-sparse' in spec and ('+metis' not in spec or '+lapack' not in spec): raise InstallError('mfem+suite-sparse must be built with ' + - '+metis and +lapack!') - if 'metis@5:' in spec and '%clang' in spec and ('^cmake %gcc' not in spec): + '+metis and +lapack!') + if 'metis@5:' in spec and '%clang' in spec and ( + '^cmake %gcc' not in spec): raise InstallError('To work around CMake bug with clang, must ' + 'build mfem with mfem[+variants] %clang ' + '^cmake %gcc to force CMake to build with gcc') @@ -86,15 +91,17 @@ class Mfem(Package): if '+lapack' in spec: lapack_lib = '-L{0} -llapack -L{1} -lblas'.format( spec['lapack'].prefix.lib, spec['blas'].prefix.lib) - options.extend(['MFEM_USE_LAPACK=YES', - 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, - 'LAPACK_LIB=%s' % lapack_lib]) + options.extend([ + 'MFEM_USE_LAPACK=YES', + 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, + 'LAPACK_LIB=%s' % lapack_lib]) if '+hypre' in spec: - options.extend(['HYPRE_DIR=%s' % spec['hypre'].prefix, - 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include, - 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + - ' -lHYPRE']) + options.extend([ + 'HYPRE_DIR=%s' % spec['hypre'].prefix, + 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include, + 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + + ' -lHYPRE']) if '+metis' in spec: metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib @@ -102,22 +109,26 @@ class Mfem(Package): metis_str = 'MFEM_USE_METIS_5=YES' else: metis_str = 'MFEM_USE_METIS_5=NO' - options.extend([metis_str, - 'METIS_DIR=%s' % spec['metis'].prefix, - 'METIS_OPT=-I%s' % spec['metis'].prefix.include, - 'METIS_LIB=%s' % metis_lib]) + options.extend([ + metis_str, + 'METIS_DIR=%s' % spec['metis'].prefix, + 'METIS_OPT=-I%s' % spec['metis'].prefix.include, + 'METIS_LIB=%s' % metis_lib]) - if '+mpi' in spec: options.extend(['MFEM_USE_MPI=YES']) + if '+mpi' in spec: + options.extend(['MFEM_USE_MPI=YES']) if '+suite-sparse' in spec: ssp = spec['suite-sparse'].prefix ss_lib = '-L%s' % ssp.lib ss_lib += (' -lumfpack -lcholmod -lcolamd -lamd -lcamd' + - ' -lccolamd -lsuitesparseconfig') + ' -lccolamd -lsuitesparseconfig') no_librt_archs = ['darwin-i686', 'darwin-x86_64'] - no_rt = any(map(lambda a: spec.satisfies('='+a), no_librt_archs)) - if not no_rt: ss_lib += ' -lrt' + no_rt = any(map(lambda a: spec.satisfies('=' + a), + no_librt_archs)) + if not no_rt: + ss_lib += ' -lrt' ss_lib += (' ' + metis_lib + ' ' + lapack_lib) options.extend(['MFEM_USE_SUITESPARSE=YES', @@ -125,10 +136,11 @@ class Mfem(Package): 'SUITESPARSE_OPT=-I%s' % ssp.include, 'SUITESPARSE_LIB=%s' % ss_lib]) - if '+debug' in spec: options.extend(['MFEM_DEBUG=YES']) + if '+debug' in spec: + options.extend(['MFEM_DEBUG=YES']) # Dirty hack to cope with URL redirect - tgz_file = string.split(self.url,'/')[-1] + tgz_file = string.split(self.url, '/')[-1] tar = which('tar') tar('xzvf', tgz_file) cd(glob.glob('mfem*')[0]) @@ -138,12 +150,12 @@ class Mfem(Package): make('all') # Run a small test before installation - args = ['-m', join_path('data','star.mesh'), '--no-visualization'] + args = ['-m', join_path('data', 'star.mesh'), '--no-visualization'] if '+mpi' in spec: Executable(join_path(spec['mpi'].prefix.bin, 'mpirun'))('-np', '4', - join_path('examples','ex1p'), + join_path('examples', 'ex1p'), *args) else: Executable(join_path('examples', 'ex1'))(*args) diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py index 6ea64f5313..71a233ff3e 100644 --- a/var/spack/repos/builtin/packages/mkl/package.py +++ b/var/spack/repos/builtin/packages/mkl/package.py @@ -12,9 +12,9 @@ class Mkl(IntelInstaller): mirror, see http://software.llnl.gov/spack/mirrors.html. To set the threading layer at run time set MKL_THREADING_LAYER - variable to one of the following values: INTEL, SEQUENTIAL, PGI. + variable to one of the following values: INTEL (default), SEQUENTIAL, PGI. To set interface layer at run time, use set the MKL_INTERFACE_LAYER - variable to LP64 or ILP64. + variable to LP64 (default) or ILP64. """ homepage = "https://software.intel.com/en-us/intel-mkl" @@ -38,6 +38,13 @@ class Mkl(IntelInstaller): for f in os.listdir(mkl_dir): os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f)) + # Unfortunately MKL libs are natively distrubted in prefix/lib/intel64. + # To make MKL play nice with Spack, symlink all files to prefix/lib: + mkl_lib_dir = os.path.join(prefix, "lib", "intel64") + for f in os.listdir(mkl_lib_dir): + os.symlink(os.path.join(mkl_lib_dir, f), + os.path.join(self.prefix, "lib", f)) + def setup_dependent_package(self, module, dspec): # For now use Single Dynamic Library: # To set the threading layer at run time, use the @@ -53,6 +60,7 @@ class Mkl(IntelInstaller): name = 'libmkl_rt.%s' % dso_suffix libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib) + # Now set blas/lapack libs: self.spec.blas_shared_lib = join_path(libdir, name) self.spec.lapack_shared_lib = self.spec.blas_shared_lib diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py index 92eb976f8b..71cacd5dfe 100644 --- a/var/spack/repos/builtin/packages/mpc/package.py +++ b/var/spack/repos/builtin/packages/mpc/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpc(Package): """Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the diff --git a/var/spack/repos/builtin/packages/mpe2/package.py b/var/spack/repos/builtin/packages/mpe2/package.py index f69ea2d65b..a129d59949 100644 --- a/var/spack/repos/builtin/packages/mpe2/package.py +++ b/var/spack/repos/builtin/packages/mpe2/package.py @@ -24,8 +24,9 @@ ############################################################################## from spack import * + class Mpe2(Package): - """Message Passing Extensions (MPE) -- Parallel, shared X window graphics""" + """Message Passing Extensions (MPE): Parallel, shared X window graphics""" homepage = "http://www.mcs.anl.gov/research/projects/perfvis/software/MPE/" url = "ftp://ftp.mcs.anl.gov/pub/mpi/mpe/mpe2-1.3.0.tar.gz" diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py index ed3926a8ab..5777cd1926 100644 --- a/var/spack/repos/builtin/packages/mpfr/package.py +++ b/var/spack/repos/builtin/packages/mpfr/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpfr(Package): """The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.""" diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py index e659663d90..f3feaaaa42 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpibash/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Mpibash(Package): """Parallel scripting right from the Bourne-Again Shell (Bash)""" homepage = "http://www.ccs3.lanl.gov/~pakin/software/mpibash-4.3.html" diff --git a/var/spack/repos/builtin/packages/mpileaks/package.py b/var/spack/repos/builtin/packages/mpileaks/package.py index 51bc66a0eb..ec4e9b30cc 100644 --- a/var/spack/repos/builtin/packages/mpileaks/package.py +++ b/var/spack/repos/builtin/packages/mpileaks/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class Mpileaks(Package): - """Tool to detect and report leaked MPI objects like MPI_Requests and MPI_Datatypes.""" + """Tool to detect and report leaked MPI objects like MPI_Requests and + MPI_Datatypes.""" homepage = "https://github.com/hpc/mpileaks" url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index 3380c7f823..490e99dd83 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -24,34 +24,40 @@ ############################################################################## from spack import * + class Mrnet(Package): """The MRNet Multi-Cast Reduction Network.""" homepage = "http://paradyn.org/mrnet" url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz" list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet" - version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9') + version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', + commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9') version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd') version('4.1.0', '5a248298b395b329e2371bf25366115c') version('4.0.0', 'd00301c078cba57ef68613be32ceea2f') - # Add a patch that brings mrnet-5.0.1 up to date with the current development tree - # The development tree contains fixes needed for the krell based tools - variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.") + # Add a patch that brings mrnet-5.0.1 up to date with the current + # development tree The development tree contains fixes needed for the + # krell based tools + variant('krellpatch', default=False, + description="Build MRNet with krell openspeedshop based patch.") patch('krell-5.0.1.patch', when='@5.0.1+krellpatch') - variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries") + variant('lwthreads', default=False, + description="Also build the MRNet LW threadsafe libraries") parallel = False depends_on("boost") def install(self, spec, prefix): - # Build the MRNet LW thread safe libraries when the krelloptions variant is present + # Build the MRNet LW thread safe libraries when the krelloptions + # variant is present if '+lwthreads' in spec: - configure("--prefix=%s" %prefix, "--enable-shared", "--enable-ltwt-threadsafe") + configure("--prefix=%s" % prefix, "--enable-shared", + "--enable-ltwt-threadsafe") else: - configure("--prefix=%s" %prefix, "--enable-shared") + configure("--prefix=%s" % prefix, "--enable-shared") make() make("install") - diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py index d42ac255d0..9a726e2356 100644 --- a/var/spack/repos/builtin/packages/msgpack-c/package.py +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class MsgpackC(Package): """A small, fast binary interchange format convertible to/from JSON""" homepage = "http://www.msgpack.org" diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index b85a6d2b94..32bc42a9c3 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -36,15 +36,24 @@ class Mumps(Package): version('5.0.1', 'b477573fdcc87babe861f62316833db0') - variant('mpi', default=True, description='Activate the compilation of MUMPS with the MPI support') - variant('scotch', default=False, description='Activate Scotch as a possible ordering library') - variant('ptscotch', default=False, description='Activate PT-Scotch as a possible ordering library') - variant('metis', default=False, description='Activate Metis as a possible ordering library') - variant('parmetis', default=False, description='Activate Parmetis as a possible ordering library') - variant('double', default=True, description='Activate the compilation of dmumps') - variant('float', default=True, description='Activate the compilation of smumps') - variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps') - variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') + variant('mpi', default=True, + description='Compile MUMPS with MPI support') + variant('scotch', default=False, + description='Activate Scotch as a possible ordering library') + variant('ptscotch', default=False, + description='Activate PT-Scotch as a possible ordering library') + variant('metis', default=False, + description='Activate Metis as a possible ordering library') + variant('parmetis', default=False, + description='Activate Parmetis as a possible ordering library') + variant('double', default=True, + description='Activate the compilation of dmumps') + variant('float', default=True, + description='Activate the compilation of smumps') + variant('complex', default=True, + description='Activate the compilation of cmumps and/or zmumps') + variant('idx64', default=False, + description='Use int64_t/integer*8 as default index type') variant('shared', default=True, description='Build shared libraries') depends_on('scotch + esmumps', when='~ptscotch+scotch') @@ -61,8 +70,10 @@ class Mumps(Package): # end before install # def patch(self): def write_makefile_inc(self): - if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: # NOQA: ignore=E501 - raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: ignore=E501 + if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and ( + '+mpi' not in self.spec): + raise RuntimeError( + 'You cannot use the variants parmetis or ptscotch without mpi') makefile_conf = ["LIBBLAS = %s" % to_link_flags( self.spec['blas'].blas_shared_lib) @@ -115,7 +126,7 @@ class Mumps(Package): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: ignore=E501 + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # noqa 'OPTL = %s -O ' % fpic, 'OPTC = %s -O -DINTSIZE64' % fpic]) else: @@ -148,13 +159,13 @@ class Mumps(Package): # 10.10. Use gfortran. (Homebrew) makefile_conf.extend([ 'LIBEXT=.dylib', - 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib), # NOQA: ignore=E501 + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib), # noqa 'RANLIB=echo' ]) else: makefile_conf.extend([ 'LIBEXT=.so', - 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, # NOQA: ignore=E501 + 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, # noqa 'RANLIB=echo' ]) else: diff --git a/var/spack/repos/builtin/packages/munge/package.py b/var/spack/repos/builtin/packages/munge/package.py index ebe3e18882..51455006e9 100644 --- a/var/spack/repos/builtin/packages/munge/package.py +++ b/var/spack/repos/builtin/packages/munge/package.py @@ -25,12 +25,14 @@ from spack import * import os + class Munge(Package): """ MUNGE Uid 'N' Gid Emporium """ homepage = "https://code.google.com/p/munge/" url = "https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2" - version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01', url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2') + version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01', + url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2') depends_on('openssl') depends_on('libgcrypt') @@ -41,4 +43,3 @@ class Munge(Package): make() make("install") - diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py index 47d1855329..1373c8cd7b 100644 --- a/var/spack/repos/builtin/packages/muparser/package.py +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Muparser(Package): """C++ math expression parser library.""" homepage = "http://muparser.beltoforion.de/" diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py index 64b7324415..81817e48dc 100644 --- a/var/spack/repos/builtin/packages/muster/package.py +++ b/var/spack/repos/builtin/packages/muster/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Muster(Package): """The Muster library provides implementations of sequential and parallel K-Medoids clustering algorithms. It is intended as a diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index da386445bb..17124a0572 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -40,7 +40,8 @@ class Mvapich2(Package): provides('mpi@:2.2', when='@1.9') # MVAPICH2-1.9 supports MPI 2.2 provides('mpi@:3.0', when='@2.0:') # MVAPICH2-2.0 supports MPI 3.0 - variant('debug', default=False, description='Enables debug information and error messages at run-time') + variant('debug', default=False, + description='Enable debug info and error messages at run-time') ########## # TODO : Process managers should be grouped into the same variant, @@ -51,10 +52,14 @@ class Mvapich2(Package): GFORKER = 'gforker' REMSHELL = 'remshell' SLURM_INCOMPATIBLE_PMS = (HYDRA, GFORKER, REMSHELL) - variant(SLURM, default=False, description='Sets slurm as the only process manager') - variant(HYDRA, default=False, description='Sets hydra as one of the process managers') - variant(GFORKER, default=False, description='Sets gforker as one of the process managers') - variant(REMSHELL, default=False, description='Sets remshell as one of the process managers') + variant(SLURM, default=False, + description='Set slurm as the only process manager') + variant(HYDRA, default=False, + description='Set hydra as one of the process managers') + variant(GFORKER, default=False, + description='Set gforker as one of the process managers') + variant(REMSHELL, default=False, + description='Set remshell as one of the process managers') ########## ########## @@ -67,15 +72,28 @@ class Mvapich2(Package): NEMESIS = 'nemesis' MRAIL = 'mrail' SUPPORTED_NETWORKS = (PSM, SOCK, NEMESIS, NEMESISIB, NEMESISIBTCP) - variant(PSM, default=False, description='Configures a build for QLogic PSM-CH3') - variant(SOCK, default=False, description='Configures a build for TCP/IP-CH3') - variant(NEMESISIBTCP, default=False, description='Configures a build for both OFA-IB-Nemesis and TCP/IP-Nemesis') - variant(NEMESISIB, default=False, description='Configures a build for OFA-IB-Nemesis') - variant(NEMESIS, default=False, description='Configures a build for TCP/IP-Nemesis') - variant(MRAIL, default=False, description='Configures a build for OFA-IB-CH3') + variant( + PSM, default=False, + description='Configure for QLogic PSM-CH3') + variant( + SOCK, default=False, + description='Configure for TCP/IP-CH3') + variant( + NEMESISIBTCP, default=False, + description='Configure for both OFA-IB-Nemesis and TCP/IP-Nemesis') + variant( + NEMESISIB, default=False, + description='Configure for OFA-IB-Nemesis') + variant( + NEMESIS, default=False, + description='Configure for TCP/IP-Nemesis') + variant( + MRAIL, default=False, + description='Configure for OFA-IB-CH3') ########## # FIXME : CUDA support is missing + depends_on('libpciaccess') def url_for_version(self, version): base_url = "http://mvapich.cse.ohio-state.edu/download" diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py index 254a5f1595..113c48c18f 100644 --- a/var/spack/repos/builtin/packages/mxml/package.py +++ b/var/spack/repos/builtin/packages/mxml/package.py @@ -1,3 +1,27 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## from spack import * diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py index 63269a50b1..792e3fe3c7 100644 --- a/var/spack/repos/builtin/packages/nag/package.py +++ b/var/spack/repos/builtin/packages/nag/package.py @@ -43,8 +43,8 @@ class Nag(Package): def url_for_version(self, version): # TODO: url and checksum are architecture dependent # TODO: We currently only support x86_64 - return 'http://www.nag.com/downloads/impl/npl6a%sna_amd64.tgz' % \ - str(version).replace('.', '') + return 'http://www.nag.com/downloads/impl/npl6a%sna_amd64.tgz' % str( + version).replace('.', '') def install(self, spec, prefix): # Set installation directories diff --git a/var/spack/repos/builtin/packages/nasm/package.py b/var/spack/repos/builtin/packages/nasm/package.py index c955e6d13e..9faccccaae 100644 --- a/var/spack/repos/builtin/packages/nasm/package.py +++ b/var/spack/repos/builtin/packages/nasm/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Nasm(Package): """NASM (Netwide Assembler) is an 80x86 assembler designed for portability and modularity. It includes a disassembler as well.""" diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py index 68bddd6957..d59ca09381 100644 --- a/var/spack/repos/builtin/packages/nccmp/package.py +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Nccmp(Package): """Compare NetCDF Files""" homepage = "http://nccmp.sourceforge.net/" diff --git a/var/spack/repos/builtin/packages/ncdu/package.py b/var/spack/repos/builtin/packages/ncdu/package.py index 0f2f9cda45..2147319d3f 100644 --- a/var/spack/repos/builtin/packages/ncdu/package.py +++ b/var/spack/repos/builtin/packages/ncdu/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Ncdu(Package): """ Ncdu is a disk usage analyzer with an ncurses interface. It is designed @@ -38,15 +39,15 @@ class Ncdu(Package): version('1.11', '9e44240a5356b029f05f0e70a63c4d12') version('1.10', '7535decc8d54eca811493e82d4bfab2d') - version('1.9' , '93258079db897d28bb8890e2db89b1fb') - version('1.8' , '94d7a821f8a0d7ba8ef3dd926226f7d5') - version('1.7' , '172047c29d232724cc62e773e82e592a') + version('1.9', '93258079db897d28bb8890e2db89b1fb') + version('1.8', '94d7a821f8a0d7ba8ef3dd926226f7d5') + version('1.7', '172047c29d232724cc62e773e82e592a') depends_on("ncurses") def install(self, spec, prefix): configure('--prefix=%s' % prefix, - '--with-ncurses=%s' % spec['ncurses']) + '--with-ncurses=%s' % spec['ncurses']) make() make("install") diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py index 4bc4da68e3..16d72b4593 100644 --- a/var/spack/repos/builtin/packages/nco/package.py +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class Nco(Package): """The NCO toolkit manipulates and analyzes data stored in @@ -39,9 +39,9 @@ class Nco(Package): depends_on('netcdf') depends_on('antlr@2.7.7+cxx') # (required for ncap2) - depends_on('gsl') # (desirable for ncap2) + depends_on('gsl') # (desirable for ncap2) depends_on('udunits2') # (allows dimensional unit transformations) - # depends_on('opendap') # (enables network transparency), + # depends_on('opendap') # (enables network transparency), def install(self, spec, prefix): opts = [ diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index 3ab2b0477d..aaacbac7b1 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -24,11 +24,14 @@ ############################################################################## from spack import * + class Ncurses(Package): - """The ncurses (new curses) library is a free software emulation of curses - in System V Release 4.0, and more. It uses terminfo format, supports pads and - color and multiple highlights and forms characters and function-key mapping, - and has all the other SYSV-curses enhancements over BSD curses. + """The ncurses (new curses) library is a free software emulation of + curses in System V Release 4.0, and more. It uses terminfo format, + supports pads and color and multiple highlights and forms + characters and function-key mapping, and has all the other + SYSV-curses enhancements over BSD curses. + """ homepage = "http://invisible-island.net/ncurses/ncurses.html" diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index b39e17ca49..f61e6984b5 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Ncview(Package): """Simple viewer for NetCDF files.""" homepage = "http://meteora.ucsd.edu/~pierce/ncview_home_page.html" diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py index 3c9dd4054a..dc41add03f 100644 --- a/var/spack/repos/builtin/packages/ndiff/package.py +++ b/var/spack/repos/builtin/packages/ndiff/package.py @@ -24,11 +24,15 @@ ############################################################################## from spack import * + class Ndiff(Package): - """The ndiff tool is a binary utility that compares putatively similar files - while ignoring small numeric differernces. This utility is most often used - to compare files containing a lot of floating-point numeric data that - may be slightly different due to numeric error.""" + """The ndiff tool is a binary utility that compares putatively similar + files while ignoring small numeric differernces. This utility is + most often used to compare files containing a lot of + floating-point numeric data that may be slightly different due to + numeric error. + + """ homepage = "http://ftp.math.utah.edu/pub/ndiff/" url = "http://ftp.math.utah.edu/pub/ndiff/ndiff-2.00.tar.gz" diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py index 994c51c0da..2c3ab73309 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class NetcdfCxx(Package): """Deprecated C++ compatibility bindings for NetCDF. These do NOT read or write NetCDF-4 files, and are no longer diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index ad4ee59640..ab40c14340 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -26,9 +26,11 @@ from spack import * class Netcdf(Package): - """NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data.""" + """NetCDF is a set of software libraries and self-describing, + machine-independent data formats that support the creation, access, + and sharing of array-oriented scientific data. + + """ homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz" @@ -74,18 +76,19 @@ class Netcdf(Package): "--enable-dap" ] - # Make sure Netcdf links against Spack's curl - # Otherwise it may pick up system's curl, which could lead to link errors: - # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0' + # Make sure Netcdf links against Spack's curl, otherwise + # otherwise it may pick up system's curl, which can give link + # errors, e.g.: + # undefined reference to `SSL_CTX_use_certificate_chain_file` LIBS.append("-lcurl") CPPFLAGS.append("-I%s" % spec['curl'].prefix.include) - LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib) + LDFLAGS.append("-L%s" % spec['curl'].prefix.lib) if '+mpi' in spec: config_args.append('--enable-parallel4') CPPFLAGS.append("-I%s/include" % spec['hdf5'].prefix) - LDFLAGS.append( "-L%s/lib" % spec['hdf5'].prefix) + LDFLAGS.append("-L%s/lib" % spec['hdf5'].prefix) # HDF4 support # As of NetCDF 4.1.3, "--with-hdf4=..." is no longer a valid option @@ -93,13 +96,13 @@ class Netcdf(Package): if '+hdf4' in spec: config_args.append("--enable-hdf4") CPPFLAGS.append("-I%s/include" % spec['hdf'].prefix) - LDFLAGS.append( "-L%s/lib" % spec['hdf'].prefix) - LIBS.append( "-l%s" % "jpeg") + LDFLAGS.append("-L%s/lib" % spec['hdf'].prefix) + LIBS.append("-l%s" % "jpeg") if 'szip' in spec: CPPFLAGS.append("-I%s/include" % spec['szip'].prefix) - LDFLAGS.append( "-L%s/lib" % spec['szip'].prefix) - LIBS.append( "-l%s" % "sz") + LDFLAGS.append("-L%s/lib" % spec['szip'].prefix) + LIBS.append("-l%s" % "sz") # Fortran support # In version 4.2+, NetCDF-C and NetCDF-Fortran have split. diff --git a/var/spack/repos/builtin/packages/netgauge/package.py b/var/spack/repos/builtin/packages/netgauge/package.py index be9292fabb..b57cdbe5f3 100644 --- a/var/spack/repos/builtin/packages/netgauge/package.py +++ b/var/spack/repos/builtin/packages/netgauge/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Netgauge(Package): """Netgauge is a high-precision network parameter measurement tool. It supports benchmarking of many different network protocols diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 70015baf1c..08c94a5c9b 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -26,11 +26,12 @@ from spack import * class NetlibLapack(Package): - """ - LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix - inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value - decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the - scientific community. + """LAPACK version 3.X is a comprehensive FORTRAN library that does + linear algebra operations including matrix inversions, least squared + solutions to linear sets of equations, eigenvector analysis, singular + value decomposition, etc. It is a very comprehensive and reputable + package that has found extensive use in the scientific community. + """ homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" @@ -44,9 +45,11 @@ class NetlibLapack(Package): variant('debug', default=False, description='Activates the Debug build type') variant('shared', default=True, description="Build shared library version") - variant('external-blas', default=False, description='Build lapack with an external blas') + variant('external-blas', default=False, + description='Build lapack with an external blas') - variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface') + variant('lapacke', default=True, + description='Activates the build of the LAPACKE C interface') # virtual dependency provides('blas', when='~external-blas') @@ -55,26 +58,30 @@ class NetlibLapack(Package): depends_on('cmake', type='build') depends_on('blas', when='+external-blas') - def patch(self): # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name. if self.spec.satisfies('@3.6.0:'): - filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', - '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True) + filter_file( + '${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', + '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', + 'CBLAS/CMakeLists.txt', string=True) def install_one(self, spec, prefix, shared): - cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'), - '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), - '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] + cmake_args = [ + '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ( + 'Debug' if '+debug' in spec else 'Release'), + '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] if spec.satisfies('@3.6.0:'): - cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS + cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS if '+external-blas' in spec: - # TODO : the mechanism to specify the library should be more general, + # TODO : mechanism to specify the library should be more general, # TODO : but this allows to have an hook to an external blas cmake_args.extend([ '-DUSE_OPTIMIZED_BLAS:BOOL=ON', - '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a') + '-DBLAS_LIBRARIES:PATH=%s' % join_path( + spec['blas'].prefix.lib, 'libblas.a') ]) cmake_args.extend(std_cmake_args) @@ -85,7 +92,6 @@ class NetlibLapack(Package): make() make("install") - def install(self, spec, prefix): # Always build static libraries. self.install_one(spec, prefix, False) @@ -94,15 +100,17 @@ class NetlibLapack(Package): if '+shared' in spec: self.install_one(spec, prefix, True) - def setup_dependent_package(self, module, dspec): # This is WIP for a prototype interface for virtual packages. # We can update this as more builds start depending on BLAS/LAPACK. - libdir = find_library_path('libblas.a', self.prefix.lib64, self.prefix.lib) + libdir = find_library_path( + 'libblas.a', self.prefix.lib64, self.prefix.lib) self.spec.blas_static_lib = join_path(libdir, 'libblas.a') self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a') if '+shared' in self.spec: - self.spec.blas_shared_lib = join_path(libdir, 'libblas.%s' % dso_suffix) - self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix) + self.spec.blas_shared_lib = join_path( + libdir, 'libblas.%s' % dso_suffix) + self.spec.lapack_shared_lib = join_path( + libdir, 'liblapack.%s' % dso_suffix) diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index f7733249cf..49b8633209 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -39,7 +39,8 @@ class NetlibScalapack(Package): # versions before 2.0.0 are not using cmake and requires blacs as # a separated package - variant('shared', default=True, description='Build the shared library version') + variant('shared', default=True, + description='Build the shared library version') variant('fpic', default=False, description="Build with -fpic compiler option") provides('scalapack') diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py index 56e4836611..02e9ef5f1e 100644 --- a/var/spack/repos/builtin/packages/nettle/package.py +++ b/var/spack/repos/builtin/packages/nettle/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Nettle(Package): """The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts.""" diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py new file mode 100644 index 0000000000..54f3dbf915 --- /dev/null +++ b/var/spack/repos/builtin/packages/nextflow/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Nextflow(Package): + """Data-driven computational pipelines""" + + homepage = "http://www.nextflow.io" + + version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a', + url='https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow', + expand=False) + + depends_on('jdk') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install("nextflow", join_path(prefix.bin, "nextflow")) + set_executable(join_path(prefix.bin, "nextflow")) diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py index e3f3819289..dcd00576dd 100644 --- a/var/spack/repos/builtin/packages/ninja/package.py +++ b/var/spack/repos/builtin/packages/ninja/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Ninja(Package): """ A small, fast Make alternative """ homepage = "https://martine.github.io/ninja/" @@ -35,7 +36,6 @@ class Ninja(Package): extends('python') def install(self, spec, prefix): - sh = which('sh') python('configure.py', '--bootstrap') cp = which('cp') diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index 97164165e0..fb897f560b 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -25,6 +25,7 @@ from spack import * import sys + class Numdiff(Package): """Numdiff is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric @@ -35,7 +36,7 @@ class Numdiff(Package): version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') - depends_on('gettext', when=sys.platform=='darwin', type='build') + depends_on('gettext', when=sys.platform == 'darwin', type='build') def install(self, spec, prefix): options = ['--prefix=%s' % prefix] diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py new file mode 100644 index 0000000000..9488d3b7a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/ocaml/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Ocaml(Package): + """OCaml is an industrial strength programming language supporting + functional, imperative and object-oriented styles""" + + homepage = "http://ocaml.org/" + url = "http://caml.inria.fr/pub/distrib/ocaml-4.03/ocaml-4.03.0.tar.gz" + + version('4.03.0', '43812739ea1b4641cf480f57f977c149') + + depends_on('ncurses') + + def install(self, spec, prefix): + configure('-prefix', '{0}'.format(prefix)) + + make('world.opt') + make('install') diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 108c8f8a41..4f9f7b2e12 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -40,7 +40,8 @@ class Oce(Package): version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') version('0.16', '7a4b4df5a104d75a537e25e7dd387eca') - variant('tbb', default=True, description='Build with Intel Threading Building Blocks') + variant('tbb', default=True, + description='Build with Intel Threading Building Blocks') depends_on('cmake@2.8:', type='build') depends_on('tbb', when='+tbb') diff --git a/var/spack/repos/builtin/packages/ompss/package.py b/var/spack/repos/builtin/packages/ompss/package.py index c0848ffd70..02925974ea 100644 --- a/var/spack/repos/builtin/packages/ompss/package.py +++ b/var/spack/repos/builtin/packages/ompss/package.py @@ -26,19 +26,18 @@ from spack import * import os import glob -# working config lines for ompss 14.06 : -#./nanox-0.7/config.log: $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-mcc=/usr/gapps/exmatex/ompss/ --with-hwloc=/usr -#./mcxx-1.99.2/config.log: $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel class Ompss(Package): - """OmpSs is an effort to integrate features from the StarSs - programming model developed by BSC into a single programming - model. In particular, our objective is to extend OpenMP with - new directives to support asynchronous parallelism and - heterogeneity (devices like GPUs). However, it can also be - understood as new directives extending other accelerator based - APIs like CUDA or OpenCL. Our OmpSs environment is built on top - of our Mercurium compiler and Nanos++ runtime system.""" + """OmpSs is an effort to integrate features from the StarSs programming + model developed by BSC into a single programming model. In + particular, our objective is to extend OpenMP with new directives + to support asynchronous parallelism and heterogeneity (devices + like GPUs). However, it can also be understood as new directives + extending other accelerator based APIs like CUDA or OpenCL. Our + OmpSs environment is built on top of our Mercurium compiler and + Nanos++ runtime system. + + """ homepage = "http://pm.bsc.es/" url = "http://pm.bsc.es/sites/default/files/ftp/ompss/releases/ompss-14.10.tar.gz" list_url = 'http://pm.bsc.es/ompss-downloads' @@ -47,7 +46,7 @@ class Ompss(Package): # all dependencies are optional, really depends_on("mpi") - #depends_on("openmp") + # depends_on("openmp") depends_on("hwloc") depends_on("extrae") @@ -61,14 +60,22 @@ class Ompss(Package): openmp_options = ["--enable-tl-openmp-profile"] if spec.satisfies('%intel'): - openmp_options.append( "--enable-tl-openmp-intel" ) + openmp_options.append("--enable-tl-openmp-intel") os.chdir(glob.glob('./nanox-*').pop()) - configure("--prefix=%s" % prefix, "--with-mcc=%s" % prefix, "--with-extrae=%s" % spec['extrae'].prefix, "--with-hwloc=%s" % spec['hwloc'].prefix) + configure("--prefix=%s" % prefix, + "--with-mcc=%s" % prefix, + "--with-extrae=%s" % + spec['extrae'].prefix, + "--with-hwloc=%s" % spec['hwloc'].prefix) make() make("install") os.chdir(glob.glob('../mcxx-*').pop()) - configure("--prefix=%s" % prefix, "--with-nanox=%s" % prefix, "--enable-ompss", "--with-mpi=%s" % mpi.prefix, *openmp_options) + configure("--prefix=%s" % prefix, + "--with-nanox=%s" % prefix, + "--enable-ompss", + "--with-mpi=%s" % mpi.prefix, + *openmp_options) make() make("install") diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py index 800c04ae0e..40159e4c6c 100644 --- a/var/spack/repos/builtin/packages/ompt-openmp/package.py +++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py @@ -24,8 +24,14 @@ ############################################################################## from spack import * + class OmptOpenmp(Package): - """LLVM/Clang OpenMP runtime with OMPT support. This is a fork of the OpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP mirror. This library provides a drop-in replacement of the OpenMP runtimes for GCC, Intel and LLVM/Clang.""" + """LLVM/Clang OpenMP runtime with OMPT support. This is a fork of the + OpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP + mirror. This library provides a drop-in replacement of the OpenMP + runtimes for GCC, Intel and LLVM/Clang. + + """ homepage = "https://github.com/OpenMPToolsInterface/LLVM-openmp" url = "http://github.com/khuck/LLVM-openmp/archive/v0.1.tar.gz" @@ -35,13 +41,9 @@ class OmptOpenmp(Package): def install(self, spec, prefix): with working_dir("runtime/build", create=True): - - # FIXME: Modify the configure line to suit your build system here. - cmake('-DCMAKE_C_COMPILER=%s' % self.compiler.cc, + cmake('-DCMAKE_C_COMPILER=%s' % self.compiler.cc, '-DCMAKE_CXX_COMPILER=%s' % self.compiler.cxx, '-DCMAKE_INSTALL_PREFIX=%s' % prefix, '..', *std_cmake_args) - - # FIXME: Add logic to build and install here make() make("install") diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py index 510fff9fc2..e901f8ed39 100644 --- a/var/spack/repos/builtin/packages/opari2/package.py +++ b/var/spack/repos/builtin/packages/opari2/package.py @@ -25,18 +25,24 @@ from spack import * + class Opari2(Package): """ - OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and - runtime library calls with calls to the POMP2 measurement interface. OPARI2 will provide you with a new - initialization method that allows for multi-directory and parallel builds as well as the usage of pre-instrumented - libraries. Furthermore, an efficient way of tracking parent-child relationships was added. Additionally, we extended - OPARI2 to support instrumentation of OpenMP 3.0 tied tasks. + OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid + codes. It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. OPARI2 will provide you with a new + initialization method that allows for multi-directory and parallel builds + as well as the usage of pre-instrumented libraries. Furthermore, an + efficient way of tracking parent-child relationships was added. + Additionally, we extended OPARI2 to support instrumentation of OpenMP 3.0 + tied tasks. """ homepage = "http://www.vi-hps.org/projects/score-p" url = "http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.2.tar.gz" + version('2.0', '72350dbdb6139f2e68a5055a4f0ba16c', + url='http://www.vi-hps.org/upload/packages/opari2/opari2-2.0.tar.gz') version('1.1.4', '245d3d11147a06de77909b0805f530c0', url='http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.4.tar.gz') version('1.1.2', '9a262c7ca05ff0ab5f7775ae96f3539e') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index d09ebd6739..37f7a7005d 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -37,9 +37,12 @@ class Openblas(Package): version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') - variant('shared', default=True, description="Build shared libraries as well as static libs.") # NOQA: ignore=E501 - variant('openmp', default=False, description="Enable OpenMP support.") - variant('fpic', default=True, description="Build position independent code") # NOQA: ignore=E501 + variant('shared', default=True, + description="Build shared libraries as well as static libs.") + variant('openmp', default=False, + description="Enable OpenMP support.") + variant('fpic', default=True, + description="Build position independent code") # virtual dependency provides('blas') diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py index ff551d0b92..8f592342b0 100644 --- a/var/spack/repos/builtin/packages/opencv/package.py +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -23,51 +23,186 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +from glob import glob class Opencv(Package): + """OpenCV is released under a BSD license and hence it's free for both + academic and commercial use. It has C++, C, Python and Java interfaces and + supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for + computational efficiency and with a strong focus on real-time applications. + Written in optimized C/C++, the library can take advantage of multi-core + processing. Enabled with OpenCL, it can take advantage of the hardware + acceleration of the underlying heterogeneous compute platform. Adopted all + around the world, OpenCV has more than 47 thousand people of user community + and estimated number of downloads exceeding 9 million. Usage ranges from + interactive art, to mines inspection, stitching maps on the web or through + advanced robotics. """ - OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C, - Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for - computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library - can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware - acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than - 47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from - interactive art, to mines inspection, stitching maps on the web or through advanced robotics. - """ + homepage = 'http://opencv.org/' url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz' version('3.1.0', '70e1dd07f0aa06606f1bc0e3fa15abd3') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds a debug version of the libraries') variant('eigen', default=True, description='Activates support for eigen') variant('ipp', default=True, description='Activates support for IPP') + variant('jasper', default=True, description='Activates support for JasPer') + variant('cuda', default=False, description='Activates support for CUDA') + variant('gtk', default=False, description='Activates support for GTK') + variant('vtk', default=False, description='Activates support for VTK') + variant('qt', default=False, description='Activates support for QT') + variant('python', default=False, + description='Enables the build of Python extensions') + variant('java', default=False, + description='Activates support for Java') + + depends_on('cmake', type='build') + depends_on('eigen', when='+eigen', type='build') depends_on('zlib') depends_on('libpng') depends_on('libjpeg-turbo') depends_on('libtiff') - depends_on('python') - depends_on('py-numpy') + depends_on('jasper', when='+jasper') + depends_on('cuda', when='+cuda') + depends_on('gtkplus', when='+gtk') + depends_on('vtk', when='+vtk') + depends_on('qt', when='+qt') + depends_on('jdk', when='+java') + depends_on('py-numpy', when='+python') - depends_on('eigen', when='+eigen', type='build') - depends_on('cmake', type='build') - - # FIXME : GUI extensions missing - # FIXME : CUDA extensions still missing + extends('python', when='+python') def install(self, spec, prefix): cmake_options = [] cmake_options.extend(std_cmake_args) - cmake_options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), - '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), - '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF', - '-DWITH_IPP:BOOL=%s' % ('ON' if '+ipp' in spec else 'OFF')]) + cmake_options.extend([ + '-DCMAKE_BUILD_TYPE:STRING={0}'.format(( + 'Debug' if '+debug' in spec else 'Release')), + '-DBUILD_SHARED_LIBS:BOOL={0}'.format(( + 'ON' if '+shared' in spec else 'OFF')), + '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF', + '-DWITH_IPP:BOOL={0}'.format(( + 'ON' if '+ipp' in spec else 'OFF')), + '-DWITH_CUDA:BOOL={0}'.format(( + 'ON' if '+cuda' in spec else 'OFF')), + '-DWITH_QT:BOOL={0}'.format(( + 'ON' if '+qt' in spec else 'OFF')), + '-DWITH_VTK:BOOL={0}'.format(( + 'ON' if '+vtk' in spec else 'OFF')), + '-DBUILD_opencv_java:BOOL={0}'.format(( + 'ON' if '+java' in spec else 'OFF')), + ]) + + # Media I/O + zlib = spec['zlib'] + cmake_options.extend([ + '-DZLIB_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(zlib.prefix.lib, + 'libz.{0}'.format(dso_suffix))), + '-DZLIB_INCLUDE_DIR:PATH={0}'.format(zlib.prefix.include) + ]) + + libpng = spec['libpng'] + cmake_options.extend([ + '-DPNG_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(libpng.prefix.lib, + 'libpng.{0}'.format(dso_suffix))), + '-DPNG_INCLUDE_DIR:PATH={0}'.format(libpng.prefix.include) + ]) + + libjpeg = spec['libjpeg-turbo'] + cmake_options.extend([ + '-DJPEG_LIBRARY:FILEPATH={0}'.format( + join_path(libjpeg.prefix.lib, + 'libjpeg.{0}'.format(dso_suffix))), + '-DJPEG_INCLUDE_DIR:PATH={0}'.format(libjpeg.prefix.include) + ]) + + libtiff = spec['libtiff'] + cmake_options.extend([ + '-DTIFF_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(libtiff.prefix.lib, + 'libtiff.{0}'.format(dso_suffix))), + '-DTIFF_INCLUDE_DIR:PATH={0}'.format(libtiff.prefix.include) + ]) + + jasper = spec['jasper'] + cmake_options.extend([ + '-DJASPER_LIBRARY_{0}:FILEPATH={1}'.format(( + 'DEBUG' if '+debug' in spec else 'RELEASE'), + join_path(jasper.prefix.lib, + 'libjasper.{0}'.format(dso_suffix))), + '-DJASPER_INCLUDE_DIR:PATH={0}'.format(jasper.prefix.include) + ]) + + # GUI + if '+gtk' not in spec: + cmake_options.extend([ + '-DWITH_GTK:BOOL=OFF', + '-DWITH_GTK_2_X:BOOL=OFF' + ]) + elif '^gtkplus@3:' in spec: + cmake_options.extend([ + '-DWITH_GTK:BOOL=ON', + '-DWITH_GTK_2_X:BOOL=OFF' + ]) + elif '^gtkplus@2:3' in spec: + cmake_options.extend([ + '-DWITH_GTK:BOOL=OFF', + '-DWITH_GTK_2_X:BOOL=ON' + ]) + + # Python + if '+python' in spec: + python = spec['python'] + + try: + python_lib = glob(join_path( + python.prefix.lib, 'libpython*.{0}'.format(dso_suffix)))[0] + except KeyError: + raise InstallError('Cannot find libpython') + + try: + python_include_dir = glob(join_path(python.prefix.include, + 'python*'))[0] + except KeyError: + raise InstallError('Cannot find python include directory') + + if '^python@3:' in spec: + python_exe = join_path(python.prefix.bin, 'python3') + cmake_options.extend([ + '-DBUILD_opencv_python3=ON', + '-DPYTHON3_EXECUTABLE={0}'.format(python_exe), + '-DPYTHON3_LIBRARY={0}'.format(python_lib), + '-DPYTHON3_INCLUDE_DIR={0}'.format(python_include_dir), + '-DBUILD_opencv_python2=OFF', + ]) + elif '^python@2:3' in spec: + python_exe = join_path(python.prefix.bin, 'python2') + cmake_options.extend([ + '-DBUILD_opencv_python2=ON', + '-DPYTHON2_EXECUTABLE={0}'.format(python_exe), + '-DPYTHON2_LIBRARY={0}'.format(python_lib), + '-DPYTHON2_INCLUDE_DIR={0}'.format(python_include_dir), + '-DBUILD_opencv_python3=OFF', + ]) + else: + cmake_options.extend([ + '-DBUILD_opencv_python2=OFF', + '-DBUILD_opencv_python3=OFF' + ]) with working_dir('spack_build', create=True): cmake('..', *cmake_options) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 3fcf942f05..b0efe27def 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -108,7 +108,8 @@ class Openmpi(Package): depends_on('sqlite', when='+sqlite3') def url_for_version(self, version): - return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) # NOQA: ignore=E501 + return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % ( + version.up_to(2), version) def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index 4e2694a53c..5e141060b2 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -################################################################################ +########################################################################## # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved. # # This program is free software; you can redistribute it and/or modify it under @@ -38,50 +38,72 @@ # You should have received a copy of the GNU General Public License along with # this program; if not, write to the Free Software Foundation, Inc., 59 Temple # Place, Suite 330, Boston, MA 02111-1307 USA -################################################################################ +########################################################################## from spack import * + class Openspeedshop(Package): - """OpenSpeedShop is a community effort by The Krell Institute with current direct funding from DOEs NNSA. - It builds on top of a broad list of community infrastructures, most notably Dyninst and MRNet from UW, - libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an open source multi platform Linux performance - tool which is targeted to support performance analysis of applications running on both single node and - large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Blue Gene and Cray platforms. OpenSpeedShop development - is hosted by the Krell Institute. The infrastructure and base components of OpenSpeedShop are released - as open source code primarily under LGPL. + """OpenSpeedShop is a community effort by The Krell Institute with + current direct funding from DOEs NNSA. It builds on top of a broad + list of community infrastructures, most notably Dyninst and MRNet + from UW, libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an + open source multi platform Linux performance tool which is targeted + to support performance analysis of applications running on both + single node and large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Blue + Gene and Cray platforms. OpenSpeedShop development is hosted by the + Krell Institute. The infrastructure and base components of + OpenSpeedShop are released as open source code primarily under LGPL. + """ homepage = "http://www.openspeedshop.org" - url = "https://github.com/OpenSpeedShop" + url = "https://github.com/OpenSpeedShop" version('2.2', '16cb051179c2038de4e8a845edf1d573') # Use when the git repository is available - version('2.2', branch='master', git='https://github.com/OpenSpeedShop/openspeedshop.git') + version('2.2', branch='master', + git='https://github.com/OpenSpeedShop/openspeedshop.git') # Optional mirror template - #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/openspeedshop-2.2.tar.gz" - #version('2.2', '643337740dc6c2faca60f42d3620b0e1') + # url="file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/openspeedshop-2.2.tar.gz" + # version('2.2', '643337740dc6c2faca60f42d3620b0e1') parallel = False - variant('offline', default=True, description="build with offline instrumentor enabled.") - variant('cbtf', default=False, description="build with cbtf instrumentor enabled.") - variant('runtime', default=False, description="build only the runtime libraries and collectors.") - variant('frontend', default=False, description="build only the front-end tool using the runtime_dir to point to the target build.") - variant('cuda', default=False, description="build with cuda packages included.") - variant('ptgf', default=False, description="build with the PTGF based gui package enabled.") - variant('rtfe', default=False, description="build for generic cluster platforms that have different processors on the fe and be nodes.") + variant('offline', default=True, + description="build with offline instrumentor enabled.") + variant('cbtf', default=False, + description="build with cbtf instrumentor enabled.") + variant('runtime', default=False, + description="build only the runtime libraries and collectors.") + variant('frontend', default=False, + description="build only the front-end tool using the runtime_dir " + "to point to the target build.") + variant('cuda', default=False, + description="build with cuda packages included.") + variant('ptgf', default=False, + description="build with the PTGF based gui package enabled.") + variant('rtfe', default=False, + description="build for generic cluster platforms that have " + "different processors on the fe and be nodes.") # MPI variants - variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.") - variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.") - variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.") - variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.") - variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.") - variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") + variant('openmpi', default=False, + description="Build mpi experiment collector for openmpi MPI.") + variant('mpt', default=False, + description="Build mpi experiment collector for SGI MPT MPI.") + variant('mvapich2', default=False, + description="Build mpi experiment collector for mvapich2 MPI.") + variant('mvapich', default=False, + description="Build mpi experiment collector for mvapich MPI.") + variant('mpich2', default=False, + description="Build mpi experiment collector for mpich2 MPI.") + variant('mpich', default=False, + description="Build mpi experiment collector for mpich MPI.") depends_on("cmake@3.0.2", type='build') - # Dependencies for openspeedshop that are common to all the variants of the OpenSpeedShop build + # Dependencies for openspeedshop that are common to all the variants of + # the OpenSpeedShop build depends_on("bison") depends_on("flex") depends_on("binutils@2.24+krellpatch") @@ -111,11 +133,13 @@ class Openspeedshop(Package): depends_on("mrnet@5.0.1:+lwthreads+krellpatch", when='+cbtf') def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions): - # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings + # Sets build type parameters into cmakeOptions the options that will + # enable the cbtf-krell built type settings - compile_flags="-O2 -g" + compile_flags = "-O2 -g" BuildTypeOptions = [] - # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs + # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the + # stdcmakeargs for word in cmakeOptions[:]: if word.startswith('-DCMAKE_BUILD_TYPE'): cmakeOptions.remove(word) @@ -124,63 +148,64 @@ class Openspeedshop(Package): if word.startswith('-DCMAKE_C_FLAGS'): cmakeOptions.remove(word) BuildTypeOptions.extend([ - '-DCMAKE_BUILD_TYPE=None', - '-DCMAKE_CXX_FLAGS=%s' % compile_flags, - '-DCMAKE_C_FLAGS=%s' % compile_flags + '-DCMAKE_BUILD_TYPE=None', + '-DCMAKE_CXX_FLAGS=%s' % compile_flags, + '-DCMAKE_C_FLAGS=%s' % compile_flags ]) cmakeOptions.extend(BuildTypeOptions) def set_mpi_cmakeOptions(self, spec, cmakeOptions): - # Appends to cmakeOptions the options that will enable the appropriate MPI implementations - + # Appends to cmakeOptions the options that will enable the appropriate + # MPI implementations + MPIOptions = [] # openmpi if '+openmpi' in spec: MPIOptions.extend([ - '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix + '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix ]) # mpich if '+mpich' in spec: MPIOptions.extend([ - '-DMPICH_DIR=%s' % spec['mpich'].prefix + '-DMPICH_DIR=%s' % spec['mpich'].prefix ]) # mpich2 if '+mpich2' in spec: MPIOptions.extend([ - '-DMPICH2_DIR=%s' % spec['mpich2'].prefix + '-DMPICH2_DIR=%s' % spec['mpich2'].prefix ]) # mvapich if '+mvapich' in spec: MPIOptions.extend([ - '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix + '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix ]) # mvapich2 if '+mvapich2' in spec: MPIOptions.extend([ - '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix + '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix ]) # mpt if '+mpt' in spec: MPIOptions.extend([ - '-DMPT_DIR=%s' % spec['mpt'].prefix + '-DMPT_DIR=%s' % spec['mpt'].prefix ]) cmakeOptions.extend(MPIOptions) - def install(self, spec, prefix): - #openmpi_prefix_path = "/opt/openmpi-1.8.2" - #mvapich_prefix_path = "/usr/local/tools/mvapich-gnu" - #'-DOPENMPI_DIR=%s' % spec['openmpi'].prefix, - #'-DOPENMPI_DIR=%s' % openmpi_prefix_path, - #'-DMVAPICH_DIR=%s' % mvapich_prefix_path, + # openmpi_prefix_path = "/opt/openmpi-1.8.2" + # mvapich_prefix_path = "/usr/local/tools/mvapich-gnu" + # '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix, + # '-DOPENMPI_DIR=%s' % openmpi_prefix_path, + # '-DMVAPICH_DIR=%s' % mvapich_prefix_path, - # FIXME: How do we make this dynamic in spack? That is, can we specify the paths to cuda dynamically? - # WAITING for external package support. - #if '+cuda' in spec: + # FIXME: How do we make this dynamic in spack? + # FIXME: That is, can we specify the paths to cuda dynamically? + # WAITING for external package support. + # if '+cuda' in spec: # cuda_prefix_path = "/usr/local/cuda-6.0" # cupti_prefix_path = "/usr/local/cuda-6.0/extras/CUPTI" @@ -190,19 +215,20 @@ class Openspeedshop(Package): with working_dir('build_runtime', create=True): cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DINSTRUMENTOR=%s' % instrumentor_setting, - '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, - '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - '-DPAPI_DIR=%s' % spec['papi'].prefix - ]) - + cmakeOptions.extend([ + '-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + '-DINSTRUMENTOR=%s' % instrumentor_setting, + '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, + '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + '-DPAPI_DIR=%s' % spec['papi'].prefix]) + # Add any MPI implementations coming from variant settings self.set_mpi_cmakeOptions(spec, cmakeOptions) cmakeOptions.extend(std_cmake_args) - # Adjust the build options to the favored ones for this build + # Adjust the build options to the favored ones for this + # build self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) cmake('..', *cmakeOptions) @@ -214,43 +240,49 @@ class Openspeedshop(Package): cmake_prefix_path = join_path(spec['dyninst'].prefix) with working_dir('build', create=True): - #python_vers=join_path(spec['python'].version[:2]) - #'-DOPENMPI_DIR=%s' % openmpi_prefix_path, - #'-DMVAPICH_DIR=%s' % mvapich_prefix_path, - #'-DMPICH_DIR=%s' % spec['mpich'].prefix, - #'-DMPICH2_DIR=%s' % spec['mpich2'].prefix, - #'-DBoost_NO_SYSTEM_PATHS=TRUE', - #'-DBOOST_ROOT=%s' % spec['boost'].prefix, - #'-DOPENMPI_DIR=%s' % spec['openmpi'].prefix, + # python_vers=join_path(spec['python'].version[:2]) + # '-DOPENMPI_DIR=%s' % openmpi_prefix_path, + # '-DMVAPICH_DIR=%s' % mvapich_prefix_path, + # '-DMPICH_DIR=%s' % spec['mpich'].prefix, + # '-DMPICH2_DIR=%s' % spec['mpich2'].prefix, + # '-DBoost_NO_SYSTEM_PATHS=TRUE', + # '-DBOOST_ROOT=%s' % spec['boost'].prefix, + # '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix, - python_vers='%d.%d' % spec['python'].version[:2] + python_vers = '%d.%d' % spec['python'].version[:2] cmakeOptions = [] - cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DINSTRUMENTOR=%s' % instrumentor_setting, - '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - '-DLIBELF_DIR=%s' % spec['libelf'].prefix, - '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, - '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, - '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - '-DPAPI_DIR=%s' % spec['papi'].prefix, - '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix, - '-DQTLIB_DIR=%s' % spec['qt'].prefix, - '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'), - '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers, - '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so', - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DDYNINST_DIR=%s' % spec['dyninst'].prefix - ]) + cmakeOptions.extend([ + '-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DINSTRUMENTOR=%s' % instrumentor_setting, + '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + '-DLIBELF_DIR=%s' % spec['libelf'].prefix, + '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, + '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix, + '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + '-DPAPI_DIR=%s' % spec['papi'].prefix, + '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix, + '-DQTLIB_DIR=%s' % spec['qt'].prefix, + '-DPYTHON_EXECUTABLE=%s' % join_path( + spec['python'].prefix, '/bin/python'), + '-DPYTHON_INCLUDE_DIR=%s' % join_path( + spec['python'].prefix.include, + 'python' + python_vers), + '-DPYTHON_LIBRARY=%s' % join_path( + spec['python'].prefix.lib, + 'libpython' + python_vers + '.so'), + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DDYNINST_DIR=%s' % spec['dyninst'].prefix]) # Add any MPI implementations coming from variant settings self.set_mpi_cmakeOptions(spec, cmakeOptions) cmakeOptions.extend(std_cmake_args) - # Adjust the build options to the favored ones for this build + # Adjust the build options to the favored ones for this + # build self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions) cmake('..', *cmakeOptions) @@ -261,160 +293,171 @@ class Openspeedshop(Package): elif '+cbtf' in spec: instrumentor_setting = "cbtf" - resolve_symbols = "symtabapi" - cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) + ':' + join_path(spec['dyninst'].prefix) - #runtime_platform_cray = "cray" - #if '+cray' in spec: + cmake_prefix_path = ':'.join(spec['cbtf'].prefix, + spec['cbtf-krell'].prefix, + spec['dyninst'].prefix) + + # resolve_symbols = "symtabapi" + # runtime_platform_cray = "cray" + # if '+cray' in spec: # if '+runtime' in spec: - # #-DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_INSTALL_DIR} \ - # with working_dir('build_cbtf_cray_runtime', create=True): - # python_vers='%d.%d' % spec['python'].version[:2] - # cmake('..', - # '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - # '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - # '-DRUNTIME_PLATFORM=%s' % runtime_platform_cray, - # '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - # '-DRESOLVE_SYMBOLS=%s' % resolve_symbols, - # '-DINSTRUMENTOR=%s' % instrumentor_setting, - # '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - # '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, - # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % spec['cbtf-krell'].prefix, - # '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - # '-DLIBELF_DIR=%s' % spec['libelf'].prefix, - # '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, - # '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, - # '-DPAPI_DIR=%s' % spec['papi'].prefix, - # '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, - # '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, - # '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - # '-DBoost_NO_SYSTEM_PATHS=TRUE', - # '-DBOOST_ROOT=%s' % spec['boost'].prefix, - # *std_cmake_args) + # #-DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_INSTALL_DIR} \ + # with working_dir('build_cbtf_cray_runtime', create=True): + # python_vers='%d.%d' % spec['python'].version[:2] + # cmake('..', + # '-DCMAKE_INSTALL_PREFIX=%s' % prefix, + # '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + # '-DRUNTIME_PLATFORM=%s' % runtime_platform_cray, + # '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + # '-DRESOLVE_SYMBOLS=%s' % resolve_symbols, + # '-DINSTRUMENTOR=%s' % instrumentor_setting, + # '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + # '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % spec['cbtf-krell'].prefix, + # '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + # '-DLIBELF_DIR=%s' % spec['libelf'].prefix, + # '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, + # '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix, + # '-DPAPI_DIR=%s' % spec['papi'].prefix, + # '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, + # '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix, + # '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + # '-DBoost_NO_SYSTEM_PATHS=TRUE', + # '-DBOOST_ROOT=%s' % spec['boost'].prefix, + # *std_cmake_args) # make("clean") # make() # make("install") - - #elif '+mic' in spec: - # comment out else and shift over the default case below until arch detection is in - #else: + # elif '+mic' in spec: + # comment out else and shift over the default case below + # until arch detection is in else: if '+runtime' in spec: with working_dir('build_cbtf_runtime', create=True): - python_vers='%d.%d' % spec['python'].version[:2] - cmake('..', - '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DINSTRUMENTOR=%s' % instrumentor_setting, - '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - '-DLIBELF_DIR=%s' % spec['libelf'].prefix, - '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, - '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'), - '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers, - '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so', - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - *std_cmake_args) + python_vers = '%d.%d' % spec['python'].version[:2] + cmake( + '..', + '-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DINSTRUMENTOR=%s' % instrumentor_setting, + '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + '-DLIBELF_DIR=%s' % spec['libelf'].prefix, + '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + '-DPYTHON_EXECUTABLE=%s' % join_path( + spec['python'].prefix, 'bin', 'python'), + '-DPYTHON_INCLUDE_DIR=%s' % join_path( + spec['python'].prefix.include, + 'python' + python_vers), + '-DPYTHON_LIBRARY=%s' % join_path( + spec['python'].prefix.lib, + 'libpython' + python_vers + '.so'), + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + *std_cmake_args) + make("clean") make() make("install") else: with working_dir('build_cbtf', create=True): - python_vers='%d.%d' % spec['python'].version[:2] - #python_vers=join_path(spec['python'].version[:2]) - cmake('..', - '-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, - '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, - '-DINSTRUMENTOR=%s' % instrumentor_setting, - '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, - '-DLIBELF_DIR=%s' % spec['libelf'].prefix, - '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, - '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix, - '-DCBTF_DIR=%s' % spec['cbtf'].prefix, - '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, - '-DQTLIB_DIR=%s' % spec['qt'].prefix, - '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'), - '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers, - '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so', - '-DBoost_NO_SYSTEM_PATHS=TRUE', - '-DBOOST_ROOT=%s' % spec['boost'].prefix, - '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, - '-DMRNET_DIR=%s' % spec['mrnet'].prefix, - *std_cmake_args) + python_vers = '%d.%d' % spec['python'].version[:2] + # python_vers=join_path(spec['python'].version[:2]) + cmake( + '..', + '-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64, + '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path, + '-DINSTRUMENTOR=%s' % instrumentor_setting, + '-DBINUTILS_DIR=%s' % spec['binutils'].prefix, + '-DLIBELF_DIR=%s' % spec['libelf'].prefix, + '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix, + '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix, + '-DCBTF_DIR=%s' % spec['cbtf'].prefix, + '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix, + '-DQTLIB_DIR=%s' % spec['qt'].prefix, + '-DPYTHON_EXECUTABLE=%s' % join_path( + spec['python'].prefix, 'bin', 'python'), + '-DPYTHON_INCLUDE_DIR=%s' % join_path( + spec['python'].prefix.include, + 'python' + python_vers), + '-DPYTHON_LIBRARY=%s' % join_path( + spec['python'].prefix.lib, + 'libpython' + python_vers + '.so'), + '-DBoost_NO_SYSTEM_PATHS=TRUE', + '-DBOOST_ROOT=%s' % spec['boost'].prefix, + '-DDYNINST_DIR=%s' % spec['dyninst'].prefix, + '-DMRNET_DIR=%s' % spec['mrnet'].prefix, + *std_cmake_args) + make("clean") make() make("install") - #if '+frontend' in spec: - # with working_dir('build_frontend', create=True): - # tbd - - - - #if '+cbtf' in spec: - # if cray build type detected: - # if '+runtime' in spec: - # with working_dir('build_cray_cbtf_compute', create=True): - # tbd - # else: - # with working_dir('build_cray_cbtf_frontend', create=True): - # tbd - # with working_dir('build_cray_osscbtf_frontend', create=True): - # tbd - # fi - # elif '+intelmic' in spec: - # if '+runtime' in spec: - # with working_dir('build_intelmic_cbtf_compute', create=True): - # tbd - # else: - # with working_dir('build_intelmic_cbtf_frontend', create=True): - # tbd - # with working_dir('build_intelmic_osscbtf_frontend', create=True): - # fi - # else - # with working_dir('build_cluster_cbtf', create=True): - # tbd - # with working_dir('build_cluster osscbtf', create=True): - # tbd - # fi - #elif '+offline' in spec: - # if cray build type detected: - # if '+runtime' in spec: - # with working_dir('build_cray_ossoff_compute', create=True): - # tbd - # else: - # with working_dir('build_cray_ossoff_frontend', create=True): - # tbd - # fi - # elif '+intelmic' in spec: - # if '+runtime' in spec: - # with working_dir('build_intelmic_ossoff_compute', create=True): - # tbd - # else: - # with working_dir('build_intelmic_ossoff_frontend', create=True): - # tbd - # fi - # elif bgq build type detected: - # if '+runtime' in spec: - # with working_dir('build_bgq_ossoff_compute', create=True): - # tbd - # else: - # with working_dir('build_bgq_ossoff_frontend', create=True): - # tbd - # fi - # else - # with working_dir('build_cluster ossoff', create=True): - # tbd - # fi - #fi - - - +# if '+frontend' in spec: +# with working_dir('build_frontend', create=True): +# tbd + +# if '+cbtf' in spec: +# if cray build type detected: +# if '+runtime' in spec: +# with working_dir('build_cray_cbtf_compute', create=True): +# tbd +# else: +# with working_dir('build_cray_cbtf_frontend', create=True): +# tbd +# with working_dir('build_cray_osscbtf_frontend', create=True): +# tbd +# fi +# elif '+intelmic' in spec: +# if '+runtime' in spec: +# with working_dir('build_intelmic_cbtf_compute', create=True): +# tbd +# else: +# with working_dir('build_intelmic_cbtf_frontend', create=True): +# tbd +# with working_dir('build_intelmic_osscbtf_frontend', create=True): +# fi +# else +# with working_dir('build_cluster_cbtf', create=True): +# tbd +# with working_dir('build_cluster osscbtf', create=True): +# tbd +# fi +# elif '+offline' in spec: +# if cray build type detected: +# if '+runtime' in spec: +# with working_dir('build_cray_ossoff_compute', create=True): +# tbd +# else: +# with working_dir('build_cray_ossoff_frontend', create=True): +# tbd +# fi +# elif '+intelmic' in spec: +# if '+runtime' in spec: +# with working_dir('build_intelmic_ossoff_compute', create=True): +# tbd +# else: +# with working_dir('build_intelmic_ossoff_frontend', create=True): +# tbd +# fi +# elif bgq build type detected: +# if '+runtime' in spec: +# with working_dir('build_bgq_ossoff_compute', create=True): +# tbd +# else: +# with working_dir('build_bgq_ossoff_frontend', create=True): +# tbd +# fi +# else +# with working_dir('build_cluster ossoff', create=True): +# tbd +# fi +# fi diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index b9eada9e83..8d9049a8f7 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -34,7 +34,7 @@ class Openssl(Package): Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.""" homepage = "http://www.openssl.org" - url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz" + url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz" version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') version('1.0.1r', '1abd905e079542ccae948af37e393d28') @@ -52,7 +52,7 @@ class Openssl(Package): if '@system' in self.spec: return '@system (reserved version for system openssl)' else: - return super(Openssl, self).url_for_version(self.spec) + return super(Openssl, self).url_for_version(self.version) def handle_fetch_error(self, error): tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has " diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py new file mode 100644 index 0000000000..2c81d92cc0 --- /dev/null +++ b/var/spack/repos/builtin/packages/opium/package.py @@ -0,0 +1,55 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Opium(Package): + """DFT pseudopotential generation project""" + + homepage = "https://opium.sourceforge.net/index.html" + url = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz" + + version('3.8', 'f710c0f869e70352b4a510c31e13bf9f') + + depends_on('blas') + depends_on('lapack') + + def install(self, spec, prefix): + options = [ + 'LDFLAGS=%s %s' % ( + to_link_flags(spec['lapack'].lapack_shared_lib), + to_link_flags(spec['blas'].blas_shared_lib) + ) + ] + + configure(*options) + with working_dir("src", create=False): + make("all-subdirs") + make("opium") + + # opium not have a make install :-(( + mkdirp(self.prefix.bin) + install(join_path(self.stage.source_path, 'opium'), + self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py index 2104bf842b..161ba6254a 100644 --- a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class OsuMicroBenchmarks(Package): """The Ohio MicroBenchmark suite is a collection of independent MPI message passing performance microbenchmarks developed and written at @@ -41,7 +42,6 @@ class OsuMicroBenchmarks(Package): depends_on('mpi') depends_on('cuda', when='+cuda') - def install(self, spec, prefix): config_args = [ 'CC=%s' % spec['mpi'].prefix.bin + '/mpicc', diff --git a/var/spack/repos/builtin/packages/otf/package.py b/var/spack/repos/builtin/packages/otf/package.py index 4a7a00b212..39eb5a85aa 100644 --- a/var/spack/repos/builtin/packages/otf/package.py +++ b/var/spack/repos/builtin/packages/otf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Otf(Package): """To improve scalability for very large and massively parallel traces the Open Trace Format (OTF) is developed at ZIH as a diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py index 131836f8ac..ee39f448eb 100644 --- a/var/spack/repos/builtin/packages/otf2/package.py +++ b/var/spack/repos/builtin/packages/otf2/package.py @@ -27,8 +27,8 @@ from spack import * class Otf2(Package): - """ - The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. + """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. """ homepage = "http://www.vi-hps.org/score-p" @@ -46,10 +46,10 @@ class Otf2(Package): url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz") def install(self, spec, prefix): - configure_args=["--prefix=%s" % prefix, - "--enable-shared", - "CFLAGS=-fPIC", - "CXXFLAGS=-fPIC"] + configure_args = ["--prefix=%s" % prefix, + "--enable-shared", + "CFLAGS=-fPIC", + "CXXFLAGS=-fPIC"] configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 4bbf0c1311..114fd00011 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -24,46 +24,42 @@ ############################################################################## from spack import * + class P4est(Package): - """Dynamic management of a collection (a forest) of adaptive octrees in parallel""" + """Dynamic management of a collection (a forest) of adaptive octrees in + parallel""" homepage = "http://www.p4est.org" url = "http://p4est.github.io/release/p4est-1.1.tar.gz" version('1.1', '37ba7f4410958cfb38a2140339dbf64f') - variant('tests', default=True, description='Run small tests') - # build dependencies depends_on('automake', type='build') depends_on('autoconf', type='build') depends_on('libtool@2.4.2:', type='build') # other dependencies - depends_on('lua') # Needed for the submodule sc + depends_on('lua') # Needed for the submodule sc depends_on('mpi') depends_on('zlib') def install(self, spec, prefix): - options = ['--enable-mpi', - '--enable-shared', - '--disable-vtk-binary', - '--without-blas', - 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', - 'CFLAGS=-O2', - 'CC=%s' % self.spec['mpi'].mpicc, - 'CXX=%s' % self.spec['mpi'].mpicxx, - 'FC=%s' % self.spec['mpi'].mpifc, - 'F77=%s' % self.spec['mpi'].mpif77 - ] + options = [ + '--enable-mpi', + '--enable-shared', + '--disable-vtk-binary', + '--without-blas', + 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', + 'CFLAGS=-O2', + 'CC=%s' % self.spec['mpi'].mpicc, + 'CXX=%s' % self.spec['mpi'].mpicxx, + 'FC=%s' % self.spec['mpi'].mpifc, + 'F77=%s' % self.spec['mpi'].mpif77 + ] configure('--prefix=%s' % prefix, *options) make() - # Make tests optional as sometimes mpiexec can't be run with an error: - # mpiexec has detected an attempt to run as root. - # Running at root is *strongly* discouraged as any mistake (e.g., in - # defining TMPDIR) or bug can result in catastrophic damage to the OS - # file system, leaving your system in an unusable state. - if '+tests' in self.spec: - make("check") + if self.run_tests: + make("check") make("install") diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py index a04f6d64e0..2da20e9dc2 100644 --- a/var/spack/repos/builtin/packages/pango/package.py +++ b/var/spack/repos/builtin/packages/pango/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Pango(Package): """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It can be used anywhere @@ -31,8 +32,11 @@ class Pango(Package): far has been done in the context of the GTK+ widget toolkit.""" homepage = "http://www.pango.org" url = "http://ftp.gnome.org/pub/gnome/sources/pango/1.36/pango-1.36.8.tar.xz" + list_url = "http://ftp.gnome.org/pub/gnome/sources/pango/" + list_depth = 2 version('1.36.8', '217a9a753006275215fa9fa127760ece') + version('1.40.1', '6fc88c6529890d6c8e03074d57a3eceb') depends_on("harfbuzz") depends_on("cairo") diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index ecd958407f..5c4abe1730 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -28,6 +28,7 @@ import os import sys from llnl.util.filesystem import fix_darwin_install_name + class Papi(Package): """PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance @@ -47,7 +48,7 @@ class Papi(Package): def install(self, spec, prefix): with working_dir("src"): - configure_args=["--prefix=%s" % prefix] + configure_args = ["--prefix=%s" % prefix] # PAPI uses MPI if MPI is present; since we don't require # an MPI package, we ensure that all attempts to use MPI diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py index 97d36d94a4..c91b01c964 100644 --- a/var/spack/repos/builtin/packages/paradiseo/package.py +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -23,40 +23,50 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import sys + class Paradiseo(Package): - """A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics.""" + """A C++ white-box object-oriented framework dedicated to the reusable + design of metaheuristics.""" homepage = "http://paradiseo.gforge.inria.fr/" - # Installing from the development version is a better option at this + # Installing from the development version is a better option at this # point than using the very old supplied packages version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git') - # This is a version that the package formula author has tested successfully. - # However, the clone is very large (~1Gb git history). The history in the - # head version has been trimmed significantly. - version('dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git', - commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6') - variant('mpi', default=True, description='Compile with parallel and distributed metaheuristics module') - variant('smp', default=True, description='Compile with symmetric multi-processing module ') - variant('edo', default=True, description='Compile with (Experimental) EDO module') - #variant('tests', default=False, description='Compile with build tests') - #variant('doc', default=False, description='Compile with documentation') - variant('debug', default=False, description='Builds a debug version of the libraries') + # This is a version that the package formula author has tested + # successfully. However, the clone is very large (~1Gb git + # history). The history in the head version has been trimmed + # significantly. + version( + 'dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git', + commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6') + + variant('mpi', default=True, + description='Compile with parallel and distributed ' + 'metaheuristics module') + variant('smp', default=True, + description='Compile with symmetric multi-processing module ') + variant('edo', default=True, + description='Compile with (Experimental) EDO module') + + # variant('tests', default=False, description='Compile with build tests') + # variant('doc', default=False, description='Compile with documentation') + variant('debug', default=False, + description='Builds a debug version of the libraries') variant('openmp', default=False, description='Enable OpenMP support') variant('gnuplot', default=False, description='Enable GnuPlot support') - + # Required dependencies - depends_on ("cmake", type='build') + depends_on("cmake", type='build') # Optional dependencies - depends_on ("mpi", when="+mpi") - depends_on ("doxygen", when='+doc', type='build') - depends_on ("gnuplot", when='+gnuplot') - depends_on ("eigen", when='+edo', type='build') - depends_on ("boost~mpi", when='+edo~mpi') - depends_on ("boost+mpi", when='+edo+mpi') + depends_on("mpi", when="+mpi") + depends_on("doxygen", when='+doc', type='build') + depends_on("gnuplot", when='+gnuplot') + depends_on("eigen", when='+edo', type='build') + depends_on("boost~mpi", when='+edo~mpi') + depends_on("boost+mpi", when='+edo+mpi') # Patches patch('enable_eoserial.patch') @@ -69,16 +79,21 @@ class Paradiseo(Package): options.extend(std_cmake_args) options.extend([ - '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ( + 'Debug' if '+debug' in spec else 'Release'), '-DINSTALL_TYPE:STRING=MIN', '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'), - '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler + # Note: This requires a C++11 compatible compiler + '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'), - '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'), - '-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'), - '-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE') + '-DENABLE_CMAKE_TESTING:BOOL=%s' % ( + 'TRUE' if '+tests' in spec else 'FALSE'), + '-DENABLE_OPENMP:BOOL=%s' % ( + 'TRUE' if '+openmp' in spec else 'FALSE'), + '-DENABLE_GNUPLOT:BOOL=%s' % ( + 'TRUE' if '+gnuplot' in spec else 'FALSE') ]) - + with working_dir('spack-build', create=True): # Configure cmake('..', *options) diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index deee46df8f..be4a8bc38b 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class ParallelNetcdf(Package): """Parallel netCDF (PnetCDF) is a library providing high-performance parallel I/O while still maintaining file-format compatibility with @@ -37,12 +38,14 @@ class ParallelNetcdf(Package): variant('cxx', default=True, description='Build the C++ Interface') variant('fortran', default=True, description='Build the Fortran Interface') - variant('fpic', default=True, description='Produce position-independent code (for use with shared libraries)') + variant('fpic', default=True, + description='Produce position-independent code (for shared libs)') depends_on("m4", type='build') depends_on("mpi") - # See: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL + # See: + # https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL def install(self, spec, prefix): args = list() if '+fpic' in spec: @@ -53,7 +56,7 @@ class ParallelNetcdf(Package): args.append('--disable-fortran') args.extend(["--prefix=%s" % prefix, - "--with-mpi=%s" % spec['mpi'].prefix]) + "--with-mpi=%s" % spec['mpi'].prefix]) configure(*args) make() make("install") diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py index 50ce6b79fb..1b6e3ce8e6 100644 --- a/var/spack/repos/builtin/packages/paraver/package.py +++ b/var/spack/repos/builtin/packages/paraver/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Paraver(Package): """"A very powerful performance visualization and analysis tool based on traces that can be used to analyse any information that @@ -36,7 +37,7 @@ class Paraver(Package): version('4.5.3', '625de9ec0d639acd18d1aaa644b38f72') depends_on("boost") - #depends_on("extrae") + # depends_on("extrae") depends_on("wx") depends_on("wxpropgrid") @@ -47,8 +48,11 @@ class Paraver(Package): make("install") os.chdir("../paraver-kernel") - #"--with-extrae=%s" % spec['extrae'].prefix, - configure("--prefix=%s" % prefix, "--with-ptools-common-files=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization") + # "--with-extrae=%s" % spec['extrae'].prefix, + configure("--prefix=%s" % prefix, + "--with-ptools-common-files=%s" % prefix, + "--with-boost=%s" % spec['boost'].prefix, + "--with-boost-serialization=boost_serialization") make() make("install") @@ -58,8 +62,11 @@ class Paraver(Package): make("install") os.chdir("../wxparaver") - #"--with-extrae=%s" % spec['extrae'].prefix, - configure("--prefix=%s" % prefix, "--with-paraver=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization", "--with-wxdir=%s" % spec['wx'].prefix.bin) + # "--with-extrae=%s" % spec['extrae'].prefix, + configure("--prefix=%s" % prefix, + "--with-paraver=%s" % prefix, + "--with-boost=%s" % spec['boost'].prefix, + "--with-boost-serialization=boost_serialization", + "--with-wxdir=%s" % spec['wx'].prefix.bin) make() make("install") - diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 75f5272006..68c781734e 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Paraview(Package): homepage = 'http://www.paraview.org' url = 'http://www.paraview.org/files/v5.0/ParaView-v' @@ -52,23 +53,22 @@ class Paraview(Package): depends_on('cmake', type='build') depends_on('bzip2') depends_on('freetype') - #depends_on('hdf5+mpi', when='+mpi') - #depends_on('hdf5~mpi', when='~mpi') + # depends_on('hdf5+mpi', when='+mpi') + # depends_on('hdf5~mpi', when='~mpi') depends_on('jpeg') depends_on('libpng') depends_on('libtiff') depends_on('libxml2') - #depends_on('netcdf') - #depends_on('netcdf-cxx') - #depends_on('protobuf') # version mismatches? - #depends_on('sqlite') # external version not supported + # depends_on('netcdf') + # depends_on('netcdf-cxx') + # depends_on('protobuf') # version mismatches? + # depends_on('sqlite') # external version not supported depends_on('zlib') def url_for_version(self, version): """Handle ParaView version-based custom URLs.""" return self._url_str % (version.up_to(2), version) - def install(self, spec, prefix): with working_dir('spack-build', create=True): def feature_to_bool(feature, on='ON', off='OFF'): @@ -80,34 +80,46 @@ class Paraview(Package): return feature_to_bool(feature, on='OFF', off='ON') feature_args = std_cmake_args[:] - feature_args.append('-DPARAVIEW_BUILD_QT_GUI:BOOL=%s' % feature_to_bool('+qt')) - feature_args.append('-DPARAVIEW_ENABLE_PYTHON:BOOL=%s' % feature_to_bool('+python')) + feature_args.append( + '-DPARAVIEW_BUILD_QT_GUI:BOOL=%s' % feature_to_bool('+qt')) + feature_args.append('-DPARAVIEW_ENABLE_PYTHON:BOOL=%s' % + feature_to_bool('+python')) if '+python' in spec: - feature_args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s/bin/python' % spec['python'].prefix) - feature_args.append('-DPARAVIEW_USE_MPI:BOOL=%s' % feature_to_bool('+mpi')) + feature_args.append( + '-DPYTHON_EXECUTABLE:FILEPATH=%s/bin/python' + % spec['python'].prefix) + feature_args.append('-DPARAVIEW_USE_MPI:BOOL=%s' % + feature_to_bool('+mpi')) if '+mpi' in spec: - feature_args.append('-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix) - feature_args.append('-DVTK_ENABLE_TCL_WRAPPING:BOOL=%s' % feature_to_bool('+tcl')) - feature_args.append('-DVTK_OPENGL_HAS_OSMESA:BOOL=%s' % feature_to_bool('+osmesa')) - feature_args.append('-DVTK_USE_X:BOOL=%s' % nfeature_to_bool('+osmesa')) - feature_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL')) + feature_args.append( + '-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix) + feature_args.append( + '-DVTK_ENABLE_TCL_WRAPPING:BOOL=%s' % feature_to_bool('+tcl')) + feature_args.append('-DVTK_OPENGL_HAS_OSMESA:BOOL=%s' % + feature_to_bool('+osmesa')) + feature_args.append('-DVTK_USE_X:BOOL=%s' % + nfeature_to_bool('+osmesa')) + feature_args.append( + '-DVTK_RENDERING_BACKEND:STRING=%s' % + feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL')) feature_args.extend(std_cmake_args) if 'darwin' in self.spec.architecture: feature_args.append('-DVTK_USE_X:BOOL=OFF') - feature_args.append('-DPARAVIEW_DO_UNIX_STYLE_INSTALLS:BOOL=ON') + feature_args.append( + '-DPARAVIEW_DO_UNIX_STYLE_INSTALLS:BOOL=ON') cmake('..', - '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix, - '-DBUILD_TESTING:BOOL=OFF', - '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON', - '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF', - '-DVTK_USE_SYSTEM_JPEG:BOOL=ON', - '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON', - '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF', - '-DVTK_USE_SYSTEM_TIFF:BOOL=ON', - '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON', - *feature_args) + '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix, + '-DBUILD_TESTING:BOOL=OFF', + '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON', + '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF', + '-DVTK_USE_SYSTEM_JPEG:BOOL=ON', + '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON', + '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF', + '-DVTK_USE_SYSTEM_TIFF:BOOL=ON', + '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON', + *feature_args) make() make('install') diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index b2ceadc128..2750df2bdb 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -38,8 +38,10 @@ class Parmetis(Package): version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628') version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds the library in debug mode') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') depends_on('cmake@2.8:', type='build') # build dependency @@ -48,9 +50,9 @@ class Parmetis(Package): patch('enable_external_metis.patch') # bug fixes from PETSc developers - # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ # NOQA: ignore=E501 + # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch') - # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ # NOQA: ignore=E501 + # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') def url_for_version(self, version): diff --git a/var/spack/repos/builtin/packages/parpack/package.py b/var/spack/repos/builtin/packages/parpack/package.py index 5930dada85..84bc88b3b0 100644 --- a/var/spack/repos/builtin/packages/parpack/package.py +++ b/var/spack/repos/builtin/packages/parpack/package.py @@ -26,6 +26,7 @@ from spack import * import os import shutil + class Parpack(Package): """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" @@ -52,13 +53,13 @@ class Parpack(Package): mf.filter('^PLAT.*', 'PLAT = ') mf.filter('^home.*', 'home = %s' % os.getcwd()) mf.filter('^BLASdir.*', 'BLASdir = %s' % self.spec['blas'].prefix) - mf.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix) + mf.filter('^LAPACKdir.*', 'LAPACKdir = %s' % + self.spec['lapack'].prefix) mf.filter('^MAKE.*', 'MAKE = make') # build the library in our own prefix. mf.filter('^ARPACKLIB.*', 'PARPACKLIB = %s/libparpack.a' % os.getcwd()) - def install(self, spec, prefix): with working_dir('PARPACK/SRC/MPI'): make('all') diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py index 3860875bcc..cd1f679062 100644 --- a/var/spack/repos/builtin/packages/patchelf/package.py +++ b/var/spack/repos/builtin/packages/patchelf/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class Patchelf(Package): - """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + """PatchELF is a small utility to modify the dynamic linker and RPATH of + ELF executables.""" homepage = "https://nixos.org/patchelf.html" url = "http://nixos.org/releases/patchelf/patchelf-0.8/patchelf-0.8.tar.gz" diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py index a43729a1ac..6f306ab0f9 100644 --- a/var/spack/repos/builtin/packages/pcre/package.py +++ b/var/spack/repos/builtin/packages/pcre/package.py @@ -29,7 +29,6 @@ class Pcre(Package): """The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.""" - homepage = "http://www.pcre.org""" url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2" @@ -46,6 +45,7 @@ class Pcre(Package): configure_args = ['--prefix=%s' % prefix] if '+utf' in spec: configure_args.append('--enable-utf') + configure_args.append('--enable-unicode-properties') configure(*configure_args) make() diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py index b013685f05..a2739e0584 100644 --- a/var/spack/repos/builtin/packages/pcre2/package.py +++ b/var/spack/repos/builtin/packages/pcre2/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Pcre2(Package): """The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py index 60136fc0cd..074d28540b 100644 --- a/var/spack/repos/builtin/packages/pdt/package.py +++ b/var/spack/repos/builtin/packages/pdt/package.py @@ -27,17 +27,21 @@ from spack import * class Pdt(Package): - """ - Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages - and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements - a standard program representation, the program database (PDB), that can be accessed in a uniform way through a - class library supporting common PDB operations. + """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich + program knowledge accessible to developers of static and dynamic + analysis tools. PDT implements a standard program representation, + the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations. + """ homepage = "https://www.cs.uoregon.edu/research/pdt/home.php" - url = "https://www.cs.uoregon.edu/research/tau/pdt_releases/pdt-3.21.tar.gz" - version('3.21', '8df94298b71703decf680709a4ddf68f') - version('3.19', 'ba5591994998771fdab216699e362228') + version('3.21', '3092ca0d8833b69992c17e63ae66c263') + version('3.19', '5c5e1e6607086aa13bf4b1b9befc5864') + + def url_for_version(self, version): + return 'https://www.cs.uoregon.edu/research/tau/pdt_releases/pdtoolkit-%s.tar.gz' % (version) def install(self, spec, prefix): configure('-prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py new file mode 100644 index 0000000000..d71a7492ba --- /dev/null +++ b/var/spack/repos/builtin/packages/perl/package.py @@ -0,0 +1,75 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +# +# Author: George Hartzell <hartzell@alerce.com> +# Date: July 21, 2016 +# Author: Justin Too <justin@doubleotoo.com> +# Date: September 6, 2015 +# +from spack import * + + +class Perl(Package): + """Perl 5 is a highly capable, feature-rich programming language with over + 27 years of development.""" + homepage = "http://www.perl.org" + url = "http://www.cpan.org/src/5.0/perl-5.22.2.tar.gz" + + version('5.24.0', 'c5bf7f3285439a2d3b6a488e14503701') + version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b') + version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd') + # 5.18.4 fails with gcc-5 + # https://rt.perl.org/Public/Bug/Display.html?id=123784 + # version('5.18.4' , '1f9334ff730adc05acd3dd7130d295db') + + # Installing cpanm alongside the core makes it safe and simple for + # people/projects to install their own sets of perl modules. Not + # having it in core increases the "energy of activation" for doing + # things cleanly. + variant('cpanm', default=True, + description='Optionally install cpanm with the core packages.') + + resource( + name="cpanm", + url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz", + md5="e87f55fbcb3c13a4754500c18e89219f", + destination="cpanm", + placement="cpanm" + ) + + def install(self, spec, prefix): + configure = Executable('./Configure') + configure("-des", "-Dprefix=" + prefix) + make() + if self.run_tests: + make("test") + make("install") + + if '+cpanm' in spec: + with working_dir(join_path('cpanm', 'cpanm')): + perl = Executable(join_path(prefix.bin, 'perl')) + perl('Makefile.PL') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 11f5c36c22..66e1abdf1a 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -44,18 +44,25 @@ class Petsc(Package): version('3.5.1', 'a557e029711ebf425544e117ffa44d8f') version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d') - variant('shared', default=True, description='Enables the build of shared libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') variant('mpi', default=True, description='Activates MPI support') - variant('double', default=True, description='Switches between single and double precision') + variant('double', default=True, + description='Switches between single and double precision') variant('complex', default=False, description='Build with complex numbers') variant('debug', default=False, description='Compile in debug mode') - variant('metis', default=True, description='Activates support for metis and parmetis') - variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)') + variant('metis', default=True, + description='Activates support for metis and parmetis') + variant('hdf5', default=True, + description='Activates support for HDF5 (only parallel)') variant('boost', default=True, description='Activates support for Boost') - variant('hypre', default=True, description='Activates support for Hypre (only parallel)') - variant('mumps', default=True, description='Activates support for MUMPS (only parallel)') - variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)') + variant('hypre', default=True, + description='Activates support for Hypre (only parallel)') + variant('mumps', default=True, + description='Activates support for MUMPS (only parallel)') + variant('superlu-dist', default=True, + description='Activates support for SuperluDist (only parallel)') # Virtual dependencies depends_on('blas') @@ -74,7 +81,7 @@ class Petsc(Package): # Hypre does not support complex numbers. # Also PETSc prefer to build it without internal superlu, likely due to # conflict in headers see - # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py # NOQA: ignore=E501 + # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py depends_on('hypre~internal-superlu', when='+hypre+mpi~complex') depends_on('superlu-dist@:4.3', when='@:3.6.4+superlu-dist+mpi') depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi') @@ -85,17 +92,21 @@ class Petsc(Package): if '~mpi' in self.spec: compiler_opts = [ '--with-cc=%s' % os.environ['CC'], - '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), # NOQA: ignore=E501 - '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), # NOQA: ignore=E501 + '--with-cxx=%s' % (os.environ['CXX'] + if self.compiler.cxx is not None else '0'), + '--with-fc=%s' % (os.environ['FC'] + if self.compiler.fc is not None else '0'), '--with-mpi=0' ] - error_message_fmt = '\t{library} support requires "+mpi" to be activated' # NOQA: ignore=E501 + error_message_fmt = \ + '\t{library} support requires "+mpi" to be activated' # If mpi is disabled (~mpi), it's an error to have any of these # enabled. This generates a list of any such errors. - errors = [error_message_fmt.format(library=x) - for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist') # NOQA: ignore=E501 - if ('+' + x) in self.spec] + errors = [ + error_message_fmt.format(library=x) + for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist') + if ('+' + x) in self.spec] if errors: errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) @@ -110,8 +121,10 @@ class Petsc(Package): options = ['--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ - '--with-precision=%s' % ('double' if '+double' in spec else 'single'), # NOQA: ignore=E501 - '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), # NOQA: ignore=E501 + '--with-precision=%s' % ( + 'double' if '+double' in spec else 'single'), + '--with-scalar-type=%s' % ( + 'complex' if '+complex' in spec else 'real'), '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'), '--with-debugging=%s' % ('1' if '+debug' in spec else '0'), '--with-blas-lapack-dir=%s' % spec['lapack'].prefix @@ -120,11 +133,13 @@ class Petsc(Package): for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis', 'mumps', 'scalapack'): options.append( - '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) # NOQA: ignore=E501 + '--with-{library}={value}'.format( + library=library, value=('1' if library in spec else '0')) ) if library in spec: options.append( - '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) # NOQA: ignore=E501 + '--with-{library}-dir={path}'.format( + library=library, path=spec[library].prefix) ) # PETSc does not pick up SuperluDist from the dir as they look for # superlu_dist_4.1.a @@ -158,13 +173,25 @@ class Petsc(Package): run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun')) run('ex50', '-da_grid_x', '4', '-da_grid_y', '4') if 'superlu-dist' in spec: - run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 + run('ex50', + '-da_grid_x', '4', + '-da_grid_y', '4', + '-pc_type', 'lu', + '-pc_factor_mat_solver_package', 'superlu_dist') if 'mumps' in spec: - run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 + run('ex50', + '-da_grid_x', '4', + '-da_grid_y', '4', + '-pc_type', 'lu', + '-pc_factor_mat_solver_package', 'mumps') if 'hypre' in spec: - run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 + run('ex50', + '-da_grid_x', '4', + '-da_grid_y', '4', + '-pc_type', 'hypre', + '-pc_hypre_type', 'boomeramg') def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up PETSC_DIR for everyone using PETSc package diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py index 7170c65303..c58d563682 100644 --- a/var/spack/repos/builtin/packages/pgi/package.py +++ b/var/spack/repos/builtin/packages/pgi/package.py @@ -41,6 +41,7 @@ class Pgi(Package): homepage = "http://www.pgroup.com/" url = "file://%s/pgi-16.3.tar.gz" % os.getcwd() + version('16.5', 'a40e8852071b5d600cb42f31631b3de1') version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427') variant('network', default=True, diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py index e7b18ce7a8..e19bb9e470 100644 --- a/var/spack/repos/builtin/packages/pidx/package.py +++ b/var/spack/repos/builtin/packages/pidx/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Pidx(Package): """PIDX Parallel I/O Library. diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py index 34d8dfea0d..3d7e332a3f 100644 --- a/var/spack/repos/builtin/packages/pixman/package.py +++ b/var/spack/repos/builtin/packages/pixman/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Pixman(Package): """The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and diff --git a/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch new file mode 100644 index 0000000000..9538f23875 --- /dev/null +++ b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch @@ -0,0 +1,34 @@ +From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001 +From: coypu <coypu@sdf.org> +Date: Wed, 2 Mar 2016 19:43:10 +0200 +Subject: [PATCH 2/2] gdate: Suppress string format literal warning + +Newer versions of GCC emit an error here, but we know it's safe. +https://bugzilla.gnome.org/761550 +--- + glib/glib/gdate.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/glib/glib/gdate.c b/glib/glib/gdate.c +index 4aece02..92c34d2 100644 +--- a/glib/glib/gdate.c ++++ b/glib/glib/gdate.c +@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate *d, + * + * Returns: number of characters written to the buffer, or 0 the buffer was too small + */ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wformat-nonliteral" ++ + gsize + g_date_strftime (gchar *s, + gsize slen, +@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s, + return retval; + #endif + } ++ ++#pragma GCC diagnostic pop +-- +2.7.1 + diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py index ddbc151767..45e8e8b74e 100644 --- a/var/spack/repos/builtin/packages/pkg-config/package.py +++ b/var/spack/repos/builtin/packages/pkg-config/package.py @@ -24,23 +24,29 @@ ############################################################################## from spack import * + class PkgConfig(Package): - """pkg-config is a helper tool used when compiling applications and libraries""" + """pkg-config is a helper tool used when compiling applications + and libraries""" + homepage = "http://www.freedesktop.org/wiki/Software/pkg-config/" url = "http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz" - version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d') + version('0.29.1', 'f739a28cae4e0ca291f82d1d41ef107d') + version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d') parallel = False + # The following patch is needed for gcc-6.1 + patch('g_date_strftime.patch') + def install(self, spec, prefix): - configure("--prefix=%s" %prefix, - "--enable-shared", - "--with-internal-glib") # There's a bootstrapping problem here; - # glib uses pkg-config as well, so - # break the cycle by using the internal - # glib. + configure("--prefix={0}".format(prefix), + "--enable-shared", + # There's a bootstrapping problem here; + # glib uses pkg-config as well, so break + # the cycle by using the internal glib. + "--with-internal-glib") make() make("install") - diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py new file mode 100644 index 0000000000..b670b4c2b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -0,0 +1,112 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import subprocess + +from spack import * + + +class Plumed(Package): + """PLUMED is an open source library for free energy calculations in + molecular systems which works together with some of the most popular + molecular dynamics engines. + + Free energy calculations can be performed as a function of many order + parameters with a particular focus on biological problems, using state + of the art methods such as metadynamics, umbrella sampling and + Jarzynski-equation based steered MD. + + The software, written in C++, can be easily interfaced with both fortran + and C/C++ codes. + """ + homepage = 'http://www.plumed.org/' + url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz' + + version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8') + + variant('shared', default=True, description='Builds shared libraries') + variant('mpi', default=True, description='Activates MPI support') + variant('gsl', default=True, description='Activates GSL support') + + depends_on('zlib') + depends_on('blas') + depends_on('lapack') + + depends_on('mpi', when='+mpi') + depends_on('gsl', when='+gsl') + + # Dictionary mapping PLUMED versions to the patches it provides + # interactively + plumed_patches = { + '2.2.3': { + 'amber-14': '1', + 'gromacs-4.5.7': '2', + 'gromacs-4.6.7': '3', + 'gromacs-5.0.7': '4', + 'gromacs-5.1.2': '5', + 'lammps-6Apr13': '6', + 'namd-2.8': '7', + 'namd-2.9': '8', + 'espresso-5.0.2': '9' + } + } + + def apply_patch(self, other): + plumed = subprocess.Popen( + [join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'], + stdin=subprocess.PIPE + ) + opts = Plumed.plumed_patches[str(self.version)] + search = '{0.name}-{0.version}'.format(other) + choice = opts[search] + '\n' + plumed.stdin.write(choice) + plumed.wait() + + def setup_dependent_package(self, module, ext_spec): + # Make plumed visible from dependent packages + module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed')) + + def install(self, spec, prefix): + # From plumed docs : + # Also consider that this is different with respect to what some other + # configure script does in that variables such as MPICXX are + # completely ignored here. In case you work on a machine where CXX is + # set to a serial compiler and MPICXX to a MPI compiler, to compile + # with MPI you should use: + # + # > ./configure CXX="$MPICXX" + configure_opts = [ + 'CXX={0}'.format(spec['mpi'].mpicxx) + ] if '+mpi' in self.spec else [] + + configure_opts.extend([ + '--prefix={0}'.format(prefix), + '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'), + '--enable-mpi={0}'.format('yes' if '+mpi' in spec else 'no'), + '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no') + ]) + + configure(*configure_opts) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/pmgr_collective/package.py b/var/spack/repos/builtin/packages/pmgr_collective/package.py index a6e3b8e2a2..f6466a7954 100644 --- a/var/spack/repos/builtin/packages/pmgr_collective/package.py +++ b/var/spack/repos/builtin/packages/pmgr_collective/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PmgrCollective(Package): """PMGR_COLLECTIVE provides a scalable network for bootstrapping MPI jobs.""" diff --git a/var/spack/repos/builtin/packages/ppl/package.py b/var/spack/repos/builtin/packages/ppl/package.py index a54c6ce221..73404103f0 100644 --- a/var/spack/repos/builtin/packages/ppl/package.py +++ b/var/spack/repos/builtin/packages/ppl/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Ppl(Package): """The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py new file mode 100644 index 0000000000..d627e8a0b6 --- /dev/null +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Prank(Package): + """A powerful multiple sequence alignment browser.""" + + homepage = "http://wasabiapp.org/software/prank/" + url = "http://wasabiapp.org/download/prank/prank.source.140603.tgz" + + version('150803', '71ac2659e91c385c96473712c0a23e8a') + + depends_on('mafft') + depends_on('exonerate') + depends_on('bpp-suite') # for bppancestor + + def install(self, spec, prefix): + with working_dir('src'): + make() + mkdirp(prefix.bin) + install('prank', prefix.bin) diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py index 20dd4f5f69..06ab6108b6 100644 --- a/var/spack/repos/builtin/packages/proj/package.py +++ b/var/spack/repos/builtin/packages/proj/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Proj(Package): """Cartographic Projections""" homepage = "https://github.com/OSGeo/proj.4/wiki" diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py index d4befc34ab..bf0073b16a 100644 --- a/var/spack/repos/builtin/packages/protobuf/package.py +++ b/var/spack/repos/builtin/packages/protobuf/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Protobuf(Package): """Google's data interchange format.""" diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py index 192dd86e0e..6296d0cee6 100644 --- a/var/spack/repos/builtin/packages/psi4/package.py +++ b/var/spack/repos/builtin/packages/psi4/package.py @@ -39,7 +39,15 @@ class Psi4(Package): # Required dependencies depends_on('blas') depends_on('lapack') - depends_on('boost+chrono+filesystem+python+regex+serialization+system+timer+thread') + depends_on('boost' + '+chrono' + '+filesystem' + '+python' + '+regex' + '+serialization' + '+system' + '+timer' + '+thread') depends_on('python') depends_on('cmake', type='build') depends_on('py-numpy', type=nolink) diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py index 05f4616ff5..ca59105b4c 100644 --- a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py +++ b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PySqlalchemy(Package): """The Python SQL Toolkit and Object Relational Mapper""" diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py index ace9320424..2549972a6d 100644 --- a/var/spack/repos/builtin/packages/py-argcomplete/package.py +++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyArgcomplete(Package): """Bash tab completion for argparse.""" diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py index e1ea71fb67..a47b7ffa33 100644 --- a/var/spack/repos/builtin/packages/py-astroid/package.py +++ b/var/spack/repos/builtin/packages/py-astroid/package.py @@ -43,4 +43,3 @@ class PyAstroid(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py index 507664949b..f6c08e2728 100644 --- a/var/spack/repos/builtin/packages/py-autopep8/package.py +++ b/var/spack/repos/builtin/packages/py-autopep8/package.py @@ -1,5 +1,6 @@ from spack import * + class PyAutopep8(Package): """Automatic pep8 formatter""" homepage = "https://github.com/hhatto/autopep8" @@ -13,4 +14,3 @@ class PyAutopep8(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py index bcc889756e..c3edf9735b 100644 --- a/var/spack/repos/builtin/packages/py-biopython/package.py +++ b/var/spack/repos/builtin/packages/py-biopython/package.py @@ -24,8 +24,13 @@ ############################################################################## from spack import * + class PyBiopython(Package): - """It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.""" + """A distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. + + """ homepage = "http://biopython.org/wiki/Main_Page" url = "http://biopython.org/DIST/biopython-1.65.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py index 8d7a2343d1..e6fc6aa983 100644 --- a/var/spack/repos/builtin/packages/py-blessings/package.py +++ b/var/spack/repos/builtin/packages/py-blessings/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyBlessings(Package): """A nicer, kinder way to write to the terminal """ homepage = "https://github.com/erikrose/blessings" diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index 2483fab85f..ad2ee749d3 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -24,8 +24,9 @@ ############################################################################## from spack import * + class PyBottleneck(Package): - """Bottleneck is a collection of fast NumPy array functions written in Cython.""" + """A collection of fast NumPy array functions written in Cython.""" homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0" url = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py index e54d50fa50..3c1044783f 100644 --- a/var/spack/repos/builtin/packages/py-cffi/package.py +++ b/var/spack/repos/builtin/packages/py-cffi/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyCffi(Package): """Foreign Function Interface for Python calling C code""" homepage = "http://cffi.readthedocs.org/en/latest/" diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py index b7eaf58cd6..c2a698b0bd 100644 --- a/var/spack/repos/builtin/packages/py-coverage/package.py +++ b/var/spack/repos/builtin/packages/py-coverage/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyCoverage(Package): """ Testing coverage checker for python """ # FIXME: add a proper url for your package's homepage here. diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index 2deaa2f74e..5f50e3b6c2 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyCsvkit(Package): """A library of utilities for working with CSV, the king of tabular file formats""" diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 5ccc508697..4b3e1cabe1 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyCython(Package): """The Cython compiler for writing C extensions for the Python language.""" homepage = "https://pypi.python.org/pypi/cython" diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py index b7dbab3d97..4bc2c6fc99 100644 --- a/var/spack/repos/builtin/packages/py-dask/package.py +++ b/var/spack/repos/builtin/packages/py-dask/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyDask(Package): """Minimal task scheduling abstraction""" homepage = "https://github.com/dask/dask/" diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py index dfd1e143d9..40945232c1 100644 --- a/var/spack/repos/builtin/packages/py-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-dateutil/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyDateutil(Package): """Extensions to the standard Python datetime module.""" homepage = "https://pypi.python.org/pypi/dateutil" diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py index 09c93de428..7f83bce75e 100644 --- a/var/spack/repos/builtin/packages/py-dbf/package.py +++ b/var/spack/repos/builtin/packages/py-dbf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyDbf(Package): """Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro .dbf files (including memos)""" diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index bd78f262f4..9101b07a0d 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -24,8 +24,11 @@ ############################################################################## from spack import * + class PyDecorator(Package): - """The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.""" + """The aim of the decorator module it to simplify the usage of decorators + for the average programmer, and to popularize decorators by showing + various non-trivial examples.""" homepage = "https://github.com/micheles/decorator" url = "https://pypi.python.org/packages/source/d/decorator/decorator-4.0.9.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-epydoc/package.py b/var/spack/repos/builtin/packages/py-epydoc/package.py index b370075e02..9d4b93dad4 100644 --- a/var/spack/repos/builtin/packages/py-epydoc/package.py +++ b/var/spack/repos/builtin/packages/py-epydoc/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyEpydoc(Package): - """Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings.""" + """Epydoc is a tool for generating API documentation documentation for + Python modules, based on their docstrings.""" homepage = "https://pypi.python.org/pypi/epydoc" url = "https://pypi.python.org/packages/source/e/epydoc/epydoc-3.0.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py index 11ba639b85..c3d37f6b98 100644 --- a/var/spack/repos/builtin/packages/py-funcsigs/package.py +++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class PyFuncsigs(Package): """Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2.""" @@ -38,6 +38,3 @@ class PyFuncsigs(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - - - diff --git a/var/spack/repos/builtin/packages/py-genders/package.py b/var/spack/repos/builtin/packages/py-genders/package.py index 44f6cb1ef4..f919a7e6c2 100644 --- a/var/spack/repos/builtin/packages/py-genders/package.py +++ b/var/spack/repos/builtin/packages/py-genders/package.py @@ -24,16 +24,19 @@ ############################################################################## from spack import * + class PyGenders(Package): - """Genders is a static cluster configuration database used for cluster configuration management. It is used by a variety of tools and scripts for management of large clusters.""" + """Genders is a static cluster configuration database used for cluster + configuration management. It is used by a variety of tools and scripts + for management of large clusters.""" homepage = "https://github.com/chaos/genders" url = "https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz" - version('1.22', '9ea59a024dcbddb85b0ed25ddca9bc8e', url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz') + version('1.22', '9ea59a024dcbddb85b0ed25ddca9bc8e', + url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz') extends('python') def install(self, spec, prefix): - configure("--prefix=%s" %prefix) + configure("--prefix=%s" % prefix) make(parallel=False) make("install") - diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py index b08b03d1f1..a448a66e51 100644 --- a/var/spack/repos/builtin/packages/py-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyGnuplot(Package): - """Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program.""" + """Gnuplot.py is a Python package that allows you to create graphs from + within Python using the gnuplot plotting program.""" homepage = "http://gnuplot-py.sourceforge.net/" url = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index f96cb9b4cd..90a67c51bd 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -43,6 +43,7 @@ class PyH5py(Package): # Build dependencies depends_on('py-cython@0.19:', type='build') depends_on('pkg-config', type='build') + depends_on('py-setuptools', type='build') depends_on('hdf5@1.8.4:') depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py index b583609953..ac3291e21e 100644 --- a/var/spack/repos/builtin/packages/py-ipython/package.py +++ b/var/spack/repos/builtin/packages/py-ipython/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyIpython(Package): - """IPython provides a rich toolkit to help you make the most out of using Python interactively.""" + """IPython provides a rich toolkit to help you make the most out of using + Python interactively.""" homepage = "https://pypi.python.org/pypi/ipython" url = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py index fd1d6b4419..32acf75131 100644 --- a/var/spack/repos/builtin/packages/py-jdcal/package.py +++ b/var/spack/repos/builtin/packages/py-jdcal/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyJdcal(Package): """Julian dates from proleptic Gregorian and Julian calendars""" diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py index 57f26e3b90..943edf521a 100644 --- a/var/spack/repos/builtin/packages/py-jinja2/package.py +++ b/var/spack/repos/builtin/packages/py-jinja2/package.py @@ -48,4 +48,3 @@ class PyJinja2(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py index 38cc81b895..b873625bdb 100644 --- a/var/spack/repos/builtin/packages/py-lockfile/package.py +++ b/var/spack/repos/builtin/packages/py-lockfile/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyLockfile(Package): """The lockfile package exports a LockFile class which provides a simple API for locking files. Unlike the Windows msvcrt.locking diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py index 6dab4a40e4..ac1b933e43 100644 --- a/var/spack/repos/builtin/packages/py-logilab-common/package.py +++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py @@ -39,4 +39,3 @@ class PyLogilabCommon(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py index 56741ec11f..18a8dc0e68 100644 --- a/var/spack/repos/builtin/packages/py-mako/package.py +++ b/var/spack/repos/builtin/packages/py-mako/package.py @@ -24,12 +24,13 @@ ############################################################################## from spack import * + class PyMako(Package): - """A super-fast templating language that borrows the best - ideas from the existing templating languages.""" + """A super-fast templating language that borrows the best + ideas from the existing templating languages.""" homepage = "https://pypi.python.org/pypi/mako" - url = "https://pypi.python.org/packages/source/M/Mako/Mako-1.0.1.tar.gz" + url = "https://pypi.python.org/packages/source/M/Mako/Mako-1.0.1.tar.gz" version('1.0.1', '9f0aafd177b039ef67b90ea350497a54') diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py index ee396de7be..0a039d1d47 100644 --- a/var/spack/repos/builtin/packages/py-markupsafe/package.py +++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py @@ -48,4 +48,3 @@ class PyMarkupsafe(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index b5eb8a53c4..c454a47ec3 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -25,6 +25,7 @@ from spack import * import os + class PyMatplotlib(Package): """Python plotting package.""" homepage = "https://pypi.python.org/pypi/matplotlib" @@ -65,12 +66,12 @@ class PyMatplotlib(Package): if str(self.version) in ['1.4.2', '1.4.3']: # hack to fix configuration file config_file = None - for p,d,f in os.walk(prefix.lib): + for p, d, f in os.walk(prefix.lib): for file in f: if file.find('matplotlibrc') != -1: config_file = join_path(p, 'matplotlibrc') print config_file - if config_file == None: + if config_file is None: raise InstallError('could not find config file') filter_file(r'backend : pyside', 'backend : Qt4Agg', diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-meep/package.py new file mode 100644 index 0000000000..269ac55c67 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-meep/package.py @@ -0,0 +1,75 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PyMeep(Package): + """Python-meep is a wrapper around libmeep. It allows the scripting of + Meep-simulations with Python""" + + homepage = "https://launchpad.net/python-meep" + url = "https://launchpad.net/python-meep/1.4/1.4/+download/python-meep-1.4.2.tar" + + version('1.4.2', 'f8913542d18b0dda92ebc64f0a10ce56') + + variant('mpi', default=True, description='Enable MPI support') + + extends('python') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-matplotlib', type=nolink) + + depends_on('mpi', when='+mpi') + depends_on('meep~mpi', when='~mpi') + depends_on('meep+mpi', when='+mpi') + + # As of SWIG 3.0.3, Python-style comments are now treated as + # pre-processor directives. Use older SWIG. But not too old, + # or else it can't handle newer C++ compilers and flags. + depends_on('swig@1.3.39:3.0.2') + + def install(self, spec, prefix): + setup = 'setup-mpi.py' if '+mpi' in spec else 'setup.py' + + include_dirs = [ + spec['meep'].prefix.include, + spec['py-numpy'].include + ] + + library_dirs = [ + spec['meep'].prefix.lib + ] + + if '+mpi' in spec: + include_dirs.append(spec['mpi'].prefix.include) + library_dirs.append(spec['mpi'].prefix.lib) + + include_flags = '-I{0}'.format(','.join(include_dirs)) + library_flags = '-L{0}'.format(','.join(library_dirs)) + + python(setup, 'clean', '--all') + python(setup, 'build_ext', include_flags, library_flags) + python(setup, 'install', '--prefix={0}'.format(prefix)) + python(setup, 'bdist', include_flags, library_flags) diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py index f4c178de67..2c70535f19 100644 --- a/var/spack/repos/builtin/packages/py-mock/package.py +++ b/var/spack/repos/builtin/packages/py-mock/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyMock(Package): """mock is a library for testing in Python. It allows you to replace parts of your system under test with mock objects and make assertions about how diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py index a749e16779..1f0e52804e 100644 --- a/var/spack/repos/builtin/packages/py-mpi4py/package.py +++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py @@ -24,8 +24,14 @@ ############################################################################## from spack import * + class PyMpi4py(Package): - """This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.""" + """This package provides Python bindings for the Message Passing + Interface (MPI) standard. It is implemented on top of the + MPI-1/MPI-2 specification and exposes an API which grounds on the + standard MPI-2 C++ bindings. + + """ homepage = "https://pypi.python.org/pypi/mpi4py" url = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py index 899ff053a9..e5bae34694 100644 --- a/var/spack/repos/builtin/packages/py-mpmath/package.py +++ b/var/spack/repos/builtin/packages/py-mpmath/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyMpmath(Package): """A Python library for arbitrary-precision floating-point arithmetic.""" homepage = "http://mpmath.org" diff --git a/var/spack/repos/builtin/packages/py-mx/package.py b/var/spack/repos/builtin/packages/py-mx/package.py index d0f9f7cadf..f5631916f6 100644 --- a/var/spack/repos/builtin/packages/py-mx/package.py +++ b/var/spack/repos/builtin/packages/py-mx/package.py @@ -24,8 +24,14 @@ ############################################################################## from spack import * + class PyMx(Package): - """The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types.""" + """The eGenix.com mx Base Distribution for Python is a collection of + professional quality software tools which enhance Python's + usability in many important areas such as fast text searching, + date/time processing and high speed data types. + + """ homepage = "http://www.egenix.com/products/python/mxBase/" url = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py index 46b44f34dd..693fda6dbb 100644 --- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py +++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyMysqldb1(Package): """Legacy mysql bindings for python""" homepage = "https://github.com/farcepest/MySQLdb1" @@ -36,4 +37,3 @@ class PyMysqldb1(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py index 9a354cb1c1..e4f67d75a6 100644 --- a/var/spack/repos/builtin/packages/py-netcdf/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyNetcdf(Package): """Python interface to the netCDF Library.""" homepage = "http://unidata.github.io/netcdf4-python" diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index d545717628..79ad420f8f 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyNetworkx(Package): - """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.""" + """NetworkX is a Python package for the creation, manipulation, and study + of the structure, dynamics, and functions of complex networks.""" homepage = "http://networkx.github.io/" url = "https://pypi.python.org/packages/source/n/networkx/networkx-1.11.tar.gz" @@ -34,6 +36,7 @@ class PyNetworkx(Package): extends('python') depends_on('py-decorator', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index d15a1784d1..eb3dd77219 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -36,7 +36,7 @@ class PyNose(Package): version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') - extends('python', ignore=r'bin/nosetests.*$') + extends('python') depends_on('py-setuptools', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index fd8d7dc0c6..b3b2e1d47d 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import re + class PyNumexpr(Package): """Fast numerical expression evaluator for NumPy""" diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 2febdac658..f800b5e834 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import platform class PyNumpy(Package): @@ -48,6 +49,18 @@ class PyNumpy(Package): depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') + def setup_dependent_package(self, module, dep_spec): + python_version = self.spec['python'].version.up_to(2) + arch = '{0}-{1}'.format(platform.system().lower(), platform.machine()) + + self.spec.include = join_path( + self.prefix.lib, + 'python{0}'.format(python_version), + 'site-packages', + 'numpy-{0}-py{1}-{2}.egg'.format( + self.spec.version, python_version, arch), + 'numpy/core/include') + def install(self, spec, prefix): libraries = [] library_dirs = [] diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 624da58ff3..fa32cb879f 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyOpenpyxl(Package): """A Python library to read/write Excel 2007 xlsx/xlsm files""" diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 8bd4227faf..37234ae652 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -23,10 +23,18 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class PyPandas(Package): - """pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language.""" + """pandas is a Python package providing fast, flexible, and expressive + data structures designed to make working with relational or + labeled data both easy and intuitive. It aims to be the + fundamental high-level building block for doing practical, real + world data analysis in Python. Additionally, it has the broader + goal of becoming the most powerful and flexible open source data + analysis / manipulation tool available in any language. + + """ homepage = "http://pandas.pydata.org/" url = "https://pypi.python.org/packages/source/p/pandas/pandas-0.16.0.tar.gz#md5=bfe311f05dc0c351f8955fbd1e296e73" diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py index 8502b0b364..a0cfe0e5a5 100644 --- a/var/spack/repos/builtin/packages/py-pbr/package.py +++ b/var/spack/repos/builtin/packages/py-pbr/package.py @@ -23,10 +23,11 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class PyPbr(Package): - """PBR is a library that injects some useful and sensible default behaviors into your setuptools run.""" + """PBR is a library that injects some useful and sensible default + behaviors into your setuptools run.""" homepage = "https://pypi.python.org/pypi/pbr" url = "https://pypi.python.org/packages/source/p/pbr/pbr-1.8.1.tar.gz" @@ -38,5 +39,3 @@ class PyPbr(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - - diff --git a/var/spack/repos/builtin/packages/py-pep8/package.py b/var/spack/repos/builtin/packages/py-pep8/package.py index ffcc2b318c..87d1da9ab0 100644 --- a/var/spack/repos/builtin/packages/py-pep8/package.py +++ b/var/spack/repos/builtin/packages/py-pep8/package.py @@ -1,5 +1,6 @@ from spack import * + class PyPep8(Package): """python pep8 format checker""" homepage = "https://github.com/PyCQA/pycodestyle" @@ -12,4 +13,3 @@ class PyPep8(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py index 608f4e16c1..51d9cc2046 100644 --- a/var/spack/repos/builtin/packages/py-periodictable/package.py +++ b/var/spack/repos/builtin/packages/py-periodictable/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPeriodictable(Package): """nose extends the test loading and running features of unittest, making it easier to write, find and run tests.""" diff --git a/var/spack/repos/builtin/packages/py-pexpect/package.py b/var/spack/repos/builtin/packages/py-pexpect/package.py index dd95af9643..8a99c0473b 100644 --- a/var/spack/repos/builtin/packages/py-pexpect/package.py +++ b/var/spack/repos/builtin/packages/py-pexpect/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPexpect(Package): """Pexpect allows easy control of interactive console applications.""" homepage = "https://pypi.python.org/pypi/pexpect" diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py index a3a4b7a9f7..d5b3313a98 100644 --- a/var/spack/repos/builtin/packages/py-phonopy/package.py +++ b/var/spack/repos/builtin/packages/py-phonopy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPhonopy(Package): """Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.""" diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index 13a09f63cf..1d8b3faa6f 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -53,12 +53,15 @@ class PyPillow(Package): variant('tiff', default=False, description='Access to TIFF files') variant('freetype', default=False, description='Font related services') variant('lcms', default=False, description='Color management') - variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality') + variant('jpeg2000', default=False, + description='Provide JPEG 2000 functionality') # Spack does not (yet) support these modes of building # variant('webp', default=False, description='Provide the WebP format') - # variant('webpmux', default=False, description='WebP metadata, relies on WebP support') # NOQA: ignore=E501 - # variant('imagequant', default=False, description='Provide improved color quantization') # NOQA: ignore=E501 + # variant('webpmux', default=False, + # description='WebP metadata, relies on WebP support') + # variant('imagequant', default=False, + # description='Provide improved color quantization') # Required dependencies extends('python') diff --git a/var/spack/repos/builtin/packages/py-pmw/package.py b/var/spack/repos/builtin/packages/py-pmw/package.py index 062bfe9c03..e0a332a6bf 100644 --- a/var/spack/repos/builtin/packages/py-pmw/package.py +++ b/var/spack/repos/builtin/packages/py-pmw/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyPmw(Package): - """Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts.""" + """Pmw is a toolkit for building high-level compound widgets, or + megawidgets, constructed using other widgets as component parts.""" homepage = "https://pypi.python.org/pypi/Pmw" url = "https://pypi.python.org/packages/source/P/Pmw/Pmw-2.0.0.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index 02f37d8b78..a79c2e477b 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -43,4 +43,3 @@ class PyPy2neo(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-pychecker/package.py b/var/spack/repos/builtin/packages/py-pychecker/package.py index 137c5f491c..e81c3dbc9b 100644 --- a/var/spack/repos/builtin/packages/py-pychecker/package.py +++ b/var/spack/repos/builtin/packages/py-pychecker/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPychecker(Package): """""" homepage = "http://pychecker.sourceforge.net/" diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py index 9afba50077..ef1b772ffc 100644 --- a/var/spack/repos/builtin/packages/py-pycparser/package.py +++ b/var/spack/repos/builtin/packages/py-pycparser/package.py @@ -24,14 +24,14 @@ ############################################################################## from spack import * + class PyPycparser(Package): - """pycparser is a complete parser of the C language, written in pure python""" + """A complete parser of the C language, written in pure python.""" homepage = "https://github.com/eliben/pycparser" url = "https://pypi.python.org/packages/source/p/pycparser/pycparser-2.13.tar.gz" version('2.13', 'e4fe1a2d341b22e25da0d22f034ef32f') - extends('python') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py index 0c4a7a36cc..bf781daf83 100644 --- a/var/spack/repos/builtin/packages/py-pyelftools/package.py +++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyPyelftools(Package): - """A pure-Python library for parsing and analyzing ELF files and DWARF debugging information""" + """A pure-Python library for parsing and analyzing ELF files and DWARF + debugging information""" homepage = "https://pypi.python.org/pypi/pyelftools" url = "https://pypi.python.org/packages/source/p/pyelftools/pyelftools-0.23.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py index 0ca15dd10d..2d22bd9f03 100644 --- a/var/spack/repos/builtin/packages/py-pygments/package.py +++ b/var/spack/repos/builtin/packages/py-pygments/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPygments(Package): """Pygments is a syntax highlighting package written in Python.""" homepage = "https://pypi.python.org/pypi/pygments" diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py index 7107b2987f..c505d44530 100644 --- a/var/spack/repos/builtin/packages/py-pylint/package.py +++ b/var/spack/repos/builtin/packages/py-pylint/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import re + class PyPylint(Package): """array processing for numbers, strings, records, and objects.""" diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py index f762789dea..6fef71304c 100644 --- a/var/spack/repos/builtin/packages/py-pypar/package.py +++ b/var/spack/repos/builtin/packages/py-pypar/package.py @@ -24,12 +24,16 @@ ############################################################################## from spack import * + class PyPypar(Package): - """Pypar is an efficient but easy-to-use module that allows programs written in Python to run in parallel on multiple processors and communicate using MPI.""" + """Pypar is an efficient but easy-to-use module that allows programs + written in Python to run in parallel on multiple processors and + communicate using MPI.""" homepage = "http://code.google.com/p/pypar/" url = "https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz" - version('2.1.5_108', '7a1f28327d2a3b679f9455c843d850b8', url='https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz') + version('2.1.5_108', '7a1f28327d2a3b679f9455c843d850b8', + url='https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz') extends('python') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py index 0423aa3bdb..67d255b02d 100644 --- a/var/spack/repos/builtin/packages/py-pyparsing/package.py +++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPyparsing(Package): """A Python Parsing Module.""" homepage = "https://pypi.python.org/pypi/pyparsing" diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py index 05fb7aa22c..de68bfaa90 100644 --- a/var/spack/repos/builtin/packages/py-pyqt/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPyqt(Package): """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework and runs on all platforms supported by Qt diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py index cd174ce658..1cb3e4745f 100644 --- a/var/spack/repos/builtin/packages/py-pyside/package.py +++ b/var/spack/repos/builtin/packages/py-pyside/package.py @@ -25,6 +25,7 @@ from spack import * import os + class PyPyside(Package): """Python bindings for Qt.""" homepage = "https://pypi.python.org/pypi/pyside" @@ -43,7 +44,8 @@ class PyPyside(Package): # Figure out the special RPATH pypkg = self.spec['python'].package rpath = self.rpath - rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'PySide')) + rpath.append(os.path.join( + self.prefix, pypkg.site_packages_dir, 'PySide')) # Add Spack's standard CMake args to the sub-builds. # They're called BY setup.py so we have to patch it. @@ -61,7 +63,6 @@ class PyPyside(Package): r'#rpath_cmd(pyside_path, srcpath)', 'pyside_postinstall.py') - def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix, diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py index 58ed067b21..f87e74211f 100644 --- a/var/spack/repos/builtin/packages/py-pytables/package.py +++ b/var/spack/repos/builtin/packages/py-pytables/package.py @@ -23,10 +23,11 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import re + class PyPytables(Package): - """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.""" + """PyTables is a package for managing hierarchical datasets and designed to + efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" url = "https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz" @@ -37,6 +38,7 @@ class PyPytables(Package): depends_on('py-numpy', type=nolink) depends_on('py-numexpr', type=nolink) depends_on('py-cython', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): env["HDF5_DIR"] = spec['hdf5'].prefix diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py index c2c7c4de4f..a30dc00ba4 100644 --- a/var/spack/repos/builtin/packages/py-python-daemon/package.py +++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPythonDaemon(Package): """Library to implement a well-behaved Unix daemon process. @@ -47,4 +48,3 @@ class PyPythonDaemon(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index caf2c90e73..96f686d591 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPytz(Package): """World timezone definitions, modern and historical.""" homepage = "https://pypi.python.org/pypi/pytz" diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py index c0e22ba681..8da391fac1 100644 --- a/var/spack/repos/builtin/packages/py-pyyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyPyyaml(Package): """PyYAML is a YAML parser and emitter for Python.""" homepage = "http://pyyaml.org/wiki/PyYAML" diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py index 8f4771f0eb..f86d813766 100644 --- a/var/spack/repos/builtin/packages/py-rpy2/package.py +++ b/var/spack/repos/builtin/packages/py-rpy2/package.py @@ -24,10 +24,16 @@ ############################################################################## from spack import * + class PyRpy2(Package): - """rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.""" + """rpy2 is a redesign and rewrite of rpy. It is providing a low-level + interface to R from Python, a proposed high-level interface, + including wrappers to graphical libraries, as well as R-like + structures and functions. + + """ homepage = "https://pypi.python.org/pypi/rpy2" - url = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz" + url = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz" version('2.5.4', '115a20ac30883f096da2bdfcab55196d') version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f') diff --git a/var/spack/repos/builtin/packages/py-scientificpython/package.py b/var/spack/repos/builtin/packages/py-scientificpython/package.py index 7f7eb76b73..e2273dc164 100644 --- a/var/spack/repos/builtin/packages/py-scientificpython/package.py +++ b/var/spack/repos/builtin/packages/py-scientificpython/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyScientificpython(Package): """ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 26c286e4be..fbeb5c95ca 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -42,6 +42,7 @@ class PyScikitImage(Package): depends_on('py-six', type=nolink) depends_on('py-scipy', type=nolink) depends_on('py-matplotlib', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 1a6112bcf3..3cd7ea74f3 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyScikitLearn(Package): """""" homepage = "https://pypi.python.org/pypi/scikit-learn" diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index ea3731cf1b..cab516e1df 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyScipy(Package): """Scientific Library for Python.""" homepage = "http://www.scipy.org/" @@ -41,7 +42,8 @@ class PyScipy(Package): if 'atlas' in spec: # libatlas.so actually isn't always installed, but this # seems to make the build autodetect things correctly. - env['ATLAS'] = join_path(spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix) + env['ATLAS'] = join_path( + spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix) else: env['BLAS'] = spec['blas'].blas_shared_lib env['LAPACK'] = spec['lapack'].lapack_shared_lib diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py index 27188e1417..0713f26ebc 100644 --- a/var/spack/repos/builtin/packages/py-shiboken/package.py +++ b/var/spack/repos/builtin/packages/py-shiboken/package.py @@ -25,8 +25,9 @@ from spack import * import os + class PyShiboken(Package): - """Shiboken generates bindings for C++ libraries using CPython source code.""" + """Shiboken generates bindings for C++ libraries using CPython.""" homepage = "https://shiboken.readthedocs.org/" url = "https://pypi.python.org/packages/source/S/Shiboken/Shiboken-1.2.2.tar.gz" @@ -45,7 +46,8 @@ class PyShiboken(Package): # They're called BY setup.py so we have to patch it. pypkg = self.spec['python'].package rpath = self.rpath - rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'Shiboken')) + rpath.append(os.path.join( + self.prefix, pypkg.site_packages_dir, 'Shiboken')) filter_file( r'OPTION_CMAKE,', @@ -61,7 +63,6 @@ class PyShiboken(Package): r'#rpath_cmd(shiboken_path, srcpath)', 'shiboken_postinstall.py') - def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix, diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py index fc8e7f5296..9d97f08433 100644 --- a/var/spack/repos/builtin/packages/py-sip/package.py +++ b/var/spack/repos/builtin/packages/py-sip/package.py @@ -25,8 +25,10 @@ from spack import * import os + class PySip(Package): - """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + """SIP is a tool that makes it very easy to create Python bindings for C + and C++ libraries.""" homepage = "http://www.riverbankcomputing.com/software/sip/intro" url = "http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index eb4846d5af..da0c7aa003 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PySix(Package): """Python 2 and 3 compatibility utilities.""" homepage = "https://pypi.python.org/pypi/six" diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py index d00f1d128b..2295a6a0c3 100644 --- a/var/spack/repos/builtin/packages/py-sphinx/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PySphinx(Package): """Sphinx Documentation Generator.""" homepage = "http://sphinx-doc.org" diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py index 5e38fc5be1..3d8b86ac4d 100644 --- a/var/spack/repos/builtin/packages/py-sympy/package.py +++ b/var/spack/repos/builtin/packages/py-sympy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PySympy(Package): """SymPy is a Python library for symbolic mathematics.""" homepage = "https://pypi.python.org/pypi/sympy" diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py index b10244acdd..03e9528ad7 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tappy/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyTappy(Package): """Python TAP interface module for unit tests""" homepage = "https://github.com/mblayman/tappy" diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py index 56056ebad1..672a3ee587 100644 --- a/var/spack/repos/builtin/packages/py-tuiview/package.py +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyTuiview(Package): """ TuiView is a lightweight raster GIS with powerful raster attribute diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py index 2ce83cd24c..edf1e7b0d7 100644 --- a/var/spack/repos/builtin/packages/py-twisted/package.py +++ b/var/spack/repos/builtin/packages/py-twisted/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyTwisted(Package): """An asynchronous networking framework written in Python""" homepage = "https://twistedmatrix.com/" diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py index 48ba84e7bc..943fb250f6 100644 --- a/var/spack/repos/builtin/packages/py-urwid/package.py +++ b/var/spack/repos/builtin/packages/py-urwid/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyUrwid(Package): """A full-featured console UI library""" homepage = "http://urwid.org/" @@ -37,4 +38,3 @@ class PyUrwid(Package): def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) - diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index d6b33ae175..0ed567df95 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import shutil + class PyVirtualenv(Package): """virtualenv is a tool to create isolated Python environments.""" diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py index 9e383a9a19..f0ad340835 100644 --- a/var/spack/repos/builtin/packages/py-wheel/package.py +++ b/var/spack/repos/builtin/packages/py-wheel/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyWheel(Package): """A built-package format for Python.""" diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py index 9220f90340..81c3c928c0 100644 --- a/var/spack/repos/builtin/packages/py-xlrd/package.py +++ b/var/spack/repos/builtin/packages/py-xlrd/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyXlrd(Package): """Library for developers to extract data from Microsoft Excel (tm) spreadsheet files""" diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py index f7fe4037a1..bc26b82b07 100644 --- a/var/spack/repos/builtin/packages/py-yapf/package.py +++ b/var/spack/repos/builtin/packages/py-yapf/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class PyYapf(Package): """ Yet Another Python Formatter """ homepage = "https://github.com/google/yapf" diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index f755527607..c4e6754969 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -55,7 +55,8 @@ class Python(Package): extendable = True variant('tk', default=False, description='Provide support for Tkinter') - variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings') + variant('ucs4', default=False, + description='Enable UCS4 (wide) unicode strings') # From https://docs.python.org/2/c-api/unicode.html: Python's default # builds use a 16-bit type for Py_UNICODE and store Unicode values # internally as UCS2. It is also possible to build a UCS4 version of Python @@ -117,7 +118,8 @@ class Python(Package): config_args.append('--with-wide-unicode') elif spec.satisfies('@3.3:'): # https://docs.python.org/3.3/whatsnew/3.3.html - raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond') # NOQA: ignore=E501 + raise ValueError( + '+ucs4 variant not compatible with Python 3.3 and beyond') if spec.satisfies('@3:'): config_args.append('--without-ensurepip') diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py index f7cbcc2736..2733d8b652 100644 --- a/var/spack/repos/builtin/packages/qhull/package.py +++ b/var/spack/repos/builtin/packages/qhull/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Qhull(Package): """Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furt hest-site @@ -44,7 +45,7 @@ class Qhull(Package): # https://github.com/qhull/qhull/pull/5 patch('qhull-iterator.patch', when='@1.0') - + depends_on('cmake', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py index 314950dc36..f6b4c80cf4 100644 --- a/var/spack/repos/builtin/packages/qrupdate/package.py +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Qrupdate(Package): """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index f33e5c2d0e..e496a3e4d5 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Qt(Package): """Qt is a comprehensive cross-platform C++ application framework.""" homepage = 'http://qt.io' @@ -37,15 +38,17 @@ class Qt(Package): version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb') version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009') - # Add patch for compile issues with qt3 found with use in the OpenSpeedShop project - variant('krellpatch', default=False, description="Build with openspeedshop based patch.") + # Add patch for compile issues with qt3 found with use in the + # OpenSpeedShop project + variant('krellpatch', default=False, + description="Build with openspeedshop based patch.") variant('mesa', default=False, description="Depend on mesa.") variant('gtk', default=False, description="Build with gtkplus.") patch('qt3krell.patch', when='@3.3.8b+krellpatch') # Use system openssl for security. - #depends_on("openssl") + # depends_on("openssl") depends_on("glib") depends_on("gtkplus", when='+gtk') @@ -69,43 +72,39 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def url_for_version(self, version): url = "http://download.qt.io/archive/qt/" if version >= Version('5'): url += "%s/%s/single/qt-everywhere-opensource-src-%s.tar.gz" % \ - (version.up_to(2), version, version) + (version.up_to(2), version, version) elif version >= Version('4.8'): url += "%s/%s/qt-everywhere-opensource-src-%s.tar.gz" % \ - (version.up_to(2), version, version) + (version.up_to(2), version, version) elif version >= Version('4.6'): url += "%s/qt-everywhere-opensource-src-%s.tar.gz" % \ - (version.up_to(2), version) + (version.up_to(2), version) elif version >= Version('4.0'): url += "%s/qt-x11-opensource-src-%s.tar.gz" % \ - (version.up_to(2), version) + (version.up_to(2), version) elif version >= Version('3'): url += "%s/qt-x11-free-%s.tar.gz" % \ - (version.up_to(1), version) + (version.up_to(1), version) elif version >= Version('2.1'): url += "%s/qt-x11-%s.tar.gz" % \ - (version.up_to(1), version) + (version.up_to(1), version) else: url += "%s/qt-%s.tar.gz" % \ - (version.up_to(1), version) + (version.up_to(1), version) return url - def setup_environment(self, spack_env, env): env.set('QTDIR', self.prefix) - def setup_dependent_environment(self, spack_env, run_env, dspec): spack_env.set('QTDIR', self.prefix) - def patch(self): if self.spec.satisfies('@4'): qmake_conf = 'mkspecs/common/g++-base.conf' @@ -117,11 +116,14 @@ class Qt(Package): return # Fix qmake compilers in the default mkspec - filter_file(r'^QMAKE_COMPILER *=.*$', 'QMAKE_COMPILER = cc', qmake_conf) - filter_file(r'^QMAKE_CC *=.*$', 'QMAKE_CC = cc', qmake_conf) - filter_file(r'^QMAKE_CXX *=.*$', 'QMAKE_CXX = c++', qmake_conf) - filter_file(r'^QMAKE_LFLAGS_NOUNDEF *\+?=.*$', 'QMAKE_LFLAGS_NOUNDEF =', qmake_unix_conf) - + filter_file(r'^QMAKE_COMPILER *=.*$', + 'QMAKE_COMPILER = cc', qmake_conf) + filter_file(r'^QMAKE_CC *=.*$', + 'QMAKE_CC = cc', qmake_conf) + filter_file(r'^QMAKE_CXX *=.*$', + 'QMAKE_CXX = c++', qmake_conf) + filter_file(r'^QMAKE_LFLAGS_NOUNDEF *\+?=.*$', + 'QMAKE_LFLAGS_NOUNDEF =', qmake_unix_conf) @property def common_config_args(self): @@ -155,7 +157,7 @@ class Qt(Package): @when('@3') def configure(self): # An user report that this was necessary to link Qt3 on ubuntu - os.environ['LD_LIBRARY_PATH'] = os.getcwd()+'/lib' + os.environ['LD_LIBRARY_PATH'] = os.getcwd() + '/lib' configure('-prefix', self.prefix, '-v', '-thread', @@ -169,17 +171,16 @@ class Qt(Package): '-no-webkit', *self.common_config_args) - @when('@5') def configure(self): configure('-no-eglfs', '-no-directfb', '-qt-xcb', - # If someone wants to get a webkit build working, be my guest! + # If someone wants to get a webkit build working, be my + # guest! '-skip', 'qtwebkit', *self.common_config_args) - def install(self, spec, prefix): self.configure() make() diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py index 47b5706063..2eaff0a240 100644 --- a/var/spack/repos/builtin/packages/qthreads/package.py +++ b/var/spack/repos/builtin/packages/qthreads/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Qthreads(Package): """The qthreads API is designed to make using large numbers of threads convenient and easy, and to allow portable access to diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py new file mode 100644 index 0000000000..4c5d14a90f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RBase64enc(Package): + """This package provides tools for handling base64 encoding. It is more + flexible than the orphaned base64 package.""" + + homepage = "http://www.rforge.net/base64enc" + url = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc" + + version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py new file mode 100644 index 0000000000..1f2f541fec --- /dev/null +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RBoot(Package): + """Functions and datasets for bootstrapping from the book "Bootstrap + Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, + CUP), originally written by Angelo Canty for S.""" + + homepage = "https://cran.r-project.org/package=boot" + url = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/boot" + + version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py new file mode 100644 index 0000000000..111606d576 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RBrew(Package): + """brew implements a templating framework for mixing text and R code for + report generation. brew template syntax is similar to PHP, Ruby's erb + module, Java Server Pages, and Python's psp module.""" + + homepage = "https://cran.r-project.org/package=brew" + url = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/brew" + + version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py new file mode 100644 index 0000000000..f4a3824983 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCar(Package): + """Functions and Datasets to Accompany J. Fox and S. Weisberg, An R + Companion to Applied Regression, Second Edition, Sage, 2011.""" + + homepage = "https://r-forge.r-project.org/projects/car/" + url = "https://cran.r-project.org/src/contrib/car_2.1-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/car" + + version('2.1-2', '0f78ad74ef7130126d319acec23951a0') + + extends('R') + + depends_on('r-mass', type=nolink) + depends_on('r-mgcv', type=nolink) + depends_on('r-nnet', type=nolink) + depends_on('r-pbkrtest', type=nolink) + depends_on('r-quantreg', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py new file mode 100644 index 0000000000..460526c7d3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCaret(Package): + """Misc functions for training and plotting classification and regression + models.""" + + homepage = "https://github.com/topepo/caret/" + url = "https://cran.r-project.org/src/contrib/caret_6.0-70.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/caret" + + version('6.0-70', '202d7abb6a679af716ea69fb2573f108') + + extends('R') + + depends_on('r-lattice', type=nolink) + depends_on('r-ggplot2', type=nolink) + depends_on('r-car', type=nolink) + depends_on('r-foreach', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-nlme', type=nolink) + depends_on('r-reshape2', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py new file mode 100644 index 0000000000..9cd9d76e9e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RChron(Package): + """Chronological objects which can handle dates and times.""" + + homepage = "https://cran.r-project.org/package=chron" + url = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/chron" + + version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py new file mode 100644 index 0000000000..f541ea3611 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RClass(Package): + """Various functions for classification, including k-nearest neighbour, + Learning Vector Quantization and Self-Organizing Maps.""" + + homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" + url = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/class" + + version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') + + extends('R') + + depends_on('r-mass', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py new file mode 100644 index 0000000000..0fdf2ce5de --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCluster(Package): + """Methods for Cluster analysis. Much extended the original from Peter + Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw + (1990) "Finding Groups in Data".""" + + homepage = "https://cran.r-project.org/web/packages/cluster/index.html" + url = "https://cran.r-project.org/src/contrib/cluster_2.0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/cluster" + + version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py new file mode 100644 index 0000000000..bea2f78c82 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCodetools(Package): + """Code analysis tools for R.""" + + homepage = "https://cran.r-project.org/web/packages/codetools/index.html" + url = "https://cran.r-project.org/src/contrib/codetools_0.2-14.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/codetools" + + version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py new file mode 100644 index 0000000000..1e0befbca9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCrayon(Package): + """Colored terminal output on terminals that support 'ANSI' color and + highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is + automatically detected. Colors and highlighting can be combined and nested. + New styles can also be created easily. This package was inspired by the + 'chalk' 'JavaScript' project.""" + + homepage = "https://github.com/gaborcsardi/crayon" + url = "https://cran.r-project.org/src/contrib/crayon_1.3.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/crayon" + + version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py new file mode 100644 index 0000000000..1d8f837922 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RCubature(Package): + """Adaptive multivariate integration over hypercubes""" + + homepage = "https://cran.r-project.org/package=cubature" + url = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/cubature" + + version('1.1-2', '5617e1d82baa803a3814d92461da45c9') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index c6e8f22a94..24c0eadb2d 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -38,8 +38,9 @@ class RCurl(Package): homepage = "https://github.com/jeroenooms/curl" url = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl" + list_url = "https://cran.r-project.org/src/contrib/Archive/curl" + version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') extends('R') diff --git a/var/spack/repos/builtin/packages/r-datatable/package.py b/var/spack/repos/builtin/packages/r-datatable/package.py new file mode 100644 index 0000000000..8b50643341 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-datatable/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDatatable(Package): + """Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, + fast add/modify/delete of columns by group using no copies at all, list + columns and a fast file reader (fread). Offers a natural and flexible + syntax, for faster development.""" + + homepage = "https://github.com/Rdatatable/data.table/wiki" + url = "https://cran.r-project.org/src/contrib/data.table_1.9.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/data.table" + + version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372') + + extends('R') + + depends_on('r-chron') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 5f0b7b8779..75506dd257 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -36,14 +36,14 @@ class RDevtools(Package): extends('R') - depends_on('r-httr') - depends_on('r-memoise') - depends_on('r-whisker') - depends_on('r-digest') - depends_on('r-rstudioapi') - depends_on('r-jsonlite') - depends_on('r-git2r') - depends_on('r-withr') + depends_on('r-httr', type=nolink) + depends_on('r-memoise', type=nolink) + depends_on('r-whisker', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-rstudioapi', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-git2r', type=nolink) + depends_on('r-withr', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py new file mode 100644 index 0000000000..7ff3b8548b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDiagrammer(Package): + """Create graph diagrams and flowcharts using R.""" + + homepage = "https://github.com/rich-iannone/DiagrammeR" + url = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/DiagrammeR" + + version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-igraph', type=nolink) + depends_on('r-influencer', type=nolink) + depends_on('r-rstudioapi@0.6:', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-visnetwork', type=nolink) + depends_on('r-scales', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py new file mode 100644 index 0000000000..7cebfd9e58 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDoparallel(Package): + """Provides a parallel backend for the %dopar% function using the parallel + package.""" + + homepage = "https://cran.r-project.org/web/packages/doParallel/index.html" + url = "https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/doParallel" + + version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') + + extends('R') + + depends_on('r-foreach', type=nolink) + depends_on('r-iterators', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index b065e0b817..ded7651278 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -36,14 +36,15 @@ class RDplyr(Package): version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef') extends('R') - depends_on('r-assertthat') - depends_on('r-R6') - depends_on('r-rcpp') - depends_on('r-tibble') - depends_on('r-magrittr') - depends_on('r-lazyeval') - depends_on('r-dbi') - depends_on('r-bh') + + depends_on('r-assertthat', type=nolink) + depends_on('r-R6', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-tibble', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-dbi', type=nolink) + depends_on('r-bh', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py new file mode 100644 index 0000000000..f134ee8913 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDt(Package): + """Data objects in R can be rendered as HTML tables using the JavaScript + library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' + library has been included in this R package. The package name 'DT' is an + abbreviation of 'DataTables'.""" + + homepage = "http://rstudio.github.io/DT" + url = "https://cran.r-project.org/src/contrib/DT_0.1.tar.gz" + + version('0.1', '5c8df984921fa484784ec4b8a4fb6f3c') + + extends('R') + + depends_on('r-htmltools', type=nolink) + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-magrittr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py new file mode 100644 index 0000000000..9b01d7aa18 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDygraphs(Package): + """An R interface to the 'dygraphs' JavaScript charting library (a copy of + which is included in the package). Provides rich facilities for charting + time-series data in R, including highly configurable series- and + axis-display and interactive features like zoom/pan and series/point + highlighting.""" + + homepage = "https://cran.r-project.org/web/packages/dygraphs/index.html" + url = "https://cran.r-project.org/src/contrib/dygraphs_0.9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/dygraphs" + + version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') + + extends('R') + + depends_on('r-magrittr', type=nolink) + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-zoo', type=nolink) + depends_on('r-xts', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py new file mode 100644 index 0000000000..c2e7166403 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RE1071(Package): + """Functions for latent class analysis, short time Fourier transform, fuzzy + clustering, support vector machines, shortest path computation, bagged + clustering, naive Bayes classifier, ...""" + + homepage = "https://cran.r-project.org/package=e1071" + url = "https://cran.r-project.org/src/contrib/e1071_1.6-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/e1071" + + version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') + + extends('R') + + depends_on('r-class', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py new file mode 100644 index 0000000000..2a7324ae99 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RForeach(Package): + """Support for the foreach looping construct. Foreach is an idiom that + allows for iterating over elements in a collection, without the use of an + explicit loop counter. This package in particular is intended to be used + for its return value, rather than for its side effects. In that sense, it + is similar to the standard lapply function, but doesn't require the + evaluation of a function. Using foreach without side effects also + facilitates executing the loop in parallel.""" + + homepage = "https://cran.r-project.org/web/packages/foreach/index.html" + url = "https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/foreach" + + version('1.4.3', 'ef45768126661b259f9b8994462c49a0') + + extends('R') + + depends_on('r-codetools', type=nolink) + depends_on('r-iterators', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py new file mode 100644 index 0000000000..0a09a1145b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -0,0 +1,59 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGdata(Package): + """Various R programming tools for data manipulation, including: - medical + unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects + ('bindData', 'cbindX', 'combine', 'interleave'), - character vector + operations ('centerText', 'startsWith', 'trim'), - factor manipulation + ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R + objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', + 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel + formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', + 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - + extricating components of date & time objects ('getYear', 'getMonth', + 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data + frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', + 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', + 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames + ('frameApply', 'wideByFactor'), - value of last evaluated expression + ('ans'), and - wrapper for 'sample' that ensures consistent behavior for + both scalar and vector arguments ('resample').""" + + homepage = "https://cran.r-project.org/package=gdata" + url = "https://cran.r-project.org/src/contrib/gdata_2.17.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gdata" + + version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') + + extends('R') + + depends_on('r-gtools', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py new file mode 100644 index 0000000000..21ae07fd41 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGeosphere(Package): + """Spherical trigonometry for geographic applications. That is, compute + distances and related measures for angular (longitude/latitude) + locations.""" + + homepage = "https://cran.r-project.org/package=geosphere" + url = "https://cran.r-project.org/src/contrib/geosphere_1.5-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/geosphere" + + version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') + + extends('R') + + depends_on('r-sp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py new file mode 100644 index 0000000000..2dfca19b51 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -0,0 +1,57 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGgmap(Package): + """A collection of functions to visualize spatial data and models on top of + static maps from various online sources (e.g Google Maps and Stamen Maps). + It includes tools common to those tasks, including functions for + geolocation and routing.""" + + homepage = "https://github.com/dkahle/ggmap" + url = "https://cran.r-project.org/src/contrib/ggmap_2.6.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggmap" + + version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') + + extends('R') + + depends_on('r-ggplot2', type=nolink) + depends_on('r-proto', type=nolink) + depends_on('r-rgooglemaps', type=nolink) + depends_on('r-png', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-reshape2', type=nolink) + depends_on('r-rjson', type=nolink) + depends_on('r-mapproj', type=nolink) + depends_on('r-jpeg', type=nolink) + depends_on('r-geosphere', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-scales', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index 2d1f53af26..a8cf21930f 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -42,12 +42,12 @@ class RGgplot2(Package): extends('R') - depends_on('r-digest') - depends_on('r-gtable') - depends_on('r-mass') - depends_on('r-plyr') - depends_on('r-reshape2') - depends_on('r-scales') + depends_on('r-digest', type=nolink) + depends_on('r-gtable', type=nolink) + depends_on('r-mass', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-reshape2', type=nolink) + depends_on('r-scales', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 8fc1f397c8..29b2069ae9 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -38,13 +38,13 @@ class RGgvis(Package): extends('R') - depends_on('r-assertthat') - depends_on('r-jsonlite') - depends_on('r-shiny') - depends_on('r-magrittr') - depends_on('r-dplyr') - depends_on('r-lazyeval') - depends_on('r-htmltools') + depends_on('r-assertthat', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-shiny', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-dplyr', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-htmltools', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py new file mode 100644 index 0000000000..af6e1d1b63 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGlmnet(Package): + """Extremely efficient procedures for fitting the entire lasso or + elastic-net regularization path for linear regression, logistic and + multinomial regression models, Poisson regression and the Cox model. Two + recent additions are the multiple-response Gaussian, and the grouped + multinomial. The algorithm uses cyclical coordinate descent in a path-wise + fashion, as described in the paper linked to via the URL below.""" + + homepage = "http://www.jstatsoft.org/v33/i01/" + url = "https://cran.r-project.org/src/contrib/glmnet_2.0-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/glmnet" + + version('2.0-5', '049b18caa29529614cd684db3beaec2a') + + extends('R') + + depends_on('r-matrix', type=nolink) + depends_on('r-foreach', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py new file mode 100644 index 0000000000..bcb7caa0fb --- /dev/null +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGooglevis(Package): + """R interface to Google Charts API, allowing users to create interactive + charts based on data frames. Charts are displayed locally via the R HTTP + help server. A modern browser with an Internet connection is required and + for some charts a Flash player. The data remains local and is not uploaded + to Google.""" + + homepage = "https://github.com/mages/googleVis#googlevis" + url = "https://cran.r-project.org/src/contrib/googleVis_0.6.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/googleVis" + + version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') + + extends('R') + + depends_on('r-jsonlite', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py new file mode 100644 index 0000000000..a2f55b4470 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGridbase(Package): + """Integration of base and grid graphics.""" + + homepage = "https://cran.r-project.org/web/packages/gridBase/index.html" + url = "https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase" + + version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index d215d10678..537426d42f 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -37,7 +37,7 @@ class RGridextra(Package): extends('R') - depends_on('r-gtable') + depends_on('r-gtable', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py new file mode 100644 index 0000000000..367bb30f87 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -0,0 +1,60 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGtools(Package): + """Functions to assist in R programming, including: - assist in developing, + updating, and maintaining R and R packages ('ask', 'checkRVersion', + 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse + logit transformations ('logit', 'inv.logit'), - test if a value is missing, + empty or contains only NA and NULL values ('invalid'), - manipulate R's + .Last function ('addLast'), - define macros ('defmacro'), - detect odd and + even integers ('odd', 'even'), - convert strings containing non-ASCII + characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a + binary search ('binsearch'), - sort strings containing both numeric and + character components ('mixedsort'), - create a factor variable from the + quantiles of a continuous variable ('quantcut'), - enumerate permutations + and combinations ('combinations', 'permutation'), - calculate and convert + between fold-change and log-ratio ('foldchange', 'logratio2foldchange', + 'foldchange2logratio'), - calculate probabilities and generate random + numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply + a function over adjacent subsets of a vector ('running'), - modify the + TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of + data frames, even if the column names don't match ('smartbind'), - generate + significance stars from p-values ('stars.pval'), - convert characters + to/from ASCII codes.""" + + homepage = "https://cran.r-project.org/package=gtools" + url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gtools" + + version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 0aea564372..21cdbe9184 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -36,8 +36,8 @@ class RHtmltools(Package): extends('R') - depends_on('r-digest') - depends_on('r-rcpp') + depends_on('r-digest', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py new file mode 100644 index 0000000000..8090776f06 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RHtmlwidgets(Package): + """A framework for creating HTML widgets that render in various contexts + including the R console, 'R Markdown' documents, and 'Shiny' web + applications.""" + + homepage = "https://github.com/ramnathv/htmlwidgets" + url = "https://cran.r-project.org/src/contrib/htmlwidgets_0.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/htmlwidgets" + + version('0.6', '7fa522d2eda97593978021bda9670c0e') + + extends('R') + + depends_on('r-htmltools', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-yaml', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index 6ab12bcf9d..57025d3a3c 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -42,7 +42,7 @@ class RHttpuv(Package): extends('R') - depends_on('r-rcpp') + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index 77ec34ab03..227594fc0d 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -38,11 +38,11 @@ class RHttr(Package): extends('R') - depends_on('r-jsonlite') - depends_on('r-mime') - depends_on('r-curl') - depends_on('r-openssl') - depends_on('r-R6') + depends_on('r-jsonlite', type=nolink) + depends_on('r-mime', type=nolink) + depends_on('r-curl', type=nolink) + depends_on('r-openssl', type=nolink) + depends_on('r-R6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py new file mode 100644 index 0000000000..37925d4e02 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RIgraph(Package): + """Routines for simple graphs and network analysis. It can handle large + graphs very well and provides functions for generating random and regular + graphs, graph visualization, centrality methods and much more.""" + + homepage = "http://igraph.org/" + url = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/igraph" + + version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') + + extends('R') + + depends_on('r-matrix', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-nmf', type=nolink) + depends_on('r-irlba', type=nolink) + depends_on('gmp') + depends_on('libxml2') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py new file mode 100644 index 0000000000..dd525daf2b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RInfluencer(Package): + """Provides functionality to compute various node centrality measures on + networks. Included are functions to compute betweenness centrality (by + utilizing Madduri and Bader's SNAP library), implementations of Burt's + constraint and effective network size (ENS) metrics, Borgatti's algorithm + to identify key players, and Valente's bridging metric. On Unix systems, + the betweenness, Key Players, and bridging implementations are parallelized + with OpenMP, which may run faster on systems which have OpenMP + configured.""" + + homepage = "https://github.com/rcc-uchicago/influenceR" + url = "https://cran.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" + + version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') + + extends('R') + + depends_on('r-igraph', type=nolink) + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py new file mode 100644 index 0000000000..42cc142e8a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RIrlba(Package): + """Fast and memory efficient methods for truncated singular and eigenvalue + decompositions and principal component analysis of large sparse or dense + matrices.""" + + homepage = "https://cran.r-project.org/web/packages/irlba/index.html" + url = "https://cran.r-project.org/src/contrib/irlba_2.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/irlba" + + version('2.0.0', '557674cf8b68fea5b9f231058c324d26') + + extends('R') + + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py new file mode 100644 index 0000000000..f5a3489e7d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RIterators(Package): + """Support for iterators, which allow a programmer to traverse through all + the elements of a vector, list, or other collection of data.""" + + homepage = "https://cran.r-project.org/web/packages/iterators/index.html" + url = "https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/iterators" + + version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py new file mode 100644 index 0000000000..ef940720f8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RJpeg(Package): + """This package provides an easy and simple way to read, write and display + bitmap images stored in the JPEG format. It can read and write both files + and in-memory raw vectors.""" + + homepage = "http://www.rforge.net/jpeg/" + url = "https://cran.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/jpeg" + + version('0.1-8', '696007451d14395b1ed1d0e9af667a57') + + extends('R') + + depends_on('jpeg') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 6e231ed345..d1cb4b52c1 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -38,9 +38,10 @@ class RJsonlite(Package): use with dynamic data in systems and applications.""" homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz" + url = "https://cran.r-project.org/src/contrib/jsonlite_1.0.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + version('1.0', 'c8524e086de22ab39b8ac8000220cc87') version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') extends('R') diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py new file mode 100644 index 0000000000..2a91100c34 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RLeaflet(Package): + """Create and customize interactive maps using the 'Leaflet' JavaScript + library and the 'htmlwidgets' package. These maps can be used directly from + the R console, from 'RStudio', in Shiny apps and R Markdown documents.""" + + homepage = "http://rstudio.github.io/leaflet/" + url = "https://cran.r-project.org/src/contrib/leaflet_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/leaflet" + + version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') + + extends('R') + + depends_on('r-base64enc', type=nolink) + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-markdown', type=nolink) + depends_on('r-png', type=nolink) + depends_on('r-rcolorbrewer', type=nolink) + depends_on('r-raster', type=nolink) + depends_on('r-scales', type=nolink) + depends_on('r-sp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py new file mode 100644 index 0000000000..c52d9d0e27 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RLme4(Package): + """Fit linear and generalized linear mixed-effects models. The models and + their components are represented using S4 classes and methods. The core + computational algorithms are implemented using the 'Eigen' C++ library for + numerical linear algebra and 'RcppEigen' "glue".""" + + homepage = "https://github.com/lme4/lme4/" + url = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lme4" + + version('1.1-12', 'da8aaebb67477ecb5631851c46207804') + + extends('R') + + depends_on('r-matrix', type=nolink) + depends_on('r-mass', type=nolink) + depends_on('r-lattice', type=nolink) + depends_on('r-nlme', type=nolink) + depends_on('r-minqa', type=nolink) + depends_on('r-nloptr', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-rcppeigen', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py new file mode 100644 index 0000000000..31a36f1f7e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RLmtest(Package): + """A collection of tests, data sets, and examples for diagnostic checking + in linear regression models. Furthermore, some generic tools for inference + in parametric models are provided.""" + + homepage = "https://cran.r-project.org/package=lmtest" + url = "https://cran.r-project.org/src/contrib/lmtest_0.9-34.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lmtest" + + version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') + + extends('R') + + depends_on('r-zoo', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 88576911f0..2e5661fa4d 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -40,7 +40,8 @@ class RLubridate(Package): version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') extends('R') - depends_on('r-stringr') + + depends_on('r-stringr', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index f6ba97740b..2b8f95351a 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -39,7 +39,7 @@ class RMagic(Package): extends('R') - depends_on('r-abind') + depends_on('r-abind', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py new file mode 100644 index 0000000000..0f8bbe199b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMapproj(Package): + """Converts latitude/longitude into projected coordinates.""" + + homepage = "https://cran.r-project.org/package=mapproj" + url = "https://cran.r-project.org/src/contrib/mapproj_1.2-4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mapproj" + + version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') + + extends('R') + + depends_on('r-maps', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py new file mode 100644 index 0000000000..1e0bfd2d43 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMaps(Package): + """Display of maps. Projection code and larger maps are in separate + packages ('mapproj' and 'mapdata').""" + + homepage = "https://cran.r-project.org/" + url = "https://cran.r-project.org/src/contrib/maps_3.1.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/maps" + + version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py new file mode 100644 index 0000000000..8d045a4ed4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMaptools(Package): + """Set of tools for manipulating and reading geographic data, in particular + ESRI shapefiles; C code used from shapelib. It includes binary access to + GSHHG shoreline files. The package also provides interface wrappers for + exchanging spatial objects with packages such as PBSmapping, spatstat, + maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.""" + + homepage = "http://r-forge.r-project.org/projects/maptools/" + url = "https://cran.r-project.org/src/contrib/maptools_0.8-39.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/maptools" + + version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') + + extends('R') + + depends_on('r-sp', type=nolink) + depends_on('r-foreign', type=nolink) + depends_on('r-lattice', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py new file mode 100644 index 0000000000..c34727d2b0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMarkdown(Package): + """Provides R bindings to the 'Sundown' 'Markdown' rendering library + (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting + syntax that can be converted to 'XHTML' or other formats. See + http://en.wikipedia.org/wiki/Markdown for more information about + 'Markdown'.""" + + homepage = "https://github.com/rstudio/markdown" + url = "https://cran.r-project.org/src/contrib/markdown_0.7.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/markdown" + + version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') + + extends('R') + + depends_on('r-mime', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index fbd8a7b4df..1b45dc55ca 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -37,7 +37,7 @@ class RMatrix(Package): extends('R') - depends_on('r-lattice') + depends_on('r-lattice', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py new file mode 100644 index 0000000000..3cdce6fea6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMatrixmodels(Package): + """Modelling with sparse and dense 'Matrix' matrices, using modular + prediction and response module classes.""" + + homepage = "http://matrix.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels" + + version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') + + extends('R') + + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index 6a0fb78650..81f3ff1dab 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -37,7 +37,7 @@ class RMemoise(Package): extends('R') - depends_on('r-digest') + depends_on('r-digest', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py new file mode 100644 index 0000000000..4c49462ba2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMgcv(Package): + """GAMs, GAMMs and other generalized ridge regression with multiple + smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() + function, a wide variety of smoothers, JAGS support and distributions + beyond the exponential family.""" + + homepage = "https://cran.r-project.org/package=mgcv" + url = "https://cran.r-project.org/src/contrib/mgcv_1.8-13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv" + + version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') + + extends('R') + + depends_on('r-nlme', type=nolink) + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index fb079f44c5..5e78889a76 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -30,9 +30,10 @@ class RMime(Package): from /etc/mime.types in UNIX-type systems.""" homepage = "https://github.com/yihui/mime" - url = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz" + url = "https://cran.r-project.org/src/contrib/mime_0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') extends('R') diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py new file mode 100644 index 0000000000..16cff20b41 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMinqa(Package): + """Derivative-free optimization by quadratic approximation based on an + interface to Fortran implementations by M. J. D. Powell.""" + + homepage = "http://optimizer.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/minqa" + + version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') + + extends('R') + + depends_on('r-rcpp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py new file mode 100644 index 0000000000..54416502d9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMultcomp(Package): + """Simultaneous tests and confidence intervals for general linear + hypotheses in parametric models, including linear, generalized linear, + linear mixed effects, and survival models. The package includes demos + reproducing analyzes presented in the book "Multiple Comparisons Using R" + (Bretz, Hothorn, Westfall, 2010, CRC Press).""" + + homepage = "http://multcomp.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp" + + version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') + + extends('R') + + depends_on('r-mvtnorm', type=nolink) + depends_on('r-survival', type=nolink) + depends_on('r-thdata', type=nolink) + depends_on('r-sandwich', type=nolink) + depends_on('r-codetools', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 3216c95e00..b96b90f9c7 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -40,7 +40,7 @@ class RMunsell(Package): extends('R') - depends_on('r-colorspace') + depends_on('r-colorspace', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py new file mode 100644 index 0000000000..b3f7db60c6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMvtnorm(Package): + """Computes multivariate normal and t probabilities, quantiles, random + deviates and densities.""" + + homepage = "http://mvtnorm.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm" + + version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py new file mode 100644 index 0000000000..11bf7abb38 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -0,0 +1,56 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNcdf4(Package): + """Provides a high-level R interface to data files written using Unidata's + netCDF library (version 4 or earlier), which are binary data files that are + portable across platforms and include metadata information in addition to + the data sets. Using this package, netCDF files (either version 4 or + "classic" version 3) can be opened and data sets read in easily. It is also + easy to create new netCDF dimensions, variables, and files, in either + version 3 or 4 format, and manipulate existing netCDF files. This package + replaces the former ncdf package, which only worked with netcdf version 3 + files. For various reasons the names of the functions have had to be + changed from the names in the ncdf package. The old ncdf package is still + available at the URL given below, if you need to have backward + compatibility. It should be possible to have both the ncdf and ncdf4 + packages installed simultaneously without a problem. However, the ncdf + package does not provide an interface for netcdf version 4 files.""" + + homepage = "http://cirrus.ucsd.edu/~pierce/ncdf" + url = "https://cran.r-project.org/src/contrib/ncdf4_1.15.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ncdf4" + + version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') + + extends('R') + + depends_on('netcdf') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py new file mode 100644 index 0000000000..8884f7cf1b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNetworkd3(Package): + """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs + from 'R'.""" + + homepage = "http://cran.r-project.org/package=networkD3" + url = "https://cran.r-project.org/src/contrib/networkD3_0.2.12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/networkD3" + + version('0.2.12', '356fe4be59698e6fb052644bd9659d84') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-igraph', type=nolink) + depends_on('r-magrittr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py new file mode 100644 index 0000000000..1b6bb114e1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNlme(Package): + """Fit and compare Gaussian linear and nonlinear mixed-effects models.""" + + homepage = "https://cran.r-project.org/package=nlme" + url = "https://cran.r-project.org/src/contrib/nlme_3.1-128.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/nlme" + + version('3.1-128', '3d75ae7380bf123761b95a073eb55008') + + extends('R') + + depends_on('r-lattice', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py new file mode 100644 index 0000000000..58cb585c49 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNloptr(Package): + """nloptr is an R interface to NLopt. NLopt is a free/open-source library + for nonlinear optimization, providing a common interface for a number of + different free optimization routines available online as well as original + implementations of various other algorithms. See + http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more + information on the available algorithms. During installation on Unix the + NLopt code is downloaded and compiled from the NLopt website.""" + + homepage = "https://cran.r-project.org/package=nloptr" + url = "https://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/nloptr" + + version('1.0.4', '9af69a613349b236fd377d0a107f484c') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py new file mode 100644 index 0000000000..c30a1ac101 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -0,0 +1,60 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNmf(Package): + """Provides a framework to perform Non-negative Matrix Factorization (NMF). + The package implements a set of already published algorithms and seeding + methods, and provides a framework to test, develop and plug new/custom + algorithms. Most of the built-in algorithms have been optimized in C++, and + the main interface function provides an easy way of performing parallel + computations on multicore machines..""" + + homepage = "http://renozao.github.io/NMF" + url = "https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/NMF" + + version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') + + extends('R') + + depends_on('r-pkgmaker', type=nolink) + depends_on('r-registry', type=nolink) + depends_on('r-rngtools', type=nolink) + depends_on('r-cluster', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-gridbase', type=nolink) + depends_on('r-colorspace', type=nolink) + depends_on('r-rcolorbrewer', type=nolink) + depends_on('r-foreach', type=nolink) + depends_on('r-doparallel', type=nolink) + depends_on('r-ggplot2', type=nolink) + depends_on('r-reshape2', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py new file mode 100644 index 0000000000..be048f5ad0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNnet(Package): + """Software for feed-forward neural networks with a single hidden layer, + and for multinomial log-linear models.""" + + homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" + url = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/nnet" + + version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py new file mode 100644 index 0000000000..bff7d0f195 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RNp(Package): + """This package provides a variety of nonparametric (and semiparametric) + kernel methods that seamlessly handle a mix of continuous, unordered, and + ordered factor data types. We would like to gratefully acknowledge support + from the Natural Sciences and Engineering Research Council of Canada + (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council + of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic + Research Computing Network (SHARCNET:www.sharcnet.ca).""" + + homepage = "https://github.com/JeffreyRacine/R-Package-np/" + url = "https://cran.r-project.org/src/contrib/np_0.60-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/np" + + version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') + + extends('R') + + depends_on('r-boot', type=nolink) + depends_on('r-cubature', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py new file mode 100644 index 0000000000..40b6f96927 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPbkrtest(Package): + """Test in mixed effects models. Attention is on mixed effects models as + implemented in the 'lme4' package. This package implements a parametric + bootstrap test and a Kenward Roger modification of F-tests for linear mixed + effects models and a parametric bootstrap test for generalized linear mixed + models.""" + + homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/" + url = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest" + + version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') + + extends('R') + + depends_on('r-lme4', type=nolink) + depends_on('r-matrix', type=nolink) + depends_on('r-mass', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py new file mode 100644 index 0000000000..87daec5ad0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPkgmaker(Package): + """This package provides some low-level utilities to use for package + development. It currently provides managers for multiple package specific + options and registries, vignette, unit test and bibtex related utilities. + It serves as a base package for packages like NMF, RcppOctave, doRNG, and + as an incubator package for other general purposes utilities, that will + eventually be packaged separately. It is still under heavy development and + changes in the interface(s) are more than likely to happen.""" + + homepage = "https://renozao.github.io/pkgmaker" + url = "https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pkgmaker" + + version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') + + extends('R') + + depends_on('r-registry', type=nolink) + depends_on('r-codetools', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-xtable', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py new file mode 100644 index 0000000000..d1d61dbc4d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPlotrix(Package): + """Lots of plots, various labeling, axis and color scaling functions.""" + + homepage = "https://cran.r-project.org/package=plotrix" + url = "https://cran.r-project.org/src/contrib/plotrix_3.6-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix" + + version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index 192e7e8b18..fe4512347a 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -42,7 +42,7 @@ class RPlyr(Package): extends('R') - depends_on('r-rcpp') + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py new file mode 100644 index 0000000000..d3a80a4e16 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPng(Package): + """This package provides an easy and simple way to read, write and display + bitmap images stored in the PNG format. It can read and write both files + and in-memory raw vectors.""" + + homepage = "http://www.rforge.net/png/" + url = "https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/png" + + version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') + + extends('R') + + depends_on('libpng') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py new file mode 100644 index 0000000000..102d86d2fa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPraise(Package): + """Build friendly R packages that praise their users if they have done + something good, or they just need it to feel better.""" + + homepage = "https://github.com/gaborcsardi/praise" + url = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz" + + version('1.0.0', '9318724cec0454884b5f762bee2da6a1') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py new file mode 100644 index 0000000000..07ace3ad29 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RProto(Package): + """An object oriented system using object-based, also called + prototype-based, rather than class-based object oriented ideas.""" + + homepage = "http://r-proto.googlecode.com/" + url = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/proto" + + version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py new file mode 100644 index 0000000000..ecfbf49055 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RQuantmod(Package): + """Specify, build, trade, and analyse quantitative financial trading + strategies.""" + + homepage = "http://www.quantmod.com/" + url = "https://cran.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/quantmod" + + version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') + + extends('R') + + depends_on('r-xts', type=nolink) + depends_on('r-zoo', type=nolink) + depends_on('r-ttr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py new file mode 100644 index 0000000000..89a26070ba --- /dev/null +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RQuantreg(Package): + """Estimation and inference methods for models of conditional quantiles: + Linear and nonlinear parametric and non-parametric (total variation + penalized) models for conditional quantiles of a univariate response + and several methods for handling censored survival data. Portfolio + selection methods based on expected shortfall risk are also + included.""" + + homepage = "https://cran.r-project.org/package=quantreg" + url = "https://cran.r-project.org/src/contrib/quantreg_5.26.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg" + + version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') + + extends('R') + + depends_on('r-sparsem', type=nolink) + depends_on('r-matrix', type=nolink) + depends_on('r-matrixmodels', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py new file mode 100644 index 0000000000..1066c217f4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRandomforest(Package): + """Classification and regression based on a forest of trees using random + inputs.""" + + homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/" + url = "https://cran.r-project.org/src/contrib/randomForest_4.6-12.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest" + + version('4.6-12', '071c03af974198e861f1475c5bab9e7a') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py new file mode 100644 index 0000000000..39f4256703 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRaster(Package): + """Reading, writing, manipulating, analyzing and modeling of gridded + spatial data. The package implements basic and high-level functions. + Processing of very large files is supported.""" + + homepage = "http://cran.r-project.org/package=raster" + url = "https://cran.r-project.org/src/contrib/raster_2.5-8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/raster" + + version('2.5-8', '2a7db931c74d50516e82d04687c0a577') + + extends('R') + + depends_on('r-sp', type=nolink) + depends_on('r-rcpp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 2428f4af3b..94580a8700 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -37,9 +37,10 @@ class RRcpp(Package): last two.""" homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" - url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz" + url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.6.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp" + version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') extends('R') diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 3175628a73..ecf9256ab3 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -48,8 +48,8 @@ class RRcppeigen(Package): extends('R') - depends_on('r-matrix') - depends_on('r-rcpp') + depends_on('r-matrix', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py new file mode 100644 index 0000000000..119a84718a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRegistry(Package): + """Provides a generic infrastructure for creating and using registries.""" + + homepage = "https://cran.r-project.org/web/packages/registry/index.html" + url = "https://cran.r-project.org/src/contrib/registry_0.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/registry" + + version('0.3', '85345b334ec81eb3da6edcbb27c5f421') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index a96a314008..769e82aff9 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -37,9 +37,9 @@ class RReshape2(Package): extends('R') - depends_on('r-plyr') - depends_on('r-stringr') - depends_on('r-rcpp') + depends_on('r-plyr', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py new file mode 100644 index 0000000000..0d28b68b94 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRgooglemaps(Package): + """This package serves two purposes: (i) Provide a comfortable R interface + to query the Google server for static maps, and (ii) Use the map as a + background image to overlay plots within R. This requires proper coordinate + scaling.""" + + homepage = "https://cran.r-project.org/package=RgoogleMaps" + url = "https://cran.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RgoogleMaps" + + version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') + + extends('R') + + depends_on('r-png', type=nolink) + depends_on('r-rjsonio', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py new file mode 100644 index 0000000000..94ca45f485 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRjson(Package): + """Converts R object into JSON objects and vice-versa.""" + + homepage = "https://cran.r-project.org/package=rjson" + url = "https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rjson" + + version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py new file mode 100644 index 0000000000..b56dfbe21d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -0,0 +1,55 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRjsonio(Package): + """This is a package that allows conversion to and from data in Javascript + object notation (JSON) format. This allows R objects to be inserted into + Javascript/ECMAScript/ActionScript code and allows R programmers to read + and convert JSON content to R objects. This is an alternative to rjson + package. Originally, that was too slow for converting large R objects to + JSON and was not extensible. rjson's performance is now similar to this + package, and perhaps slightly faster in some cases. This package uses + methods and is readily extensible by defining methods for different + classes, vectorized operations, and C code and callbacks to R functions for + deserializing JSON objects to R. The two packages intentionally share the + same basic interface. This package (RJSONIO) has many additional options to + allow customizing the generation and processing of JSON content. This + package uses libjson rather than implementing yet another JSON parser. The + aim is to support other general projects by building on their work, + providing feedback and benefit from their ongoing development.""" + + homepage = "https://cran.r-project.org/package=RJSONIO" + url = "https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO" + + version('1.3-0', '72c395622ba8d1435ec43849fd32c830') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 086374df07..bc42c51ca9 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -36,7 +36,7 @@ class RRmysql(Package): extends('R') - depends_on('r-dbi') + depends_on('r-dbi', type=nolink) depends_on('mariadb') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py new file mode 100644 index 0000000000..2f33cd9f88 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRngtools(Package): + """This package contains a set of functions for working with Random Number + Generators (RNGs). In particular, it defines a generic S4 framework for + getting/setting the current RNG, or RNG data that are embedded into objects + for reproducibility. Notably, convenient default methods greatly facilitate + the way current RNG settings can be changed.""" + + homepage = "https://renozao.github.io/rngtools" + url = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools" + + version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') + + extends('R') + + depends_on('r-pkgmaker', type=nolink) + depends_on('r-stringr', type=nolink) + depends_on('r-digest', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py new file mode 100644 index 0000000000..4f4b8dcafa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRoxygen2(Package): + """A 'Doxygen'-like in-source documentation system for Rd, collation, and + 'NAMESPACE' files.""" + + homepage = "https://github.com/klutometis/roxygen" + url = "https://cran.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/roxygen2" + + version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') + + extends('R') + + depends_on('r-stringr', type=nolink) + depends_on('r-stringi', type=nolink) + depends_on('r-brew', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-rcpp', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 53e1978ffe..999fb4a1b9 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -44,7 +44,7 @@ class RRpostgresql(Package): extends('R') - depends_on('r-dbi') + depends_on('r-dbi', type=nolink) depends_on('postgresql') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index 7c03ab8950..c7d41f0fb3 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -38,7 +38,7 @@ class RRsqlite(Package): extends('R') - depends_on('r-dbi') + depends_on('r-dbi', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 00fd5116d9..1d0052563b 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -44,13 +44,13 @@ class RRstan(Package): extends('R') - depends_on('r-ggplot2') - depends_on('r-stanheaders') - depends_on('r-inline') - depends_on('r-gridextra') - depends_on('r-rcpp') - depends_on('r-rcppeigen') - depends_on('r-bh') + depends_on('r-ggplot2', type=nolink) + depends_on('r-stanheaders', type=nolink) + depends_on('r-inline', type=nolink) + depends_on('r-gridextra', type=nolink) + depends_on('r-rcpp', type=nolink) + depends_on('r-rcppeigen', type=nolink) + depends_on('r-bh', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 0ef2d9b987..bf9b35fe5b 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -33,6 +33,7 @@ class RRstudioapi(Package): url = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') extends('R') diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py new file mode 100644 index 0000000000..ffd62b1b14 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RSandwich(Package): + """Model-robust standard error estimators for cross-sectional, time series, + and longitudinal data.""" + + homepage = "https://cran.r-project.org/package=sandwich" + url = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich" + + version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') + + extends('R') + + depends_on('r-zoo', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index 046a05d48e..44bd5a5a2a 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -37,12 +37,12 @@ class RScales(Package): extends('R') - depends_on('r-rcolorbrewer') - depends_on('r-dichromat') - depends_on('r-plyr') - depends_on('r-munsell') - depends_on('r-labeling') - depends_on('r-rcpp') + depends_on('r-rcolorbrewer', type=nolink) + depends_on('r-dichromat', type=nolink) + depends_on('r-plyr', type=nolink) + depends_on('r-munsell', type=nolink) + depends_on('r-labeling', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index a9a9532910..a80860f4a5 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -39,13 +39,13 @@ class RShiny(Package): extends('R') - depends_on('r-httpuv') - depends_on('r-mime') - depends_on('r-jsonlite') - depends_on('r-xtable') - depends_on('r-digest') - depends_on('r-htmltools') - depends_on('r-R6') + depends_on('r-httpuv', type=nolink) + depends_on('r-mime', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-xtable', type=nolink) + depends_on('r-digest', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-R6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py new file mode 100644 index 0000000000..bb7589d490 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RSp(Package): + """Classes and methods for spatial data; the classes document where the + spatial location information resides, for 2D or 3D data. Utility functions + are provided, e.g. for plotting data as maps, spatial selection, as well as + methods for retrieving coordinates, for subsetting, print, summary, etc.""" + + homepage = "https://github.com/edzer/sp/" + url = "https://cran.r-project.org/src/contrib/sp_1.2-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/sp" + + version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') + + extends('R') + + depends_on('r-lattice', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py new file mode 100644 index 0000000000..c4dabf5c15 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RSparsem(Package): + """Some basic linear algebra functionality for sparse matrices is provided: + including Cholesky decomposition and backsolving as well as standard R + subsetting and Kronecker products.""" + + homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html" + url = "https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM" + + version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index 01fd969522..08ded95833 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -40,8 +40,8 @@ class RStringr(Package): extends('R') - depends_on('r-stringi') - depends_on('r-magrittr') + depends_on('r-stringi', type=nolink) + depends_on('r-magrittr', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py new file mode 100644 index 0000000000..646793f7a4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RSurvey(Package): + """Summary statistics, two-sample tests, rank tests, generalised linear + models, cumulative link models, Cox models, loglinear models, and general + maximum pseudolikelihood estimation for multistage stratified, + cluster-sampled, unequally weighted survey samples. Variances by Taylor + series linearisation or replicate weights. Post-stratification, + calibration, and raking. Two-phase subsampling designs. Graphics. PPS + sampling without replacement. Principal components, factor analysis.""" + + homepage = "http://r-survey.r-forge.r-project.org/survey/" + url = "https://cran.r-project.org/src/contrib/survey_3.30-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/survey" + + version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py new file mode 100644 index 0000000000..cfba9298fe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RSurvival(Package): + """Contains the core survival analysis routines, including definition of + Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox + models, and parametric accelerated failure time models.""" + + homepage = "https://cran.r-project.org/package=survival" + url = "https://cran.r-project.org/src/contrib/survival_2.39-5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/survival" + + version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') + + extends('R') + + depends_on('r-matrix', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py new file mode 100644 index 0000000000..a85aa8baef --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RTarifx(Package): + """A collection of various utility and convenience functions.""" + + homepage = "https://cran.r-project.org/package=taRifx" + url = "https://cran.r-project.org/src/contrib/taRifx_1.0.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/taRifx" + + version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') + + extends('R') + + depends_on('r-reshape2', type=nolink) + depends_on('r-plyr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py new file mode 100644 index 0000000000..60dfd2afcd --- /dev/null +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RTestthat(Package): + """A unit testing system designed to be fun, flexible and easy to set + up.""" + + homepage = "https://github.com/hadley/testthat" + url = "https://cran.r-project.org/src/contrib/testthat_1.0.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/testthat" + + version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') + + extends('R') + + depends_on('r-digest', type=nolink) + depends_on('r-crayon', type=nolink) + depends_on('r-praise', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-R6', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-thdata/package.py b/var/spack/repos/builtin/packages/r-thdata/package.py new file mode 100644 index 0000000000..e1cf050181 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-thdata/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RThdata(Package): + """Contains data sets used in other packages Torsten Hothorn maintains.""" + + homepage = "https://cran.r-project.org/package=TH.data" + url = "https://cran.r-project.org/src/contrib/TH.data_1.0-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data" + + version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') + + extends('R') + + depends_on('r-survival', type=nolink) + depends_on('r-mass', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py new file mode 100644 index 0000000000..89ecce8bfc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RThreejs(Package): + """Create interactive 3D scatter plots, network plots, and globes using the + 'three.js' visualization library ("http://threejs.org").""" + + homepage = "http://bwlewis.github.io/rthreejs" + url = "https://cran.r-project.org/src/contrib/threejs_0.2.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/threejs" + + version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-base64enc', type=nolink) + depends_on('r-matrix', type=nolink) + depends_on('r-jsonlite', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 837c3df603..c601de3c88 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -37,9 +37,9 @@ class RTibble(Package): extends('R') - depends_on('r-assertthat') - depends_on('r-lazyeval') - depends_on('r-rcpp') + depends_on('r-assertthat', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index 2db7b174c2..d82ae278fe 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -37,12 +37,12 @@ class RTidyr(Package): version('0.5.1', '3cadc869510c054ed93d374ab44120bd') extends('R') - depends_on('r-tibble') - depends_on('r-dplyr') - depends_on('r-stringi') - depends_on('r-lazyeval') - depends_on('r-magrittr') - depends_on('r-rcpp') + depends_on('r-tibble', type=nolink) + depends_on('r-dplyr', type=nolink) + depends_on('r-stringi', type=nolink) + depends_on('r-lazyeval', type=nolink) + depends_on('r-magrittr', type=nolink) + depends_on('r-rcpp', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py new file mode 100644 index 0000000000..c9b40a8262 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RTtr(Package): + """Functions and data to construct technical trading rules with R.""" + + homepage = "https://github.com/joshuaulrich/TTR" + url = "https://cran.r-project.org/src/contrib/TTR_0.23-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/TTR" + + version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') + + extends('R') + + depends_on('r-xts', type=nolink) + depends_on('r-zoo', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py new file mode 100644 index 0000000000..06e609b1ef --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RVcd(Package): + """Visualization techniques, data sets, summary and inference procedures + aimed particularly at categorical data. Special emphasis is given to highly + extensible grid graphics. The package was package was originally inspired + by the book "Visualizing Categorical Data" by Michael Friendly and is now + the main support package for a new book, "Discrete Data Analysis with R" by + Michael Friendly and David Meyer (2015).""" + + homepage = "https://cran.r-project.org/package=vcd" + url = "https://cran.r-project.org/src/contrib/vcd_1.4-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/vcd" + + version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') + + extends('R') + + depends_on('r-mass', type=nolink) + depends_on('r-colorspace', type=nolink) + depends_on('r-lmtest', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py new file mode 100644 index 0000000000..90d55bbb2f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RVisnetwork(Package): + """Provides an R interface to the 'vis.js' JavaScript charting library. It + allows an interactive visualization of networks.""" + + homepage = "https://github.com/datastorm-open/visNetwork" + url = "https://cran.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/visNetwork" + + version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') + + extends('R') + + depends_on('r-htmlwidgets', type=nolink) + depends_on('r-htmltools', type=nolink) + depends_on('r-jsonlite', type=nolink) + depends_on('r-magrittr', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 4ee7163be1..332c80fb92 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -33,13 +33,13 @@ class RXlconnect(Package): url = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect" - version('0.2-11', '9d1769a103cda05665df399cc335017d', - url='https://cran.r-project.org/src/contrib/Archive/XLConnect/XLConnect_0.2-11.tar.gz') + version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') + version('0.2-11', '9d1769a103cda05665df399cc335017d') extends('R') - depends_on('r-xlconnectjars') - depends_on('r-rjava') + depends_on('r-xlconnectjars', type=nolink) + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index c1fb365883..26e822d2b7 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -32,12 +32,12 @@ class RXlconnectjars(Package): url = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars" - version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb', - url='https://cran.r-project.org/src/contrib/Archive/XLConnectJars/XLConnectJars_0.2-9.tar.gz') + version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') + version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') extends('R') - depends_on('r-rjava') + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 99d41dbb94..6fed09296d 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -37,8 +37,8 @@ class RXlsx(Package): extends('R') - depends_on('r-rjava') - depends_on('r-xlsxjars') + depends_on('r-rjava', type=nolink) + depends_on('r-xlsxjars', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index 80e86d0c73..19f0006ce9 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -37,7 +37,7 @@ class RXlsxjars(Package): extends('R') - depends_on('r-rjava') + depends_on('r-rjava', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py new file mode 100644 index 0000000000..591c887f32 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RXml(Package): + """Many approaches for both reading and creating XML (and HTML) documents + (including DTDs), both local and accessible via HTTP or FTP. Also offers + access to an 'XPath' "interpreter".""" + + homepage = "http://www.omegahat.net/RSXML" + url = "https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/XML" + + version('3.98-1', '1a7f3ce6f264eeb109bfa57bedb26c14') + + extends('R') + + depends_on('libxml2') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py new file mode 100644 index 0000000000..d8a4b62d27 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RXts(Package): + """Provide for uniform handling of R's different time-based data classes by + extending zoo, maximizing native format information preservation and + allowing for user level customization and extension, while simplifying + cross-class interoperability.""" + + homepage = "http://r-forge.r-project.org/projects/xts/" + url = "https://cran.r-project.org/src/contrib/xts_0.9-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/xts" + + version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') + + extends('R') + + depends_on('r-zoo', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py new file mode 100644 index 0000000000..b68f26e9b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RYaml(Package): + """This package implements the libyaml YAML 1.1 parser and emitter + (http://pyyaml.org/wiki/LibYAML) for R.""" + + homepage = "https://cran.r-project.org/web/packages/yaml/index.html" + url = "https://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/yaml" + + version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py new file mode 100644 index 0000000000..d889cacbee --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RZoo(Package): + """An S3 class with methods for totally ordered indexed observations. It is + particularly aimed at irregular time series of numeric vectors/matrices and + factors. zoo's key design goals are independence of a particular + index/date/time class and consistency with ts and base R by providing + methods to extend standard generics.""" + + homepage = "http://zoo.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/zoo_1.7-13.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/zoo" + + version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') + + extends('R') + + depends_on('r-lattice', type=nolink) + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py index b6300a1dfa..e9db4b4fc8 100644 --- a/var/spack/repos/builtin/packages/raja/package.py +++ b/var/spack/repos/builtin/packages/raja/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Raja(Package): """RAJA Parallel Framework.""" homepage = "http://software.llnl.gov/RAJA/" @@ -31,6 +32,6 @@ class Raja(Package): version('git', git='https://github.com/LLNL/RAJA.git', branch="master") def install(self, spec, prefix): - cmake('.',*std_cmake_args) - make() - make('install') + cmake('.', *std_cmake_args) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py index 96692ac7c1..4f4f2b2e10 100644 --- a/var/spack/repos/builtin/packages/ravel/package.py +++ b/var/spack/repos/builtin/packages/ravel/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Ravel(Package): """Ravel is a parallel communication trace visualization tool that orders events according to logical time.""" diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py index 039bf725eb..abb6ba04ce 100644 --- a/var/spack/repos/builtin/packages/readline/package.py +++ b/var/spack/repos/builtin/packages/readline/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Readline(Package): """The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index bcd317eb8f..02b09f0126 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -22,12 +22,13 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -#------------------------------------------------------------------------------ +# ----------------------------------------------------------------------------- # Author: Justin Too <too1@llnl.gov> -#------------------------------------------------------------------------------ +# ----------------------------------------------------------------------------- from spack import * + class Rose(Package): """A compiler infrastructure to build source-to-source program transformation and analysis tools. @@ -36,7 +37,8 @@ class Rose(Package): homepage = "http://rosecompiler.org/" url = "https://github.com/rose-compiler/edg4x-rose" - version('master', branch='master', git='https://github.com/rose-compiler/edg4x-rose.git') + version('master', branch='master', + git='https://github.com/rose-compiler/edg4x-rose.git') patch('add_spack_compiler_recognition.patch') @@ -60,4 +62,3 @@ class Rose(Package): "--with-boost=" + boost.prefix, "--disable-boost-version-check") make("install-core") - diff --git a/var/spack/repos/builtin/packages/rsync/package.py b/var/spack/repos/builtin/packages/rsync/package.py index a9f8d4cfda..4e741b255f 100644 --- a/var/spack/repos/builtin/packages/rsync/package.py +++ b/var/spack/repos/builtin/packages/rsync/package.py @@ -24,8 +24,9 @@ ############################################################################## from spack import * + class Rsync(Package): - """rsync is an open source utility that provides fast incremental file transfer.""" + """An open source utility that provides fast incremental file transfer.""" homepage = "https://rsync.samba.org" url = "https://download.samba.org/pub/rsync/rsync-3.1.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py index 65f81ce534..629dfb4649 100644 --- a/var/spack/repos/builtin/packages/rust/package.py +++ b/var/spack/repos/builtin/packages/rust/package.py @@ -6,6 +6,7 @@ def get_submodules(): git = which('git') git('submodule', 'update', '--init', '--recursive') + class Rust(Package): """The rust programming language toolchain""" homepage = "http://www.rust-lang.org" diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index f5c7f4431f..6b0b224785 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -24,19 +24,27 @@ ############################################################################## from spack import * + class Samtools(Package): - """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating + """SAM Tools provide various utilities for manipulating alignments in + the SAM format, including sorting, merging, indexing and generating alignments in a per-position format""" homepage = "www.htslib.org" - version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2") + url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" - depends_on("zlib") - depends_on("mpc") - parallel=False - patch("samtools1.2.patch",level=0) + version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88') + version('1.2', '988ec4c3058a6ceda36503eebecd4122') - def install(self, spec, prefix): - make("prefix=%s" % prefix, "install") + depends_on("ncurses") + depends_on("htslib", when='@1.3.1:') # htslib became standalone + depends_on('zlib', when='@1.2') # needed for builtin htslib + def install(self, spec, prefix): + if self.spec.version >= Version('1.3.1'): + configure('--prefix={0}'.format(prefix), '--with-ncurses') + make() + make('install') + else: + make("prefix=%s" % prefix) + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch b/var/spack/repos/builtin/packages/samtools/samtools1.2.patch deleted file mode 100644 index ead3ab4e2c..0000000000 --- a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- Makefile 2015-02-03 08:27:34.000000000 -0800 -+++ Makefile.new 2015-07-21 10:38:27.881406892 -0700 -@@ -26,7 +26,7 @@ - CFLAGS = -g -Wall -O2 - LDFLAGS = - LDLIBS = --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o - AOBJS= bam_index.o bam_plcmd.o sam_view.o \ -@@ -37,7 +37,7 @@ - faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o - INCLUDES= -I. -I$(HTSDIR) --LIBCURSES= -lcurses # -lXCurses -+#LIBCURSES= -lcurses # -lXCurses - - prefix = /usr/local - exec_prefix = $(prefix) diff --git a/var/spack/repos/builtin/packages/scalasca/package.py b/var/spack/repos/builtin/packages/scalasca/package.py index 98e43ee75a..228d814aed 100644 --- a/var/spack/repos/builtin/packages/scalasca/package.py +++ b/var/spack/repos/builtin/packages/scalasca/package.py @@ -27,10 +27,12 @@ from spack import * class Scalasca(Package): - """ - Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and - analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particular those - concerning communication and synchronization - and offers guidance in exploring their causes. + """Scalasca is a software tool that supports the performance optimization + of parallel programs by measuring and analyzing their runtime + behavior. The analysis identifies potential performance + bottlenecks - in particular those concerning communication and + synchronization - and offers guidance in exploring their causes. + """ homepage = "http://www.scalasca.org" @@ -44,7 +46,8 @@ class Scalasca(Package): depends_on("mpi") ########## - # Hard-code dependencies for Scalasca according to what stated in the release page + # Hard-code dependencies for Scalasca according to what stated in the + # release page # The OTF2 library path should be detected automatically from SCOREP # SCALASCA 2.2.2 depends_on("scorep@1.4:", when='@2.2.2') @@ -60,4 +63,4 @@ class Scalasca(Package): "--enable-shared"] configure(*configure_args) make() - make("install")
\ No newline at end of file + make("install") diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py index 40ae4176dd..2c32bde4a1 100644 --- a/var/spack/repos/builtin/packages/scons/package.py +++ b/var/spack/repos/builtin/packages/scons/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Scons(Package): """SCons is a software construction tool""" homepage = "http://scons.org" diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py index 633511a15a..d40e08740f 100644 --- a/var/spack/repos/builtin/packages/scorep/package.py +++ b/var/spack/repos/builtin/packages/scorep/package.py @@ -28,20 +28,28 @@ from spack import * class Scorep(Package): """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event - tracing, and online analysis of HPC applications. + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. """ homepage = "http://www.vi-hps.org/projects/score-p" url = "http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.3.tar.gz" + version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888', + url='http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz') version('1.4.2', '3b9a042b13bdd5836452354e6567f71e', url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.4.2.tar.gz') version('1.3', '9db6f957b7f51fa01377a9537867a55c', url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.3.tar.gz') ########## - # Dependencies for SCORE-P are quite tight. See the homepage for more information. + # Dependencies for SCORE-P are quite tight. See the homepage for more + # information. + # SCOREP 2.0.2 + depends_on('otf2@2.0', when='@2.0.2') + depends_on('opari2@2.0', when='@2.0.2') + depends_on('cube@4.3:4.4', when='@2.0.2') # SCOREP 1.4.2 depends_on('otf2@1.5:1.6', when='@1.4.2') depends_on('opari2@1.1.4', when='@1.4.2') @@ -56,17 +64,18 @@ class Scorep(Package): depends_on("papi") def install(self, spec, prefix): - configure = Executable( join_path(self.stage.source_path, 'configure') ) + configure = Executable(join_path(self.stage.source_path, 'configure')) with working_dir('spack-build', create=True): - configure_args = ["--prefix=%s" % prefix, - "--with-otf2=%s" % spec['otf2'].prefix.bin, - "--with-opari2=%s" % spec['opari2'].prefix.bin, - "--with-cube=%s" % spec['cube'].prefix.bin, - "--with-papi-header=%s" % spec['papi'].prefix.include, - "--with-papi-lib=%s" % spec['papi'].prefix.lib, - "--enable-shared", - "CFLAGS=-fPIC", - "CXXFLAGS=-fPIC"] + configure_args = [ + "--prefix=%s" % prefix, + "--with-otf2=%s" % spec['otf2'].prefix.bin, + "--with-opari2=%s" % spec['opari2'].prefix.bin, + "--with-cube=%s" % spec['cube'].prefix.bin, + "--with-papi-header=%s" % spec['papi'].prefix.include, + "--with-papi-lib=%s" % spec['papi'].prefix.lib, + "--enable-shared", + "CFLAGS=-fPIC", + "CXXFLAGS=-fPIC"] configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index c2bad20c2f..94a323ce90 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -39,11 +39,16 @@ class Scotch(Package): version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e') version('5.1.10b', 'f587201d6cf5cf63527182fbfba70753') - variant('mpi', default=False, description='Activate the compilation of parallel libraries') - variant('compression', default=True, description='Activate the posibility to use compressed files') - variant('esmumps', default=False, description='Activate the compilation of esmumps needed by mumps') - variant('shared', default=True, description='Build a shared version of the library') - variant('metis', default=True, description='Build metis and parmetis wrapper libraries') + variant('mpi', default=False, + description='Activate the compilation of parallel libraries') + variant('compression', default=True, + description='Activate the posibility to use compressed files') + variant('esmumps', default=False, + description='Activate the compilation of esmumps needed by mumps') + variant('shared', default=True, + description='Build a shared version of the library') + variant('metis', default=True, + description='Build metis and parmetis wrapper libraries') depends_on('flex', type='build') depends_on('bison', type='build') diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py index b638688e7b..2b01c60b3e 100644 --- a/var/spack/repos/builtin/packages/scr/package.py +++ b/var/spack/repos/builtin/packages/scr/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Scr(Package): """SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart @@ -34,8 +35,10 @@ class Scr(Package): depends_on("mpi") # depends_on("dtcmp") - version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd', url='http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz') - version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e', url='https://github.com/hpc/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz') + version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd', + url='http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz') + version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e', + url='https://github.com/hpc/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz') def install(self, spec, prefix): configure("--prefix=" + prefix, diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py new file mode 100644 index 0000000000..ca168c176c --- /dev/null +++ b/var/spack/repos/builtin/packages/seqtk/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Seqtk(Package): + """Toolkit for processing sequences in FASTA/Q formats.""" + + homepage = "https://github.com/lh3/seqtk" + url = "https://github.com/lh3/seqtk/archive/v1.1.tar.gz" + + version('1.2', '255ffe05bf2f073dc57abcff97f11a37') + version('1.1', 'ebf5cc57698a217150c2250494e039a2') + + depends_on('zlib') + + def install(self, spec, prefix): + make() + mkdirp(prefix.bin) + install('seqtk', prefix.bin) + set_executable(join_path(prefix.bin, 'seqtk')) diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index 017a09977a..5113c88bdf 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -38,7 +38,8 @@ class Silo(Package): variant('fortran', default=True, description='Enable Fortran support') variant('shared', default=True, description='Build shared libraries') - variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files') + variant('silex', default=False, + description='Builds Silex, a GUI for viewing Silo files') depends_on('hdf5') depends_on('qt', when='+silex') @@ -55,8 +56,10 @@ class Silo(Package): configure( '--prefix=%s' % prefix, - '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib), - '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib), + '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, + spec['hdf5'].prefix.lib), + '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, + spec['zlib'].prefix.lib), '--enable-install-lite-headers', *config_args) diff --git a/var/spack/repos/builtin/packages/snappy/package.py b/var/spack/repos/builtin/packages/snappy/package.py index 836063f933..1e94980c92 100644 --- a/var/spack/repos/builtin/packages/snappy/package.py +++ b/var/spack/repos/builtin/packages/snappy/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import os from spack import * + class Snappy(Package): """A fast compressor/decompressor: https://code.google.com/p/snappy""" diff --git a/var/spack/repos/builtin/packages/sparsehash/package.py b/var/spack/repos/builtin/packages/sparsehash/package.py index a72a5ce105..e5abd42ae6 100644 --- a/var/spack/repos/builtin/packages/sparsehash/package.py +++ b/var/spack/repos/builtin/packages/sparsehash/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Sparsehash(Package): """Sparse and dense hash-tables for C++ by Google""" homepage = "https://github.com/sparsehash/sparsehash" diff --git a/var/spack/repos/builtin/packages/spindle/package.py b/var/spack/repos/builtin/packages/spindle/package.py index bcdc7543a3..213d41e970 100644 --- a/var/spack/repos/builtin/packages/spindle/package.py +++ b/var/spack/repos/builtin/packages/spindle/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Spindle(Package): """Spindle improves the library-loading performance of dynamically linked HPC applications. Without Spindle large MPI jobs can diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py index 21bb6f03a7..096aa24c02 100644 --- a/var/spack/repos/builtin/packages/spot/package.py +++ b/var/spack/repos/builtin/packages/spot/package.py @@ -23,16 +23,17 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class Spot(Package): - """Spot is a C++11 library for omega-automata manipulation and model checking.""" + """Spot is a C++11 library for omega-automata manipulation and model + checking.""" homepage = "https://spot.lrde.epita.fr/index.html" url = "http://www.lrde.epita.fr/dload/spot/spot-1.99.3.tar.gz" version('1.99.3', 'd53adcb2d0fe7c69f45d4e595a58254e') - #depends_on("gcc@4.8:", type='build') + # depends_on("gcc@4.8:", type='build') depends_on("python@3.2:") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py index 5e7ae4fb8b..513f8ec6d4 100644 --- a/var/spack/repos/builtin/packages/sqlite/package.py +++ b/var/spack/repos/builtin/packages/sqlite/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Sqlite(Package): """SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQL database access without diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py index a03713397b..ec2fae5e9b 100644 --- a/var/spack/repos/builtin/packages/stat/package.py +++ b/var/spack/repos/builtin/packages/stat/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Stat(Package): """Library to create, manipulate, and export graphs Graphlib.""" homepage = "http://paradyn.org/STAT/STAT.html" @@ -49,13 +50,14 @@ class Stat(Package): configure_args = [ "--enable-gui", "--prefix=%s" % prefix, - "--disable-examples", # Examples require MPI: avoid this dependency. + # Examples require MPI: avoid this dependency. + "--disable-examples", "--with-launchmon=%s" % spec['launchmon'].prefix, "--with-mrnet=%s" % spec['mrnet'].prefix, "--with-graphlib=%s" % spec['graphlib'].prefix, "--with-stackwalker=%s" % spec['dyninst'].prefix, "--with-libdwarf=%s" % spec['libdwarf'].prefix - ] + ] if '+dysect' in spec: configure_args.append('--enable-dysectapi') configure(*configure_args) diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index 68ee397857..26d143e4aa 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -#import os + class Subversion(Package): """Apache Subversion - an open source version control system.""" @@ -41,39 +41,40 @@ class Subversion(Package): # Optional: We need swig if we want the Perl, Python or Ruby # bindings. - #depends_on('swig') - #depends_on('python') - #depends_on('perl') - #depends_on('ruby') + # depends_on('swig') + # depends_on('python') + # depends_on('perl') + # depends_on('ruby') def install(self, spec, prefix): # configure, build, install: - # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html + # Ref: + # http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html options = ['--prefix=%s' % prefix] options.append('--with-apr=%s' % spec['apr'].prefix) options.append('--with-apr-util=%s' % spec['apr-util'].prefix) options.append('--with-zlib=%s' % spec['zlib'].prefix) options.append('--with-sqlite=%s' % spec['sqlite'].prefix) options.append('--with-serf=%s' % spec['serf'].prefix) - #options.append('--with-swig=%s' % spec['swig'].prefix) + # options.append('--with-swig=%s' % spec['swig'].prefix) configure(*options) make() make('install') # python bindings - #make('swig-py', + # make('swig-py', # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') - #make('install-swig-py', + # make('install-swig-py', # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') # perl bindings - #make('swig-pl') - #make('install-swig-pl') + # make('swig-pl') + # make('install-swig-pl') # ruby bindings - #make('swig-rb') - #make('isntall-swig-rb') + # make('swig-rb') + # make('isntall-swig-rb') diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index e52b90eb8a..7582954ab1 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -36,11 +36,15 @@ class Sundials(Package): version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95') variant('mpi', default=True, description='Enable MPI support') - variant('lapack', default=True, description='Build with external BLAS/LAPACK libraries') - variant('klu', default=False, description='Build with SuiteSparse KLU libraries') - variant('superlu', default=False, description='Build with SuperLU_MT libraries') + variant('lapack', default=True, + description='Build with external BLAS/LAPACK libraries') + variant('klu', default=False, + description='Build with SuiteSparse KLU libraries') + variant('superlu', default=False, + description='Build with SuperLU_MT libraries') variant('openmp', default=False, description='Enable OpenMP support') - variant('pthread', default=True, description='Enable POSIX threads support') + variant('pthread', default=True, + description='Enable POSIX threads support') depends_on('cmake', type='build') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index e51d7224d9..4b3354e379 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -57,7 +57,7 @@ class SuperluDist(Package): 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, 'FLIBS =', - 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', # NOQA: ignore=E501 + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', # noqa 'ARCH = ar', 'ARCHFLAGS = cr', 'RANLIB = true', diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py index 5a9429d6e5..e849273e08 100644 --- a/var/spack/repos/builtin/packages/superlu-mt/package.py +++ b/var/spack/repos/builtin/packages/superlu-mt/package.py @@ -37,11 +37,13 @@ class SuperluMt(Package): version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91') - variant('blas', default=True, description='Build with external BLAS library') + variant('blas', default=True, + description='Build with external BLAS library') # Must choose one or the other variant('openmp', default=False, description='Build with OpenMP support') - variant('pthread', default=True, description='Build with POSIX threads support') + variant('pthread', default=True, + description='Build with POSIX threads support') # NOTE: must link with a single-threaded BLAS library depends_on('blas', when='+blas') diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index 620d658a10..636aa26bd2 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -38,9 +38,11 @@ class Swiftsim(Package): homepage = 'http://icc.dur.ac.uk/swift/' url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0' - version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', commit='254cc1b563b2f88ddcf437b1f71da123bb9db733') + version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', + commit='254cc1b563b2f88ddcf437b1f71da123bb9db733') - variant('mpi', default=True, description='Enable distributed memory parallelism') + variant('mpi', default=True, + description='Enable distributed memory parallelism') # Build dependencies depends_on('autoconf', type='build') diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index f552621821..b43246dcee 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -22,9 +22,9 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## - from spack import * + class Swig(Package): """SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, @@ -38,6 +38,7 @@ class Swig(Package): homepage = "http://www.swig.org" url = "http://prdownloads.sourceforge.net/swig/swig-3.0.8.tar.gz" + version('3.0.10', 'bb4ab8047159469add7d00910e203124') version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97') version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4') diff --git a/var/spack/repos/builtin/packages/szip/package.py b/var/spack/repos/builtin/packages/szip/package.py index fd3a2a209d..b2ca6f3995 100644 --- a/var/spack/repos/builtin/packages/szip/package.py +++ b/var/spack/repos/builtin/packages/szip/package.py @@ -24,10 +24,13 @@ ############################################################################## from spack import * + class Szip(Package): - """Szip is an implementation of the extended-Rice lossless compression algorithm. - It provides lossless compression of scientific data, and is provided with HDF - software products.""" + """An implementation of the extended-Rice lossless compression algorithm. + It provides lossless compression of scientific data, and is provided + with HDF software products. + + """ homepage = "https://www.hdfgroup.org/doc_resource/SZIP/" url = "http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch b/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch new file mode 100644 index 0000000000..e5c183b720 --- /dev/null +++ b/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch @@ -0,0 +1,482 @@ +diff --git a/Makefile.in b/Makefile.in +index f9f1d1d..b403e46 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +@@ -1583,9 +1583,10 @@ distcheck: dist + && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ + && am__cwd=`pwd` \ + && $(am__cd) $(distdir)/_build \ +- && ../configure --srcdir=.. --prefix="$$dc_install_base" \ ++ && ../configure \ + $(AM_DISTCHECK_CONFIGURE_FLAGS) \ + $(DISTCHECK_CONFIGURE_FLAGS) \ ++ --srcdir=.. --prefix="$$dc_install_base" \ + && $(MAKE) $(AM_MAKEFLAGS) \ + && $(MAKE) $(AM_MAKEFLAGS) dvi \ + && $(MAKE) $(AM_MAKEFLAGS) check \ +diff --git a/aclocal.m4 b/aclocal.m4 +index 0e09589..804c0b3 100644 +--- a/aclocal.m4 ++++ b/aclocal.m4 +@@ -1,4 +1,4 @@ +-# generated automatically by aclocal 1.14 -*- Autoconf -*- ++# generated automatically by aclocal 1.14.1 -*- Autoconf -*- + + # Copyright (C) 1996-2013 Free Software Foundation, Inc. + +@@ -35,7 +35,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION], + [am__api_version='1.14' + dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to + dnl require some minimum version. Point them to the right macro. +-m4_if([$1], [1.14], [], ++m4_if([$1], [1.14.1], [], + [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl + ]) + +@@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], []) + # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. + # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. + AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], +-[AM_AUTOMAKE_VERSION([1.14])dnl ++[AM_AUTOMAKE_VERSION([1.14.1])dnl + m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl + _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) +diff --git a/config.h.in b/config.h.in +index 6646ea5..8571ef4 100644 +--- a/config.h.in ++++ b/config.h.in +@@ -617,7 +617,7 @@ + */ + #undef HAVE_ALLOCA_H + +-/* define to 1 if we have <attr/xattr.h> header */ ++/* Define to 1 if you have the <attr/xattr.h> header file. */ + #undef HAVE_ATTR_XATTR_H + + /* Define to 1 if you have the <bp-sym.h> header file. */ +@@ -924,21 +924,12 @@ + /* Define to 1 if you have the <features.h> header file. */ + #undef HAVE_FEATURES_H + +-/* Define to 1 if you have the `fgetxattr' function. */ +-#undef HAVE_FGETXATTR +- +-/* Define to 1 if you have the `flistxattr' function. */ +-#undef HAVE_FLISTXATTR +- + /* Define to 1 if you have the `flockfile' function. */ + #undef HAVE_FLOCKFILE + + /* Define to 1 if fseeko (and presumably ftello) exists and is declared. */ + #undef HAVE_FSEEKO + +-/* Define to 1 if you have the `fsetxattr' function. */ +-#undef HAVE_FSETXATTR +- + /* Define to 1 if you have the `fstatat' function. */ + #undef HAVE_FSTATAT + +@@ -990,9 +981,6 @@ + /* Define to 1 if you have the `gettimeofday' function. */ + #undef HAVE_GETTIMEOFDAY + +-/* Define to 1 if you have the `getxattr' function. */ +-#undef HAVE_GETXATTR +- + /* Define to 1 if you have the `grantpt' function. */ + #undef HAVE_GRANTPT + +@@ -1045,12 +1033,6 @@ + /* Define to 1 if you have the `lchown' function. */ + #undef HAVE_LCHOWN + +-/* Define to 1 if you have the `lgetxattr' function. */ +-#undef HAVE_LGETXATTR +- +-/* Define to 1 if you have the `attr' library (-lattr). */ +-#undef HAVE_LIBATTR +- + /* Define to 1 if you have the <libgen.h> header file. */ + #undef HAVE_LIBGEN_H + +@@ -1069,12 +1051,6 @@ + /* Define to 1 if you have the <linux/fd.h> header file. */ + #undef HAVE_LINUX_FD_H + +-/* Define to 1 if you have the `listxattr' function. */ +-#undef HAVE_LISTXATTR +- +-/* Define to 1 if you have the `llistxattr' function. */ +-#undef HAVE_LLISTXATTR +- + /* Define to 1 if you have the <locale.h> header file. */ + #undef HAVE_LOCALE_H + +@@ -1087,9 +1063,6 @@ + /* Define to 1 if the system has the type 'long long int'. */ + #undef HAVE_LONG_LONG_INT + +-/* Define to 1 if you have the `lsetxattr' function. */ +-#undef HAVE_LSETXATTR +- + /* Define to 1 if you have the `lstat' function. */ + #undef HAVE_LSTAT + +@@ -1867,9 +1840,6 @@ + /* Define to 1 if you have the `setlocale' function. */ + #undef HAVE_SETLOCALE + +-/* Define to 1 if you have the `setxattr' function. */ +-#undef HAVE_SETXATTR +- + /* Define to 1 if you have the <sgtty.h> header file. */ + #undef HAVE_SGTTY_H + +@@ -2074,7 +2044,7 @@ + /* Define to 1 if you have the <sys/wait.h> header file. */ + #undef HAVE_SYS_WAIT_H + +-/* define to 1 if we have <sys/xattr.h> header */ ++/* Define to 1 if you have the <sys/xattr.h> header file. */ + #undef HAVE_SYS_XATTR_H + + /* Define if struct tm has the tm_gmtoff member. */ +diff --git a/configure b/configure +index cfdd721..8cf6e91 100755 +--- a/configure ++++ b/configure +@@ -663,8 +663,6 @@ RSH + LIBOBJS + TAR_COND_GRANTPT_FALSE + TAR_COND_GRANTPT_TRUE +-TAR_LIB_ATTR_FALSE +-TAR_LIB_ATTR_TRUE + TAR_COND_XATTR_H_FALSE + TAR_COND_XATTR_H_TRUE + GNULIB_TEST_WARN_CFLAGS +@@ -34994,41 +34992,6 @@ else + TAR_COND_XATTR_H_FALSE= + fi + +- if false; then +- TAR_LIB_ATTR_TRUE= +- TAR_LIB_ATTR_FALSE='#' +-else +- TAR_LIB_ATTR_TRUE='#' +- TAR_LIB_ATTR_FALSE= +-fi +- +- if test "$ac_cv_header_sys_xattr_h" = yes; then +- for ac_func in getxattr fgetxattr lgetxattr \ +- setxattr fsetxattr lsetxattr \ +- listxattr flistxattr llistxattr +-do : +- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" +-if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +- cat >>confdefs.h <<_ACEOF +-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +-_ACEOF +- # only when functions are present +- +-$as_echo "#define HAVE_SYS_XATTR_H 1" >>confdefs.h +- +- if test "$with_xattrs" != no; then +- +-$as_echo "#define HAVE_XATTRS /**/" >>confdefs.h +- +- fi +- +-fi +-done +- +- fi +- +- # If <sys/xattr.h> is not found, then check for <attr/xattr.h> + if test "$ac_cv_header_sys_xattr_h" != yes; then + for ac_header in attr/xattr.h + do : +@@ -35050,13 +35013,20 @@ else + TAR_COND_XATTR_H_FALSE= + fi + +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for fgetxattr in -lattr" >&5 +-$as_echo_n "checking for fgetxattr in -lattr... " >&6; } +-if ${ac_cv_lib_attr_fgetxattr+:} false; then : ++ fi ++ ++ if test "$with_xattrs" != no; then ++ for i in getxattr fgetxattr lgetxattr \ ++ setxattr fsetxattr lsetxattr \ ++ listxattr flistxattr llistxattr ++ do ++ as_ac_Search=`$as_echo "ac_cv_search_$i" | $as_tr_sh` ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing $i" >&5 ++$as_echo_n "checking for library containing $i... " >&6; } ++if eval \${$as_ac_Search+:} false; then : + $as_echo_n "(cached) " >&6 + else +- ac_check_lib_save_LIBS=$LIBS +-LIBS="-lattr $LIBS" ++ ac_func_search_save_LIBS=$LIBS + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -35066,67 +35036,56 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext + #ifdef __cplusplus + extern "C" + #endif +-char fgetxattr (); ++char $i (); + int + main () + { +-return fgetxattr (); ++return $i (); + ; + return 0; + } + _ACEOF +-if ac_fn_c_try_link "$LINENO"; then : +- ac_cv_lib_attr_fgetxattr=yes +-else +- ac_cv_lib_attr_fgetxattr=no ++for ac_lib in '' attr; do ++ if test -z "$ac_lib"; then ++ ac_res="none required" ++ else ++ ac_res=-l$ac_lib ++ LIBS="-l$ac_lib $ac_func_search_save_LIBS" ++ fi ++ if ac_fn_c_try_link "$LINENO"; then : ++ eval "$as_ac_Search=\$ac_res" + fi + rm -f core conftest.err conftest.$ac_objext \ +- conftest$ac_exeext conftest.$ac_ext +-LIBS=$ac_check_lib_save_LIBS +-fi +-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_attr_fgetxattr" >&5 +-$as_echo "$ac_cv_lib_attr_fgetxattr" >&6; } +-if test "x$ac_cv_lib_attr_fgetxattr" = xyes; then : +- cat >>confdefs.h <<_ACEOF +-#define HAVE_LIBATTR 1 +-_ACEOF +- +- LIBS="-lattr $LIBS" +- ++ conftest$ac_exeext ++ if eval \${$as_ac_Search+:} false; then : ++ break + fi ++done ++if eval \${$as_ac_Search+:} false; then : + +- if test "$ac_cv_lib_attr_fgetxattr" = yes; then +- TAR_LIB_ATTR_TRUE= +- TAR_LIB_ATTR_FALSE='#' + else +- TAR_LIB_ATTR_TRUE='#' +- TAR_LIB_ATTR_FALSE= ++ eval "$as_ac_Search=no" ++fi ++rm conftest.$ac_ext ++LIBS=$ac_func_search_save_LIBS + fi ++eval ac_res=\$$as_ac_Search ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 ++$as_echo "$ac_res" >&6; } ++eval ac_res=\$$as_ac_Search ++if test "$ac_res" != no; then : ++ test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +- if test "$ac_cv_header_attr_xattr_h" = yes; then +- for ac_func in getxattr fgetxattr lgetxattr \ +- setxattr fsetxattr lsetxattr \ +- listxattr flistxattr llistxattr +-do : +- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" +-if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +- cat >>confdefs.h <<_ACEOF +-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +-_ACEOF +- # only when functions are present ++fi + +-$as_echo "#define HAVE_ATTR_XATTR_H 1" >>confdefs.h ++ eval found=\$ac_cv_search_$i ++ test "$found" = "no" && break ++ done + +- if test "$with_xattrs" != no; then ++ if test "$found" != no; then + + $as_echo "#define HAVE_XATTRS /**/" >>confdefs.h + +- fi +- +-fi +-done +- + fi + fi + +@@ -38187,18 +38146,10 @@ if test -z "${TAR_COND_XATTR_H_TRUE}" && test -z "${TAR_COND_XATTR_H_FALSE}"; th + as_fn_error $? "conditional \"TAR_COND_XATTR_H\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 + fi +-if test -z "${TAR_LIB_ATTR_TRUE}" && test -z "${TAR_LIB_ATTR_FALSE}"; then +- as_fn_error $? "conditional \"TAR_LIB_ATTR\" was never defined. +-Usually this means the macro was only invoked conditionally." "$LINENO" 5 +-fi + if test -z "${TAR_COND_XATTR_H_TRUE}" && test -z "${TAR_COND_XATTR_H_FALSE}"; then + as_fn_error $? "conditional \"TAR_COND_XATTR_H\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 + fi +-if test -z "${TAR_LIB_ATTR_TRUE}" && test -z "${TAR_LIB_ATTR_FALSE}"; then +- as_fn_error $? "conditional \"TAR_LIB_ATTR\" was never defined. +-Usually this means the macro was only invoked conditionally." "$LINENO" 5 +-fi + if test -z "${TAR_COND_GRANTPT_TRUE}" && test -z "${TAR_COND_GRANTPT_FALSE}"; then + as_fn_error $? "conditional \"TAR_COND_GRANTPT\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 +diff --git a/doc/Makefile.in b/doc/Makefile.in +index ca44f1a..42a06b3 100644 +--- a/doc/Makefile.in ++++ b/doc/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/gnu/Makefile.in b/gnu/Makefile.in +index 03eed58..d908a03 100644 +--- a/gnu/Makefile.in ++++ b/gnu/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/lib/Makefile.in b/lib/Makefile.in +index 41a9aca..1254b8f 100644 +--- a/lib/Makefile.in ++++ b/lib/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/rmt/Makefile.in b/rmt/Makefile.in +index c3f2509..0f3dca4 100644 +--- a/rmt/Makefile.in ++++ b/rmt/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/scripts/Makefile.in b/scripts/Makefile.in +index 57c0d0d..bf344ed 100644 +--- a/scripts/Makefile.in ++++ b/scripts/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/src/Makefile.in b/src/Makefile.in +index 6f9a592..fc6fc87 100644 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +@@ -99,7 +99,6 @@ POST_UNINSTALL = : + build_triplet = @build@ + host_triplet = @host@ + bin_PROGRAMS = tar$(EXEEXT) +-@TAR_LIB_ATTR_TRUE@am__append_1 = -lattr + subdir = src + DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \ + $(top_srcdir)/build-aux/depcomp $(noinst_HEADERS) +@@ -254,7 +253,7 @@ am__DEPENDENCIES_2 = ../lib/libtar.a ../gnu/libgnu.a \ + $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) + tar_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2) \ + $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \ +- $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) ++ $(am__DEPENDENCIES_1) + AM_V_P = $(am__v_P_@AM_V@) + am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) + am__v_P_0 = false +@@ -1225,8 +1224,7 @@ tar_SOURCES = \ + AM_CPPFLAGS = -I$(top_srcdir)/gnu -I../ -I../gnu -I$(top_srcdir)/lib -I../lib + AM_CFLAGS = $(WARN_CFLAGS) $(WERROR_CFLAGS) + LDADD = ../lib/libtar.a ../gnu/libgnu.a $(LIBINTL) $(LIBICONV) +-tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) \ +- $(LIB_SELINUX) $(am__append_1) ++tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) $(LIB_SELINUX) + all: all-am + + .SUFFIXES: +diff --git a/tests/Makefile.in b/tests/Makefile.in +index 6807509..50d7689 100644 +--- a/tests/Makefile.in ++++ b/tests/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/lib/xattr-at.c b/lib/xattr-at.c +index 443ccae..009bde5 100644 +--- a/lib/xattr-at.c ++++ b/lib/xattr-at.c +@@ -18,6 +18,11 @@ + + #include <config.h> + ++/* Temporarily don't build. We are unable to build on (probably not only) ++ darwin due to lack of l*xattr callbacks (XATTR_NOFOLLOW is alternative) and ++ different function definitions. */ ++#ifdef HAVE_XATTRS ++ + #include "xattr-at.h" + #include "openat.h" + +@@ -108,3 +113,5 @@ + #undef AT_FUNC_RESULT + #undef AT_FUNC_POST_FILE_PARAM_DECLS + #undef AT_FUNC_POST_FILE_ARGS ++ ++#endif +diff --git a/src/Makefile.am b/src/Makefile.am +index 82b2d46..42daaef 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -52,7 +52,3 @@ AM_CFLAGS = $(WARN_CFLAGS) $(WERROR_CFLAGS) + LDADD = ../lib/libtar.a ../gnu/libgnu.a $(LIBINTL) $(LIBICONV) + + tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) $(LIB_SELINUX) +- +-if TAR_LIB_ATTR +-tar_LDADD += -lattr +-endif +-- +1.9.3
\ No newline at end of file diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py index c55b5165bf..f5995cb007 100644 --- a/var/spack/repos/builtin/packages/tar/package.py +++ b/var/spack/repos/builtin/packages/tar/package.py @@ -24,13 +24,21 @@ ############################################################################## from spack import * + class Tar(Package): - """GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.""" + """GNU Tar provides the ability to create tar archives, as well as various + other kinds of manipulation.""" homepage = "https://www.gnu.org/software/tar/" - url = "http://ftp.gnu.org/gnu/tar/tar-1.28.tar.gz" + url = "https://ftp.gnu.org/gnu/tar/tar-1.28.tar.gz" + version('1.29', 'cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0') version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7') + # see http://lists.gnu.org/archive/html/bug-tar/2014-08/msg00001.html and + # https://github.com/Homebrew/homebrew-core/commit/aef9a1792de4648d0322b4b04d32287532f046bb + # TODO: when=sys.platform=='darwin' ? + patch('gnutar-configure-xattrs.patch', when='@1.28') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py index 8c3b412f48..785023fd03 100644 --- a/var/spack/repos/builtin/packages/task/package.py +++ b/var/spack/repos/builtin/packages/task/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Task(Package): """Feature-rich console based todo list manager""" homepage = "http://www.taskwarrior.org" diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py index 1d7f9ed49e..d13f480374 100644 --- a/var/spack/repos/builtin/packages/taskd/package.py +++ b/var/spack/repos/builtin/packages/taskd/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Taskd(Package): """TaskWarrior task synchronization daemon""" # FIXME: add a proper url for your package's homepage here. diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index 3b181f3fa4..a77df8d37c 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -30,6 +30,7 @@ import os.path from llnl.util.filesystem import join_path + class Tau(Package): """ A portable profiling and tracing toolkit for performance @@ -45,15 +46,20 @@ class Tau(Package): version('2.23.1', '6593b47ae1e7a838e632652f0426fe72') # TODO : shmem variant missing - variant('download', default=False, description='Downloads and builds various dependencies') + variant('download', default=False, + description='Downloads and builds various dependencies') variant('scorep', default=False, description='Activates SCOREP support') variant('openmp', default=True, description='Use OpenMP threads') - variant('mpi', default=True, description='Specify use of TAU MPI wrapper library') + variant('mpi', default=True, + description='Specify use of TAU MPI wrapper library') variant('phase', default=True, description='Generate phase based profiles') - variant('comm', default=True, description=' Generate profiles with MPI communicator info') + variant('comm', default=True, + description=' Generate profiles with MPI communicator info') - # TODO : Try to build direct OTF2 support? Some parts of the OTF support library in TAU are non-conformant, - # TODO : and fail at compile-time. Further, SCOREP is compiled with OTF2 support. + # TODO : Try to build direct OTF2 support? Some parts of the OTF support + # TODO : library in TAU are non-conformant, + # TODO : and fail at compile-time. Further, SCOREP is compiled with OTF2 + # support. depends_on('pdt') # Required for TAU instrumentation depends_on('scorep', when='+scorep') depends_on('binutils', when='~download') @@ -65,13 +71,17 @@ class Tau(Package): ########## # Selecting a compiler with TAU configure is quite tricky: - # 1 - compilers are mapped to a given set of strings (and spack cc, cxx, etc. wrappers are not among them) + # 1 - compilers are mapped to a given set of strings + # (and spack cc, cxx, etc. wrappers are not among them) # 2 - absolute paths are not allowed - # 3 - the usual environment variables seems not to be checked ('CC', 'CXX' and 'FC') - # 4 - if no -cc=<compiler> -cxx=<compiler> is passed tau is built with system compiler silently + # 3 - the usual environment variables seems not to be checked + # ('CC', 'CXX' and 'FC') + # 4 - if no -cc=<compiler> -cxx=<compiler> is passed tau is built with + # system compiler silently # (regardless of what %<compiler> is used in the spec) # - # In the following we give TAU what he expects and put compilers into PATH + # In the following we give TAU what he expects and put compilers into + # PATH compiler_path = os.path.dirname(self.compiler.cc) os.environ['PATH'] = ':'.join([compiler_path, os.environ['PATH']]) compiler_options = ['-c++=%s' % self.compiler.cxx_names[0], @@ -80,7 +90,8 @@ class Tau(Package): compiler_options.append('-fortran=%s' % self.compiler.fc_names[0]) ########## - # Construct the string of custom compiler flags and append it to compiler related options + # Construct the string of custom compiler flags and append it to + # compiler related options useropt = ' '.join(useropt) useropt = "-useropt=%s" % useropt compiler_options.append(useropt) @@ -92,8 +103,9 @@ class Tau(Package): change_sed_delimiter('@', ';', 'utils/FixMakefile') change_sed_delimiter('@', ';', 'utils/FixMakefile.sed.default') - # TAU configure, despite the name , seems to be a manually written script (nothing related to autotools). - # As such it has a few #peculiarities# that make this build quite hackish. + # TAU configure, despite the name , seems to be a manually + # written script (nothing related to autotools). As such it has + # a few #peculiarities# that make this build quite hackish. options = ["-prefix=%s" % prefix, "-iowrapper", "-pdt=%s" % spec['pdt'].prefix] diff --git a/var/spack/repos/builtin/packages/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py index c88b170816..d13579b44d 100644 --- a/var/spack/repos/builtin/packages/tbb/package.py +++ b/var/spack/repos/builtin/packages/tbb/package.py @@ -35,8 +35,10 @@ class Tbb(Package): homepage = "http://www.threadingbuildingblocks.org/" # Only version-specific URL's work for TBB - version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz') # NOQA: ignore=E501 - version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz') # NOQA: ignore=E501 + version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71', + url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz') + version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', + url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz') def coerce_to_spack(self, tbb_build_subdir): for compiler in ["icc", "gcc", "clang"]: diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py index 97aa68be65..7ac55a6785 100644 --- a/var/spack/repos/builtin/packages/tetgen/package.py +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -36,7 +36,8 @@ class Tetgen(Package): url = "http://www.tetgen.org/files/tetgen1.4.3.tar.gz" version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18') - version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') + version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', + url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') depends_on('cmake@2.8.7:', when='@1.5.0:', type='build') diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py index 5c6fef0db6..ddb23e5d6f 100644 --- a/var/spack/repos/builtin/packages/texinfo/package.py +++ b/var/spack/repos/builtin/packages/texinfo/package.py @@ -27,10 +27,13 @@ from spack import * class Texinfo(Package): - """ - Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob - Chassell many years ago, loosely based on Brian Reid's Scribe and other formatting languages of the time. It is - used by many non-GNU projects as well.FIXME: put a proper description of your package here. + """Texinfo is the official documentation format of the GNU project. + + It was invented by Richard Stallman and Bob Chassell many years ago, + loosely based on Brian Reid's Scribe and other formatting languages + of the time. It is used by many non-GNU projects as well.FIXME: put a + proper description of your package here. + """ homepage = "https://www.gnu.org/software/texinfo/" url = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz" diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py new file mode 100644 index 0000000000..64158e74cb --- /dev/null +++ b/var/spack/repos/builtin/packages/texlive/package.py @@ -0,0 +1,58 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +import os + + +class Texlive(Package): + """TeX Live is a free software distribution for the TeX typesetting + system""" + + homepage = "http://www.tug.org/texlive" + + version('live', 'e671eea7f142c438959493cc42a2a59b', + url="http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz") + + # There does not seem to be a complete list of schemes. + # Examples include: + # full scheme (everything) + # medium scheme (small + more packages and languages) + # small scheme (basic + xetex, metapost, a few languages) + # basic scheme (plain and latex) + # minimal scheme (plain only) + # See: + # https://www.tug.org/texlive/doc/texlive-en/texlive-en.html#x1-25025r6 + variant('scheme', default="small", + description='Package subset to install (e.g. full, small, basic)') + + depends_on('perl') + + def install(self, spec, prefix): + env = os.environ + env['TEXLIVE_INSTALL_PREFIX'] = prefix + perl = which('perl') + scheme = spec.variants['scheme'].value + perl('./install-tl', '-scheme', scheme, + '-portable', '-profile', '/dev/null') diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 025ee2b885..755f7a80b9 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -24,12 +24,16 @@ ############################################################################## from spack import * + class Thrift(Package): - """The Apache Thrift software framework, for scalable cross-language services - development, combines a software stack with a code generation engine to build - services that work efficiently and seamlessly between C++, Java, Python, PHP, - Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml - and Delphi and other languages.""" + """Software framework for scalable cross-language services development. + + Thrift combines a software stack with a code generation engine to + build services that work efficiently and seamlessly between C++, + Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, + JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. + + """ homepage = "http://thrift.apache.org" url = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz" @@ -37,8 +41,10 @@ class Thrift(Package): version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678') # Currently only support for c-family and python - variant('c', default=True, description="Build support for C-family languages") - variant('python', default=True, description="Build support for python") + variant('c', default=True, + description="Build support for C-family languages") + variant('python', default=True, + description="Build support for python") depends_on('jdk') depends_on('autoconf', type='build') @@ -66,7 +72,8 @@ class Thrift(Package): options.append('--enable-tests=no') options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no')) - options.append('--with-python=%s' % ('yes' if '+python' in spec else 'no')) + options.append('--with-python=%s' % + ('yes' if '+python' in spec else 'no')) options.append('--with-java=%s' % ('yes' if '+java' in spec else 'no')) options.append('--with-go=%s' % ('yes' if '+go' in spec else 'no')) options.append('--with-lua=%s' % ('yes' if '+lua' in spec else 'no')) diff --git a/var/spack/repos/builtin/packages/tmuxinator/package.py b/var/spack/repos/builtin/packages/tmuxinator/package.py index b9c92ea4db..66da4006f2 100644 --- a/var/spack/repos/builtin/packages/tmuxinator/package.py +++ b/var/spack/repos/builtin/packages/tmuxinator/package.py @@ -24,17 +24,18 @@ ############################################################################## from spack import * + class Tmuxinator(Package): """A session configuration creator and manager for tmux""" homepage = "https://github.com/tmuxinator/tmuxinator" url = "https://github.com/tmuxinator/tmuxinator" version('0.6.11', - git='https://github.com/tmuxinator/tmuxinator', - tag='v0.6.11') + git='https://github.com/tmuxinator/tmuxinator', + tag='v0.6.11') extends('ruby') def install(self, spec, prefix): - gem('build', 'tmuxinator.gemspec') - gem('install', 'tmuxinator-{0}.gem'.format(self.version)) + gem('build', 'tmuxinator.gemspec') + gem('install', 'tmuxinator-{0}.gem'.format(self.version)) diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py new file mode 100644 index 0000000000..8e0e176c4c --- /dev/null +++ b/var/spack/repos/builtin/packages/tree/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Tree(Package): + """Tree is a recursive directory listing command that produces a depth + indented listing of files, which is colorized ala dircolors if + the LS_COLORS environment variable is set and output is to + tty. Tree has been ported and reported to work under the + following operating systems: Linux, FreeBSD, OS X, Solaris, + HP/UX, Cygwin, HP Nonstop and OS/2.""" + + homepage = "http://mama.indstate.edu/users/ice/tree/" + url = "http://mama.indstate.edu/users/ice/tree/src/tree-1.7.0.tgz" + + version('1.7.0', 'abe3e03e469c542d8e157cdd93f4d8a6') + + def install(self, spec, prefix): + filter_file(r'^prefix =.*', 'prefix = %s' % prefix, 'Makefile') + filter_file(r'^CFLAGS', '# use spack settings instead... CFLAGS', + 'Makefile') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py index bc8b0ec639..f4ee9ca1c9 100644 --- a/var/spack/repos/builtin/packages/triangle/package.py +++ b/var/spack/repos/builtin/packages/triangle/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Triangle(Package): """Triangle is a two-dimensional mesh generator and Delaunay triangulator. Triangle generates exact Delaunay triangulations, diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 77589bb8f9..d39e45f054 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -45,6 +45,7 @@ class Trilinos(Package): homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.4', 'db25056617c688f6f25092376a03200f') version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e') version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9') version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') @@ -55,17 +56,24 @@ class Trilinos(Package): version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - variant('metis', default=True, description='Compile with METIS and ParMETIS') - variant('mumps', default=True, description='Compile with support for MUMPS solvers') - variant('superlu-dist', default=True, description='Compile with SuperluDist solvers') - variant('hypre', default=True, description='Compile with Hypre preconditioner') + variant('metis', default=True, + description='Compile with METIS and ParMETIS') + variant('mumps', default=True, + description='Compile with support for MUMPS solvers') + variant('superlu-dist', default=True, + description='Compile with SuperluDist solvers') + variant('hypre', default=True, + description='Compile with Hypre preconditioner') variant('hdf5', default=True, description='Compile with HDF5') - variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') + variant('suite-sparse', default=True, + description='Compile with SuiteSparse solvers') # not everyone has py-numpy activated, keep it disabled by default to avoid # configure errors variant('python', default=False, description='Build python wrappers') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') + variant('debug', default=False, + description='Builds a debug version of the libraries') variant('boost', default=True, description='Compile with Boost') depends_on('cmake', type='build') @@ -138,16 +146,23 @@ class Trilinos(Package): '-DTPL_ENABLE_LAPACK=ON', '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name( spec['lapack'].lapack_shared_lib), - '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, + '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib, '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', '-DTrilinos_ENABLE_CXX11:BOOL=ON', '-DTPL_ENABLE_Netcdf:BOOL=ON', '-DTPL_ENABLE_HYPRE:BOOL=%s' % ( - 'ON' if '+hypre' in spec else 'OFF'), - '-DTPL_ENABLE_HDF5:BOOL=%s' % ( - 'ON' if '+hdf5' in spec else 'OFF'), + 'ON' if '+hypre' in spec else 'OFF') ]) + if '+hdf5' in spec: + options.extend([ + '-DTPL_ENABLE_HDF5:BOOL=ON', + '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include, + '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib + ]) + else: + options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF']) + if '+boost' in spec: options.extend([ '-DTPL_ENABLE_Boost:BOOL=ON', diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py index aed39668fd..bae6414c5b 100644 --- a/var/spack/repos/builtin/packages/udunits2/package.py +++ b/var/spack/repos/builtin/packages/udunits2/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Udunits2(Package): """Automated units conversion""" diff --git a/var/spack/repos/builtin/packages/uncrustify/package.py b/var/spack/repos/builtin/packages/uncrustify/package.py index db96bc301e..c3182d0dc8 100644 --- a/var/spack/repos/builtin/packages/uncrustify/package.py +++ b/var/spack/repos/builtin/packages/uncrustify/package.py @@ -24,8 +24,9 @@ ############################################################################## from spack import * + class Uncrustify(Package): - """Source Code Beautifier for C, C++, C#, ObjectiveC, D, Java, Pawn and VALA""" + """Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others.""" homepage = "http://uncrustify.sourceforge.net/" url = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz" diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py index d9e0ad6bcb..943e4737e1 100644 --- a/var/spack/repos/builtin/packages/unibilium/package.py +++ b/var/spack/repos/builtin/packages/unibilium/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Unibilium(Package): """A terminfo parsing library""" homepage = "https://github.com/mauke/unibilium" @@ -32,5 +33,5 @@ class Unibilium(Package): version('1.2.0', '9b1c97839a880a373da6c097443b43c4') def install(self, spec, prefix): - make("PREFIX="+prefix) - make("install", "PREFIX="+prefix) + make("PREFIX=" + prefix) + make("install", "PREFIX=" + prefix) diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py new file mode 100644 index 0000000000..181e1e6410 --- /dev/null +++ b/var/spack/repos/builtin/packages/unison/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Unison(Package): + """Unison is a file-synchronization tool for OSX, Unix, and + Windows. It allows two replicas of a collection of files and + directories to be stored on different hosts (or different disks + on the same host), modified separately, and then brought up to + date by propagating the changes in each replica to the + other.""" + + homepage = "https://www.cis.upenn.edu/~bcpierce/unison/" + url = "https://www.seas.upenn.edu/~bcpierce/unison//download/releases/stable/unison-2.48.3.tar.gz" + + version('2.48.4', '5334b78c7e68169df7de95f4c6c4b60f') + + depends_on('ocaml', type='build') + + parallel = False + + def install(self, spec, prefix): + make('./mkProjectInfo') + make('UISTYLE=text') + + mkdirp(prefix.bin) + install('unison', prefix.bin) + set_executable(join_path(prefix.bin, 'unison')) diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py index bf6972683d..99af170ca1 100644 --- a/var/spack/repos/builtin/packages/util-linux/package.py +++ b/var/spack/repos/builtin/packages/util-linux/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class UtilLinux(Package): """Util-linux is a suite of essential utilities for any Linux system.""" @@ -36,9 +36,9 @@ class UtilLinux(Package): depends_on("python@2.7:") def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "PKG_CONFIG_PATH=%s/pkgconfig" % spec['python'].prefix.lib, - "--disable-use-tty-group") + configure("--prefix=%s" % prefix, + "PKG_CONFIG_PATH=%s/pkgconfig" % spec['python'].prefix.lib, + "--disable-use-tty-group") make() make("install") diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py index afd4cc6ad0..e7ae227c27 100644 --- a/var/spack/repos/builtin/packages/valgrind/package.py +++ b/var/spack/repos/builtin/packages/valgrind/package.py @@ -27,12 +27,15 @@ from spack import * class Valgrind(Package): - """ - Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can - automatically detect many memory management and threading bugs, and profile your programs in detail. You can also - use Valgrind to build new tools. + """An instrumentation framework for building dynamic analysis. + + There are Valgrind tools that can automatically detect many memory + management and threading bugs, and profile your programs in + detail. You can also use Valgrind to build new tools. + + Valgrind is Open Source / Free Software, and is freely available + under the GNU General Public License, version 2. - Valgrind is Open Source / Free Software, and is freely available under the GNU General Public License, version 2. """ homepage = "http://valgrind.org/" url = "http://valgrind.org/downloads/valgrind-3.11.0.tar.bz2" @@ -42,7 +45,8 @@ class Valgrind(Package): version('3.10.0', '7c311a72a20388aceced1aa5573ce970') variant('mpi', default=True, description='Activates MPI support for valgrind') - variant('boost', default=True, description='Activates boost support for valgrind') + variant('boost', default=True, + description='Activates boost support for valgrind') depends_on('mpi', when='+mpi') depends_on('boost', when='+boost') diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py index e0dfb64879..01eccfab57 100644 --- a/var/spack/repos/builtin/packages/vim/package.py +++ b/var/spack/repos/builtin/packages/vim/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Vim(Package): """Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most @@ -51,7 +52,7 @@ class Vim(Package): feature_sets = ('huge', 'big', 'normal', 'small', 'tiny') for fs in feature_sets: - variant(fs, default=False, description="Use '%s' feature set" % fs) + variant(fs, default=False, description="Use '%s' feature set" % fs) variant('python', default=False, description="build with Python") depends_on('python', when='+python') @@ -66,42 +67,44 @@ class Vim(Package): # virtual dependency? def install(self, spec, prefix): - feature_set = None - for fs in self.feature_sets: - if "+" + fs in spec: - if feature_set is not None: - tty.error("Only one feature set allowed, both %s and %s specified" - % (feature_set, fs)) - feature_set = fs - if '+gui' in spec: - if feature_set is not None: - if feature_set is not 'huge': - tty.error("+gui variant requires 'huge' feature set, %s was specified" - % feature_set) - feature_set = 'huge' - if feature_set is None: - feature_set = 'normal' - - configure_args = [] - configure_args.append("--with-features=" + feature_set) - - if '+python' in spec: - configure_args.append("--enable-pythoninterp=yes") - else: - configure_args.append("--enable-pythoninterp=dynamic") - - if '+ruby' in spec: - configure_args.append("--enable-rubyinterp=yes") - else: - configure_args.append("--enable-rubyinterp=dynamic") - - if '+gui' in spec: - configure_args.append("--enable-gui=auto") - - if '+cscope' in spec: - configure_args.append("--enable-cscope") - - configure("--prefix=%s" % prefix, *configure_args) - - make() - make("install") + feature_set = None + for fs in self.feature_sets: + if "+" + fs in spec: + if feature_set is not None: + tty.error( + "Only one feature set allowed, specified %s and %s" + % (feature_set, fs)) + feature_set = fs + if '+gui' in spec: + if feature_set is not None: + if feature_set is not 'huge': + tty.error( + "+gui variant requires 'huge' feature set, " + "%s was specified" % feature_set) + feature_set = 'huge' + if feature_set is None: + feature_set = 'normal' + + configure_args = [] + configure_args.append("--with-features=" + feature_set) + + if '+python' in spec: + configure_args.append("--enable-pythoninterp=yes") + else: + configure_args.append("--enable-pythoninterp=dynamic") + + if '+ruby' in spec: + configure_args.append("--enable-rubyinterp=yes") + else: + configure_args.append("--enable-rubyinterp=dynamic") + + if '+gui' in spec: + configure_args.append("--enable-gui=auto") + + if '+cscope' in spec: + configure_args.append("--enable-cscope") + + configure("--prefix=%s" % prefix, *configure_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py index ae19fd0450..d88caeb00a 100644 --- a/var/spack/repos/builtin/packages/visit/package.py +++ b/var/spack/repos/builtin/packages/visit/package.py @@ -26,7 +26,8 @@ from spack import * class Visit(Package): - """VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.""" + """VisIt is an Open Source, interactive, scalable, visualization, + animation and analysis tool.""" homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/" url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz" @@ -42,12 +43,15 @@ class Visit(Package): with working_dir('spack-build', create=True): feature_args = std_cmake_args[:] - feature_args.extend(["-DVTK_MAJOR_VERSION=6", - "-DVTK_MINOR_VERSION=1", - "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec['qt'].prefix.bin, - "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec['python'].prefix.bin, - "-DVISIT_SILO_DIR:PATH=%s" % spec['silo'].prefix, - "-DVISIT_HDF5_DIR:PATH=%s" % spec['hdf5'].prefix]) + feature_args.extend([ + "-DVTK_MAJOR_VERSION=6", + "-DVTK_MINOR_VERSION=1", + "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec[ + 'qt'].prefix.bin, + "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec[ + 'python'].prefix.bin, + "-DVISIT_SILO_DIR:PATH=%s" % spec['silo'].prefix, + "-DVISIT_HDF5_DIR:PATH=%s" % spec['hdf5'].prefix]) cmake('../src', *feature_args) diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 5c196b5ea8..087c0e93eb 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Vtk(Package): """The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image @@ -31,9 +32,11 @@ class Vtk(Package): homepage = "http://www.vtk.org" url = "http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz" - version("7.0.0", "5fe35312db5fb2341139b8e4955c367d", url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz") + version("7.0.0", "5fe35312db5fb2341139b8e4955c367d", + url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz") - version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d', url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz") + version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d', + url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz") version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') @@ -41,7 +44,8 @@ class Vtk(Package): depends_on("qt") # VTK7 defaults to OpenGL2 rendering backend - variant('opengl2', default=True, description='Build with OpenGL instead of OpenGL2 as rendering backend') + variant('opengl2', default=True, + description='Build with OpenGL instead of OpenGL2 backend') def install(self, spec, prefix): def feature_to_bool(feature, on='ON', off='OFF'): @@ -67,7 +71,7 @@ class Vtk(Package): "-DVTK_Group_Qt=OFF", "-DModule_vtkGUISupportQt:BOOL=ON", "-DModule_vtkGUISupportQtOpenGL:BOOL=ON" - ]) + ]) if spec['qt'].satisfies('@5'): cmake_args.append("-DVTK_QT_VERSION:STRING=5") @@ -76,7 +80,8 @@ class Vtk(Package): cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY") cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY") - cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL')) + cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % + feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL')) cmake(*cmake_args) make() diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py index 532cf332e9..aff771b723 100644 --- a/var/spack/repos/builtin/packages/wget/package.py +++ b/var/spack/repos/builtin/packages/wget/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Wget(Package): """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It @@ -40,9 +41,11 @@ class Wget(Package): depends_on("openssl") def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--with-ssl=openssl", - "OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include, - "OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec['openssl'].prefix.lib) + configure( + "--prefix=%s" % prefix, + "--with-ssl=openssl", + "OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include, + "OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec[ + 'openssl'].prefix.lib) make() make("install") diff --git a/var/spack/repos/builtin/packages/wx/package.py b/var/spack/repos/builtin/packages/wx/package.py index c000824803..5a80ca1c1f 100644 --- a/var/spack/repos/builtin/packages/wx/package.py +++ b/var/spack/repos/builtin/packages/wx/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Wx(Package): """wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms @@ -43,8 +44,8 @@ class Wx(Package): depends_on('gtkplus') def install(self, spec, prefix): - configure("--prefix=%s" % prefix, "--enable-unicode", "--disable-precomp-headers") + configure("--prefix=%s" % prefix, "--enable-unicode", + "--disable-precomp-headers") make(parallel=False) make("install") - diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py index 2283e1acf1..cc9ff445d6 100644 --- a/var/spack/repos/builtin/packages/wxpropgrid/package.py +++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Wxpropgrid(Package): """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing @@ -37,8 +38,8 @@ class Wxpropgrid(Package): depends_on("wx") def install(self, spec, prefix): - configure("--prefix=%s" % prefix, "--with-wxdir=%s" % spec['wx'].prefix.bin, "--enable-unicode") + configure("--prefix=%s" % prefix, "--with-wxdir=%s" % + spec['wx'].prefix.bin, "--enable-unicode") make() make("install") - diff --git a/var/spack/repos/builtin/packages/xcb-proto/package.py b/var/spack/repos/builtin/packages/xcb-proto/package.py index efcbdf0aea..587983f6bd 100644 --- a/var/spack/repos/builtin/packages/xcb-proto/package.py +++ b/var/spack/repos/builtin/packages/xcb-proto/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class XcbProto(Package): """Protocol for libxcb""" diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index 2efccc3c08..d0c2d3d497 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/package.py @@ -24,16 +24,18 @@ ############################################################################## from spack import * + class XercesC(Package): """ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, - manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. + manipulating, and validating XML documents using the DOM, SAX, and SAX2 + APIs. """ homepage = "https://xerces.apache.org/xerces-c" - url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.3.tar.bz2" - version('3.1.3', '5e333b55cb43e6b025ddf0e5d0f0fb0d') + url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.4.tar.bz2" + version('3.1.4', 'd04ae9d8b2dee2157c6db95fa908abfd') def install(self, spec, prefix): configure("--prefix=%s" % prefix, @@ -41,4 +43,3 @@ class XercesC(Package): make("clean") make() make("install") - diff --git a/var/spack/repos/builtin/packages/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py index 963d93442f..cd50d46826 100644 --- a/var/spack/repos/builtin/packages/xorg-util-macros/package.py +++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py @@ -24,11 +24,12 @@ ############################################################################## from spack import * + class XorgUtilMacros(Package): - """The util-macros package contains the m4 macros used by all of the Xorg packages.""" + """The m4 macros used by all of the Xorg packages.""" homepage = "http://www.example.com" - url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2" + url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2" version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1') diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py index 7be6defb83..dbceaa1575 100644 --- a/var/spack/repos/builtin/packages/xproto/package.py +++ b/var/spack/repos/builtin/packages/xproto/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Xproto(Package): """The Xorg protocol headers provide the header files required to build the system, and to allow other applications to build against diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py index b3ef7808aa..a8ab959a62 100644 --- a/var/spack/repos/builtin/packages/xz/package.py +++ b/var/spack/repos/builtin/packages/xz/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Xz(Package): """XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like @@ -39,4 +40,3 @@ class Xz(Package): configure("--prefix=%s" % prefix) make() make("install") - diff --git a/var/spack/repos/builtin/packages/yasm/package.py b/var/spack/repos/builtin/packages/yasm/package.py index e05160c8ea..f14bdbcee7 100644 --- a/var/spack/repos/builtin/packages/yasm/package.py +++ b/var/spack/repos/builtin/packages/yasm/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Yasm(Package): """Yasm is a complete rewrite of the NASM-2.11.06 assembler. It supports the x86 and AMD64 instruction sets, accepts NASM and diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/zeromq/package.py index 9bdd5861e0..6a657dc39c 100644 --- a/var/spack/repos/builtin/packages/zeromq/package.py +++ b/var/spack/repos/builtin/packages/zeromq/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Zeromq(Package): """ The ZMQ networking/concurrency library and core API """ homepage = "http://zguide.zeromq.org/" @@ -38,7 +39,7 @@ class Zeromq(Package): depends_on("libsodium") def install(self, spec, prefix): - configure("--with-libsodium","--prefix=%s" % prefix) + configure("--with-libsodium", "--prefix=%s" % prefix) make() make("install") diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py index 878b65118f..a898ab03d3 100644 --- a/var/spack/repos/builtin/packages/zfp/package.py +++ b/var/spack/repos/builtin/packages/zfp/package.py @@ -24,12 +24,15 @@ ############################################################################## from spack import * + class Zfp(Package): - """zfp is an open source C library for compressed floating-point arrays that supports - very high throughput read and write random acces, target error bounds or bit rates. - Although bit-for-bit lossless compression is not always possible, zfp is usually - accurate to within machine epsilon in near-lossless mode, and is often orders of - magnitude more accurate than other lossy compressors. + """zfp is an open source C library for compressed floating-point arrays + that supports very high throughput read and write random acces, + target error bounds or bit rates. Although bit-for-bit lossless + compression is not always possible, zfp is usually accurate to + within machine epsilon in near-lossless mode, and is often orders + of magnitude more accurate than other lossy compressors. + """ homepage = "http://computation.llnl.gov/projects/floating-point-compression" diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py index e1cbdc7e28..6d799fb05a 100644 --- a/var/spack/repos/builtin/packages/zlib/package.py +++ b/var/spack/repos/builtin/packages/zlib/package.py @@ -24,11 +24,10 @@ ############################################################################## from spack import * + class Zlib(Package): - """zlib is designed to be a free, general-purpose, legally unencumbered -- - that is, not covered by any patents -- lossless data-compression library for - use on virtually any computer hardware and operating system. - """ + """A free, general-purpose, legally unencumbered lossless + data-compression library.""" homepage = "http://zlib.net" url = "http://zlib.net/zlib-1.2.8.tar.gz" diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py index 841ff3f4a2..0094395968 100644 --- a/var/spack/repos/builtin/packages/zoltan/package.py +++ b/var/spack/repos/builtin/packages/zoltan/package.py @@ -22,16 +22,22 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import re, os, glob +import re +import os +import glob from spack import * + class Zoltan(Package): - """The Zoltan library is a toolkit of parallel combinatorial algorithms for - parallel, unstructured, and/or adaptive scientific applications. Zoltan's - largest component is a suite of dynamic load-balancing and paritioning - algorithms that increase applications' parallel performance by reducing - idle time. Zoltan also has graph coloring and graph ordering algorithms, - which are useful in task schedulers and parallel preconditioners.""" + """The Zoltan library is a toolkit of parallel combinatorial algorithms + for parallel, unstructured, and/or adaptive scientific + applications. Zoltan's largest component is a suite of dynamic + load-balancing and paritioning algorithms that increase + applications' parallel performance by reducing idle time. Zoltan + also has graph coloring and graph ordering algorithms, which are + useful in task schedulers and parallel preconditioners. + + """ homepage = "http://www.cs.sandia.gov/zoltan" base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions" @@ -41,8 +47,10 @@ class Zoltan(Package): version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9') version('3.3', '5eb8f00bda634b25ceefa0122bd18d65') - variant('debug', default=False, description='Builds a debug version of the library') - variant('shared', default=True, description='Builds a shared version of the library') + variant('debug', default=False, + description='Builds a debug version of the library') + variant('shared', default=True, + description='Builds a shared version of the library') variant('fortran', default=True, description='Enable Fortran support') variant('mpi', default=False, description='Enable MPI support') @@ -51,8 +59,11 @@ class Zoltan(Package): def install(self, spec, prefix): config_args = [ - '--enable-f90interface' if '+fortan' in spec else '--disable-f90interface', - '--enable-mpi' if '+mpi' in spec else '--disable-mpi', + '--enable-f90interface' + if '+fortan' in spec else '--disable-f90interface', + + '--enable-mpi' + if '+mpi' in spec else '--disable-mpi', ] config_cflags = [ '-O0' if '+debug' in spec else '-O3', @@ -68,7 +79,8 @@ class Zoltan(Package): config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin) config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin) config_args.append('--with-mpi=%s' % spec['mpi'].prefix) - config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin) + config_args.append('--with-mpi-compilers=%s' % + spec['mpi'].prefix.bin) # NOTE: Early versions of Zoltan come packaged with a few embedded # library packages (e.g. ParMETIS, Scotch), which messes with Spack's @@ -89,13 +101,15 @@ class Zoltan(Package): make() make('install') - # NOTE: Unfortunately, Zoltan doesn't provide any configuration options for - # the extension of the output library files, so this script must change these - # extensions as a post-processing step. + # NOTE: Unfortunately, Zoltan doesn't provide any configuration + # options for the extension of the output library files, so this + # script must change these extensions as a post-processing step. if '+shared' in spec: for libpath in glob.glob('lib/*.a'): - libdir, libname = (os.path.dirname(libpath), os.path.basename(libpath)) - move(libpath, os.path.join(libdir, re.sub(r'\.a$', '.so', libname))) + libdir, libname = (os.path.dirname(libpath), + os.path.basename(libpath)) + move(libpath, os.path.join( + libdir, re.sub(r'\.a$', '.so', libname))) mkdirp(prefix) move('include', prefix) diff --git a/var/spack/repos/builtin/packages/zsh/package.py b/var/spack/repos/builtin/packages/zsh/package.py index 2c9ed4c6e7..4c27cd3ec2 100644 --- a/var/spack/repos/builtin/packages/zsh/package.py +++ b/var/spack/repos/builtin/packages/zsh/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Zsh(Package): """ Zsh is a shell designed for interactive use, although it is also a powerful |