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authorMario Melara <maamelara@gmail.com>2016-06-18 00:52:06 -0700
committerMario Melara <maamelara@gmail.com>2016-06-18 00:52:06 -0700
commit8af1c5fc8f246303ad353d5d91b3a9865cabfe49 (patch)
treebfa1f565f6417d396a533004b281577a6968d5bd
parentc703bfb54d0452418fea95839226fb5bab7e5893 (diff)
parent62b2f2a7c9d54fb864e6aae91f1f47a1b35d1828 (diff)
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Merge remote-tracking branch 'upstream/develop' into develop
"Updating NERSC branch"
-rw-r--r--.flake82
-rw-r--r--lib/spack/llnl/util/tty/__init__.py4
-rw-r--r--lib/spack/spack/database.py6
-rw-r--r--lib/spack/spack/hooks/licensing.py5
-rw-r--r--lib/spack/spack/package.py14
-rw-r--r--var/spack/repos/builtin/packages/bertini/package.py50
-rw-r--r--var/spack/repos/builtin/packages/daal/package.py28
-rw-r--r--var/spack/repos/builtin/packages/espresso/package.py24
-rw-r--r--var/spack/repos/builtin/packages/hpl/package.py119
-rw-r--r--var/spack/repos/builtin/packages/intel-parallel-studio/package.py144
-rw-r--r--var/spack/repos/builtin/packages/intel/package.py125
-rw-r--r--var/spack/repos/builtin/packages/ipp/package.py26
-rw-r--r--var/spack/repos/builtin/packages/mkl/package.py28
-rw-r--r--var/spack/repos/builtin/packages/py-astropy/package.py35
-rw-r--r--var/spack/repos/builtin/packages/py-beautifulsoup4/package.py41
-rw-r--r--var/spack/repos/builtin/packages/py-emcee/package.py41
-rw-r--r--var/spack/repos/builtin/packages/py-h5py/package.py39
-rw-r--r--var/spack/repos/builtin/packages/py-iminuit/package.py46
-rw-r--r--var/spack/repos/builtin/packages/py-nestle/package.py44
-rw-r--r--var/spack/repos/builtin/packages/py-sncosmo/package.py51
-rw-r--r--var/spack/repos/builtin/packages/py-wcsaxes/package.py43
-rw-r--r--var/spack/repos/builtin/packages/python/package.py193
22 files changed, 993 insertions, 115 deletions
diff --git a/.flake8 b/.flake8
index 12ae2efa80..286522bc48 100644
--- a/.flake8
+++ b/.flake8
@@ -19,5 +19,5 @@
# - F999: name name be undefined or undefined from star imports.
#
[flake8]
-ignore = E221,E241,E731,F403,F821,F999
+ignore = E221,E241,E731,F403,F821,F999,F405
max-line-length = 79
diff --git a/lib/spack/llnl/util/tty/__init__.py b/lib/spack/llnl/util/tty/__init__.py
index c638b113fd..ee81e11a20 100644
--- a/lib/spack/llnl/util/tty/__init__.py
+++ b/lib/spack/llnl/util/tty/__init__.py
@@ -64,12 +64,14 @@ def info(message, *args, **kwargs):
format = kwargs.get('format', '*b')
stream = kwargs.get('stream', sys.stdout)
wrap = kwargs.get('wrap', False)
+ break_long_words = kwargs.get('break_long_words', False)
cprint("@%s{==>} %s" % (format, cescape(str(message))), stream=stream)
for arg in args:
if wrap:
lines = textwrap.wrap(
- str(arg), initial_indent=indent, subsequent_indent=indent)
+ str(arg), initial_indent=indent, subsequent_indent=indent,
+ break_long_words=break_long_words)
for line in lines:
stream.write(line + '\n')
else:
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index 38bb7541e0..f941346bb1 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -311,7 +311,11 @@ class Database(object):
for spec in directory_layout.all_specs():
# Create a spec for each known package and add it.
path = directory_layout.path_for_spec(spec)
- self._add(spec, path, directory_layout)
+ old_info = old_data.get(spec.dag_hash())
+ explicit = False
+ if old_info is not None:
+ explicit = old_info.explicit
+ self._add(spec, path, directory_layout, explicit=explicit)
self._check_ref_counts()
diff --git a/lib/spack/spack/hooks/licensing.py b/lib/spack/spack/hooks/licensing.py
index 0f63b0e05a..9010b84154 100644
--- a/lib/spack/spack/hooks/licensing.py
+++ b/lib/spack/spack/hooks/licensing.py
@@ -26,7 +26,7 @@ import os
import spack
import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
+from llnl.util.filesystem import join_path, mkdirp
def pre_install(pkg):
@@ -154,6 +154,9 @@ def symlink_license(pkg):
target = pkg.global_license_file
for filename in pkg.license_files:
link_name = join_path(pkg.prefix, filename)
+ license_dir = os.path.dirname(link_name)
+ if not os.path.exists(license_dir):
+ mkdirp(license_dir)
if os.path.exists(target):
os.symlink(target, link_name)
tty.msg("Added local symlink %s to global license file" %
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 1a6c289bc7..98fd51b262 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -398,13 +398,19 @@ class Package(object):
spack.repo.get(self.extendee_spec)._check_extendable()
@property
+ def global_license_dir(self):
+ """Returns the directory where global license files for all
+ packages are stored."""
+ spack_root = ancestor(__file__, 4)
+ return join_path(spack_root, 'etc', 'spack', 'licenses')
+
+ @property
def global_license_file(self):
- """Returns the path where a global license file should be stored."""
+ """Returns the path where a global license file for this
+ particular package should be stored."""
if not self.license_files:
return
- spack_root = ancestor(__file__, 4)
- global_license_dir = join_path(spack_root, 'etc', 'spack', 'licenses')
- return join_path(global_license_dir, self.name,
+ return join_path(self.global_license_dir, self.name,
os.path.basename(self.license_files[0]))
@property
diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py
new file mode 100644
index 0000000000..8d7da705e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bertini/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 Bertini(Package):
+ """Bertini is a general-purpose solver, written in C, that was created
+ for research about polynomial continuation. It solves for the numerical
+ solution of systems of polynomial equations using homotopy continuation."""
+
+ homepage = "https://bertini.nd.edu/"
+ url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz"
+
+ version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707')
+
+ variant('mpi', default=True, description='Compile in parallel')
+
+ depends_on('flex')
+ depends_on('bison')
+ depends_on('gmp')
+ depends_on('mpfr')
+ depends_on('mpi', when='+mpi')
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/daal/package.py b/var/spack/repos/builtin/packages/daal/package.py
new file mode 100644
index 0000000000..e13dd80e19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/daal/package.py
@@ -0,0 +1,28 @@
+from spack import *
+import os
+
+from spack.pkg.builtin.intel import IntelInstaller
+
+
+class Daal(IntelInstaller):
+ """Intel Data Analytics Acceleration Library.
+
+ Note: You will have to add the download 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"""
+
+ homepage = "https://software.intel.com/en-us/daal"
+
+ version('2016.2.181', 'aad2aa70e5599ebfe6f85b29d8719d46',
+ url="file://%s/l_daal_2016.2.181.tgz" % os.getcwd())
+ version('2016.3.210', 'ad747c0dd97dace4cad03cf2266cad28',
+ url="file://%s/l_daal_2016.3.210.tgz" % os.getcwd())
+
+ def install(self, spec, prefix):
+
+ self.intel_prefix = os.path.join(prefix, "pkg")
+ IntelInstaller.install(self, spec, prefix)
+
+ daal_dir = os.path.join(self.intel_prefix, "daal")
+ for f in os.listdir(daal_dir):
+ os.symlink(os.path.join(daal_dir, f), os.path.join(self.prefix, f))
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index 63a5560137..447964f286 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -26,20 +26,28 @@ from spack import *
import os
+
class Espresso(Package):
"""
- QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials
- modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
+ QE is an integrated suite of Open-Source computer codes for
+ electronic-structure calculations and materials modeling at
+ the nanoscale. It is based on density-functional theory, plane
+ waves, and pseudopotentials.
"""
homepage = 'http://quantum-espresso.org'
url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
+ version(
+ '5.4.0',
+ '8bb78181b39bd084ae5cb7a512c1cfe7',
+ url='http://www.qe-forge.org/gf/download/frsrelease/211/968/espresso-5.4.0.tar.gz'
+ )
version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
- variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
+ variant('mpi', default=True, description='Builds with mpi support')
variant('openmp', default=False, description='Enables openMP support')
variant('scalapack', default=True, description='Enables scalapack support')
- variant('elpa', default=True, description='Use elpa as an eigenvalue solver')
+ variant('elpa', default=True, description='Uses elpa as an eigenvalue solver')
depends_on('blas')
depends_on('lapack')
@@ -47,7 +55,12 @@ class Espresso(Package):
depends_on('mpi', when='+mpi')
depends_on('fftw~mpi', when='~mpi')
depends_on('fftw+mpi', when='+mpi')
- depends_on('scalapack', when='+scalapack+mpi') # TODO : + mpi needed to avoid false dependencies installation
+ # TODO : + mpi needed to avoid false dependencies installation
+ depends_on('scalapack', when='+scalapack+mpi')
+
+ # Spurious problems running in parallel the Makefile
+ # generated by qe configure
+ parallel = False
def check_variants(self, spec):
error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
@@ -93,4 +106,3 @@ class Espresso(Package):
install(filename, prefix.bin)
else:
make('install')
-
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
new file mode 100644
index 0000000000..efd5c8bb1d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -0,0 +1,119 @@
+##############################################################################
+# 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
+import platform
+
+
+class Hpl(Package):
+ """HPL is a software package that solves a (random) dense linear system
+ in double precision (64 bits) arithmetic on distributed-memory computers.
+ It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+ homepage = "http://www.netlib.org/benchmark/hpl/"
+ url = "http://www.netlib.org/benchmark/hpl/hpl-2.2.tar.gz"
+
+ version('2.2', '0eb19e787c3dc8f4058db22c9e0c5320')
+
+ variant('openmp', default=False, description='Enable OpenMP support')
+
+ depends_on('mpi@1.1:')
+ depends_on('blas')
+
+ parallel = False
+
+ def configure(self, spec, arch):
+ # List of configuration options
+ # Order is important
+ config = []
+
+ # OpenMP support
+ if '+openmp' in spec:
+ config.append(
+ 'OMP_DEFS = {0}'.format(self.compiler.openmp_flag)
+ )
+
+ config.extend([
+ # Shell
+ 'SHELL = /bin/sh',
+ 'CD = cd',
+ 'CP = cp',
+ 'LN_S = ln -fs',
+ 'MKDIR = mkdir -p',
+ 'RM = /bin/rm -f',
+ 'TOUCH = touch',
+ # Platform identifier
+ 'ARCH = {0}'.format(arch),
+ # HPL Directory Structure / HPL library
+ 'TOPdir = {0}'.format(os.getcwd()),
+ 'INCdir = $(TOPdir)/include',
+ 'BINdir = $(TOPdir)/bin/$(ARCH)',
+ 'LIBdir = $(TOPdir)/lib/$(ARCH)',
+ 'HPLlib = $(LIBdir)/libhpl.a',
+ # Message Passing library (MPI)
+ 'MPinc = -I{0}'.format(spec['mpi'].prefix.include),
+ 'MPlib = -L{0}'.format(spec['mpi'].prefix.lib),
+ # Linear Algebra library (BLAS or VSIPL)
+ 'LAinc = {0}'.format(spec['blas'].prefix.include),
+ 'LAlib = {0}'.format(spec['blas'].blas_shared_lib),
+ # F77 / C interface
+ 'F2CDEFS = -DAdd_ -DF77_INTEGER=int -DStringSunStyle',
+ # HPL includes / libraries / specifics
+ 'HPL_INCLUDES = -I$(INCdir) -I$(INCdir)/$(ARCH) ' +
+ '-I$(LAinc) -I$(MPinc)',
+ 'HPL_LIBS = $(HPLlib) $(LAlib) $(MPlib)',
+ 'HPL_OPTS = -DHPL_DETAILED_TIMING -DHPL_PROGRESS_REPORT',
+ 'HPL_DEFS = $(F2CDEFS) $(HPL_OPTS) $(HPL_INCLUDES)',
+ # Compilers / linkers - Optimization flags
+ 'CC = {0}'.format(spec['mpi'].mpicc),
+ 'CCNOOPT = $(HPL_DEFS)',
+ 'CCFLAGS = $(HPL_DEFS) -O3',
+ 'LINKER = $(CC)',
+ 'LINKFLAGS = $(CCFLAGS) $(OMP_DEFS)',
+ 'ARCHIVER = ar',
+ 'ARFLAGS = r',
+ 'RANLIB = echo'
+ ])
+
+ # Write configuration options to include file
+ with open('Make.{0}'.format(arch), 'w') as makefile:
+ for var in config:
+ makefile.write('{0}\n'.format(var))
+
+ def install(self, spec, prefix):
+ # Arch used for file naming purposes only
+ arch = '{0}-{1}'.format(platform.system(), platform.processor())
+
+ # Generate Makefile include
+ self.configure(spec, arch)
+
+ make('arch={0}'.format(arch))
+
+ # Manual installation
+ install_tree(join_path('bin', arch), prefix.bin)
+ install_tree(join_path('lib', arch), prefix.lib)
+ install_tree(join_path('include', arch), prefix.include)
+ install_tree('man', prefix.man)
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
new file mode 100644
index 0000000000..493ca16417
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -0,0 +1,144 @@
+from spack import *
+import os
+import re
+
+from spack.pkg.builtin.intel import IntelInstaller, filter_pick, \
+ get_all_components
+
+
+class IntelParallelStudio(IntelInstaller):
+ """Intel Parallel Studio.
+
+ Note: You will have to add the download 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"""
+
+ homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
+
+ # 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
+ % os.getcwd())
+ version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
+ url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501
+ version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
+ url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501
+ version('composer.2016.3', '3208eeabee951fc27579177b593cefe9',
+ url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501
+ % os.getcwd())
+ version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
+ url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501
+ version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
+ url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501
+
+ variant('rpath', default=True, description="Add rpath to .cfg files")
+ variant('newdtags', default=False,
+ description="Allow use of --enable-new-dtags in MPI wrappers")
+ variant('all', default=False,
+ description="Install all files with the requested edition")
+ variant('mpi', default=True,
+ description="Install the Intel MPI library and ITAC tool")
+ variant('mkl', default=True, description="Install the Intel MKL library")
+ variant('daal',
+ default=True, description="Install the Intel DAAL libraries")
+ variant('ipp', default=True, description="Install the Intel IPP libraries")
+ variant('tools', default=True, description="""Install the Intel Advisor,\
+VTune Amplifier, and Inspector tools""")
+
+ provides('mpi', when='@cluster:+mpi')
+ provides('mkl', when='+mkl')
+ provides('daal', when='+daal')
+ provides('ipp', when='+ipp')
+
+ def install(self, spec, prefix):
+
+ base_components = "ALL" # when in doubt, install everything
+ mpi_components = ""
+ mkl_components = ""
+ daal_components = ""
+ ipp_components = ""
+
+ if spec.satisfies('+all'):
+ base_components = "ALL"
+ else:
+ all_components = get_all_components()
+ 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)'
+ mpi_components = \
+ filter_pick(all_components, re.compile(regex).search)
+ mkl_components = \
+ filter_pick(all_components, re.compile('(mkl)').search)
+ daal_components = \
+ filter_pick(all_components, re.compile('(daal)').search)
+ ipp_components = \
+ filter_pick(all_components, re.compile('(ipp)').search)
+ regex = '(gdb|vtune|inspector|advisor)'
+ tool_components = \
+ filter_pick(all_components, re.compile(regex).search)
+
+ components = base_components
+ if not spec.satisfies('+all'):
+ if spec.satisfies('+mpi') and 'cluster' in str(spec.version):
+ components += mpi_components
+ if spec.satisfies('+mkl'):
+ components += mkl_components
+ if spec.satisfies('+daal'):
+ components += daal_components
+ if spec.satisfies('+ipp'):
+ components += ipp_components
+ if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
+ spec.satisfies('@professional')):
+ components += tool_components
+
+ 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")))
+
+ os.symlink(self.global_license_file, os.path.join(absbindir,
+ "license.lic"))
+ if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
+ spec.satisfies('@professional')):
+ os.mkdir(os.path.join(self.prefix, "inspector_xe/licenses"))
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "inspector_xe/licenses", "license.lic"))
+ os.mkdir(os.path.join(self.prefix, "advisor_xe/licenses"))
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "advisor_xe/licenses", "license.lic"))
+ os.mkdir(os.path.join(self.prefix, "vtune_amplifier_xe/licenses"))
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "vtune_amplifier_xe/licenses", "license.lic"))
+
+ if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \
+ spec.satisfies('@cluster'):
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "itac_latest", "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"]:
+ cfgfilename = os.path.join(absbindir, "%s.cfg" %
+ compiler_command)
+ with open(cfgfilename, "w") as f:
+ f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir)
+
+ os.symlink(os.path.join(self.prefix.man, "common", "man1"),
+ os.path.join(self.prefix.man, "man1"))
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
new file mode 100644
index 0000000000..ec3192380a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -0,0 +1,125 @@
+from spack import *
+import os
+import re
+
+
+def filter_pick(input_list, regex_filter):
+ """Returns the items in input_list that are found in the regex_filter"""
+ return [l for l in input_list for m in (regex_filter(l),) if m]
+
+
+def unfilter_pick(input_list, regex_filter):
+ """Returns the items in input_list that are not found in the
+ regex_filter"""
+ return [l for l in input_list for m in (regex_filter(l),) if not m]
+
+
+def get_all_components():
+ """Returns a list of all the components associated with the downloaded
+ Intel package"""
+ all_components = []
+ with open("pset/mediaconfig.xml", "r") as f:
+ lines = f.readlines()
+ for line in lines:
+ if line.find('<Abbr>') != -1:
+ component = line[line.find('<Abbr>') + 6:line.find('</Abbr>')]
+ all_components.append(component)
+ return all_components
+
+
+class IntelInstaller(Package):
+ """Base package containing common methods for installing Intel software"""
+
+ homepage = "https://software.intel.com/en-us"
+ intel_components = "ALL"
+ license_required = True
+ license_comment = '#'
+ license_files = ['Licenses/license.lic']
+ license_vars = ['INTEL_LICENSE_FILE']
+ license_url = \
+ 'https://software.intel.com/en-us/articles/intel-license-manager-faq'
+
+ @property
+ def global_license_file(self):
+ """Returns the path where a global license file should be stored."""
+ if not self.license_files:
+ return
+ return join_path(self.global_license_dir, "intel",
+ os.path.basename(self.license_files[0]))
+
+ def install(self, spec, prefix):
+
+ # Remove the installation DB, otherwise it will try to install into
+ # location of other Intel builds
+ if os.path.exists(os.path.join(os.environ["HOME"], "intel",
+ "intel_sdp_products.db")):
+ os.remove(os.path.join(os.environ["HOME"], "intel",
+ "intel_sdp_products.db"))
+
+ if not hasattr(self, "intel_prefix"):
+ self.intel_prefix = self.prefix
+
+ silent_config_filename = 'silent.cfg'
+ with open(silent_config_filename, 'w') as f:
+ f.write("""
+ACCEPT_EULA=accept
+PSET_MODE=install
+CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes
+PSET_INSTALL_DIR=%s
+ACTIVATION_LICENSE_FILE=%s
+ACTIVATION_TYPE=license_file
+PHONEHOME_SEND_USAGE_DATA=no
+CONTINUE_WITH_OPTIONAL_ERROR=yes
+COMPONENTS=%s
+""" % (self.intel_prefix, self.global_license_file, self.intel_components))
+
+ install_script = which("install.sh")
+ install_script('--silent', silent_config_filename)
+
+
+class Intel(IntelInstaller):
+ """Intel Compilers.
+
+ Note: You will have to add the download 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"""
+
+ homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
+
+ # 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
+ % os.getcwd())
+ version('16.0.3', '3208eeabee951fc27579177b593cefe9',
+ url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501
+ % os.getcwd())
+
+ variant('rpath', default=True, description="Add rpath to .cfg files")
+
+ def install(self, spec, prefix):
+ components = []
+ all_components = get_all_components()
+ regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)'
+ components = filter_pick(all_components, re.compile(regex).search)
+
+ self.intel_components = ';'.join(components)
+ IntelInstaller.install(self, spec, prefix)
+
+ absbindir = os.path.split(os.path.realpath(os.path.join(
+ self.prefix.bin, "icc")))[0]
+ abslibdir = os.path.split(os.path.realpath(os.path.join(
+ self.prefix.lib, "intel64", "libimf.a")))[0]
+
+ # symlink or copy?
+ os.symlink(self.global_license_file, os.path.join(absbindir,
+ "license.lic"))
+
+ if spec.satisfies('+rpath'):
+ for compiler_command in ["icc", "icpc", "ifort"]:
+ cfgfilename = os.path.join(absbindir, "%s.cfg" %
+ compiler_command)
+ with open(cfgfilename, "w") as f:
+ f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir)
+
+ os.symlink(os.path.join(self.prefix.man, "common", "man1"),
+ os.path.join(self.prefix.man, "man1"))
diff --git a/var/spack/repos/builtin/packages/ipp/package.py b/var/spack/repos/builtin/packages/ipp/package.py
new file mode 100644
index 0000000000..2bd931d5bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ipp/package.py
@@ -0,0 +1,26 @@
+from spack import *
+import os
+
+from spack.pkg.builtin.intel import IntelInstaller
+
+
+class Ipp(IntelInstaller):
+ """Intel Integrated Performance Primitives.
+
+ Note: You will have to add the download 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"""
+
+ homepage = "https://software.intel.com/en-us/intel-ipp"
+
+ version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3',
+ url="file://%s/l_ipp_9.0.3.210.tgz" % os.getcwd())
+
+ def install(self, spec, prefix):
+
+ self.intel_prefix = os.path.join(prefix, "pkg")
+ IntelInstaller.install(self, spec, prefix)
+
+ ipp_dir = os.path.join(self.intel_prefix, "ipp")
+ for f in os.listdir(ipp_dir):
+ os.symlink(os.path.join(ipp_dir, f), os.path.join(self.prefix, f))
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
new file mode 100644
index 0000000000..454e78d29c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -0,0 +1,28 @@
+from spack import *
+import os
+
+from spack.pkg.builtin.intel import IntelInstaller
+
+
+class Mkl(IntelInstaller):
+ """Intel Math Kernel Library.
+
+ Note: You will have to add the download 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"""
+
+ homepage = "https://software.intel.com/en-us/intel-mkl"
+
+ version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65',
+ url="file://%s/l_mkl_11.3.2.181.tgz" % os.getcwd())
+ version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
+ url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
+
+ def install(self, spec, prefix):
+
+ self.intel_prefix = os.path.join(prefix, "pkg")
+ IntelInstaller.install(self, spec, prefix)
+
+ mkl_dir = os.path.join(self.intel_prefix, "mkl")
+ for f in os.listdir(mkl_dir):
+ os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py
index 86875bbcae..a9962777dc 100644
--- a/var/spack/repos/builtin/packages/py-astropy/package.py
+++ b/var/spack/repos/builtin/packages/py-astropy/package.py
@@ -24,29 +24,38 @@
##############################################################################
from spack import *
+
class PyAstropy(Package):
- """
- The Astropy Project is a community effort to develop a single core
+ """The Astropy Project is a community effort to develop a single core
package for Astronomy in Python and foster interoperability between
- Python astronomy packages.
- """
+ Python astronomy packages."""
+
homepage = 'http://www.astropy.org/'
+ url = 'https://pypi.python.org/packages/source/a/astropy/astropy-1.1.2.tar.gz'
+ version('1.1.2', 'cbe32023b5b1177d1e2498a0d00cda51')
version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d')
- def url_for_version(self, version):
- return 'https://pypi.python.org/packages/source/a/astropy/astropy-{0}.tar.gz'.format(version)
-
+ # Required dependencies
extends('python')
+ depends_on('py-numpy')
- depends_on('cfitsio')
- depends_on('expat')
+ # Optional dependencies
depends_on('py-h5py')
- depends_on('py-numpy')
+ depends_on('py-beautifulsoup4')
+ depends_on('py-pyyaml')
depends_on('py-scipy')
+ depends_on('libxml2')
+ depends_on('py-matplotlib')
+ depends_on('py-pytz')
+ depends_on('py-scikit-image')
+ depends_on('py-pandas')
+
+ # System dependencies
+ depends_on('cfitsio')
+ depends_on('expat')
def install(self, spec, prefix):
python('setup.py', 'build', '--use-system-cfitsio',
- '--use-system-expat')
- python('setup.py', 'install', '--prefix=' + prefix)
-
+ '--use-system-expat')
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
new file mode 100644
index 0000000000..64368fe70d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/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 PyBeautifulsoup4(Package):
+ """Beautiful Soup is a Python library for pulling data out of HTML and
+ XML files. It works with your favorite parser to provide idiomatic ways
+ of navigating, searching, and modifying the parse tree."""
+
+ homepage = "https://www.crummy.com/software/BeautifulSoup"
+ url = "https://pypi.python.org/packages/source/b/beautifulsoup4/beautifulsoup4-4.4.1.tar.gz"
+
+ version('4.4.1', '8fbd9a7cac0704645fa20d1419036815')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py
new file mode 100644
index 0000000000..d57ef4bd76
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-emcee/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 PyEmcee(Package):
+ """emcee is an MIT licensed pure-Python implementation of Goodman & Weare's
+ Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler."""
+
+ homepage = "http://dan.iel.fm/emcee/current/"
+ url = "https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz"
+
+ version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7')
+
+ extends('python')
+ depends_on('py-numpy')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index a8eb027ba5..0180b658f5 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -23,23 +23,42 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
-import re
+
class PyH5py(Package):
- """The h5py package provides both a high- and low-level interface to the HDF5 library from Python."""
+ """The h5py package provides both a high- and low-level interface to the
+ HDF5 library from Python."""
+
homepage = "https://pypi.python.org/pypi/h5py"
url = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
- version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+ version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4')
version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
+ version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+
+ variant('mpi', default=False, description='Build with MPI support')
- extends('python', ignore=lambda f: re.match(r'bin/cy*', f))
- depends_on('hdf5')
- depends_on('py-numpy')
- depends_on('py-cython')
+ extends('python')
+
+ # Build dependencies
+ depends_on('py-cython@0.19:')
+ depends_on('pkg-config')
+ depends_on('hdf5@1.8.4:+mpi', when='+mpi')
+ depends_on('hdf5@1.8.4:~mpi', when='~mpi')
+ depends_on('mpi', when='+mpi')
+
+ # Build and runtime dependencies
+ depends_on('py-numpy@1.6.1:')
+
+ # Runtime dependencies
depends_on('py-six')
- depends_on('py-pkgconfig')
def install(self, spec, prefix):
- python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix)
- python('setup.py', 'install', '--prefix=%s' % prefix)
+ python('setup.py', 'configure',
+ '--hdf5={0}'.format(spec['hdf5'].prefix))
+
+ if '+mpi' in spec:
+ env['CC'] = spec['mpi'].mpicc
+ python('setup.py', 'configure', '--mpi')
+
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py
new file mode 100644
index 0000000000..47751a702d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-iminuit/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 PyIminuit(Package):
+ """Interactive IPython-Friendly Minimizer based on SEAL Minuit2."""
+
+ homepage = "https://pypi.python.org/pypi/iminuit"
+ url = "https://pypi.python.org/packages/source/i/iminuit/iminuit-1.2.tar.gz"
+
+ version('1.2', '4701ec472cae42015e26251703e6e984')
+
+ # Required dependencies
+ extends('python')
+ depends_on('py-setuptools')
+
+ # Optional dependencies
+ depends_on('py-numpy')
+ depends_on('py-matplotlib')
+ depends_on('py-cython')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py
new file mode 100644
index 0000000000..16506e3eca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nestle/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 PyNestle(Package):
+ """Nested sampling algorithms for evaluating Bayesian evidence."""
+
+ homepage = "http://kbarbary.github.io/nestle/"
+ url = "https://pypi.python.org/packages/source/n/nestle/nestle-0.1.1.tar.gz"
+
+ version('0.1.1', '4875c0f9a0a8e263c1d7f5fa6ce604c5')
+
+ # Required dependencies
+ extends('python')
+ depends_on('py-numpy')
+
+ # Optional dependencies
+ depends_on('py-scipy')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py
new file mode 100644
index 0000000000..82ae2a2e69
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sncosmo/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 PySncosmo(Package):
+ """SNCosmo is a Python library for high-level supernova cosmology
+ analysis."""
+
+ homepage = "http://sncosmo.readthedocs.io/"
+ url = "https://pypi.python.org/packages/source/s/sncosmo/sncosmo-1.2.0.tar.gz"
+
+ version('1.2.0', '028e6d1dc84ab1c17d2f3b6378b2cb1e')
+
+ # Required dependencies
+ # py-sncosmo binaries are duplicates of those from py-astropy
+ extends('python', ignore=r'bin/.*')
+ depends_on('py-numpy')
+ depends_on('py-scipy')
+ depends_on('py-astropy')
+
+ # Recommended dependencies
+ depends_on('py-matplotlib')
+ depends_on('py-iminuit')
+ depends_on('py-emcee')
+ depends_on('py-nestle')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
new file mode 100644
index 0000000000..b0adbe3658
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-wcsaxes/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 PyWcsaxes(Package):
+ """WCSAxes is a framework for making plots of Astronomical data
+ in Matplotlib."""
+
+ homepage = "http://wcsaxes.readthedocs.io/en/latest/index.html"
+ url = "https://github.com/astrofrog/wcsaxes/archive/v0.8.tar.gz"
+
+ version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920')
+
+ extends('python', ignore=r'bin/pbr')
+ depends_on('py-numpy')
+ depends_on('py-matplotlib')
+ depends_on('py-astropy')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 86c12498e1..b6a62bf742 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -22,9 +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 functools
-import glob
-import inspect
import os
import re
from contextlib import closing
@@ -37,11 +34,10 @@ from spack.util.environment import *
class Python(Package):
"""The Python programming language."""
+
homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
- extendable = True
-
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
@@ -49,6 +45,8 @@ class Python(Package):
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
+ extendable = True
+
depends_on("openssl")
depends_on("bzip2")
depends_on("readline")
@@ -64,39 +62,63 @@ class Python(Package):
# Rest of install is pretty standard except setup.py needs to
# be able to read the CPPFLAGS and LDFLAGS as it scans for the
# library and headers to build
- configure_args= [
- "--prefix=%s" % prefix,
- "--with-threads",
- "--enable-shared",
- "CPPFLAGS=-I%s/include -I%s/include -I%s/include -I%s/include -I%s/include -I%s/include" % (
- spec['openssl'].prefix, spec['bzip2'].prefix,
- spec['readline'].prefix, spec['ncurses'].prefix,
- spec['sqlite'].prefix, spec['zlib'].prefix),
- "LDFLAGS=-L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib" % (
- spec['openssl'].prefix, spec['bzip2'].prefix,
- spec['readline'].prefix, spec['ncurses'].prefix,
- spec['sqlite'].prefix, spec['zlib'].prefix)
- ]
+ cppflags = ' -I'.join([
+ spec['openssl'].prefix.include, spec['bzip2'].prefix.include,
+ spec['readline'].prefix.include, spec['ncurses'].prefix.include,
+ spec['sqlite'].prefix.include, spec['zlib'].prefix.include
+ ])
+
+ ldflags = ' -L'.join([
+ spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib,
+ spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
+ spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib
+ ])
+
+ config_args = [
+ "--prefix={0}".format(prefix),
+ "--with-threads",
+ "--enable-shared",
+ "CPPFLAGS=-I{0}".format(cppflags),
+ "LDFLAGS=-L{0}".format(ldflags)
+ ]
+
if spec.satisfies('@3:'):
- configure_args.append('--without-ensurepip')
- configure(*configure_args)
+ config_args.append('--without-ensurepip')
+
+ configure(*config_args)
+
make()
make("install")
- # Modify compiler paths in configuration files. This is necessary for
- # building site packages outside of spack
- filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
- (r'\4\5'),
- join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py'))
+ self.filter_compilers(spec, prefix)
+
+ def filter_compilers(self, spec, prefix):
+ """Run after install to tell the configuration files and Makefiles
+ to use the compilers that Spack built the package with.
+
+ If this isn't done, they'll have CC and CXX set to Spack's generic
+ cc and c++. We want them to be bound to whatever compiler
+ they were built with."""
+
+ kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
- python3_version = ''
+ dirname = join_path(prefix.lib,
+ 'python{0}'.format(self.version.up_to(2)))
+
+ config = 'config'
if spec.satisfies('@3:'):
- python3_version = '-%d.%dm' % self.version[:2]
- makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile')
- filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
- (r'\4\5'),
- makefile_filepath)
+ config = 'config-{0}m'.format(self.version.up_to(2))
+
+ files = [
+ '_sysconfigdata.py',
+ join_path(config, 'Makefile')
+ ]
+ for filename in files:
+ filter_file(env['CC'], self.compiler.cc,
+ join_path(dirname, filename), **kwargs)
+ filter_file(env['CXX'], self.compiler.cxx,
+ join_path(dirname, filename), **kwargs)
# ========================================================================
# Set up environment to make install easy for python extensions.
@@ -104,57 +126,59 @@ class Python(Package):
@property
def python_lib_dir(self):
- return os.path.join('lib', 'python%d.%d' % self.version[:2])
-
+ return join_path('lib', 'python{0}'.format(self.version.up_to(2)))
@property
def python_include_dir(self):
- return os.path.join('include', 'python%d.%d' % self.version[:2])
-
+ return join_path('include', 'python{0}'.format(self.version.up_to(2)))
@property
def site_packages_dir(self):
- return os.path.join(self.python_lib_dir, 'site-packages')
-
+ return join_path(self.python_lib_dir, 'site-packages')
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
- # TODO: do this only for actual extensions.
+ """Set PYTHONPATH to include site-packages dir for the
+ extension and any other python extensions it depends on."""
- # Set PYTHONPATH to include site-packages dir for the
- # extension and any other python extensions it depends on.
python_paths = []
for d in extension_spec.traverse():
if d.package.extends(self.spec):
- python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+ python_paths.append(join_path(d.prefix,
+ self.site_packages_dir))
pythonpath = ':'.join(python_paths)
spack_env.set('PYTHONPATH', pythonpath)
- # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+ # For run time environment set only the path for
+ # extension_spec and prepend it to PYTHONPATH
if extension_spec.package.extends(self.spec):
- run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
-
+ run_env.prepend_path('PYTHONPATH', join_path(
+ extension_spec.prefix, self.site_packages_dir))
def setup_dependent_package(self, module, ext_spec):
- """
- Called before python modules' install() methods.
+ """Called before python modules' install() methods.
In most cases, extensions will only need to have one line::
- python('setup.py', 'install', '--prefix=%s' % prefix)
- """
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))"""
+
# Python extension builds can have a global python executable function
- if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
- module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
+ if Version("3.0.0") <= self.version < Version("4.0.0"):
+ module.python = Executable(join_path(self.spec.prefix.bin,
+ 'python3'))
else:
- module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
+ module.python = Executable(join_path(self.spec.prefix.bin,
+ 'python'))
# Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
- module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir)
- module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
- module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir)
-
- # Make the site packages directory for extensions, if it does not exist already.
+ module.python_lib_dir = join_path(ext_spec.prefix,
+ self.python_lib_dir)
+ module.python_include_dir = join_path(ext_spec.prefix,
+ self.python_include_dir)
+ module.site_packages_dir = join_path(ext_spec.prefix,
+ self.site_packages_dir)
+
+ # Make the site packages directory for extensions
if ext_spec.package.is_extension:
mkdirp(module.site_packages_dir)
@@ -167,25 +191,28 @@ class Python(Package):
ignore_arg = args.get('ignore', lambda f: False)
# Always ignore easy-install.pth, as it needs to be merged.
- patterns = [r'easy-install\.pth$']
+ patterns = [r'site-packages/easy-install\.pth$']
# Ignore pieces of setuptools installed by other packages.
+ # Must include directory name or it will remove all site*.py files.
if ext_pkg.name != 'py-setuptools':
- patterns.append(r'/site[^/]*\.pyc?$')
- patterns.append(r'setuptools\.pth')
- patterns.append(r'bin/easy_install[^/]*$')
- patterns.append(r'setuptools.*egg$')
+ patterns.extend([
+ r'bin/easy_install[^/]*$',
+ r'site-packages/setuptools[^/]*\.egg$',
+ r'site-packages/setuptools\.pth$',
+ r'site-packages/site[^/]*\.pyc?$',
+ r'site-packages/__pycache__/site[^/]*\.pyc?$'
+ ])
if ext_pkg.name != 'py-numpy':
patterns.append(r'bin/f2py$')
return match_predicate(ignore_arg, patterns)
-
def write_easy_install_pth(self, exts):
paths = []
for ext in sorted(exts.values()):
- ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir)
- easy_pth = "%s/easy-install.pth" % ext_site_packages
+ ext_site_packages = join_path(ext.prefix, self.site_packages_dir)
+ easy_pth = join_path(ext_site_packages, "easy-install.pth")
if not os.path.isfile(easy_pth):
continue
@@ -195,15 +222,18 @@ class Python(Package):
line = line.rstrip()
# Skip lines matching these criteria
- if not line: continue
- if re.search(r'^(import|#)', line): continue
- if (ext.name != 'py-setuptools' and
- re.search(r'setuptools.*egg$', line)): continue
+ if not line:
+ continue
+ if re.search(r'^(import|#)', line):
+ continue
+ if ((ext.name != 'py-setuptools' and
+ re.search(r'setuptools.*egg$', line))):
+ continue
paths.append(line)
- site_packages = os.path.join(self.prefix, self.site_packages_dir)
- main_pth = "%s/easy-install.pth" % site_packages
+ site_packages = join_path(self.prefix, self.site_packages_dir)
+ main_pth = join_path(site_packages, "easy-install.pth")
if not paths:
if os.path.isfile(main_pth):
@@ -211,15 +241,22 @@ class Python(Package):
else:
with closing(open(main_pth, 'w')) as f:
- f.write("import sys; sys.__plen = len(sys.path)\n")
+ f.write("""
+import sys
+sys.__plen = len(sys.path)
+""")
for path in paths:
- f.write("%s\n" % path)
- f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; "
- "p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n")
-
+ f.write("{0}\n".format(path))
+ f.write("""
+new = sys.path[sys.__plen:]
+del sys.path[sys.__plen:]
+p = getattr(sys, '__egginsert', 0)
+sys.path[p:p] = new
+sys.__egginsert = p + len(new)
+""")
def activate(self, ext_pkg, **args):
- ignore=self.python_ignore(ext_pkg, args)
+ ignore = self.python_ignore(ext_pkg, args)
args.update(ignore=ignore)
super(Python, self).activate(ext_pkg, **args)
@@ -228,12 +265,12 @@ class Python(Package):
exts[ext_pkg.name] = ext_pkg.spec
self.write_easy_install_pth(exts)
-
def deactivate(self, ext_pkg, **args):
args.update(ignore=self.python_ignore(ext_pkg, args))
super(Python, self).deactivate(ext_pkg, **args)
exts = spack.install_layout.extension_map(self.spec)
- if ext_pkg.name in exts: # Make deactivate idempotent.
+ # Make deactivate idempotent
+ if ext_pkg.name in exts:
del exts[ext_pkg.name]
self.write_easy_install_pth(exts)