diff options
82 files changed, 422 insertions, 344 deletions
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index ace6cfded6..40eb6a7aa8 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -60,7 +60,9 @@ __all__ = [ 'fix_darwin_install_name', 'force_remove', 'force_symlink', + 'copy', 'install', + 'copy_tree', 'install_tree', 'is_exe', 'join_path', @@ -264,27 +266,98 @@ def unset_executable_mode(path): os.chmod(path, mode) -def install(src, dest): - """Manually install a file to a particular location.""" - tty.debug("Installing %s to %s" % (src, dest)) +def copy(src, dest, _permissions=False): + """Copies the file *src* to the file or directory *dest*. + + If *dest* specifies a directory, the file will be copied into *dest* + using the base filename from *src*. + + Parameters: + src (str): the file to copy + dest (str): the destination file or directory + _permissions (bool): for internal use only + """ + if _permissions: + tty.debug('Installing {0} to {1}'.format(src, dest)) + else: + tty.debug('Copying {0} to {1}'.format(src, dest)) # Expand dest to its eventual full path if it is a directory. if os.path.isdir(dest): dest = join_path(dest, os.path.basename(src)) shutil.copy(src, dest) - set_install_permissions(dest) - copy_mode(src, dest) + + if _permissions: + set_install_permissions(dest) + copy_mode(src, dest) + + +def install(src, dest): + """Installs the file *src* to the file or directory *dest*. + + Same as :py:func:`copy` with the addition of setting proper + permissions on the installed file. + + Parameters: + src (str): the file to install + dest (str): the destination file or directory + """ + copy(src, dest, _permissions=True) -def install_tree(src, dest, **kwargs): - """Manually install a directory tree to a particular location.""" - tty.debug("Installing %s to %s" % (src, dest)) - shutil.copytree(src, dest, **kwargs) +def copy_tree(src, dest, symlinks=True, _permissions=False): + """Recursively copy an entire directory tree rooted at *src*. - for s, d in traverse_tree(src, dest, follow_nonexisting=False): - set_install_permissions(d) - copy_mode(s, d) + If the destination directory *dest* does not already exist, it will + be created as well as missing parent directories. + + If *symlinks* is true, symbolic links in the source tree are represented + as symbolic links in the new tree and the metadata of the original links + will be copied as far as the platform allows; if false, the contents and + metadata of the linked files are copied to the new tree. + + Parameters: + src (str): the directory to copy + dest (str): the destination directory + symlinks (bool): whether or not to preserve symlinks + _permissions (bool): for internal use only + """ + if _permissions: + tty.debug('Installing {0} to {1}'.format(src, dest)) + else: + tty.debug('Copying {0} to {1}'.format(src, dest)) + + mkdirp(dest) + + for s, d in traverse_tree(src, dest, order='pre', follow_nonexisting=True): + if symlinks and os.path.islink(s): + # Note that this won't rewrite absolute links into the old + # root to point at the new root. Should we handle that case? + target = os.readlink(s) + os.symlink(os.path.abspath(target), d) + elif os.path.isdir(s): + mkdirp(d) + else: + shutil.copyfile(s, d) + + if _permissions: + set_install_permissions(d) + copy_mode(s, d) + + +def install_tree(src, dest, symlinks=True): + """Recursively install an entire directory tree rooted at *src*. + + Same as :py:func:`copy_tree` with the addition of setting proper + permissions on the installed files and directories. + + Parameters: + src (str): the directory to install + dest (str): the destination directory + symlinks (bool): whether or not to preserve symlinks + """ + copy_tree(src, dest, symlinks, _permissions=True) def is_exe(path): diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py new file mode 100644 index 0000000000..7701185dbe --- /dev/null +++ b/lib/spack/spack/test/llnl/util/filesystem.py @@ -0,0 +1,209 @@ +############################################################################## +# Copyright (c) 2013-2018, 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/spack/spack +# Please also see the NOTICE and LICENSE files 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 ``llnl/util/filesystem.py``""" + +import llnl.util.filesystem as fs +import os +import pytest + + +@pytest.fixture() +def stage(tmpdir_factory): + """Creates a stage with the directory structure for the tests.""" + + s = tmpdir_factory.mktemp('filesystem_test') + + with s.as_cwd(): + # Create source file hierarchy + fs.touchp('source/1') + fs.touchp('source/a/b/2') + fs.touchp('source/a/b/3') + fs.touchp('source/c/4') + fs.touchp('source/c/d/5') + fs.touchp('source/c/d/6') + fs.touchp('source/c/d/e/7') + + # Create symlink + os.symlink(os.path.abspath('source/1'), 'source/2') + + # Create destination directory + fs.mkdirp('dest') + + yield s + + +class TestCopy: + """Tests for ``filesystem.copy``""" + + def test_file_dest(self, stage): + """Test using a filename as the destination.""" + + with fs.working_dir(str(stage)): + fs.copy('source/1', 'dest/1') + + assert os.path.exists('dest/1') + assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode + + def test_dir_dest(self, stage): + """Test using a directory as the destination.""" + + with fs.working_dir(str(stage)): + fs.copy('source/1', 'dest') + + assert os.path.exists('dest/1') + assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode + + +class TestInstall: + """Tests for ``filesystem.install``""" + + def test_file_dest(self, stage): + """Test using a filename as the destination.""" + + with fs.working_dir(str(stage)): + fs.install('source/1', 'dest/1') + + assert os.path.exists('dest/1') + assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode + + def test_dir_dest(self, stage): + """Test using a directory as the destination.""" + + with fs.working_dir(str(stage)): + fs.install('source/1', 'dest') + + assert os.path.exists('dest/1') + assert os.stat('source/1').st_mode == os.stat('dest/1').st_mode + + +class TestCopyTree: + """Tests for ``filesystem.copy_tree``""" + + def test_existing_dir(self, stage): + """Test copying to an existing directory.""" + + with fs.working_dir(str(stage)): + fs.copy_tree('source', 'dest') + + assert os.path.exists('dest/a/b/2') + + def test_non_existing_dir(self, stage): + """Test copying to a non-existing directory.""" + + with fs.working_dir(str(stage)): + fs.copy_tree('source', 'dest/sub/directory') + + assert os.path.exists('dest/sub/directory/a/b/2') + + def test_symlinks_true(self, stage): + """Test copying with symlink preservation.""" + + with fs.working_dir(str(stage)): + fs.copy_tree('source', 'dest', symlinks=True) + + assert os.path.exists('dest/2') + assert os.path.islink('dest/2') + + def test_symlinks_false(self, stage): + """Test copying without symlink preservation.""" + + with fs.working_dir(str(stage)): + fs.copy_tree('source', 'dest', symlinks=False) + + assert os.path.exists('dest/2') + assert not os.path.islink('dest/2') + + +class TestInstallTree: + """Tests for ``filesystem.install_tree``""" + + def test_existing_dir(self, stage): + """Test installing to an existing directory.""" + + with fs.working_dir(str(stage)): + fs.install_tree('source', 'dest') + + assert os.path.exists('dest/a/b/2') + + def test_non_existing_dir(self, stage): + """Test installing to a non-existing directory.""" + + with fs.working_dir(str(stage)): + fs.install_tree('source', 'dest/sub/directory') + + assert os.path.exists('dest/sub/directory/a/b/2') + + def test_symlinks_true(self, stage): + """Test installing with symlink preservation.""" + + with fs.working_dir(str(stage)): + fs.install_tree('source', 'dest', symlinks=True) + + assert os.path.exists('dest/2') + assert os.path.islink('dest/2') + + def test_symlinks_false(self, stage): + """Test installing without symlink preservation.""" + + with fs.working_dir(str(stage)): + fs.install_tree('source', 'dest', symlinks=False) + + assert os.path.exists('dest/2') + assert not os.path.islink('dest/2') + + +def test_move_transaction_commit(tmpdir): + + fake_library = tmpdir.mkdir('lib').join('libfoo.so') + fake_library.write('Just some fake content.') + + old_md5 = fs.hash_directory(str(tmpdir)) + + with fs.replace_directory_transaction(str(tmpdir.join('lib'))): + fake_library = tmpdir.mkdir('lib').join('libfoo.so') + fake_library.write('Other content.') + new_md5 = fs.hash_directory(str(tmpdir)) + + assert old_md5 != fs.hash_directory(str(tmpdir)) + assert new_md5 == fs.hash_directory(str(tmpdir)) + + +def test_move_transaction_rollback(tmpdir): + + fake_library = tmpdir.mkdir('lib').join('libfoo.so') + fake_library.write('Just some fake content.') + + h = fs.hash_directory(str(tmpdir)) + + try: + with fs.replace_directory_transaction(str(tmpdir.join('lib'))): + assert h != fs.hash_directory(str(tmpdir)) + fake_library = tmpdir.mkdir('lib').join('libfoo.so') + fake_library.write('Other content.') + raise RuntimeError('') + except RuntimeError: + pass + + assert h == fs.hash_directory(str(tmpdir)) diff --git a/lib/spack/spack/test/util/filesystem.py b/lib/spack/spack/test/util/filesystem.py deleted file mode 100644 index 86c3332bb5..0000000000 --- a/lib/spack/spack/test/util/filesystem.py +++ /dev/null @@ -1,61 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 llnl.util.filesystem as fs - - -def test_move_transaction_commit(tmpdir): - - fake_library = tmpdir.mkdir('lib').join('libfoo.so') - fake_library.write('Just some fake content.') - - old_md5 = fs.hash_directory(str(tmpdir)) - - with fs.replace_directory_transaction(str(tmpdir.join('lib'))): - fake_library = tmpdir.mkdir('lib').join('libfoo.so') - fake_library.write('Other content.') - new_md5 = fs.hash_directory(str(tmpdir)) - - assert old_md5 != fs.hash_directory(str(tmpdir)) - assert new_md5 == fs.hash_directory(str(tmpdir)) - - -def test_move_transaction_rollback(tmpdir): - - fake_library = tmpdir.mkdir('lib').join('libfoo.so') - fake_library.write('Just some fake content.') - - h = fs.hash_directory(str(tmpdir)) - - try: - with fs.replace_directory_transaction(str(tmpdir.join('lib'))): - assert h != fs.hash_directory(str(tmpdir)) - fake_library = tmpdir.mkdir('lib').join('libfoo.so') - fake_library.write('Other content.') - raise RuntimeError('') - except RuntimeError: - pass - - assert h == fs.hash_directory(str(tmpdir)) diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py index f5fa8f32fd..ff280fc747 100644 --- a/var/spack/repos/builtin/packages/alglib/package.py +++ b/var/spack/repos/builtin/packages/alglib/package.py @@ -26,7 +26,6 @@ from spack import * import glob import os import sys -import shutil class Alglib(MakefilePackage): @@ -48,7 +47,7 @@ class Alglib(MakefilePackage): make_file_src = join_path(os.path.dirname(self.module.__file__), 'Makefile') make_file = join_path(self.stage.source_path, 'src', 'Makefile') - shutil.copy(make_file_src, make_file) + copy(make_file_src, make_file) filter_file(r'so', dso_suffix, make_file) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/arlecore/package.py b/var/spack/repos/builtin/packages/arlecore/package.py index 97d152d28c..31daa17f85 100644 --- a/var/spack/repos/builtin/packages/arlecore/package.py +++ b/var/spack/repos/builtin/packages/arlecore/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Arlecore(Package): @@ -37,4 +36,4 @@ class Arlecore(Package): depends_on('r', type=('build', 'run')) def install(self, spec, prefix): - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/atom-dft/package.py b/var/spack/repos/builtin/packages/atom-dft/package.py index d16d3283dc..644b064fb7 100644 --- a/var/spack/repos/builtin/packages/atom-dft/package.py +++ b/var/spack/repos/builtin/packages/atom-dft/package.py @@ -22,9 +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 ############################################################################## - from spack import * -import shutil class AtomDft(MakefilePackage): @@ -40,7 +38,7 @@ class AtomDft(MakefilePackage): depends_on('xmlf90') def edit(self, spec, prefix): - shutil.copyfile('arch.make.sample', 'arch.make') + copy('arch.make.sample', 'arch.make') @property def build_targets(self): diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py index c34376bac1..4907854a73 100644 --- a/var/spack/repos/builtin/packages/autodock-vina/package.py +++ b/var/spack/repos/builtin/packages/autodock-vina/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile -from shutil import copymode import sys @@ -66,7 +64,5 @@ class AutodockVina(MakefilePackage): def install(self, spec, prefix): with working_dir(self.build_directory): mkdirp(prefix.bin) - copyfile("vina", join_path(prefix.bin, "vina")) - copymode("vina", join_path(prefix.bin, "vina")) - copyfile("vina_split", join_path(prefix.bin, "vina_split")) - copymode("vina_split", join_path(prefix.bin, "vina_split")) + install('vina', prefix.bin) + install('vina_split', prefix.bin) diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py index b6e476b55c..eb86367fb0 100644 --- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py +++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py @@ -24,7 +24,6 @@ ############################################################################## from spack import * import os -import shutil import glob import llnl.util.tty as tty @@ -94,7 +93,7 @@ class Bcl2fastq2(Package): tty.msg("cwd sez: {0}".format(os.getcwd())) tarball = glob.glob(join_path('spack-expanded-archive', 'bcl2fastq2*.tar.gz'))[0] - shutil.move(tarball, '.') + copy(tarball, '.') os.rmdir('spack-expanded-archive') tar = which('tar') tarball = os.path.basename(tarball) diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py index ae43dff5f5..8ea38bf293 100644 --- a/var/spack/repos/builtin/packages/bioawk/package.py +++ b/var/spack/repos/builtin/packages/bioawk/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile -from shutil import copymode class Bioawk(MakefilePackage): @@ -45,7 +43,5 @@ class Bioawk(MakefilePackage): def install(self, spec, prefix): mkdirp(prefix.bin) - copyfile("bioawk", join_path(prefix.bin, "bioawk")) - copymode("bioawk", join_path(prefix.bin, "bioawk")) - copyfile("maketab", join_path(prefix.bin, "maketab")) - copymode("maketab", join_path(prefix.bin, "maketab")) + install('bioawk', prefix.bin) + install('maketab', prefix.bin) diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py index 30435af0e3..c72eba1b68 100644 --- a/var/spack/repos/builtin/packages/biopieces/package.py +++ b/var/spack/repos/builtin/packages/biopieces/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Biopieces(Package): @@ -79,7 +78,7 @@ class Biopieces(Package): depends_on('scan-for-matches') def install(self, spec, prefix): - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): # Note: user will need to set environment variables on their own, diff --git a/var/spack/repos/builtin/packages/casper/package.py b/var/spack/repos/builtin/packages/casper/package.py index 2a0f04b64d..1469ec68df 100644 --- a/var/spack/repos/builtin/packages/casper/package.py +++ b/var/spack/repos/builtin/packages/casper/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Casper(MakefilePackage): @@ -43,7 +42,7 @@ class Casper(MakefilePackage): conflicts('%gcc@7.1.0') def install(self, spec, prefix): - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): run_env.prepend_path('PATH', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/charm/package.py b/var/spack/repos/builtin/packages/charm/package.py index 4135fc8ca7..b4fc48ae9f 100644 --- a/var/spack/repos/builtin/packages/charm/package.py +++ b/var/spack/repos/builtin/packages/charm/package.py @@ -249,7 +249,7 @@ class Charm(Package): tmppath = filepath + ".tmp" # Skip dangling symbolic links try: - shutil.copy2(filepath, tmppath) + copy(filepath, tmppath) os.remove(filepath) os.rename(tmppath, filepath) except (IOError, OSError): diff --git a/var/spack/repos/builtin/packages/chlorop/package.py b/var/spack/repos/builtin/packages/chlorop/package.py index 96fdf70be4..96b348c840 100644 --- a/var/spack/repos/builtin/packages/chlorop/package.py +++ b/var/spack/repos/builtin/packages/chlorop/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util import os @@ -47,7 +46,7 @@ class Chlorop(Package): def install(self, spec, prefix): os.rename('chlorop', 'bin/chlorop') - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): run_env.set('CHLOROP', self.prefix) diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py index 74717b88d4..7136680c4b 100644 --- a/var/spack/repos/builtin/packages/chombo/package.py +++ b/var/spack/repos/builtin/packages/chombo/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import glob @@ -71,8 +70,8 @@ class Chombo(MakefilePackage): # Set remaining variables in Make.defs.local # Make.defs.local.template.patch ensures lines for USE_TIMER, # USE_LAPACK and lapackincflags are present - copyfile('./lib/mk/Make.defs.local.template', - './lib/mk/Make.defs.local') + copy('./lib/mk/Make.defs.local.template', + './lib/mk/Make.defs.local') defs_file = FileFilter('./lib/mk/Make.defs.local') diff --git a/var/spack/repos/builtin/packages/clapack/package.py b/var/spack/repos/builtin/packages/clapack/package.py index 73c4414d31..dd0076db43 100644 --- a/var/spack/repos/builtin/packages/clapack/package.py +++ b/var/spack/repos/builtin/packages/clapack/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Clapack(MakefilePackage): @@ -46,7 +45,7 @@ class Clapack(MakefilePackage): depends_on('atlas', when='+external-blas') def edit(self, spec, prefix): - install('make.inc.example', 'make.inc') + copy('make.inc.example', 'make.inc') if '+external-blas' in spec: make_inc = FileFilter('make.inc') make_inc.filter(r'^BLASLIB.*', @@ -60,4 +59,4 @@ class Clapack(MakefilePackage): make('lib') def install(self, spec, prefix): - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/codar-cheetah/package.py b/var/spack/repos/builtin/packages/codar-cheetah/package.py index c2754f5f8a..de9a12eb6e 100644 --- a/var/spack/repos/builtin/packages/codar-cheetah/package.py +++ b/var/spack/repos/builtin/packages/codar-cheetah/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class CodarCheetah(Package): @@ -42,4 +41,4 @@ class CodarCheetah(Package): depends_on('savanna') def install(self, spec, prefix): - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/comd/package.py b/var/spack/repos/builtin/packages/comd/package.py index 2aed00a924..baa9c89d59 100644 --- a/var/spack/repos/builtin/packages/comd/package.py +++ b/var/spack/repos/builtin/packages/comd/package.py @@ -22,9 +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 ############################################################################## - from spack import * -import shutil class Comd(MakefilePackage): @@ -58,7 +56,7 @@ class Comd(MakefilePackage): def edit(self, spec, prefix): with working_dir('src-mpi') or working_dir('src-openmp'): - shutil.copy('Makefile.vanilla', 'Makefile') + copy('Makefile.vanilla', 'Makefile') @property def build_targets(self): diff --git a/var/spack/repos/builtin/packages/cosp2/package.py b/var/spack/repos/builtin/packages/cosp2/package.py index 001206132a..5eb59d53e6 100644 --- a/var/spack/repos/builtin/packages/cosp2/package.py +++ b/var/spack/repos/builtin/packages/cosp2/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import shutil class Cosp2(MakefilePackage): @@ -62,7 +61,7 @@ class Cosp2(MakefilePackage): if '+double' in spec: filter_file('DOUBLE_PRECISION = O.*', 'DOUBLE_PRECISION = OFF', 'Makefile.vanilla') - shutil.copy('Makefile.vanilla', 'Makefile') + copy('Makefile.vanilla', 'Makefile') def install(self, spec, prefix): install_tree('bin/', prefix.bin) diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 4aa79a4592..52eecc61ed 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import shutil import copy from spack import * @@ -266,8 +265,7 @@ class Cp2k(Package): lib_dir = join_path('lib', cp2k_architecture, cp2k_version) mkdirp(lib_dir) try: - shutil.copy(env['LIBSMM_PATH'], - join_path(lib_dir, 'libsmm.a')) + copy(env['LIBSMM_PATH'], join_path(lib_dir, 'libsmm.a')) except KeyError: raise KeyError('Point environment variable LIBSMM_PATH to ' 'the absolute path of the libsmm.a file') @@ -315,4 +313,4 @@ class Cp2k(Package): 'VERSION={0}'.format(cp2k_version)) env['PWD'] = pwd_backup exe_dir = join_path('exe', cp2k_architecture) - shutil.copytree(exe_dir, self.prefix.bin) + install_tree(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 6286941b84..dfd2adb4eb 100644 --- a/var/spack/repos/builtin/packages/cppcheck/package.py +++ b/var/spack/repos/builtin/packages/cppcheck/package.py @@ -23,11 +23,9 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os -import shutil -class Cppcheck(Package): +class Cppcheck(MakefilePackage): """A tool for static C/C++ code analysis.""" homepage = "http://cppcheck.sourceforge.net/" url = "https://downloads.sourceforge.net/project/cppcheck/cppcheck/1.78/cppcheck-1.78.tar.bz2" @@ -41,12 +39,13 @@ class Cppcheck(Package): depends_on('py-pygments', when='+htmlreport', type='run') + def build(self, spec, prefix): + make('CFGDIR={0}'.format(prefix.cfg)) + def install(self, spec, prefix): - # cppcheck does not have a configure script - make("CFGDIR=%s" % os.path.join(prefix, 'cfg')) - # manually install the final cppcheck binary + # Manually install the final cppcheck binary mkdirp(prefix.bin) install('cppcheck', prefix.bin) - shutil.copytree('cfg', os.path.join(prefix, 'cfg')) + install_tree('cfg', prefix.cfg) if spec.satisfies('+htmlreport'): install('htmlreport/cppcheck-htmlreport', prefix.bin) diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py index 2752a1458f..a9958537c3 100644 --- a/var/spack/repos/builtin/packages/cudnn/package.py +++ b/var/spack/repos/builtin/packages/cudnn/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Cudnn(Package): @@ -40,4 +39,4 @@ class Cudnn(Package): depends_on('cuda@8:') def install(self, spec, prefix): - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/farmhash/package.py b/var/spack/repos/builtin/packages/farmhash/package.py index 23c9af82a4..a8aa8f2c9f 100644 --- a/var/spack/repos/builtin/packages/farmhash/package.py +++ b/var/spack/repos/builtin/packages/farmhash/package.py @@ -24,7 +24,6 @@ ############################################################################## from spack import * import os.path -from shutil import copyfile class Farmhash(CMakePackage): @@ -36,5 +35,5 @@ class Farmhash(CMakePackage): version('92e897', commit='92e897b282426729f4724d91a637596c7e2fe28f') def patch(self): - copyfile(join_path(os.path.dirname(__file__), "CMakeLists.txt"), - "CMakeLists.txt") + copy(join_path(os.path.dirname(__file__), "CMakeLists.txt"), + "CMakeLists.txt") diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py index 1b0eb876ae..c793713618 100644 --- a/var/spack/repos/builtin/packages/fastqc/package.py +++ b/var/spack/repos/builtin/packages/fastqc/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree, mkpath -from distutils.file_util import copy_file class Fastqc(Package): @@ -43,15 +41,15 @@ class Fastqc(Package): patch('fastqc.patch', level=0) def install(self, spec, prefix): - mkpath(self.prefix.bin) - mkpath(self.prefix.lib) - copy_file('fastqc', self.prefix.bin) + mkdir(prefix.bin) + mkdir(prefix.lib) + install('fastqc', prefix.bin) for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']: - copy_file(j, self.prefix.lib) + install(j, prefix.lib) for d in ['Configuration', 'net', 'org', 'Templates', 'uk']: - copy_tree(d, join_path(self.prefix.lib, d)) + install_tree(d, join_path(prefix.lib, d)) chmod = which('chmod') - chmod('+x', join_path(self.prefix.bin, 'fastqc')) + chmod('+x', prefix.bin.fastqc) # In theory the 'run' dependency on 'jdk' above should take # care of this for me. In practice, it does not. @@ -59,5 +57,4 @@ class Fastqc(Package): """Add <prefix> to the path; the package has a script at the top level. """ - run_env.prepend_path('PATH', join_path(self.spec['java'].prefix, - 'bin')) + run_env.prepend_path('PATH', self.spec['java'].prefix.bin) diff --git a/var/spack/repos/builtin/packages/fermisciencetools/package.py b/var/spack/repos/builtin/packages/fermisciencetools/package.py index bdac786766..556123dd09 100644 --- a/var/spack/repos/builtin/packages/fermisciencetools/package.py +++ b/var/spack/repos/builtin/packages/fermisciencetools/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Fermisciencetools(Package): @@ -42,4 +41,4 @@ class Fermisciencetools(Package): version('11r5p3', 'cf050ddddfe9251b6ebe8d3fd7de3c3f') def install(self, spec, prefix): - copy_tree('x86_64-unknown-linux-gnu-libc2.17', prefix) + install_tree('x86_64-unknown-linux-gnu-libc2.17', prefix) diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py index c14865622d..00d00db220 100644 --- a/var/spack/repos/builtin/packages/fsl/package.py +++ b/var/spack/repos/builtin/packages/fsl/package.py @@ -25,7 +25,6 @@ from spack import * from spack.environment import EnvironmentModifications import os -import distutils.dir_util class Fsl(Package): @@ -68,7 +67,7 @@ class Fsl(Package): build = Executable('./build') build() - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): if not self.stage.source_path: diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py index 8ca12f133a..f7ce7c1714 100644 --- a/var/spack/repos/builtin/packages/gatk/package.py +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import glob import os.path import re @@ -62,7 +61,7 @@ class Gatk(Package): # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "gatk.sh") script = join_path(prefix.bin, "gatk") - copyfile(script_sh, script) + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the diff --git a/var/spack/repos/builtin/packages/gaussian/package.py b/var/spack/repos/builtin/packages/gaussian/package.py index e928d475ad..c14c830b0e 100644 --- a/var/spack/repos/builtin/packages/gaussian/package.py +++ b/var/spack/repos/builtin/packages/gaussian/package.py @@ -24,7 +24,6 @@ ############################################################################## from spack import * import os -import shutil class Gaussian(Package): @@ -36,7 +35,7 @@ class Gaussian(Package): version('09', '7d4c95b535e68e48af183920df427e4e') def install(self, spec, prefix): - shutil.copytree(os.getcwd(), prefix.bin) + install_tree('.', prefix.bin) patch_install_files = ['flc', 'linda8.2/opteron-linux/bin/flc', 'linda8.2/opteron-linux/bin/LindaLauncher', diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 0bfcd26e2b..7bf95acb94 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -28,7 +28,6 @@ from llnl.util import tty import glob import os -import shutil import sys @@ -207,7 +206,7 @@ class Gcc(AutotoolsPackage): new_dispatch_dir = join_path(prefix, 'include', 'dispatch') mkdirp(new_dispatch_dir) new_header = join_path(new_dispatch_dir, 'object.h') - shutil.copyfile('/usr/include/dispatch/object.h', new_header) + install('/usr/include/dispatch/object.h', new_header) filter_file(r'typedef void \(\^dispatch_block_t\)\(void\)', 'typedef void* dispatch_block_t', new_header) diff --git a/var/spack/repos/builtin/packages/genomefinisher/package.py b/var/spack/repos/builtin/packages/genomefinisher/package.py index 7599c37505..2083c3b22b 100644 --- a/var/spack/repos/builtin/packages/genomefinisher/package.py +++ b/var/spack/repos/builtin/packages/genomefinisher/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import os @@ -49,13 +48,13 @@ class Genomefinisher(Package): # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "genomefinisher.sh") - script = join_path(prefix.bin, "genomefinisher") - copyfile(script_sh, script) + script = prefix.bin.genomefinisher + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the jar file # jar file. - java = join_path(self.spec['jdk'].prefix, 'bin', 'java') + java = spec['jdk'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file(jar_file, join_path(prefix.bin, jar_file), diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 7c3499bfe1..3e8a11d69e 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -24,7 +24,6 @@ ############################################################################## import sys from spack import * -from distutils.dir_util import copy_tree class Git(AutotoolsPackage): @@ -241,7 +240,7 @@ class Git(AutotoolsPackage): @run_after('install') def install_completions(self): - copy_tree('contrib/completion', self.prefix.share) + install_tree('contrib/completion', self.prefix.share) @run_after('install') def install_manpages(self): diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 6a004d8e64..87a0286950 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -25,7 +25,6 @@ from spack import * import os.path -import shutil class Glib(AutotoolsPackage): @@ -117,7 +116,7 @@ class Glib(AutotoolsPackage): dtrace_copy = join_path(self.dtrace_copy_path, 'dtrace') with working_dir(self.dtrace_copy_path, create=True): - shutil.copy(dtrace, dtrace_copy) + copy(dtrace, dtrace_copy) filter_file( '^#!/usr/bin/python', '#!/usr/bin/env python', diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py index c7794a40e9..730f423d55 100644 --- a/var/spack/repos/builtin/packages/go-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/go-bootstrap/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 os -import shutil -import glob from spack import * # THIS PACKAGE SHOULD NOT EXIST @@ -75,15 +72,7 @@ class GoBootstrap(Package): with working_dir('src'): bash('{0}.bash'.format('all' if self.run_tests else 'make')) - try: - os.makedirs(prefix) - except OSError: - pass - for f in glob.glob('*'): - if os.path.isdir(f): - shutil.copytree(f, os.path.join(prefix, f)) - else: - shutil.copy2(f, os.path.join(prefix, f)) + install_tree('.', prefix) def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('GOROOT_BOOTSTRAP', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index e7c96af8af..48055f7722 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import shutil -import glob import llnl.util.tty as tty from spack import * @@ -101,15 +99,7 @@ class Go(Package): with working_dir('src'): bash('{0}.bash'.format('all' if self.run_tests else 'make')) - try: - os.makedirs(prefix) - except OSError: - pass - for f in glob.glob('*'): - if os.path.isdir(f): - shutil.copytree(f, os.path.join(prefix, f)) - else: - shutil.copy2(f, os.path.join(prefix, f)) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): spack_env.set('GOROOT_FINAL', self.spec.prefix) @@ -123,10 +113,9 @@ class Go(Package): In most cases, extensions will only need to set GOPATH and use go:: - env = os.environ env['GOPATH'] = self.source_path + ':' + env['GOPATH'] go('get', '<package>', env=env) - shutil.copytree('bin', os.path.join(prefix, '/bin')) + install_tree('bin', prefix.bin) """ # Add a go command/compiler for extensions module.go = self.spec['go'].command diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py index e88041dd8b..0df3f3bf81 100644 --- a/var/spack/repos/builtin/packages/grackle/package.py +++ b/var/spack/repos/builtin/packages/grackle/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os.path -import shutil import inspect from spack import * @@ -78,7 +77,7 @@ class Grackle(Package): 'clib', 'Make.mach.{0}'.format(grackle_architecture) ) - shutil.copy(template, makefile) + copy(template, makefile) for key, value in substitutions.items(): filter_file(key, value, makefile) diff --git a/var/spack/repos/builtin/packages/gradle/package.py b/var/spack/repos/builtin/packages/gradle/package.py index 055aac845f..f7ad851e9f 100644 --- a/var/spack/repos/builtin/packages/gradle/package.py +++ b/var/spack/repos/builtin/packages/gradle/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Gradle(Package): @@ -81,4 +80,4 @@ class Gradle(Package): depends_on('java') def install(self, spec, prefix): - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/gurobi/package.py b/var/spack/repos/builtin/packages/gurobi/package.py index aebb6bf6c6..9720313b7e 100644 --- a/var/spack/repos/builtin/packages/gurobi/package.py +++ b/var/spack/repos/builtin/packages/gurobi/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree import os @@ -58,5 +57,4 @@ class Gurobi(Package): run_env.set('GUROBI_HOME', self.prefix) def install(self, spec, prefix): - with working_dir('linux64'): - copy_tree('.', prefix) + install_tree('linux64', prefix) diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py index b0ff9536c7..0e0d6dd352 100644 --- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py +++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py @@ -34,13 +34,13 @@ def _install_shlib(name, src, dst): if sys.platform == "darwin": shlib0 = name + ".0.dylib" shlib = name + ".dylib" - shutil.copyfile(join_path(src, shlib0), join_path(dst, shlib0)) + install(join_path(src, shlib0), join_path(dst, shlib0)) os.symlink(shlib0, join_path(dst, shlib)) else: shlib000 = name + ".so.0.0.0" shlib0 = name + ".so.0" shlib = name + ".dylib" - shutil.copyfile(join_path(src, shlib000), join_path(dst, shlib000)) + install(join_path(src, shlib000), join_path(dst, shlib000)) os.symlink(shlib000, join_path(dst, shlib0)) os.symlink(shlib0, join_path(dst, shlib)) diff --git a/var/spack/repos/builtin/packages/igvtools/package.py b/var/spack/repos/builtin/packages/igvtools/package.py index 03e8dee653..410a409d63 100644 --- a/var/spack/repos/builtin/packages/igvtools/package.py +++ b/var/spack/repos/builtin/packages/igvtools/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import os @@ -47,13 +46,13 @@ class Igvtools(Package): # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "igvtools.sh") - script = join_path(prefix.bin, "igvtools") - copyfile(script_sh, script) + script = prefix.bin.igvtools + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['jdk'].prefix, 'bin', 'java') + java = spec['jdk'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file(jar_file, join_path(prefix.bin, jar_file), diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index b39c32bc07..f6f78b9501 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -25,7 +25,6 @@ # # Author: Justin Too <too1@llnl.gov> # -import distutils.dir_util from spack import * @@ -72,7 +71,7 @@ class Jdk(Package): return url.format(version, minor_version) def install(self, spec, prefix): - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): run_env.set('JAVA_HOME', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/jmol/package.py b/var/spack/repos/builtin/packages/jmol/package.py index eda8dbe877..cd9cbf1c83 100644 --- a/var/spack/repos/builtin/packages/jmol/package.py +++ b/var/spack/repos/builtin/packages/jmol/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Jmol(Package): @@ -38,7 +37,7 @@ class Jmol(Package): depends_on('java', type='run') def install(self, spec, prefix): - copy_tree('jmol-{0}'.format(self.version), prefix) + install_tree('jmol-{0}'.format(self.version), prefix) def setup_environment(self, spack_env, run_env): run_env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/kaldi/package.py b/var/spack/repos/builtin/packages/kaldi/package.py index 69981c85ca..7dbe7d9a3b 100644 --- a/var/spack/repos/builtin/packages/kaldi/package.py +++ b/var/spack/repos/builtin/packages/kaldi/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree from os.path import join from fnmatch import fnmatch import os @@ -105,7 +104,7 @@ class Kaldi(Package): # Does not use Autotools install(join(root, name), prefix.bin) mkdir(prefix.lib) - copy_tree('lib', prefix.lib) + install_tree('lib', prefix.lib) for root, dirs, files in os.walk('.'): for name in files: diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py index cf66732170..75b7b9411e 100644 --- a/var/spack/repos/builtin/packages/leveldb/package.py +++ b/var/spack/repos/builtin/packages/leveldb/package.py @@ -26,7 +26,7 @@ import glob from spack import * -class Leveldb(Package): +class Leveldb(MakefilePackage): """LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.""" @@ -39,21 +39,14 @@ class Leveldb(Package): depends_on("snappy") def install(self, spec, prefix): - make() + mkdirp(prefix.lib.pkgconfig) - mkdirp(prefix.include) - mkdirp(prefix.lib) - mkdirp(join_path(prefix.lib, 'pkgconfig')) + libraries = glob.glob('out-shared/libleveldb.*') + libraries += glob.glob('out-static/libleveldb.*') + for library in libraries: + install(library, prefix.lib) - cp = which('cp') - - # cp --preserve=links libleveldb.* prefix/lib - args = glob.glob('out-shared/libleveldb.*') \ - + glob.glob('out-static/libleveldb.*') - args.append(prefix.lib) - cp('--preserve=links', *args) - - cp('-r', 'include/leveldb', prefix.include) + install_tree('include/leveldb', prefix.include) with open(join_path(prefix.lib, 'pkgconfig', 'leveldb.pc'), 'w') as f: f.write('prefix={0}\n'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/libgridxc/package.py b/var/spack/repos/builtin/packages/libgridxc/package.py index 42a2a05517..f2db4ab13f 100644 --- a/var/spack/repos/builtin/packages/libgridxc/package.py +++ b/var/spack/repos/builtin/packages/libgridxc/package.py @@ -22,9 +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 ############################################################################## - from spack import * -import shutil class Libgridxc(Package): @@ -42,7 +40,7 @@ class Libgridxc(Package): sh = which('sh') with working_dir('build', create=True): sh('../src/config.sh') - shutil.copyfile('../extra/fortran.mk', 'fortran.mk') + copy('../extra/fortran.mk', 'fortran.mk') def install(self, spec, prefix): with working_dir('build'): diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py index df57201d7e..d9ff4a251a 100644 --- a/var/spack/repos/builtin/packages/libiconv/package.py +++ b/var/spack/repos/builtin/packages/libiconv/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import shutil class Libiconv(AutotoolsPackage): @@ -46,6 +45,6 @@ class Libiconv(AutotoolsPackage): args = ['--enable-extra-encodings'] # A hack to patch config.guess in the libcharset sub directory - shutil.copyfile('./build-aux/config.guess', - 'libcharset/build-aux/config.guess') + copy('./build-aux/config.guess', + 'libcharset/build-aux/config.guess') return args diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 2ecd61d75a..3be612fecc 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -504,10 +504,9 @@ class Llvm(CMakePackage): if not self.spec.satisfies('+lldb platform=darwin'): return codesign = which('codesign') - cp = which('cp') mkdir('tmp') llvm_check_file = join_path('tmp', 'llvm_check') - cp('/usr/bin/false', llvm_check_file) + copy('/usr/bin/false', llvm_check_file) try: codesign('-f', '-s', 'lldb_codesign', '--dryrun', diff --git a/var/spack/repos/builtin/packages/masurca/package.py b/var/spack/repos/builtin/packages/masurca/package.py index 9c35f45657..a1786cd7f3 100644 --- a/var/spack/repos/builtin/packages/masurca/package.py +++ b/var/spack/repos/builtin/packages/masurca/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Masurca(Package): @@ -44,4 +43,4 @@ class Masurca(Package): def install(self, spec, prefix): installer = Executable('./install.sh') installer() - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/maven/package.py b/var/spack/repos/builtin/packages/maven/package.py index aef6ddeaee..abd4cca16c 100644 --- a/var/spack/repos/builtin/packages/maven/package.py +++ b/var/spack/repos/builtin/packages/maven/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Maven(Package): @@ -39,4 +38,4 @@ class Maven(Package): def install(self, spec, prefix): # install pre-built distribution - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/mefit/package.py b/var/spack/repos/builtin/packages/mefit/package.py index cbd05eb656..61e74dfbbe 100644 --- a/var/spack/repos/builtin/packages/mefit/package.py +++ b/var/spack/repos/builtin/packages/mefit/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Mefit(Package): @@ -41,7 +40,7 @@ class Mefit(Package): depends_on('casper %gcc@4.8.5') def install(self, spec, prefix): - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): run_env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 9e26473f21..7d76ee8db9 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -440,7 +440,7 @@ class Mfem(Package): # installed shared mfem library: with working_dir('config'): os.rename('config.mk', 'config.mk.orig') - shutil.copyfile(str(self.config_mk), 'config.mk') + copy(str(self.config_mk), 'config.mk') shutil.copystat('config.mk.orig', 'config.mk') if '+examples' in spec: diff --git a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py index f72b0fff4f..57cb59eb20 100644 --- a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py +++ b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py @@ -23,10 +23,9 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree -class MpixLaunchSwift(Package): +class MpixLaunchSwift(MakefilePackage): """Library that allows a child MPI application to be launched inside a subset of processes in a parent MPI application. """ @@ -42,5 +41,4 @@ class MpixLaunchSwift(Package): depends_on('swig', type='build') def install(self, spec, prefix): - make() - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/mrtrix3/package.py b/var/spack/repos/builtin/packages/mrtrix3/package.py index a61a19cc4c..26b083daf5 100644 --- a/var/spack/repos/builtin/packages/mrtrix3/package.py +++ b/var/spack/repos/builtin/packages/mrtrix3/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Mrtrix3(Package): @@ -53,9 +52,7 @@ class Mrtrix3(Package): build = Executable('./build') configure() build() - # install_tree('.', prefix) does not work since the prefix - # directory already exists by this point - distutils.dir_util.copy_tree('.', prefix) + install_tree('.', prefix) def setup_environment(self, spac_env, run_env): run_env.prepend_path('PATH', self.prefix) diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py index 837ae1a5c8..6179cacd84 100644 --- a/var/spack/repos/builtin/packages/namd/package.py +++ b/var/spack/repos/builtin/packages/namd/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import platform -import shutil import sys import os from spack import * @@ -58,8 +57,8 @@ class Namd(MakefilePackage): def _copy_arch_file(self, lib): config_filename = 'arch/{0}.{1}'.format(self.arch, lib) - shutil.copy('arch/Linux-x86_64.{0}'.format(lib), - config_filename) + copy('arch/Linux-x86_64.{0}'.format(lib), + config_filename) if lib == 'tcl': filter_file(r'-ltcl8\.5', '-ltcl{0}'.format(self.spec['tcl'].version.up_to(2)), diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py index 573acb664c..218fc31eb9 100644 --- a/var/spack/repos/builtin/packages/ncl/package.py +++ b/var/spack/repos/builtin/packages/ncl/package.py @@ -25,7 +25,6 @@ from spack import * import glob import os -import shutil import tempfile @@ -263,8 +262,8 @@ class Ncl(Package): triangle_src = join_path(self.stage.source_path, 'triangle_src') triangle_dst = join_path(self.stage.source_path, 'ni', 'src', 'lib', 'hlu') - shutil.copy(join_path(triangle_src, 'triangle.h'), triangle_dst) - shutil.copy(join_path(triangle_src, 'triangle.c'), triangle_dst) + copy(join_path(triangle_src, 'triangle.h'), triangle_dst) + copy(join_path(triangle_src, 'triangle.c'), triangle_dst) @staticmethod def delete_files(*filenames): diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index c54cbcd71f..cc1b6a7287 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -26,7 +26,6 @@ from spack import * from glob import glob from os.path import exists, join from os import makedirs -from shutil import copy class Ncurses(AutotoolsPackage): @@ -109,7 +108,7 @@ class Ncurses(AutotoolsPackage): if not exists(path): makedirs(path) for header in headers: - copy(header, path) + install(header, path) @property def libs(self): diff --git a/var/spack/repos/builtin/packages/occa/package.py b/var/spack/repos/builtin/packages/occa/package.py index a27d3c6b34..ff9285518e 100644 --- a/var/spack/repos/builtin/packages/occa/package.py +++ b/var/spack/repos/builtin/packages/occa/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os -import shutil class Occa(Package): @@ -63,12 +61,7 @@ class Occa(Package): def install(self, spec, prefix): # The build environment is set by the 'setup_environment' method. # Copy the source to the installation directory and build OCCA there. - for file in os.listdir('.'): - dest = join_path(prefix, os.path.basename(file)) - if os.path.isdir(file): - shutil.copytree(file, dest) - else: - shutil.copy2(file, dest) + install_tree('.', prefix) make('-C', prefix) if self.run_tests: diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py index c730d34756..931f951a09 100644 --- a/var/spack/repos/builtin/packages/pexsi/package.py +++ b/var/spack/repos/builtin/packages/pexsi/package.py @@ -25,7 +25,6 @@ import inspect import os.path -import shutil from spack import * @@ -99,7 +98,7 @@ class Pexsi(MakefilePackage): self.stage.source_path, 'make.inc' ) - shutil.copy(template, makefile) + copy(template, makefile) for key, value in substitutions: filter_file(key, value, makefile) diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py index cca0ae2f7b..6cab04e592 100644 --- a/var/spack/repos/builtin/packages/picard/package.py +++ b/var/spack/repos/builtin/packages/picard/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import glob import os.path import re @@ -69,13 +68,13 @@ class Picard(Package): # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "picard.sh") - script = join_path(prefix.bin, "picard") - copyfile(script_sh, script) + script = prefix.bin.picard + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['java'].prefix, 'bin', 'java') + java = self.spec['java'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'), diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py index 8fba2c2376..0fec636fba 100644 --- a/var/spack/repos/builtin/packages/pilon/package.py +++ b/var/spack/repos/builtin/packages/pilon/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import os.path @@ -47,13 +46,13 @@ class Pilon(Package): # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "pilon.sh") - script = join_path(prefix.bin, "pilon") - copyfile(script_sh, script) + script = prefix.bin.pilon + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['java'].prefix, 'bin', 'java') + java = self.spec['java'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file('pilon-{0}.jar', join_path(prefix.bin, jar_file), diff --git a/var/spack/repos/builtin/packages/pindel/package.py b/var/spack/repos/builtin/packages/pindel/package.py index 479128707b..d0acc28472 100644 --- a/var/spack/repos/builtin/packages/pindel/package.py +++ b/var/spack/repos/builtin/packages/pindel/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copytree, copyfile class Pindel(MakefilePackage): @@ -51,9 +50,8 @@ class Pindel(MakefilePackage): # def edit(self, spec, prefix): - makefile2 = join_path(self.build_directory, 'Makefile2') - copyfile(join_path(self.build_directory, 'Makefile'), makefile2) - myedit = FileFilter(makefile2) + copy('Makefile', 'Makefile2') + myedit = FileFilter('Makefile2') myedit.filter('-include Makefile.local', '#removed include') myedit.filter('@false', '#removed autofailure') @@ -69,6 +67,4 @@ class Pindel(MakefilePackage): install('src/pindel2vcf', prefix.bin) install('src/sam2pindel', prefix.bin) install('src/pindel2vcf4tcga', prefix.bin) - copytree(join_path(self.build_directory, 'demo'), - prefix.doc, - symlinks=True) + install_tree('demo', prefix.doc) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 94e6b61bd4..5b8c7e94e3 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -27,7 +27,6 @@ import os import platform import re import sys -import shutil import llnl.util.tty as tty from llnl.util.lang import match_predicate @@ -709,7 +708,7 @@ class Python(AutotoolsPackage): if not path_contains_subdirectory(src, bin_dir): view.link(src, dst) elif not os.path.islink(src): - shutil.copy2(src, dst) + copy(src, dst) if 'script' in get_filetype(src): filter_file( self.spec.prefix, os.path.abspath(view.root), dst) diff --git a/var/spack/repos/builtin/packages/qbox/package.py b/var/spack/repos/builtin/packages/qbox/package.py index 19d83773a8..805a567e55 100644 --- a/var/spack/repos/builtin/packages/qbox/package.py +++ b/var/spack/repos/builtin/packages/qbox/package.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 shutil from spack import * @@ -88,6 +86,6 @@ class Qbox(MakefilePackage): def install(self, spec, prefix): mkdir(prefix.src) install('src/qb', prefix.src) - shutil.move('test', prefix) - shutil.move('xml', prefix) - shutil.move('util', prefix) + install_tree('test', prefix) + install_tree('xml', prefix) + install_tree('util', prefix) diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py index bb71f15b8f..7e745dc304 100644 --- a/var/spack/repos/builtin/packages/qorts/package.py +++ b/var/spack/repos/builtin/packages/qorts/package.py @@ -24,7 +24,6 @@ ############################################################################## from spack import * import os.path -from shutil import copyfile class Qorts(RPackage): @@ -59,7 +58,7 @@ class Qorts(RPackage): # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh") script = self.prefix.bin.QoRTs - copyfile(script_sh, script) + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index 6ae13af9f5..52d11f5bbb 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import shutil from spack import * @@ -142,7 +141,7 @@ class R(AutotoolsPackage): # dependencies in Spack. src_makeconf = join_path(self.etcdir, 'Makeconf') dst_makeconf = join_path(self.etcdir, 'Makeconf.spack') - shutil.copy(src_makeconf, dst_makeconf) + install(src_makeconf, dst_makeconf) # ======================================================================== # Set up environment to make install easy for R extensions. diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index 72aa492f3d..6177bb5710 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -24,7 +24,6 @@ ############################################################################## from spack import * import inspect -import distutils.dir_util class Repeatmasker(Package): @@ -78,4 +77,4 @@ class Repeatmasker(Package): with open(config_answers_filename, 'r') as f: inspect.getmodule(self).perl('configure', input=f) - distutils.dir_util.copy_tree(".", prefix.bin) + install_tree('.', prefix.bin) diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py index 9fe5bcc096..cc58cb7e0e 100644 --- a/var/spack/repos/builtin/packages/rna-seqc/package.py +++ b/var/spack/repos/builtin/packages/rna-seqc/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import os.path @@ -51,12 +50,12 @@ class RnaSeqc(Package): # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "rna-seqc.sh") script = join_path(prefix.bin, "rna-seqc") - copyfile(script_sh, script) + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['jdk'].prefix, 'bin', 'java') + java = self.spec['jdk'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file), diff --git a/var/spack/repos/builtin/packages/rockstar/package.py b/var/spack/repos/builtin/packages/rockstar/package.py index f77403495f..ba4134f731 100644 --- a/var/spack/repos/builtin/packages/rockstar/package.py +++ b/var/spack/repos/builtin/packages/rockstar/package.py @@ -22,10 +22,8 @@ # 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 distutils.dir_util import copy_tree class Rockstar(MakefilePackage): @@ -59,7 +57,7 @@ class Rockstar(MakefilePackage): def install(self, spec, prefix): # Install all files and directories - copy_tree(".", prefix) + install_tree('.', prefix) mkdir(prefix.bin) mkdir(prefix.lib) diff --git a/var/spack/repos/builtin/packages/savanna/package.py b/var/spack/repos/builtin/packages/savanna/package.py index 1e5ea83f5b..126c79a5ba 100644 --- a/var/spack/repos/builtin/packages/savanna/package.py +++ b/var/spack/repos/builtin/packages/savanna/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Savanna(MakefilePackage): @@ -46,4 +45,4 @@ class Savanna(MakefilePackage): depends_on('tau', when='+tau') def install(self, spec, prefix): - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/sbt/package.py b/var/spack/repos/builtin/packages/sbt/package.py index d5eecc145c..5ad2bd2745 100644 --- a/var/spack/repos/builtin/packages/sbt/package.py +++ b/var/spack/repos/builtin/packages/sbt/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import shutil class Sbt(Package): @@ -40,5 +39,5 @@ class Sbt(Package): depends_on('java') def install(self, spec, prefix): - shutil.copytree('bin', join_path(prefix, 'bin'), symlinks=True) - shutil.copytree('conf', join_path(prefix, 'conf'), symlinks=True) + install_tree('bin', prefix.bin) + install_tree('conf', prefix.conf) diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py index 7ec0a5351e..8fc0ecd489 100644 --- a/var/spack/repos/builtin/packages/scr/package.py +++ b/var/spack/repos/builtin/packages/scr/package.py @@ -25,7 +25,6 @@ from spack import * import os -import shutil class Scr(CMakePackage): @@ -151,4 +150,4 @@ class Scr(CMakePackage): if spec.variants['copy_config'].value: dest_path = self.get_abs_path_rel_prefix( spec.variants['scr_config'].value) - shutil.copyfile(spec.variants['copy_config'].value, dest_path) + install(spec.variants['copy_config'].value, dest_path) diff --git a/var/spack/repos/builtin/packages/sctk/package.py b/var/spack/repos/builtin/packages/sctk/package.py index 089b8c04fc..97326572ff 100644 --- a/var/spack/repos/builtin/packages/sctk/package.py +++ b/var/spack/repos/builtin/packages/sctk/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Sctk(Package): @@ -49,5 +48,4 @@ class Sctk(Package): make('config') make('all') make('install') - mkdirp(prefix.bin) - copy_tree('bin', prefix.bin) + install_tree('bin', prefix.bin) diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py index 44652ccee0..2d8c7900ce 100644 --- a/var/spack/repos/builtin/packages/snpeff/package.py +++ b/var/spack/repos/builtin/packages/snpeff/package.py @@ -24,7 +24,6 @@ ############################################################################## from spack import * import os.path -from shutil import copyfile class Snpeff(Package): @@ -45,13 +44,13 @@ class Snpeff(Package): # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "snpEff.sh") - script = join_path(prefix.bin, "snpEff") - copyfile(script_sh, script) + script = prefix.bin.snpEff + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['java'].prefix.bin, 'java') + java = self.spec['java'].prefix.bin.java kwargs = {'backup': False} filter_file('^java', java, script, **kwargs) filter_file('snpEff.jar', join_path(prefix.bin, 'snpEff.jar'), diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py index 2add84ad26..5066b41e28 100644 --- a/var/spack/repos/builtin/packages/snphylo/package.py +++ b/var/spack/repos/builtin/packages/snphylo/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import distutils.dir_util class Snphylo(Package): @@ -51,7 +50,7 @@ class Snphylo(Package): with open(install_answer_input, 'r') as f: bash = which('bash') bash('./setup.sh', input=f) - distutils.dir_util.copy_tree(".", prefix) + install_tree('.', prefix) def setup_environment(self, spack_env, run_env): run_env.prepend_path('PATH', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py index 7cdd6b175f..1b318e8c78 100644 --- a/var/spack/repos/builtin/packages/spark/package.py +++ b/var/spack/repos/builtin/packages/spark/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import re -import shutil from spack import * @@ -64,7 +63,7 @@ class Spark(Package): install_dir('yarn') # required for spark to recognize binary distribution - shutil.copy('RELEASE', prefix) + install('RELEASE', prefix) @when('+hadoop') def setup_environment(self, spack_env, run_env): diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py index dad8ca0db4..83dd2f380b 100644 --- a/var/spack/repos/builtin/packages/sublime-text/package.py +++ b/var/spack/repos/builtin/packages/sublime-text/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class SublimeText(Package): @@ -57,4 +56,4 @@ class SublimeText(Package): def install(self, spec, prefix): # Sublime text comes as a pre-compiled binary. - copy_tree('.', prefix) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/supernova/package.py b/var/spack/repos/builtin/packages/supernova/package.py index 3e6ac97bc2..f358dd4939 100644 --- a/var/spack/repos/builtin/packages/supernova/package.py +++ b/var/spack/repos/builtin/packages/supernova/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree import os @@ -62,4 +61,4 @@ class Supernova(Package): # remove the broken symlinks rm('anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtcl.so', 'anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtk.so') - copy_tree('.', prefix, preserve_symlinks=1) + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py index e3d7629e1a..858a0d5eba 100644 --- a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py +++ b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os -import shutil class ThePlatinumSearcher(Package): @@ -38,7 +36,6 @@ class ThePlatinumSearcher(Package): extends("go", deptypes='build') def install(self, spec, prefix): - env = os.environ env['GOPATH'] = self.stage.source_path + ':' + env['GOPATH'] go('install', self.package, env=env) - shutil.copytree('bin', os.path.join(prefix, 'bin')) + install_tree('bin', prefix.bin) diff --git a/var/spack/repos/builtin/packages/tinyxml/package.py b/var/spack/repos/builtin/packages/tinyxml/package.py index e34315882f..afd3c7f6b5 100644 --- a/var/spack/repos/builtin/packages/tinyxml/package.py +++ b/var/spack/repos/builtin/packages/tinyxml/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile import os.path @@ -42,8 +41,8 @@ class Tinyxml(CMakePackage): return url.format(version.dotted, version.underscored) def patch(self): - copyfile(join_path(os.path.dirname(__file__), - "CMakeLists.txt"), "CMakeLists.txt") + copy(join_path(os.path.dirname(__file__), + "CMakeLists.txt"), "CMakeLists.txt") def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/trimmomatic/package.py b/var/spack/repos/builtin/packages/trimmomatic/package.py index 470ba69def..41459502ae 100644 --- a/var/spack/repos/builtin/packages/trimmomatic/package.py +++ b/var/spack/repos/builtin/packages/trimmomatic/package.py @@ -23,8 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree -from shutil import copyfile import os.path @@ -47,18 +45,18 @@ class Trimmomatic(Package): install(jar_file, prefix.bin) # Put the adapter files someplace sensible - copy_tree('adapters', join_path(self.prefix.share, 'adapters')) + install_tree('adapters', prefix.share.adapters) # Set up a helper script to call java on the jar file, # explicitly codes the path for java and the jar file. script_sh = join_path(os.path.dirname(__file__), "trimmomatic.sh") - script = join_path(prefix.bin, "trimmomatic") - copyfile(script_sh, script) + script = prefix.bin.trimmomatic + install(script_sh, script) set_executable(script) # Munge the helper script to explicitly point to java and the # jar file. - java = join_path(self.spec['java'].prefix, 'bin', 'java') + java = self.spec['java'].prefix.bin.java kwargs = {'ignore_absent': False, 'backup': False, 'string': False} filter_file('^java', java, script, **kwargs) filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file), diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index eab36f9ae4..5daad5e02f 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from distutils.dir_util import copy_tree class Trinity(MakefilePackage): @@ -59,7 +58,7 @@ class Trinity(MakefilePackage): make("plugins") def install(self, spec, prefix): - copy_tree('.', prefix.bin, preserve_symlinks=1) + install_tree('.', prefix.bin) force_remove(join_path(prefix.bin, '.gitmodules')) force_remove(join_path(prefix.bin, 'Butterfly', '.err')) force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath')) diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py index 60dcd21fff..f8b7b9adfc 100644 --- a/var/spack/repos/builtin/packages/wannier90/package.py +++ b/var/spack/repos/builtin/packages/wannier90/package.py @@ -24,7 +24,6 @@ ############################################################################## import inspect import os.path -import shutil from spack import * @@ -77,7 +76,7 @@ class Wannier90(MakefilePackage): 'make.sys' ) - shutil.copy(template, self.makefile_name) + copy(template, self.makefile_name) for key, value in substitutions.items(): filter_file(key, value, self.makefile_name) diff --git a/var/spack/repos/builtin/packages/workrave/package.py b/var/spack/repos/builtin/packages/workrave/package.py index 76434acad3..a11fd9523e 100644 --- a/var/spack/repos/builtin/packages/workrave/package.py +++ b/var/spack/repos/builtin/packages/workrave/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -from shutil import copyfile class Workrave(AutotoolsPackage): @@ -102,4 +101,4 @@ class Workrave(AutotoolsPackage): for fname in self.m4files: src = '%s/%s/%s.m4' % (self.stage.source_path, fname, fname) dest = '%s/m4/%s.m4' % (self.stage.source_path, fname) - copyfile(src, dest) + copy(src, dest) diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py index 2f4a3a349e..63ba54761e 100644 --- a/var/spack/repos/builtin/packages/yorick/package.py +++ b/var/spack/repos/builtin/packages/yorick/package.py @@ -24,8 +24,6 @@ ############################################################################## from spack import * import os -import shutil -import glob class Yorick(Package): @@ -74,13 +72,4 @@ class Yorick(Package): make() make("install") - try: - os.makedirs(prefix) - except OSError: - pass - os.chdir("relocate") - for f in glob.glob('*'): - if os.path.isdir(f): - shutil.copytree(f, os.path.join(prefix, f)) - else: - shutil.copy2(f, os.path.join(prefix, f)) + install_tree('relocate', prefix) |