install_tree, copy_tree can install into existing directory structures (#8289)
Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`. - `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory. - `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory. - `install` and `copy` are analogous single-file functions. - add more extensive tests for these functions - update packages to use these functions.
This commit is contained in:
Adam J. Stewart
Todd Gamblin
parent
c0699539d5
commit
73c978ddd9
82 changed files with 422 additions and 344 deletions
|
|
@ -60,7 +60,9 @@
|
|||
'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_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 install(src, dest):
|
||||
"""Installs the file *src* to the file or directory *dest*.
|
||||
|
||||
for s, d in traverse_tree(src, dest, follow_nonexisting=False):
|
||||
set_install_permissions(d)
|
||||
copy_mode(s, d)
|
||||
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 copy_tree(src, dest, symlinks=True, _permissions=False):
|
||||
"""Recursively copy an entire directory tree rooted at *src*.
|
||||
|
||||
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):
|
||||
|
|
|
|||
209
lib/spack/spack/test/llnl/util/filesystem.py
Normal file
209
lib/spack/spack/test/llnl/util/filesystem.py
Normal file
|
|
@ -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))
|
||||
|
|
@ -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))
|
||||
|
|
@ -26,7 +26,6 @@
|
|||
import glob
|
||||
import os
|
||||
import sys
|
||||
import shutil
|
||||
|
||||
|
||||
class Alglib(MakefilePackage):
|
||||
|
|
@ -48,7 +47,7 @@ def edit(self, spec, prefix):
|
|||
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):
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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):
|
||||
|
|
|
|||
|
|
@ -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 @@ def build(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -24,7 +24,6 @@
|
|||
##############################################################################
|
||||
from spack import *
|
||||
import os
|
||||
import shutil
|
||||
import glob
|
||||
import llnl.util.tty as tty
|
||||
|
||||
|
|
@ -94,7 +93,7 @@ def wrap():
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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,
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -249,7 +249,7 @@ def install(self, spec, prefix):
|
|||
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):
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def edit(self, spec, prefix):
|
|||
# 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')
|
||||
|
||||
|
|
|
|||
|
|
@ -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 @@ def build(self, spec, prefix):
|
|||
make('lib')
|
||||
|
||||
def install(self, spec, prefix):
|
||||
copy_tree('.', prefix)
|
||||
install_tree('.', prefix)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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):
|
||||
|
|
|
|||
|
|
@ -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 @@ def edit(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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 @@ def install(self, spec, prefix):
|
|||
'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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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")
|
||||
|
|
|
|||
|
|
@ -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 @@ def setup_environment(self, spack_env, run_env):
|
|||
"""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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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:
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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
|
||||
|
|
|
|||
|
|
@ -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',
|
||||
|
|
|
|||
|
|
@ -28,7 +28,6 @@
|
|||
|
||||
import glob
|
||||
import os
|
||||
import shutil
|
||||
import sys
|
||||
|
||||
|
||||
|
|
@ -207,7 +206,7 @@ def patch(self):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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),
|
||||
|
|
|
|||
|
|
@ -24,7 +24,6 @@
|
|||
##############################################################################
|
||||
import sys
|
||||
from spack import *
|
||||
from distutils.dir_util import copy_tree
|
||||
|
||||
|
||||
class Git(AutotoolsPackage):
|
||||
|
|
@ -241,7 +240,7 @@ def check(self):
|
|||
|
||||
@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):
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@
|
|||
from spack import *
|
||||
|
||||
import os.path
|
||||
import shutil
|
||||
|
||||
|
||||
class Glib(AutotoolsPackage):
|
||||
|
|
@ -117,7 +116,7 @@ def fix_dtrace_usr_bin_path(self):
|
|||
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',
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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 @@ def setup_dependent_package(self, module, dependent_spec):
|
|||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
'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)
|
||||
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def setup_environment(self, spack_env, run_env):
|
|||
run_env.set('GUROBI_HOME', self.prefix)
|
||||
|
||||
def install(self, spec, prefix):
|
||||
with working_dir('linux64'):
|
||||
copy_tree('.', prefix)
|
||||
install_tree('linux64', prefix)
|
||||
|
|
|
|||
|
|
@ -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))
|
||||
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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),
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@
|
|||
#
|
||||
# Author: Justin Too <too1@llnl.gov>
|
||||
#
|
||||
import distutils.dir_util
|
||||
from spack import *
|
||||
|
||||
|
||||
|
|
@ -72,7 +71,7 @@ def url_for_version(self, version):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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:
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@
|
|||
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))
|
||||
|
|
|
|||
|
|
@ -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 @@ def configure(self, spec, prefix):
|
|||
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'):
|
||||
|
|
|
|||
|
|
@ -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 @@ def configure_args(self):
|
|||
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
|
||||
|
|
|
|||
|
|
@ -504,10 +504,9 @@ def check_darwin_lldb_codesign_requirement(self):
|
|||
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',
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -440,7 +440,7 @@ def install(self, spec, prefix):
|
|||
# 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:
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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)),
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@
|
|||
from spack import *
|
||||
import glob
|
||||
import os
|
||||
import shutil
|
||||
import tempfile
|
||||
|
||||
|
||||
|
|
@ -263,8 +262,8 @@ def prepare_src_tree(self):
|
|||
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):
|
||||
|
|
|
|||
|
|
@ -26,7 +26,6 @@
|
|||
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 @@ def install(self, spec, prefix):
|
|||
if not exists(path):
|
||||
makedirs(path)
|
||||
for header in headers:
|
||||
copy(header, path)
|
||||
install(header, path)
|
||||
|
||||
@property
|
||||
def libs(self):
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@
|
|||
|
||||
import inspect
|
||||
import os.path
|
||||
import shutil
|
||||
|
||||
from spack import *
|
||||
|
||||
|
|
@ -99,7 +98,7 @@ def edit(self, spec, prefix):
|
|||
self.stage.source_path,
|
||||
'make.inc'
|
||||
)
|
||||
shutil.copy(template, makefile)
|
||||
copy(template, makefile)
|
||||
for key, value in substitutions:
|
||||
filter_file(key, value, makefile)
|
||||
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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'),
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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),
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -27,7 +27,6 @@
|
|||
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 @@ def add_files_to_view(self, view, merge_map):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def edit(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -24,7 +24,6 @@
|
|||
##############################################################################
|
||||
from spack import *
|
||||
import os.path
|
||||
from shutil import copyfile
|
||||
|
||||
|
||||
class Qorts(RPackage):
|
||||
|
|
@ -59,7 +58,7 @@ def install_jar(self):
|
|||
# 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
|
||||
|
|
|
|||
|
|
@ -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 @@ def copy_makeconf(self):
|
|||
# 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.
|
||||
|
|
|
|||
|
|
@ -24,7 +24,6 @@
|
|||
##############################################################################
|
||||
from spack import *
|
||||
import inspect
|
||||
import distutils.dir_util
|
||||
|
||||
|
||||
class Repeatmasker(Package):
|
||||
|
|
@ -78,4 +77,4 @@ def install(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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),
|
||||
|
|
|
|||
|
|
@ -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 @@ def build(self, spec, prefix):
|
|||
|
||||
def install(self, spec, prefix):
|
||||
# Install all files and directories
|
||||
copy_tree(".", prefix)
|
||||
install_tree('.', prefix)
|
||||
|
||||
mkdir(prefix.bin)
|
||||
mkdir(prefix.lib)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@
|
|||
from spack import *
|
||||
|
||||
import os
|
||||
import shutil
|
||||
|
||||
|
||||
class Scr(CMakePackage):
|
||||
|
|
@ -151,4 +150,4 @@ def copy_config(self):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
make('config')
|
||||
make('all')
|
||||
make('install')
|
||||
mkdirp(prefix.bin)
|
||||
copy_tree('bin', prefix.bin)
|
||||
install_tree('bin', prefix.bin)
|
||||
|
|
|
|||
|
|
@ -24,7 +24,6 @@
|
|||
##############################################################################
|
||||
from spack import *
|
||||
import os.path
|
||||
from shutil import copyfile
|
||||
|
||||
|
||||
class Snpeff(Package):
|
||||
|
|
@ -45,13 +44,13 @@ def install(self, spec, prefix):
|
|||
# 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'),
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install_dir(dirname):
|
|||
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):
|
||||
|
|
|
|||
|
|
@ -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 @@ def url_for_version(self, version):
|
|||
|
||||
def install(self, spec, prefix):
|
||||
# Sublime text comes as a pre-compiled binary.
|
||||
copy_tree('.', prefix)
|
||||
install_tree('.', prefix)
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
# 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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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 @@ def url_for_version(self, version):
|
|||
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
|
||||
|
|
|
|||
|
|
@ -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 @@ def install(self, spec, prefix):
|
|||
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),
|
||||
|
|
|
|||
|
|
@ -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 @@ def build(self, spec, prefix):
|
|||
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'))
|
||||
|
|
|
|||
|
|
@ -24,7 +24,6 @@
|
|||
##############################################################################
|
||||
import inspect
|
||||
import os.path
|
||||
import shutil
|
||||
|
||||
from spack import *
|
||||
|
||||
|
|
@ -77,7 +76,7 @@ def edit(self, spec, prefix):
|
|||
'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)
|
||||
|
||||
|
|
|
|||
|
|
@ -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 @@ def extra_m4(self):
|
|||
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)
|
||||
|
|
|
|||
|
|
@ -24,8 +24,6 @@
|
|||
##############################################################################
|
||||
from spack import *
|
||||
import os
|
||||
import shutil
|
||||
import glob
|
||||
|
||||
|
||||
class Yorick(Package):
|
||||
|
|
@ -74,13 +72,4 @@ def install(self, spec, prefix):
|
|||
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)
|
||||
|
|
|
|||
Loading…
Reference in a new issue