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install_tree, copy_tree can install into existing directory structures (#8289)

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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
2018-08-15 11:30:09 -05:00
committed by Todd Gamblin
parent c0699539d5
commit 73c978ddd9
82 changed files with 422 additions and 344 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
var/spack/repos/builtin/packages/alglib/package.py
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@@ -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):

3
var/spack/repos/builtin/packages/arlecore/package.py
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@@ -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)

4
var/spack/repos/builtin/packages/atom-dft/package.py
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@@ -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):

8
var/spack/repos/builtin/packages/autodock-vina/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/bcl2fastq2/package.py
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@@ -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)

8
var/spack/repos/builtin/packages/bioawk/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/biopieces/package.py
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@@ -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,

3
var/spack/repos/builtin/packages/casper/package.py
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@@ -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)

2
var/spack/repos/builtin/packages/charm/package.py
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@@ -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):

3
var/spack/repos/builtin/packages/chlorop/package.py
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@@ -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)

5
var/spack/repos/builtin/packages/chombo/package.py
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@@ -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')

5
var/spack/repos/builtin/packages/clapack/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/codar-cheetah/package.py
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@@ -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)

4
var/spack/repos/builtin/packages/comd/package.py
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@@ -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):

3
var/spack/repos/builtin/packages/cosp2/package.py
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@@ -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)

6
var/spack/repos/builtin/packages/cp2k/package.py
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@@ -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)

13
var/spack/repos/builtin/packages/cppcheck/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/cudnn/package.py
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@@ -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)

5
var/spack/repos/builtin/packages/farmhash/package.py
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@@ -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")

17
var/spack/repos/builtin/packages/fastqc/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/fermisciencetools/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/fsl/package.py
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@@ -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:

3
var/spack/repos/builtin/packages/gatk/package.py
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@@ -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

3
var/spack/repos/builtin/packages/gaussian/package.py
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@@ -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',

3
var/spack/repos/builtin/packages/gcc/package.py
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@@ -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)

7
var/spack/repos/builtin/packages/genomefinisher/package.py
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@@ -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),

3
var/spack/repos/builtin/packages/git/package.py
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@@ -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):

3
var/spack/repos/builtin/packages/glib/package.py
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@@ -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',

13
var/spack/repos/builtin/packages/go-bootstrap/package.py
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@@ -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)

15
var/spack/repos/builtin/packages/go/package.py
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@@ -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

3
var/spack/repos/builtin/packages/grackle/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/gradle/package.py
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@@ -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)

4
var/spack/repos/builtin/packages/gurobi/package.py
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@@ -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)

4
var/spack/repos/builtin/packages/hdf5-blosc/package.py
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@@ -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))

7
var/spack/repos/builtin/packages/igvtools/package.py
View File

@@ -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),

3
var/spack/repos/builtin/packages/jdk/package.py
View 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)

3
var/spack/repos/builtin/packages/jmol/package.py
View 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 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)

3
var/spack/repos/builtin/packages/kaldi/package.py
View 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
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:

21
var/spack/repos/builtin/packages/leveldb/package.py
View File

@@ -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))

4
var/spack/repos/builtin/packages/libgridxc/package.py
View File

@@ -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'):

5
var/spack/repos/builtin/packages/libiconv/package.py
View File

@@ -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

3
var/spack/repos/builtin/packages/llvm/package.py
View File

@@ -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',

3
var/spack/repos/builtin/packages/masurca/package.py
View File

@@ -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)

3
var/spack/repos/builtin/packages/maven/package.py
View 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 Maven(Package):
@@ -39,4 +38,4 @@ class Maven(Package):
def install(self, spec, prefix):
# install pre-built distribution
copy_tree('.', prefix)
install_tree('.', prefix)

3
var/spack/repos/builtin/packages/mefit/package.py
View File

@@ -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)

2
var/spack/repos/builtin/packages/mfem/package.py
View File

@@ -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:

6
var/spack/repos/builtin/packages/mpix-launch-swift/package.py
View File

@@ -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)

5
var/spack/repos/builtin/packages/mrtrix3/package.py
View File

@@ -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)

5
var/spack/repos/builtin/packages/namd/package.py
View File

@@ -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)),

5
var/spack/repos/builtin/packages/ncl/package.py
View File

@@ -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):

3
var/spack/repos/builtin/packages/ncurses/package.py
View File

@@ -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):

9
var/spack/repos/builtin/packages/occa/package.py
View File

@@ -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:

3
var/spack/repos/builtin/packages/pexsi/package.py
View File

@@ -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)

7
var/spack/repos/builtin/packages/picard/package.py
View File

@@ -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'),

7
var/spack/repos/builtin/packages/pilon/package.py
View File

@@ -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),

10
var/spack/repos/builtin/packages/pindel/package.py
View 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)

3
var/spack/repos/builtin/packages/python/package.py
View File

@@ -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)

8
var/spack/repos/builtin/packages/qbox/package.py
View File

@@ -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)

3
var/spack/repos/builtin/packages/qorts/package.py
View File

@@ -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

3
var/spack/repos/builtin/packages/r/package.py
View File

@@ -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.

3
var/spack/repos/builtin/packages/repeatmasker/package.py
View File

@@ -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)

5
var/spack/repos/builtin/packages/rna-seqc/package.py
View File

@@ -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),

4
var/spack/repos/builtin/packages/rockstar/package.py
View 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)

3
var/spack/repos/builtin/packages/savanna/package.py
View 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 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)

5
var/spack/repos/builtin/packages/sbt/package.py
View File

@@ -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)

3
var/spack/repos/builtin/packages/scr/package.py
View File

@@ -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)

4
var/spack/repos/builtin/packages/sctk/package.py
View 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 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)

7
var/spack/repos/builtin/packages/snpeff/package.py
View File

@@ -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'),

3
var/spack/repos/builtin/packages/snphylo/package.py
View File

@@ -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)

3
var/spack/repos/builtin/packages/spark/package.py
View File

@@ -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):

3
var/spack/repos/builtin/packages/sublime-text/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/supernova/package.py
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@@ -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)

5
var/spack/repos/builtin/packages/the-platinum-searcher/package.py
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@@ -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)

5
var/spack/repos/builtin/packages/tinyxml/package.py
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@@ -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

10
var/spack/repos/builtin/packages/trimmomatic/package.py
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@@ -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),

3
var/spack/repos/builtin/packages/trinity/package.py
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@@ -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'))

3
var/spack/repos/builtin/packages/wannier90/package.py
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@@ -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)

3
var/spack/repos/builtin/packages/workrave/package.py
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@@ -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)

13
var/spack/repos/builtin/packages/yorick/package.py
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@@ -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)