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flake8: fix flake8 issues with invalid escapes

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- in many files, regular strings were used in places where raw strings
  should've been used.

- convert these to raw strings and get rid of new flake8 errors
This commit is contained in:
Todd Gamblin 2018-12-31 23:25:40 -08:00
parent 6f50cd52ed
commit 5425a3dad4
22 changed files with 161 additions and 148 deletions
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2
lib/spack/spack/directory_layout.py
View file

@ -171,7 +171,7 @@ def __init__(self, root, **kwargs):
"${COMPILERNAME}-${COMPILERVER}/" "${COMPILERNAME}-${COMPILERVER}/"
"${PACKAGE}-${VERSION}-${HASH}") "${PACKAGE}-${VERSION}-${HASH}")
if self.hash_len is not None: if self.hash_len is not None:
if re.search('\${HASH:\d+}', self.path_scheme): if re.search(r'\${HASH:\d+}', self.path_scheme):
raise InvalidDirectoryLayoutParametersError( raise InvalidDirectoryLayoutParametersError(
"Conflicting options for installation layout hash length") "Conflicting options for installation layout hash length")
self.path_scheme = self.path_scheme.replace( self.path_scheme = self.path_scheme.replace(

2
lib/spack/spack/graph.py
View file

@ -3,7 +3,7 @@
# #
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
"""Functions for graphing DAGs of dependencies. r"""Functions for graphing DAGs of dependencies.
This file contains code for graphing DAGs of software packages This file contains code for graphing DAGs of software packages
(i.e. Spack specs). There are two main functions you probably care (i.e. Spack specs). There are two main functions you probably care

2
lib/spack/spack/relocate.py
View file

@ -120,7 +120,7 @@ def macho_get_paths(path_name):
if match: if match:
lhs = match.group(1).lstrip().rstrip() lhs = match.group(1).lstrip().rstrip()
rhs = match.group(2) rhs = match.group(2)
match2 = re.search('(.*) \(.*\)', rhs) match2 = re.search(r'(.*) \(.*\)', rhs)
if match2: if match2:
rhs = match2.group(1) rhs = match2.group(1)
if lhs == 'cmd': if lhs == 'cmd':

6
lib/spack/spack/test/cmd/license.py
View file

@ -61,8 +61,8 @@ def test_verify(tmpdir):
assert str(old_lgpl_header) in out assert str(old_lgpl_header) in out
assert str(correct_header) not in out assert str(correct_header) not in out
assert '3 improperly licensed files' in out assert '3 improperly licensed files' in out
assert re.search('files with no SPDX-License-Identifier:\s*1', out) assert re.search(r'files with no SPDX-License-Identifier:\s*1', out)
assert re.search('files with wrong SPDX-License-Identifier:\s*1', out) assert re.search(r'files with wrong SPDX-License-Identifier:\s*1', out)
assert re.search('files with old license header:\s*1', out) assert re.search(r'files with old license header:\s*1', out)
assert license.returncode == 1 assert license.returncode == 1

4
lib/spack/spack/test/pattern.py
View file

@ -15,10 +15,10 @@ class Base:
counter = 0 counter = 0
def add(self): def add(self):
raise NotImplemented('add not implemented') raise NotImplementedError('add not implemented')
def subtract(self): def subtract(self):
raise NotImplemented('subtract not implemented') raise NotImplementedError('subtract not implemented')
return Base return Base

146
lib/spack/spack/url.py
View file

@ -44,7 +44,7 @@
# "path" seemed like the most generic term. # "path" seemed like the most generic term.
# #
def find_list_url(url): def find_list_url(url):
"""Finds a good list URL for the supplied URL. r"""Finds a good list URL for the supplied URL.
By default, returns the dirname of the archive path. By default, returns the dirname of the archive path.
@ -148,81 +148,81 @@ def strip_version_suffixes(path):
suffix_regexes = [ suffix_regexes = [
# Download type # Download type
'[Ii]nstall', r'[Ii]nstall',
'all', r'all',
'code', r'code',
'src(_0)?', r'src(_0)?',
'[Ss]ources?', r'[Ss]ources?',
'file', r'file',
'full', r'full',
'single', r'single',
'public', r'public',
'with[a-zA-Z_-]+', r'with[a-zA-Z_-]+',
'bin', r'bin',
'binary', r'binary',
'run', r'run',
'[Uu]niversal', r'[Uu]niversal',
'jar', r'jar',
'complete', r'complete',
'dynamic', r'dynamic',
'oss', r'oss',
'gem', r'gem',
'tar', r'tar',
'sh', r'sh',
# Download version # Download version
'release', r'release',
'stable', r'stable',
'[Ff]inal', r'[Ff]inal',
'rel', r'rel',
'orig', r'orig',
'dist', r'dist',
'\+', r'\+',
# License # License
'gpl', r'gpl',
# Arch # Arch
# Needs to come before and after OS, appears in both orders # Needs to come before and after OS, appears in both orders
'ia32', r'ia32',
'intel', r'intel',
'amd64', r'amd64',
'x64', r'x64',
'x86[_-]64', r'x86[_-]64',
'x86', r'x86',
'i[36]86', r'i[36]86',
'ppc64(le)?', r'ppc64(le)?',
'armv?(7l|6l|64)', r'armv?(7l|6l|64)',
# OS # OS
'[Ll]inux(_64)?', r'[Ll]inux(_64)?',
'[Uu]ni?x', r'[Uu]ni?x',
'[Ss]un[Oo][Ss]', r'[Ss]un[Oo][Ss]',
'[Mm]ac[Oo][Ss][Xx]?', r'[Mm]ac[Oo][Ss][Xx]?',
'[Oo][Ss][Xx]', r'[Oo][Ss][Xx]',
'[Dd]arwin(64)?', r'[Dd]arwin(64)?',
'[Aa]pple', r'[Aa]pple',
'[Ww]indows', r'[Ww]indows',
'[Ww]in(64|32)?', r'[Ww]in(64|32)?',
'[Cc]ygwin(64|32)?', r'[Cc]ygwin(64|32)?',
'[Mm]ingw', r'[Mm]ingw',
# Arch # Arch
# Needs to come before and after OS, appears in both orders # Needs to come before and after OS, appears in both orders
'ia32', r'ia32',
'intel', r'intel',
'amd64', r'amd64',
'x64', r'x64',
'x86[_-]64', r'x86[_-]64',
'x86', r'x86',
'i[36]86', r'i[36]86',
'ppc64(le)?', r'ppc64(le)?',
'armv?(7l|6l|64)?', r'armv?(7l|6l|64)?',
# PyPI # PyPI
'[._-]py[23].*\.whl', r'[._-]py[23].*\.whl',
'[._-]cp[23].*\.whl', r'[._-]cp[23].*\.whl',
'[._-]win.*\.exe', r'[._-]win.*\.exe',
] ]
for regex in suffix_regexes: for regex in suffix_regexes:
@ -274,22 +274,22 @@ def strip_name_suffixes(path, version):
str(version) + '.*', str(version) + '.*',
# Download type # Download type
'install', r'install',
'src', r'src',
'(open)?[Ss]ources?', r'(open)?[Ss]ources?',
'[._-]archive', r'[._-]archive',
'[._-]std', r'[._-]std',
# Download version # Download version
'release', r'release',
'snapshot', r'snapshot',
'distrib', r'distrib',
# VCS # VCS
'0\+bzr', r'0\+bzr',
# License # License
'gpl', r'gpl',
] ]
for regex in suffix_regexes: for regex in suffix_regexes:
@ -799,7 +799,7 @@ def wildcard_version(path):
# Replace each version with a generic capture group to find versions # Replace each version with a generic capture group to find versions
# and escape everything else so it's not interpreted as a regex # and escape everything else so it's not interpreted as a regex
result = '(\d.*)'.join(re.escape(vp) for vp in vparts) result = r'(\d.*)'.join(re.escape(vp) for vp in vparts)
return result return result

36
var/spack/repos/builtin/packages/chombo/package.py
View file

@ -45,7 +45,7 @@ def edit(self, spec, prefix):
# Set fortran name mangling in Make.defs # Set fortran name mangling in Make.defs
defs_file = FileFilter('./lib/mk/Make.defs') defs_file = FileFilter('./lib/mk/Make.defs')
defs_file.filter('^\s*#\s*cppcallsfort\s*=\s*', defs_file.filter(r'^\s*#\s*cppcallsfort\s*=\s*',
'cppcallsfort = -DCH_FORT_UNDERSCORE') 'cppcallsfort = -DCH_FORT_UNDERSCORE')
# Set remaining variables in Make.defs.local # Set remaining variables in Make.defs.local
@ -57,53 +57,53 @@ def edit(self, spec, prefix):
defs_file = FileFilter('./lib/mk/Make.defs.local') defs_file = FileFilter('./lib/mk/Make.defs.local')
# Unconditional settings # Unconditional settings
defs_file.filter('^\s*#\s*DEBUG\s*=\s*', 'DEBUG = FALSE') defs_file.filter(r'^\s*#\s*DEBUG\s*=\s*', 'DEBUG = FALSE')
defs_file.filter('^\s*#\s*OPT\s*=\s*', 'OPT = TRUE') defs_file.filter(r'^\s*#\s*OPT\s*=\s*', 'OPT = TRUE')
defs_file.filter('^\s*#\s*PIC\s*=\s*', 'PIC = TRUE') defs_file.filter(r'^\s*#\s*PIC\s*=\s*', 'PIC = TRUE')
# timer code frequently fails compiles. So disable it. # timer code frequently fails compiles. So disable it.
defs_file.filter('^\s*#\s*USE_TIMER\s*=\s*', 'USE_TIMER = FALSE') defs_file.filter(r'^\s*#\s*USE_TIMER\s*=\s*', 'USE_TIMER = FALSE')
# LAPACK setup # LAPACK setup
lapack_blas = spec['lapack'].libs + spec['blas'].libs lapack_blas = spec['lapack'].libs + spec['blas'].libs
defs_file.filter('^\s*#\s*USE_LAPACK\s*=\s*', 'USE_LAPACK = TRUE') defs_file.filter(r'^\s*#\s*USE_LAPACK\s*=\s*', 'USE_LAPACK = TRUE')
defs_file.filter( defs_file.filter(
'^\s*#\s*lapackincflags\s*=\s*', r'^\s*#\s*lapackincflags\s*=\s*',
'lapackincflags = -I%s' % spec['lapack'].prefix.include) 'lapackincflags = -I%s' % spec['lapack'].prefix.include)
defs_file.filter( defs_file.filter(
'^\s*#\s*syslibflags\s*=\s*', r'^\s*#\s*syslibflags\s*=\s*',
'syslibflags = %s' % lapack_blas.ld_flags) 'syslibflags = %s' % lapack_blas.ld_flags)
# Compilers and Compiler flags # Compilers and Compiler flags
defs_file.filter('^\s*#\s*CXX\s*=\s*', 'CXX = %s' % spack_cxx) defs_file.filter(r'^\s*#\s*CXX\s*=\s*', 'CXX = %s' % spack_cxx)
defs_file.filter('^\s*#\s*FC\s*=\s*', 'FC = %s' % spack_fc) defs_file.filter(r'^\s*#\s*FC\s*=\s*', 'FC = %s' % spack_fc)
if '+mpi' in spec: if '+mpi' in spec:
defs_file.filter( defs_file.filter(
'^\s*#\s*MPICXX\s*=\s*', r'^\s*#\s*MPICXX\s*=\s*',
'MPICXX = %s' % self.spec['mpi'].mpicxx) 'MPICXX = %s' % self.spec['mpi'].mpicxx)
# Conditionally determined settings # Conditionally determined settings
defs_file.filter( defs_file.filter(
'^\s*#\s*MPI\s*=\s*', r'^\s*#\s*MPI\s*=\s*',
'MPI = %s' % ('TRUE' if '+mpi' in spec else 'FALSE')) 'MPI = %s' % ('TRUE' if '+mpi' in spec else 'FALSE'))
defs_file.filter( defs_file.filter(
'^\s*#\s*DIM\s*=\s*', r'^\s*#\s*DIM\s*=\s*',
'DIM = %s' % spec.variants['dims'].value) 'DIM = %s' % spec.variants['dims'].value)
# HDF5 settings # HDF5 settings
if '+hdf5' in spec: if '+hdf5' in spec:
defs_file.filter('^\s*#\s*USE_HDF5\s*=\s*', 'USE_HDF5 = TRUE') defs_file.filter(r'^\s*#\s*USE_HDF5\s*=\s*', 'USE_HDF5 = TRUE')
defs_file.filter( defs_file.filter(
'^\s*#\s*HDFINCFLAGS\s*=.*', r'^\s*#\s*HDFINCFLAGS\s*=.*',
'HDFINCFLAGS = -I%s' % spec['hdf5'].prefix.include) 'HDFINCFLAGS = -I%s' % spec['hdf5'].prefix.include)
defs_file.filter( defs_file.filter(
'^\s*#\s*HDFLIBFLAGS\s*=.*', r'^\s*#\s*HDFLIBFLAGS\s*=.*',
'HDFLIBFLAGS = %s' % spec['hdf5'].libs.ld_flags) 'HDFLIBFLAGS = %s' % spec['hdf5'].libs.ld_flags)
if '+mpi' in spec: if '+mpi' in spec:
defs_file.filter( defs_file.filter(
'^\s*#\s*HDFMPIINCFLAGS\s*=.*', r'^\s*#\s*HDFMPIINCFLAGS\s*=.*',
'HDFMPIINCFLAGS = -I%s' % spec['hdf5'].prefix.include) 'HDFMPIINCFLAGS = -I%s' % spec['hdf5'].prefix.include)
defs_file.filter( defs_file.filter(
'^\s*#\s*HDFMPILIBFLAGS\s*=.*', r'^\s*#\s*HDFMPILIBFLAGS\s*=.*',
'HDFMPILIBFLAGS = %s' % spec['hdf5'].libs.ld_flags) 'HDFMPILIBFLAGS = %s' % spec['hdf5'].libs.ld_flags)
def build(self, spec, prefix): def build(self, spec, prefix):

2
var/spack/repos/builtin/packages/ldc/package.py
View file

@ -59,7 +59,7 @@ def add_rpath_to_conf(self):
config_file = join_path(self.prefix.etc, 'ldc2.conf') config_file = join_path(self.prefix.etc, 'ldc2.conf')
search_for = 'switches = \[' search_for = r'switches = \['
substitute_with = 'switches = [\n' + \ substitute_with = 'switches = [\n' + \
' "-L-rpath={0}",'.format(self.prefix.lib) ' "-L-rpath={0}",'.format(self.prefix.lib)

9
var/spack/repos/builtin/packages/libceed/package.py
View file

@ -51,10 +51,11 @@ def install(self, spec, prefix):
install('ceed.h', prefix.include) install('ceed.h', prefix.include)
mkdirp(prefix.lib) mkdirp(prefix.lib)
install('libceed.%s' % dso_suffix, prefix.lib) install('libceed.%s' % dso_suffix, prefix.lib)
filter_file('^prefix=.*$', 'prefix=%s' % prefix, 'ceed.pc') filter_file(r'^prefix=.*$', 'prefix=%s' % prefix, 'ceed.pc')
filter_file('^includedir=\$\{prefix\}$', filter_file(r'^includedir=\$\{prefix\}$',
'includedir=${prefix}/include', 'ceed.pc') 'includedir=${prefix}/include', 'ceed.pc')
filter_file('^libdir=\$\{prefix\}$', 'libdir=${prefix}/lib', 'ceed.pc') filter_file(r'^libdir=\$\{prefix\}$',
filter_file('Version:.*$', 'Version: 0.1', 'ceed.pc') 'libdir=${prefix}/lib', 'ceed.pc')
filter_file(r'Version:.*$', 'Version: 0.1', 'ceed.pc')
mkdirp(prefix.lib.pkgconfig) mkdirp(prefix.lib.pkgconfig)
install('ceed.pc', prefix.lib.pkgconfig) install('ceed.pc', prefix.lib.pkgconfig)

2
var/spack/repos/builtin/packages/meraculous/package.py
View file

@ -26,7 +26,7 @@ class Meraculous(CMakePackage):
def patch(self): def patch(self):
edit = FileFilter('CMakeLists.txt') edit = FileFilter('CMakeLists.txt')
edit.filter("-static-libstdc\+\+", "") edit.filter(r"-static-libstdc\+\+", "")
def setup_environment(self, spack_env, run_env): def setup_environment(self, spack_env, run_env):
run_env.set('MERACULOUS_ROOT', self.prefix) run_env.set('MERACULOUS_ROOT', self.prefix)

6
var/spack/repos/builtin/packages/multitail/package.py
View file

@ -33,11 +33,11 @@ def edit(self, spec, prefix):
nc_include_flags = spec['ncurses'].headers.include_flags nc_include_flags = spec['ncurses'].headers.include_flags
nc_ld_flags = spec['ncurses'].libs.ld_flags nc_ld_flags = spec['ncurses'].libs.ld_flags
makefile.filter('CFLAGS\+=', 'CFLAGS+={0} '.format(nc_include_flags)) makefile.filter(r'CFLAGS\+=', 'CFLAGS+={0} '.format(nc_include_flags))
makefile.filter('LDFLAGS\+=', 'LDFLAGS+={0} '.format(nc_ld_flags)) makefile.filter(r'LDFLAGS\+=', 'LDFLAGS+={0} '.format(nc_ld_flags))
# Copy the conf file directly into place (don't worry about # Copy the conf file directly into place (don't worry about
# overwriting an existing file...) # overwriting an existing file...)
kwargs = {'ignore_absent': False, 'backup': False, 'string': True} kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
makefile.filter('cp multitail.conf $(CONFIG_FILE).new', makefile.filter(r'cp multitail.conf $(CONFIG_FILE).new',
'cp multitail.conf $(CONFIG_FILE)', **kwargs) 'cp multitail.conf $(CONFIG_FILE)', **kwargs)

4
var/spack/repos/builtin/packages/mumps/package.py
View file

@ -233,8 +233,8 @@ def write_makefile_inc(self):
# When building libpord, read AR from Makefile.inc instead of # When building libpord, read AR from Makefile.inc instead of
# going through the make command line - this prevents various # going through the make command line - this prevents various
# problems with the substring "$$@". # problems with the substring "$$@".
filter_file(' AR="\$\(AR\)"', '', 'Makefile') filter_file(r' AR="\$\(AR\)"', '', 'Makefile')
filter_file('^(INCLUDES = -I../include)', filter_file(r'^(INCLUDES = -I../include)',
'\\1\ninclude ../../Makefile.inc', '\\1\ninclude ../../Makefile.inc',
join_path('PORD', 'lib', 'Makefile')) join_path('PORD', 'lib', 'Makefile'))

2
var/spack/repos/builtin/packages/nek5000/package.py
View file

@ -158,7 +158,7 @@ def install(self, spec, prefix):
if self.compiler.name in ['xl', 'xl_r']: if self.compiler.name in ['xl', 'xl_r']:
# Use '-qextname' when compiling mxm.f # Use '-qextname' when compiling mxm.f
filter_file('\$\(OLAGS\)', '-qextname $(OLAGS)', filter_file(r'\$\(OLAGS\)', '-qextname $(OLAGS)',
join_path('postnek', 'makefile')) join_path('postnek', 'makefile'))
# Define 'rename_' function that calls 'rename' # Define 'rename_' function that calls 'rename'
with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver: with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver:

4
var/spack/repos/builtin/packages/pacbio-daligner/package.py
View file

@ -21,7 +21,7 @@ class PacbioDaligner(MakefilePackage):
def edit(self, spec, prefix): def edit(self, spec, prefix):
mkdir(prefix.bin) mkdir(prefix.bin)
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin) makefile.filter(r'DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile') gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin', gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin) 'cp ${ALL} ' + prefix.bin)

4
var/spack/repos/builtin/packages/pacbio-damasker/package.py
View file

@ -20,7 +20,7 @@ class PacbioDamasker(MakefilePackage):
def edit(self, spec, prefix): def edit(self, spec, prefix):
mkdirp(prefix.bin) mkdirp(prefix.bin)
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin) makefile.filter(r'DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile') gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin', gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin) 'cp ${ALL} ' + prefix.bin)

10
var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
View file

@ -23,12 +23,12 @@ def edit(self, spec, prefix):
mkdirp(prefix.lib) mkdirp(prefix.lib)
mkdirp(prefix.include) mkdirp(prefix.include)
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin) makefile.filter(r'DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile') gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin', gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin) 'cp ${ALL} ' + prefix.bin)
gmf.filter('rsync\s*-av\s*libdazzdb.*\s*\$\{PREFIX\}/lib', gmf.filter(r'rsync\s*-av\s*libdazzdb.*\s*\$\{PREFIX\}/lib',
'cp libdazzdb.* ' + prefix.lib) 'cp libdazzdb.* ' + prefix.lib)
gmf.filter(('rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h' gmf.filter((r'rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h'
'\)\s*\$\{PREFIX\}/include'), r'\)\s*\$\{PREFIX\}/include'),
'cp *.h ' + prefix.include) 'cp *.h ' + prefix.include)

8
var/spack/repos/builtin/packages/pacbio-dextractor/package.py
View file

@ -21,10 +21,10 @@ class PacbioDextractor(MakefilePackage):
def edit(self, spec, prefix): def edit(self, spec, prefix):
mkdirp(prefix.bin) mkdirp(prefix.bin)
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')
makefile.filter('PATH_HDF5\s*=\s*/sw/apps/hdf5/current', makefile.filter(r'PATH_HDF5\s*=\s*/sw/apps/hdf5/current',
'PATH_HDF5 = ' + spec['hdf5'].prefix) 'PATH_HDF5 = ' + spec['hdf5'].prefix)
makefile.filter('PATH_HDF5\*s=\s*/usr/local/hdf5', '') makefile.filter(r'PATH_HDF5\*s=\s*/usr/local/hdf5', '')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin) makefile.filter(r'DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile') gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin', gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin) 'cp ${ALL} ' + prefix.bin)

2
var/spack/repos/builtin/packages/pixman/package.py
View file

@ -42,7 +42,7 @@ def patch_config_h_for_intel(self):
# #
if '%intel' in self.spec: if '%intel' in self.spec:
filter_file( filter_file(
'#define HAVE_GCC_VECTOR_EXTENSIONS /\*\*/', r'#define HAVE_GCC_VECTOR_EXTENSIONS /\*\*/',
'/* #undef HAVE_GCC_VECTOR_EXTENSIONS */', '/* #undef HAVE_GCC_VECTOR_EXTENSIONS */',
config_h config_h
) )

52
var/spack/repos/builtin/packages/r-gtools/package.py
View file

@ -7,26 +7,38 @@
class RGtools(RPackage): class RGtools(RPackage):
"""Functions to assist in R programming, including: - assist in developing, """Functions to assist in R programming.
updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse Including:
logit transformations ('logit', 'inv.logit'), - test if a value is missing, - assist in developing, updating, and maintaining R and R packages
empty or contains only NA and NULL values ('invalid'), - manipulate R's ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat')
.Last function ('addLast'), - define macros ('defmacro'), - detect odd and - calculate the logit and inverse logit transformations
even integers ('odd', 'even'), - convert strings containing non-ASCII ('logit', 'inv.logit')
characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a - test if a value is missing, empty or contains only NA and NULL values
binary search ('binsearch'), - sort strings containing both numeric and ('invalid')
character components ('mixedsort'), - create a factor variable from the - manipulate R's .Last function ('addLast')
quantiles of a continuous variable ('quantcut'), - enumerate permutations - define macros ('defmacro')
and combinations ('combinations', 'permutation'), - calculate and convert - detect odd and even integers ('odd', 'even')
between fold-change and log-ratio ('foldchange', 'logratio2foldchange', - convert strings containing non-ASCII characters (like single
'foldchange2logratio'), - calculate probabilities and generate random quotes) to plain ASCII ('ASCIIfy')
numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply - perform a binary search ('binsearch')
a function over adjacent subsets of a vector ('running'), - modify the - sort strings containing both numeric and character components
TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of ('mixedsort')
data frames, even if the column names don't match ('smartbind'), - generate - create a factor variable from the quantiles of a continuous variable
significance stars from p-values ('stars.pval'), - convert characters ('quantcut')
to/from ASCII codes.""" - enumerate permutations and combinations ('combinations', 'permutation')
- calculate and convert between fold-change and log-ratio
('foldchange', 'logratio2foldchange', 'foldchange2logratio')
- calculate probabilities and generate random numbers from Dirichlet
distributions ('rdirichlet', 'ddirichlet')
- apply a function over adjacent subsets of a vector ('running')
- modify the TCP_NODELAY ('de-Nagle') flag for socket objects
- efficient 'rbind' of data frames, even if the column names don't
match ('smartbind')
- generate significance stars from p-values ('stars.pval')
- convert characters to/from ASCII codes.
"""
homepage = "https://cran.r-project.org/package=gtools" homepage = "https://cran.r-project.org/package=gtools"
url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz" url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz"

2
var/spack/repos/builtin/packages/spark/package.py
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@ -54,6 +54,6 @@ def setup_environment(self, spack_env, run_env):
# Remove whitespaces, as they can compromise syntax in # Remove whitespaces, as they can compromise syntax in
# module files # module files
hadoop_classpath = re.sub('[\s+]', '', hadoop_classpath) hadoop_classpath = re.sub(r'[\s+]', '', hadoop_classpath)
run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath) run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath)

2
var/spack/repos/builtin/packages/yorick/package.py
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@ -14,7 +14,7 @@ class Yorick(Package):
files of numbers. Yorick includes an interactive graphics package, and a files of numbers. Yorick includes an interactive graphics package, and a
binary file package capable of translating to and from the raw numeric binary file package capable of translating to and from the raw numeric
formats of all modern computers. Yorick is written in ANSI C and runs on formats of all modern computers. Yorick is written in ANSI C and runs on
most operating systems (\*nix systems, MacOS X, Windows). most operating systems (*nix systems, MacOS X, Windows).
""" """
homepage = "http://dhmunro.github.io/yorick-doc/" homepage = "http://dhmunro.github.io/yorick-doc/"

2
var/spack/repos/builtin/packages/zfp/package.py
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@ -32,7 +32,7 @@ class Zfp(MakefilePackage):
def edit(self, spec, prefix): def edit(self, spec, prefix):
config_file = FileFilter('Config') config_file = FileFilter('Config')
config_file.filter( config_file.filter(
'^\s*#\s*DEFS\s*\+=\s*-DBIT_STREAM_WORD_TYPE\s*=\s*uint8', r'^\s*#\s*DEFS\s*\+=\s*-DBIT_STREAM_WORD_TYPE\s*=\s*uint8',
'DEFS += -DBIT_STREAM_WORD_TYPE=uint%s' % 'DEFS += -DBIT_STREAM_WORD_TYPE=uint%s' %
spec.variants['bsws'].value) spec.variants['bsws'].value)