diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index f1524427816ebb9ba5137ca106319399c56c6535..f579d5664bc6da5f98b94db45b06a0a77d6c072a 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -171,7 +171,7 @@ def __init__(self, root, **kwargs):
"${COMPILERNAME}-${COMPILERVER}/"
"${PACKAGE}-${VERSION}-${HASH}")
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(
"Conflicting options for installation layout hash length")
self.path_scheme = self.path_scheme.replace(
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index 5c8c60a3bbc7be0a91fcfb5ef4fd55060cd2b664..8c481084ae408e3a7308615a7f9df5ccb7d4e3d2 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -3,7 +3,7 @@
#
# 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
(i.e. Spack specs). There are two main functions you probably care
diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 8e9a48208c19b385e31cfd626cbef3875a4bfe1a..a559ae64951e0a8e3be129b1aa49a3751791b1f8 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -120,7 +120,7 @@ def macho_get_paths(path_name):
if match:
lhs = match.group(1).lstrip().rstrip()
rhs = match.group(2)
- match2 = re.search('(.*) \(.*\)', rhs)
+ match2 = re.search(r'(.*) \(.*\)', rhs)
if match2:
rhs = match2.group(1)
if lhs == 'cmd':
diff --git a/lib/spack/spack/test/cmd/license.py b/lib/spack/spack/test/cmd/license.py
index bc77cad09614f8596a1ca31d916979f8225c7eb8..fe02cb18a52cb3b95f74504222f7c79ad5f8d385 100644
--- a/lib/spack/spack/test/cmd/license.py
+++ b/lib/spack/spack/test/cmd/license.py
@@ -61,8 +61,8 @@ def test_verify(tmpdir):
assert str(old_lgpl_header) in out
assert str(correct_header) not in out
assert '3 improperly licensed files' in out
- assert re.search('files with no SPDX-License-Identifier:\s*1', out)
- assert re.search('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 no SPDX-License-Identifier:\s*1', out)
+ assert re.search(r'files with wrong SPDX-License-Identifier:\s*1', out)
+ assert re.search(r'files with old license header:\s*1', out)
assert license.returncode == 1
diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py
index 1e3fbdaf0e2f7b7d593d2a47c0695f305cf6e380..406915bdf08ec5da950444fce52a42da1ac4cc28 100644
--- a/lib/spack/spack/test/pattern.py
+++ b/lib/spack/spack/test/pattern.py
@@ -15,10 +15,10 @@ class Base:
counter = 0
def add(self):
- raise NotImplemented('add not implemented')
+ raise NotImplementedError('add not implemented')
def subtract(self):
- raise NotImplemented('subtract not implemented')
+ raise NotImplementedError('subtract not implemented')
return Base
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index 5819d07e1ad445cba8b49c8a54ae74f2c622f6ea..387c8c957d4acdd1b82b499515a6628e621faa26 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -44,7 +44,7 @@
# "path" seemed like the most generic term.
#
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.
@@ -148,81 +148,81 @@ def strip_version_suffixes(path):
suffix_regexes = [
# Download type
- '[Ii]nstall',
- 'all',
- 'code',
- 'src(_0)?',
- '[Ss]ources?',
- 'file',
- 'full',
- 'single',
- 'public',
- 'with[a-zA-Z_-]+',
- 'bin',
- 'binary',
- 'run',
- '[Uu]niversal',
- 'jar',
- 'complete',
- 'dynamic',
- 'oss',
- 'gem',
- 'tar',
- 'sh',
+ r'[Ii]nstall',
+ r'all',
+ r'code',
+ r'src(_0)?',
+ r'[Ss]ources?',
+ r'file',
+ r'full',
+ r'single',
+ r'public',
+ r'with[a-zA-Z_-]+',
+ r'bin',
+ r'binary',
+ r'run',
+ r'[Uu]niversal',
+ r'jar',
+ r'complete',
+ r'dynamic',
+ r'oss',
+ r'gem',
+ r'tar',
+ r'sh',
# Download version
- 'release',
- 'stable',
- '[Ff]inal',
- 'rel',
- 'orig',
- 'dist',
- '\+',
+ r'release',
+ r'stable',
+ r'[Ff]inal',
+ r'rel',
+ r'orig',
+ r'dist',
+ r'\+',
# License
- 'gpl',
+ r'gpl',
# Arch
# Needs to come before and after OS, appears in both orders
- 'ia32',
- 'intel',
- 'amd64',
- 'x64',
- 'x86[_-]64',
- 'x86',
- 'i[36]86',
- 'ppc64(le)?',
- 'armv?(7l|6l|64)',
+ r'ia32',
+ r'intel',
+ r'amd64',
+ r'x64',
+ r'x86[_-]64',
+ r'x86',
+ r'i[36]86',
+ r'ppc64(le)?',
+ r'armv?(7l|6l|64)',
# OS
- '[Ll]inux(_64)?',
- '[Uu]ni?x',
- '[Ss]un[Oo][Ss]',
- '[Mm]ac[Oo][Ss][Xx]?',
- '[Oo][Ss][Xx]',
- '[Dd]arwin(64)?',
- '[Aa]pple',
- '[Ww]indows',
- '[Ww]in(64|32)?',
- '[Cc]ygwin(64|32)?',
- '[Mm]ingw',
+ r'[Ll]inux(_64)?',
+ r'[Uu]ni?x',
+ r'[Ss]un[Oo][Ss]',
+ r'[Mm]ac[Oo][Ss][Xx]?',
+ r'[Oo][Ss][Xx]',
+ r'[Dd]arwin(64)?',
+ r'[Aa]pple',
+ r'[Ww]indows',
+ r'[Ww]in(64|32)?',
+ r'[Cc]ygwin(64|32)?',
+ r'[Mm]ingw',
# Arch
# Needs to come before and after OS, appears in both orders
- 'ia32',
- 'intel',
- 'amd64',
- 'x64',
- 'x86[_-]64',
- 'x86',
- 'i[36]86',
- 'ppc64(le)?',
- 'armv?(7l|6l|64)?',
+ r'ia32',
+ r'intel',
+ r'amd64',
+ r'x64',
+ r'x86[_-]64',
+ r'x86',
+ r'i[36]86',
+ r'ppc64(le)?',
+ r'armv?(7l|6l|64)?',
# PyPI
- '[._-]py[23].*\.whl',
- '[._-]cp[23].*\.whl',
- '[._-]win.*\.exe',
+ r'[._-]py[23].*\.whl',
+ r'[._-]cp[23].*\.whl',
+ r'[._-]win.*\.exe',
]
for regex in suffix_regexes:
@@ -274,22 +274,22 @@ def strip_name_suffixes(path, version):
str(version) + '.*',
# Download type
- 'install',
- 'src',
- '(open)?[Ss]ources?',
- '[._-]archive',
- '[._-]std',
+ r'install',
+ r'src',
+ r'(open)?[Ss]ources?',
+ r'[._-]archive',
+ r'[._-]std',
# Download version
- 'release',
- 'snapshot',
- 'distrib',
+ r'release',
+ r'snapshot',
+ r'distrib',
# VCS
- '0\+bzr',
+ r'0\+bzr',
# License
- 'gpl',
+ r'gpl',
]
for regex in suffix_regexes:
@@ -799,7 +799,7 @@ def wildcard_version(path):
# Replace each version with a generic capture group to find versions
# 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
diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py
index 0044edf2402fdffb6750bc0dce16a18fd9956641..332dae343fbcf58e14f18477d7365b4f24c6f258 100644
--- a/var/spack/repos/builtin/packages/chombo/package.py
+++ b/var/spack/repos/builtin/packages/chombo/package.py
@@ -45,7 +45,7 @@ def edit(self, spec, prefix):
# Set fortran name mangling in 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')
# Set remaining variables in Make.defs.local
@@ -57,53 +57,53 @@ def edit(self, spec, prefix):
defs_file = FileFilter('./lib/mk/Make.defs.local')
# Unconditional settings
- defs_file.filter('^\s*#\s*DEBUG\s*=\s*', 'DEBUG = FALSE')
- defs_file.filter('^\s*#\s*OPT\s*=\s*', 'OPT = TRUE')
- defs_file.filter('^\s*#\s*PIC\s*=\s*', 'PIC = TRUE')
+ defs_file.filter(r'^\s*#\s*DEBUG\s*=\s*', 'DEBUG = FALSE')
+ defs_file.filter(r'^\s*#\s*OPT\s*=\s*', 'OPT = TRUE')
+ defs_file.filter(r'^\s*#\s*PIC\s*=\s*', 'PIC = TRUE')
# 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_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(
- '^\s*#\s*lapackincflags\s*=\s*',
+ r'^\s*#\s*lapackincflags\s*=\s*',
'lapackincflags = -I%s' % spec['lapack'].prefix.include)
defs_file.filter(
- '^\s*#\s*syslibflags\s*=\s*',
+ r'^\s*#\s*syslibflags\s*=\s*',
'syslibflags = %s' % lapack_blas.ld_flags)
# Compilers and Compiler flags
- defs_file.filter('^\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*CXX\s*=\s*', 'CXX = %s' % spack_cxx)
+ defs_file.filter(r'^\s*#\s*FC\s*=\s*', 'FC = %s' % spack_fc)
if '+mpi' in spec:
defs_file.filter(
- '^\s*#\s*MPICXX\s*=\s*',
+ r'^\s*#\s*MPICXX\s*=\s*',
'MPICXX = %s' % self.spec['mpi'].mpicxx)
# Conditionally determined settings
defs_file.filter(
- '^\s*#\s*MPI\s*=\s*',
+ r'^\s*#\s*MPI\s*=\s*',
'MPI = %s' % ('TRUE' if '+mpi' in spec else 'FALSE'))
defs_file.filter(
- '^\s*#\s*DIM\s*=\s*',
+ r'^\s*#\s*DIM\s*=\s*',
'DIM = %s' % spec.variants['dims'].value)
# HDF5 settings
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(
- '^\s*#\s*HDFINCFLAGS\s*=.*',
+ r'^\s*#\s*HDFINCFLAGS\s*=.*',
'HDFINCFLAGS = -I%s' % spec['hdf5'].prefix.include)
defs_file.filter(
- '^\s*#\s*HDFLIBFLAGS\s*=.*',
+ r'^\s*#\s*HDFLIBFLAGS\s*=.*',
'HDFLIBFLAGS = %s' % spec['hdf5'].libs.ld_flags)
if '+mpi' in spec:
defs_file.filter(
- '^\s*#\s*HDFMPIINCFLAGS\s*=.*',
+ r'^\s*#\s*HDFMPIINCFLAGS\s*=.*',
'HDFMPIINCFLAGS = -I%s' % spec['hdf5'].prefix.include)
defs_file.filter(
- '^\s*#\s*HDFMPILIBFLAGS\s*=.*',
+ r'^\s*#\s*HDFMPILIBFLAGS\s*=.*',
'HDFMPILIBFLAGS = %s' % spec['hdf5'].libs.ld_flags)
def build(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/ldc/package.py b/var/spack/repos/builtin/packages/ldc/package.py
index ba027538bdf302480b44dc0945326435b3aa9dfd..a1768d71b9115144574b438e7fa9840b2b76882b 100644
--- a/var/spack/repos/builtin/packages/ldc/package.py
+++ b/var/spack/repos/builtin/packages/ldc/package.py
@@ -59,7 +59,7 @@ def add_rpath_to_conf(self):
config_file = join_path(self.prefix.etc, 'ldc2.conf')
- search_for = 'switches = \['
+ search_for = r'switches = \['
substitute_with = 'switches = [\n' + \
' "-L-rpath={0}",'.format(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py
index e9eea919e2eb5e495d42a6e04bc70b938ab9ff72..578da421812a1df7d2df8183ac486f848c82207d 100644
--- a/var/spack/repos/builtin/packages/libceed/package.py
+++ b/var/spack/repos/builtin/packages/libceed/package.py
@@ -51,10 +51,11 @@ def install(self, spec, prefix):
install('ceed.h', prefix.include)
mkdirp(prefix.lib)
install('libceed.%s' % dso_suffix, prefix.lib)
- filter_file('^prefix=.*$', 'prefix=%s' % prefix, 'ceed.pc')
- filter_file('^includedir=\$\{prefix\}$',
+ filter_file(r'^prefix=.*$', 'prefix=%s' % prefix, 'ceed.pc')
+ filter_file(r'^includedir=\$\{prefix\}$',
'includedir=${prefix}/include', 'ceed.pc')
- filter_file('^libdir=\$\{prefix\}$', 'libdir=${prefix}/lib', 'ceed.pc')
- filter_file('Version:.*$', 'Version: 0.1', 'ceed.pc')
+ filter_file(r'^libdir=\$\{prefix\}$',
+ 'libdir=${prefix}/lib', 'ceed.pc')
+ filter_file(r'Version:.*$', 'Version: 0.1', 'ceed.pc')
mkdirp(prefix.lib.pkgconfig)
install('ceed.pc', prefix.lib.pkgconfig)
diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py
index 18cdd064c8527df0c69380f69ca61461a182899e..8e44be55967a0e03ab377b4d9f4125a84334aef5 100644
--- a/var/spack/repos/builtin/packages/meraculous/package.py
+++ b/var/spack/repos/builtin/packages/meraculous/package.py
@@ -26,7 +26,7 @@ class Meraculous(CMakePackage):
def patch(self):
edit = FileFilter('CMakeLists.txt')
- edit.filter("-static-libstdc\+\+", "")
+ edit.filter(r"-static-libstdc\+\+", "")
def setup_environment(self, spack_env, run_env):
run_env.set('MERACULOUS_ROOT', self.prefix)
diff --git a/var/spack/repos/builtin/packages/multitail/package.py b/var/spack/repos/builtin/packages/multitail/package.py
index 93c17279e0a1c0f2eff118e2e74dd10f5a2bea2d..0f6cd8a46bd1761f4661f31f3d63b585afd17588 100644
--- a/var/spack/repos/builtin/packages/multitail/package.py
+++ b/var/spack/repos/builtin/packages/multitail/package.py
@@ -33,11 +33,11 @@ def edit(self, spec, prefix):
nc_include_flags = spec['ncurses'].headers.include_flags
nc_ld_flags = spec['ncurses'].libs.ld_flags
- makefile.filter('CFLAGS\+=', 'CFLAGS+={0} '.format(nc_include_flags))
- makefile.filter('LDFLAGS\+=', 'LDFLAGS+={0} '.format(nc_ld_flags))
+ makefile.filter(r'CFLAGS\+=', 'CFLAGS+={0} '.format(nc_include_flags))
+ makefile.filter(r'LDFLAGS\+=', 'LDFLAGS+={0} '.format(nc_ld_flags))
# Copy the conf file directly into place (don't worry about
# overwriting an existing file...)
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)
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index f054e094e2edc83a779d3a54c7ebdb7378acd563..234708f7a2b9df20eb876b0beca0fd704ebfac40 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -233,8 +233,8 @@ def write_makefile_inc(self):
# When building libpord, read AR from Makefile.inc instead of
# going through the make command line - this prevents various
# problems with the substring "$$@".
- filter_file(' AR="\$\(AR\)"', '', 'Makefile')
- filter_file('^(INCLUDES = -I../include)',
+ filter_file(r' AR="\$\(AR\)"', '', 'Makefile')
+ filter_file(r'^(INCLUDES = -I../include)',
'\\1\ninclude ../../Makefile.inc',
join_path('PORD', 'lib', 'Makefile'))
diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py
index dbd19eb55444d69940a1fdd56df600425bb88584..a522af8cf0f7d3594c89ccbb181b302ba51195e4 100644
--- a/var/spack/repos/builtin/packages/nek5000/package.py
+++ b/var/spack/repos/builtin/packages/nek5000/package.py
@@ -158,7 +158,7 @@ def install(self, spec, prefix):
if self.compiler.name in ['xl', 'xl_r']:
# Use '-qextname' when compiling mxm.f
- filter_file('\$\(OLAGS\)', '-qextname $(OLAGS)',
+ filter_file(r'\$\(OLAGS\)', '-qextname $(OLAGS)',
join_path('postnek', 'makefile'))
# Define 'rename_' function that calls 'rename'
with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver:
diff --git a/var/spack/repos/builtin/packages/pacbio-daligner/package.py b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
index 534716d005b03dc0da689b3468b451b72a4dbb65..07738d14ee49b23d23920eae20cbdfdd841178e3 100644
--- a/var/spack/repos/builtin/packages/pacbio-daligner/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
@@ -21,7 +21,7 @@ class PacbioDaligner(MakefilePackage):
def edit(self, spec, prefix):
mkdir(prefix.bin)
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.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
+ gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin)
diff --git a/var/spack/repos/builtin/packages/pacbio-damasker/package.py b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
index f41440570a0096135886e6baa307635071e37bb3..d904e3ece2fa290c0a35486d56afa17517983a9a 100644
--- a/var/spack/repos/builtin/packages/pacbio-damasker/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
@@ -20,7 +20,7 @@ class PacbioDamasker(MakefilePackage):
def edit(self, spec, prefix):
mkdirp(prefix.bin)
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.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
+ gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin)
diff --git a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
index 2e2abca958c8b7736c6fb93535f140eca4034b02..0ccb68842b635c7242678183d35ea1f49c760564 100644
--- a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
@@ -23,12 +23,12 @@ def edit(self, spec, prefix):
mkdirp(prefix.lib)
mkdirp(prefix.include)
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.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
+ gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{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)
- gmf.filter(('rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h'
- '\)\s*\$\{PREFIX\}/include'),
+ gmf.filter((r'rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h'
+ r'\)\s*\$\{PREFIX\}/include'),
'cp *.h ' + prefix.include)
diff --git a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
index 831f64cd673c98edafed0b26932adfe666abf694..9fea4ecd78eaf28ea9819de1d5abcf6206c59e13 100644
--- a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
@@ -21,10 +21,10 @@ class PacbioDextractor(MakefilePackage):
def edit(self, spec, prefix):
mkdirp(prefix.bin)
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)
- makefile.filter('PATH_HDF5\*s=\s*/usr/local/hdf5', '')
- makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
+ makefile.filter(r'PATH_HDF5\*s=\s*/usr/local/hdf5', '')
+ makefile.filter(r'DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
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)
diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index dc3bf20f8f9b1e90ea06146d34ef65e0c7cd4338..f793d3d8b54e5655e7127a598d9d52741a6a5ef4 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -42,7 +42,7 @@ def patch_config_h_for_intel(self):
#
if '%intel' in self.spec:
filter_file(
- '#define HAVE_GCC_VECTOR_EXTENSIONS /\*\*/',
+ r'#define HAVE_GCC_VECTOR_EXTENSIONS /\*\*/',
'/* #undef HAVE_GCC_VECTOR_EXTENSIONS */',
config_h
)
diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py
index 9fa653e4bf5e68ffdccfb28154b1966814577a35..2103df512f25c2b8e43b93b99dafb5ca718abba9 100644
--- a/var/spack/repos/builtin/packages/r-gtools/package.py
+++ b/var/spack/repos/builtin/packages/r-gtools/package.py
@@ -7,26 +7,38 @@
class RGtools(RPackage):
- """Functions to assist in R programming, including: - assist in developing,
- updating, and maintaining R and R packages ('ask', 'checkRVersion',
- 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse
- logit transformations ('logit', 'inv.logit'), - test if a value is missing,
- empty or contains only NA and NULL values ('invalid'), - manipulate R's
- .Last function ('addLast'), - define macros ('defmacro'), - detect odd and
- even integers ('odd', 'even'), - convert strings containing non-ASCII
- characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a
- binary search ('binsearch'), - sort strings containing both numeric and
- character components ('mixedsort'), - create a factor variable from the
- quantiles of a continuous variable ('quantcut'), - 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."""
+ """Functions to assist in R programming.
+
+ Including:
+ - assist in developing, updating, and maintaining R and R packages
+ ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat')
+ - calculate the logit and inverse logit transformations
+ ('logit', 'inv.logit')
+ - test if a value is missing, empty or contains only NA and NULL values
+ ('invalid')
+ - manipulate R's .Last function ('addLast')
+ - define macros ('defmacro')
+ - detect odd and even integers ('odd', 'even')
+ - convert strings containing non-ASCII characters (like single
+ quotes) to plain ASCII ('ASCIIfy')
+ - perform a binary search ('binsearch')
+ - sort strings containing both numeric and character components
+ ('mixedsort')
+ - create a factor variable from the quantiles of a continuous variable
+ ('quantcut')
+ - 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"
url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz"
diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py
index e037c13f3e5cabd6c3511aaf90159e446d13e60f..9ca6a5aa26fff3453ec9c0637b819257e9f54705 100644
--- a/var/spack/repos/builtin/packages/spark/package.py
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -54,6 +54,6 @@ def setup_environment(self, spack_env, run_env):
# Remove whitespaces, as they can compromise syntax in
# 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)
diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py
index 11d85e9d54879d209b58730c8f80b14be8648873..59cc2751cf92e8a77a1b816d38bf31260cdeab88 100644
--- a/var/spack/repos/builtin/packages/yorick/package.py
+++ b/var/spack/repos/builtin/packages/yorick/package.py
@@ -14,7 +14,7 @@ class Yorick(Package):
files of numbers. Yorick includes an interactive graphics package, and a
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
- most operating systems (\*nix systems, MacOS X, Windows).
+ most operating systems (*nix systems, MacOS X, Windows).
"""
homepage = "http://dhmunro.github.io/yorick-doc/"
diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py
index efb6262ada8429304a3bd9a40d54b8b163864e74..5a69b030d7cdb1878f5c1a53e286741aa400847b 100644
--- a/var/spack/repos/builtin/packages/zfp/package.py
+++ b/var/spack/repos/builtin/packages/zfp/package.py
@@ -32,7 +32,7 @@ class Zfp(MakefilePackage):
def edit(self, spec, prefix):
config_file = FileFilter('Config')
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' %
spec.variants['bsws'].value)