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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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36
var/spack/repos/builtin/packages/chombo/package.py
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@@ -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):

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')
search_for = 'switches = \['
search_for = r'switches = \['
substitute_with = 'switches = [\n' + \
' "-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)
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)

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

@@ -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)

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_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)

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
# 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'))

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']:
# 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:

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

@@ -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)

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

@@ -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)

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.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)

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

@@ -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)

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

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

@@ -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"

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
# 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)

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
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/"

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):
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)