flake8: fix flake8 issues with invalid escapes

- 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

16 files changed, 80 insertions, 67 deletions

diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py
index 0044edf240..332dae343f 100644
--- a/var/spack/repos/builtin/packages/chombo/package.py
+++ b/var/spack/repos/builtin/packages/chombo/package.py
@@ -45,7 +45,7 @@ class Chombo(MakefilePackage):
 
         # 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 @@ class Chombo(MakefilePackage):
         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 ba027538bd..a1768d71b9 100644
--- a/var/spack/repos/builtin/packages/ldc/package.py
+++ b/var/spack/repos/builtin/packages/ldc/package.py
@@ -59,7 +59,7 @@ class Ldc(CMakePackage):
 
         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 e9eea919e2..578da42181 100644
--- a/var/spack/repos/builtin/packages/libceed/package.py
+++ b/var/spack/repos/builtin/packages/libceed/package.py
@@ -51,10 +51,11 @@ class Libceed(Package):
         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 18cdd064c8..8e44be5596 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 93c17279e0..0f6cd8a46b 100644
--- a/var/spack/repos/builtin/packages/multitail/package.py
+++ b/var/spack/repos/builtin/packages/multitail/package.py
@@ -33,11 +33,11 @@ class Multitail(MakefilePackage):
 
         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 f054e094e2..234708f7a2 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -233,8 +233,8 @@ class Mumps(Package):
                 # 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 dbd19eb554..a522af8cf0 100644
--- a/var/spack/repos/builtin/packages/nek5000/package.py
+++ b/var/spack/repos/builtin/packages/nek5000/package.py
@@ -158,7 +158,7 @@ class Nek5000(Package):
 
             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 534716d005..07738d14ee 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 f41440570a..d904e3ece2 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 2e2abca958..0ccb68842b 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 @@ class PacbioDazzDb(MakefilePackage):
         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 831f64cd67..9fea4ecd78 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 dc3bf20f8f..f793d3d8b5 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -42,7 +42,7 @@ class Pixman(AutotoolsPackage):
         #
         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 9fa653e4bf..2103df512f 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 @@ from spack import *
 
 
 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 e037c13f3e..9ca6a5aa26 100644
--- a/var/spack/repos/builtin/packages/spark/package.py
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -54,6 +54,6 @@ class Spark(Package):
 
         # 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 11d85e9d54..59cc2751cf 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 efb6262ada..5a69b030d7 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)