diff options
Diffstat (limited to 'var/spack')
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) |