make flake8 code style checks pass in o/*.py through v/*.py + other *.py files in repo

easybuild/easyblocks/__init__.py

@@ -79,7 +79,7 @@ def get_git_revision():
     VERBOSE_VERSION = LooseVersion("%s-r%s" % (VERSION, git_rev))
 
 # extend path so python finds our easyblocks in the subdirectories where they are located
-subdirs = [chr(l) for l in range(ord('a'), ord('z') + 1)] + ['0']
+subdirs = [chr(x) for x in range(ord('a'), ord('z') + 1)] + ['0']
 for subdir in subdirs:
     __path__ = extend_path(__path__, '%s.%s' % (__name__, subdir))
 

easybuild/easyblocks/o/octave.py

@@ -30,12 +30,10 @@
 """
 import os
 
-import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.modules import get_software_root
-from easybuild.tools.run import run_cmd
 
 
 EXTS_FILTER_OCTAVE_PACKAGES = ("octave --eval 'pkg list' | grep packages/%(ext_name)s-%(ext_version)s", '')

easybuild/easyblocks/o/openifs.py

@@ -52,7 +52,7 @@ def configure_step(self):
         env.setvar('OIFS_BUILD', 'opt')
         if self.toolchain.comp_family() == toolchain.GCC:
             env.setvar('OIFS_COMP', 'gnu')
-        elif self.toolchain.comp_family() == toolchain.INTELCOMP: 
+        elif self.toolchain.comp_family() == toolchain.INTELCOMP:
             env.setvar('OIFS_COMP', 'intel')
         else:
             raise EasyBuildError("Unknown compiler used, don't know how to set $OIFS_COMP.")
@@ -103,4 +103,3 @@ def sanity_check_step(self):
         }
 
         super(EB_OpenIFS, self).sanity_check_step(custom_paths=custom_paths)
-

easybuild/easyblocks/o/openssl.py

@@ -44,7 +44,7 @@ def configure_step(self, cmd_prefix=''):
         """
         Configure step
         """
- 
+
         cmd = "%s %s./config --prefix=%s threads shared %s" % (self.cfg['preconfigopts'], cmd_prefix,
                                                                self.installdir, self.cfg['configopts'])
 
@@ -65,16 +65,17 @@ def sanity_check_step(self):
 
         custom_paths = {
             'files': [os.path.join(libdir, x) for x in ['libcrypto.a', 'libcrypto.so', 'libssl.a', 'libssl.so']] +
-                     ['bin/openssl'],
+            ['bin/openssl'],
             'dirs': [],
         }
 
         if LooseVersion(self.version) < LooseVersion("1.1"):
-            custom_paths['files'].extend([os.path.join(libdir, 'libcrypto.so.1.0.0'), os.path.join(libdir, 'libssl.so.1.0.0')])
+            custom_paths['files'].extend([os.path.join(libdir, 'libcrypto.so.1.0.0'),
+                                          os.path.join(libdir, 'libssl.so.1.0.0')])
             custom_paths['dirs'].append(os.path.join(libdir, 'engines'))
         else:
-            custom_paths['files'].extend([os.path.join(libdir, 'libcrypto.so.1.1'), os.path.join(libdir, 'libssl.so.1.1')])
+            custom_paths['files'].extend([os.path.join(libdir, 'libcrypto.so.1.1'),
+                                          os.path.join(libdir, 'libssl.so.1.1')])
             custom_paths['dirs'].append(os.path.join(libdir, 'engines-1.1'))
 
         super(EB_OpenSSL, self).sanity_check_step(custom_paths=custom_paths)
-

easybuild/easyblocks/p/parmetis.py

@@ -148,7 +148,7 @@ def install_step(self):
 
             # libraries
             try:
-                src = os.path.join(self.cfg['start_dir'], 'build' ,'libmetis' ,'libmetis.a')
+                src = os.path.join(self.cfg['start_dir'], 'build', 'libmetis', 'libmetis.a')
                 dst = os.path.join(libdir, 'libmetis.a')
                 shutil.copy2(src, dst)
             except OSError as err:

easybuild/easyblocks/p/pasha.py

@@ -47,7 +47,8 @@ def configure_step(self):
             raise EasyBuildError("TBB module not loaded.")
 
         self.cfg.update('buildopts', "TBB_DIR=%s/tbb MPI_DIR='' MPI_INC='' " % tbb)
-        self.cfg.update('buildopts', 'MPI_CXX="%s" OPM_FLAG="%s"' % (os.getenv('MPICXX'), self.toolchain.get_flag('openmp')))
+        self.cfg.update('buildopts', 'MPI_CXX="%s"' % os.getenv('MPICXX'))
+        self.cfg.update('buildopts', 'OPM_FLAG="%s"' % self.toolchain.get_flag('openmp'))
         self.cfg.update('buildopts', 'MPI_LIB="" MY_CXX="%s" MPICH_IGNORE_CXX_SEEK=1' % os.getenv('CXX'))
 
     def install_step(self):
@@ -60,8 +61,8 @@ def sanity_check_step(self):
         """Custom sanity check for Pasha"""
 
         custom_paths = {
-                        'files':["bin/pasha-%s" % x for x in ["kmergen", "pregraph", "graph"]],
-                        'dirs':[],
-                       }
+            'files': ["bin/pasha-%s" % x for x in ["kmergen", "pregraph", "graph"]],
+            'dirs': [],
+        }
 
         super(EB_Pasha, self).sanity_check_step(custom_paths=custom_paths)

easybuild/easyblocks/p/pbdmpi.py

@@ -32,6 +32,7 @@
 import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.rpackage import RPackage
 
+
 class EB_pbdMPI(RPackage):
     """Support for building/installing pbdMPI."""
 

easybuild/easyblocks/p/pbdslap.py

@@ -30,6 +30,7 @@
 
 from easybuild.easyblocks.generic.rpackage import RPackage
 
+
 class EB_pbdSLAP(RPackage):
     """Support for building/installing pbdSLAP."""
 

easybuild/easyblocks/p/petsc.py

@@ -40,6 +40,7 @@
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
+from easybuild.tools.py2vs3 import string_type
 
 NO_MPI_CXX_EXT_FLAGS = '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX'
 
@@ -126,7 +127,7 @@ def configure_step(self):
                 self.cfg.update('configopts', '--with-cxxflags="%s"' % cxxflags)
                 self.cfg.update('configopts', '--with-fcflags="%s"' % os.getenv('F90FLAGS'))
 
-            if not self.toolchain.comp_family() == toolchain.GCC:  #@UndefinedVariable
+            if not self.toolchain.comp_family() == toolchain.GCC:  # @UndefinedVariable
                 self.cfg.update('configopts', '--with-gnu-compilers=0')
 
             # MPI
@@ -193,7 +194,7 @@ def configure_step(self):
 
             deps = [dep['name'] for dep in self.cfg.dependencies() if not dep['name'] in depfilter]
             for dep in deps:
-                if type(dep) == str:
+                if isinstance(dep, string_type):
                     dep = (dep, dep)
                 deproot = get_software_root(dep[0])
                 if deproot:
@@ -211,22 +212,22 @@ def configure_step(self):
                     # specified order of libs matters!
                     ss_libs = ["UMFPACK", "KLU", "CHOLMOD", "BTF", "CCOLAMD", "COLAMD", "CAMD", "AMD"]
 
-                    suitesparse_inc = [os.path.join(suitesparse, l, "Include")
-                                    for l in ss_libs]
+                    suitesparse_inc = [os.path.join(suitesparse, x, "Include")
+                                       for x in ss_libs]
                     suitesparse_inc.append(os.path.join(suitesparse, "SuiteSparse_config"))
                     inc_spec = "-include=[%s]" % ','.join(suitesparse_inc)
 
-                    suitesparse_libs = [os.path.join(suitesparse, l, "Lib", "lib%s.a" % l.lower())
-                                    for l in ss_libs]
+                    suitesparse_libs = [os.path.join(suitesparse, x, "Lib", "lib%s.a" % x.lower())
+                                        for x in ss_libs]
                     suitesparse_libs.append(os.path.join(suitesparse, "SuiteSparse_config", "libsuitesparseconfig.a"))
                     lib_spec = "-lib=[%s]" % ','.join(suitesparse_libs)
                 else:
                     # CHOLMOD and UMFPACK are part of SuiteSparse (PETSc < 3.5)
                     withdep = "--with-umfpack"
                     inc_spec = "-include=%s" % os.path.join(suitesparse, "UMFPACK", "Include")
                     # specified order of libs matters!
-                    umfpack_libs = [os.path.join(suitesparse, l, "Lib", "lib%s.a" % l.lower())
-                                    for l in ["UMFPACK", "CHOLMOD", "COLAMD", "AMD"]]
+                    umfpack_libs = [os.path.join(suitesparse, x, "Lib", "lib%s.a" % x.lower())
+                                    for x in ["UMFPACK", "CHOLMOD", "COLAMD", "AMD"]]
                     lib_spec = "-lib=[%s]" % ','.join(umfpack_libs)
 
                 self.cfg.update('configopts', ' '.join([withdep + spec for spec in ['=1', inc_spec, lib_spec]]))
@@ -249,7 +250,7 @@ def configure_step(self):
 
             if self.cfg['sourceinstall']:
                 # figure out PETSC_ARCH setting
-                petsc_arch_regex = re.compile("^\s*PETSC_ARCH:\s*(\S+)$", re.M)
+                petsc_arch_regex = re.compile(r"^\s*PETSC_ARCH:\s*(\S+)$", re.M)
                 res = petsc_arch_regex.search(out)
                 if res:
                     self.petsc_arch = res.group(1)

easybuild/easyblocks/p/pgi.py

@@ -82,7 +82,7 @@ class EB_PGI(PackedBinary):
     def extra_options():
         extra_vars = {
             'install_amd': [True, "Install AMD software components", CUSTOM],
-            'install_java': [True, "Install Java JRE for graphical debugger",  CUSTOM],
+            'install_java': [True, "Install Java JRE for graphical debugger", CUSTOM],
             'install_managed': [True, "Install OpenACC Unified Memory Evaluation package", CUSTOM],
             'install_nvidia': [True, "Install CUDA Toolkit Components", CUSTOM],
         }
@@ -133,7 +133,7 @@ def install_step(self):
             'PGI_INSTALL_MANAGED': str(self.cfg['install_managed']).lower(),
             'PGI_INSTALL_NVIDIA': str(self.cfg['install_nvidia']).lower(),
             'PGI_SILENT': 'true',
-            }
+        }
         cmd = "%s ./install" % ' '.join(['%s=%s' % x for x in sorted(pgi_env_vars.items())])
         run_cmd(cmd, log_all=True, simple=True)
 

easybuild/easyblocks/p/primer3.py

@@ -60,9 +60,10 @@ def guess_start_dir(self):
 
     def configure_step(self):
         """Configure Primer3 build by setting make options."""
-        self.cfg.update('buildopts', 'CC="%s" CPP="%s" O_OPTS="%s" all' % (os.getenv('CC'),
-                                                                         os.getenv('CXX'),
-                                                                         os.getenv('CFLAGS')))
+        self.cfg.update('buildopts', 'CC="%s"' % (os.getenv('CC')))
+        self.cfg.update('buildopts', 'CPP="%s"' % (os.getenv('CXX')))
+        self.cfg.update('buildopts', 'O_OPTS="%s"' % (os.getenv('CFLAGS')))
+        self.cfg.update('buildopts', 'all')
 
     # default build_step should be fine
 
@@ -74,10 +75,10 @@ def sanity_check_step(self):
         """Custom sanity check for Primer3."""
 
         custom_paths = {
-                        'files':["%s/%s" % (self.bindir, x) for x in ["primer3_core", "ntdpal",
-                                                                      "oligotm", "long_seq_tm_test"]],
-                        'dirs':[]
-                       }
+            'files': ["%s/%s" % (self.bindir, x) for x in ["primer3_core", "ntdpal",
+                                                           "oligotm", "long_seq_tm_test"]],
+            'dirs': []
+        }
 
         super(EB_Primer3, self).sanity_check_step(custom_paths=custom_paths)
 

easybuild/easyblocks/p/psmpi.py

@@ -73,7 +73,7 @@ def configure_step(self):
             toolchain.GCC: 'gcc',
             toolchain.INTELCOMP: 'intel',
             # TODO: Include PGI as soon as it is available as toolchain
-            #toolchain.PGI: 'pgi',
+            # toolchain.PGI: 'pgi',
         }
 
         # Set confset

easybuild/easyblocks/p/pyquante.py

@@ -46,4 +46,3 @@ def configure_step(self):
             self.log.warn("Not building Libint extension")
 
         super(EB_PyQuante, self).configure_step()
-

easybuild/easyblocks/p/pyzmq.py

@@ -44,9 +44,8 @@ def configure_step(self):
             self.sitecfg = """[build_ext]
 library_dirs = %(zmq)s/lib
 include_dirs = %(zmq)s/include
-""" % { 'zmq': root_zmq }
+""" % {'zmq': root_zmq}
         else:
             self.log.info("External ZeroMQ not found, PyZMQ will (try to) use shipped ZeroMQ.")
 
         super(EB_PyZMQ, self).configure_step()
-

easybuild/easyblocks/q/qscintilla.py

@@ -88,7 +88,7 @@ def build_step(self):
         """Custom build procedure for QScintilla."""
 
         # make sure that $CXXFLAGS is being passed down
-        self.cfg.update('buildopts', 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"')
+        self.cfg.update('buildopts', r'CXXFLAGS="$CXXFLAGS \$(DEFINES)"')
 
         super(EB_QScintilla, self).build_step()
 
@@ -117,7 +117,7 @@ def install_step(self):
             # in case PyQt5's sip was installed in directories that are specific to each version of python
             # as could happen with multi_deps
             pyqt_sipdir = find_glob_pattern(os.path.join(self.pyqt_root, 'share', 'python%s*' % pyshortver,
-                                            'site-packages', 'sip', self.pyqt_pkg_name), False)
+                                                         'site-packages', 'sip', self.pyqt_pkg_name), False)
             # fall back to a single sipdir
             if not pyqt_sipdir:
                 pyqt_sipdir = os.path.join(self.pyqt_root, 'share', 'sip', self.pyqt_pkg_name)

easybuild/easyblocks/q/qt.py

@@ -175,7 +175,7 @@ def sanity_check_step(self):
             elif myarch == POWER:
                 self.log.debug("Skipping check for qtwebengine, since it is not supported on POWER.")
             else:
-                qtwebengine_libs = ['libQt%s%s.%s' % (libversion, l, shlib_ext) for l in ['WebEngine', 'WebEngineCore']]
+                qtwebengine_libs = ['libQt%s%s.%s' % (libversion, x, shlib_ext) for x in ['WebEngine', 'WebEngineCore']]
                 custom_paths['files'].extend([os.path.join('lib', lib) for lib in qtwebengine_libs])
 
         if LooseVersion(self.version) >= LooseVersion('4'):

easybuild/easyblocks/r/__init__.py

@@ -27,4 +27,4 @@
 
 author: Kenneth Hoste (Ghent University)
 """
-from easybuild.easyblocks.r.r import *
+from easybuild.easyblocks.r.r import *  # noqa

easybuild/easyblocks/r/r.py

@@ -91,7 +91,7 @@ def configure_step(self):
         out = ConfigureMake.configure_step(self)
 
         # check output of configure command to verify BLAS/LAPACK settings
-        ext_libs_regex = re.compile("External libraries:.*BLAS\((?P<BLAS>.*)\).*LAPACK\((?P<LAPACK>.*)\)")
+        ext_libs_regex = re.compile(r"External libraries:.*BLAS\((?P<BLAS>.*)\).*LAPACK\((?P<LAPACK>.*)\)")
         res = ext_libs_regex.search(out)
         if res:
             for lib in ['BLAS', 'LAPACK']:
@@ -135,7 +135,7 @@ def sanity_check_step(self):
 
         custom_paths = {
             'files': ['bin/%s' % x for x in ['R', 'Rscript']] +
-                     [(os.path.join('lib64', 'R', f), os.path.join('lib', 'R', f)) for f in libfiles],
+            [(os.path.join('lib64', 'R', f), os.path.join('lib', 'R', f)) for f in libfiles],
             'dirs': [],
         }
         super(EB_R, self).sanity_check_step(custom_paths=custom_paths)

easybuild/easyblocks/r/rmpi.py

@@ -46,15 +46,15 @@ def run(self):
         mpi_types = {
             toolchain.MPI_TYPE_OPENMPI: "OPENMPI",
             toolchain.MPI_TYPE_MPICH: "MPICH",
-            #toolchain.MPI_TYPE_LAM: "LAM",  # no support for LAM yet
+            # toolchain.MPI_TYPE_LAM: "LAM",  # no support for LAM yet
         }
         # type of MPI
         # MPI_TYPE does not distinguish between MPICH and IntelMPI, which is why we also check mpi_family()
         mpi_type = self.toolchain.mpi_family()
         Rmpi_type = mpi_types[self.toolchain.MPI_TYPE]
-        # Rmpi versions 0.6-4 and up support INTELMPI (using --with-Rmpi-type=INTELMPI) 
+        # Rmpi versions 0.6-4 and up support INTELMPI (using --with-Rmpi-type=INTELMPI)
         if ((LooseVersion(self.version) >= LooseVersion('0.6-4')) and (mpi_type == toolchain.INTELMPI)):
-             Rmpi_type = 'INTELMPI'
+            Rmpi_type = 'INTELMPI'
 
         self.log.debug("Setting configure args for Rmpi")
         self.configureargs = [

easybuild/easyblocks/r/rosetta.py

@@ -100,9 +100,9 @@ def configure_step(self):
 
         self.detect_cxx()
         cxx_ver = None
-        if self.toolchain.comp_family() in [toolchain.GCC]:  #@UndefinedVariable
+        if self.toolchain.comp_family() in [toolchain.GCC]:  # @UndefinedVariable
             cxx_ver = '.'.join(get_software_version('GCC').split('.')[:2])
-        elif self.toolchain.comp_family() in [toolchain.INTELCOMP]:  #@UndefinedVariable
+        elif self.toolchain.comp_family() in [toolchain.INTELCOMP]:  # @UndefinedVariable
             cxx_ver = '.'.join(get_icc_version().split('.')[:2])
         else:
             raise EasyBuildError("Don't know how to determine C++ compiler version.")
@@ -137,7 +137,7 @@ def configure_step(self):
             "           'program_path': %s," % str(paths),
             "           'flags': {",
             "               'compile': %s," % str(flags),
-            #"              'mode': %s," % str(o_flags),
+            # "              'mode': %s," % str(o_flags),
             "           },",
             "           'defines': %s," % str(defines),
             "       },",
@@ -166,7 +166,7 @@ def configure_step(self):
 
         # make sure specified compiler version is accepted by patching it in
         os_fp = os.path.join(self.srcdir, "tools/build/options.settings")
-        cxxver_re = re.compile('(.*"%s".*)(,\s*"\*"\s*],.*)' % self.cxx, re.M)
+        cxxver_re = re.compile(r'(.*"%s".*)(,\s*"\*"\s*],.*)' % self.cxx, re.M)
         for line in fileinput.input(os_fp, inplace=1, backup='.orig.eb'):
             line = cxxver_re.sub(r'\1, "%s"\2' % cxx_ver, line)
             sys.stdout.write(line)
@@ -208,7 +208,7 @@ def install_step(self):
             except OSError as err:
                 raise EasyBuildError("Failed to walk build/src dir: %s", err)
             # copy binaries/libraries to install dir
-            lib_re = re.compile("^lib.*\.%s$" % shlib_ext)
+            lib_re = re.compile(r"^lib.*\.%s$" % shlib_ext)
             try:
                 for fil in os.listdir(builddir):
                     srcfile = os.path.join(builddir, fil)
@@ -278,7 +278,7 @@ def sanity_check_step(self):
         binaries = ["AbinitioRelax", "backrub", "cluster", "combine_silent", "extract_pdbs",
                     "idealize_jd2", "packstat", "relax", "score_jd2", "score"]
         custom_paths = {
-            'files':["bin/%s.%slinux%srelease" % (x, infix, self.cxx) for x in binaries],
-            'dirs':[],
+            'files': ["bin/%s.%slinux%srelease" % (x, infix, self.cxx) for x in binaries],
+            'dirs': [],
         }
         super(EB_Rosetta, self).sanity_check_step(custom_paths=custom_paths)

easybuild/easyblocks/r/ruby.py

@@ -38,7 +38,7 @@
 
 class EB_Ruby(ConfigureMake):
     """Building and installing Ruby including support for gems"""
-    
+
     def prepare_for_extensions(self):
         """Sets default class and filter for gems"""
         self.cfg['exts_defaultclass'] = 'RubyGem'

easybuild/easyblocks/s/samtools.py

@@ -59,7 +59,7 @@ def __init__(self, *args, **kwargs):
 
         if LooseVersion(self.version) < LooseVersion('1.0'):
             self.bin_files += ["bcftools/vcfutils.pl", "bcftools/bcftools"]
-            self.include_files += ["bgzf.h", "faidx.h",  "khash.h", "klist.h", "knetfile.h", "razf.h",
+            self.include_files += ["bgzf.h", "faidx.h", "khash.h", "klist.h", "knetfile.h", "razf.h",
                                    "kseq.h", "ksort.h", "kstring.h"]
         elif LooseVersion(self.version) >= LooseVersion('1.0'):
             self.bin_files += ["misc/plot-bamstats", "misc/seq_cache_populate.pl"]