diff --git a/easybuild/easyblocks/generic/binariestarball.py b/easybuild/easyblocks/generic/binariestarball.py index 9737c89224..01c2191d02 100644 --- a/easybuild/easyblocks/generic/binariestarball.py +++ b/easybuild/easyblocks/generic/binariestarball.py @@ -51,10 +51,9 @@ def install_step(self): if os.path.isfile(item): shutil.copy2(os.path.join(self.cfg['start_dir'], item), bindir) # make sure binary has executable permissions - adjust_permissions(os.path.join(bindir, item), stat.S_IXUSR|stat.S_IXGRP|stat.S_IXOTH, add=True) + adjust_permissions(os.path.join(bindir, item), stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH, add=True) self.log.debug("Copied %s to %s and fixed permissions" % (item, bindir)) else: self.log.warning("Skipping non-file %s in %s, not copying it." % (item, self.cfg['start_dir'])) except OSError as err: raise EasyBuildError("Copying binaries in %s to install dir 'bin' failed: %s", self.cfg['start_dir'], err) - diff --git a/easybuild/easyblocks/generic/binary.py b/easybuild/easyblocks/generic/binary.py index a5ab44b464..4aa5823c98 100644 --- a/easybuild/easyblocks/generic/binary.py +++ b/easybuild/easyblocks/generic/binary.py @@ -45,6 +45,7 @@ PREPEND_TO_PATH_DEFAULT = [''] + class Binary(EasyBlock): """ Support for installing software that comes in binary form. diff --git a/easybuild/easyblocks/generic/buildenv.py b/easybuild/easyblocks/generic/buildenv.py index a1a3e0112e..f882a83b8a 100644 --- a/easybuild/easyblocks/generic/buildenv.py +++ b/easybuild/easyblocks/generic/buildenv.py @@ -35,6 +35,7 @@ class BuildEnv(Bundle): """ Build environment of toolchain: only generate module file """ + def make_module_extra(self): """Add all the build environment variables.""" txt = super(BuildEnv, self).make_module_extra() diff --git a/easybuild/easyblocks/generic/bundle.py b/easybuild/easyblocks/generic/bundle.py index 4e492362e4..3eed815bd4 100644 --- a/easybuild/easyblocks/generic/bundle.py +++ b/easybuild/easyblocks/generic/bundle.py @@ -198,7 +198,8 @@ def install_step(self): comp_cnt = len(self.cfg['components']) for idx, cfg in enumerate(self.comp_cfgs): - print_msg("installing bundle component %s v%s (%d/%d)..." % (cfg['name'], cfg['version'], idx+1, comp_cnt)) + print_msg("installing bundle component %s v%s (%d/%d)..." % + (cfg['name'], cfg['version'], idx + 1, comp_cnt)) self.log.info("Installing component %s v%s using easyblock %s", cfg['name'], cfg['version'], cfg.easyblock) comp = cfg.easyblock(cfg) diff --git a/easybuild/easyblocks/generic/cmakemake.py b/easybuild/easyblocks/generic/cmakemake.py index f40381a51a..3682cc56e7 100644 --- a/easybuild/easyblocks/generic/cmakemake.py +++ b/easybuild/easyblocks/generic/cmakemake.py @@ -219,16 +219,16 @@ def configure_step(self, srcdir=None, builddir=None): if self.cfg.get('configure_cmd') == DEFAULT_CONFIGURE_CMD: command = ' '.join([ - self.cfg['preconfigopts'], - DEFAULT_CONFIGURE_CMD, - options_string, - self.cfg['configopts'], - srcdir]) + self.cfg['preconfigopts'], + DEFAULT_CONFIGURE_CMD, + options_string, + self.cfg['configopts'], + srcdir]) else: command = ' '.join([ - self.cfg['preconfigopts'], - self.cfg.get('configure_cmd'), - self.cfg['configopts']]) + self.cfg['preconfigopts'], + self.cfg.get('configure_cmd'), + self.cfg['configopts']]) (out, _) = run_cmd(command, log_all=True, simple=False) diff --git a/easybuild/easyblocks/generic/cmakepythonpackage.py b/easybuild/easyblocks/generic/cmakepythonpackage.py index 9d7b3c71be..a76be1ad3c 100644 --- a/easybuild/easyblocks/generic/cmakepythonpackage.py +++ b/easybuild/easyblocks/generic/cmakepythonpackage.py @@ -41,7 +41,7 @@ class CMakePythonPackage(CMakeMake, PythonPackage): Some packages use cmake to first build and install C Python packages and then put the Python package in lib/pythonX.Y/site-packages. - We install this in a seperate location and generate a module file + We install this in a seperate location and generate a module file which sets the PYTHONPATH. We use the default CMake implementation, and use make_module_extra from PythonPackage. diff --git a/easybuild/easyblocks/generic/conda.py b/easybuild/easyblocks/generic/conda.py index 424d8df721..c3a247c011 100644 --- a/easybuild/easyblocks/generic/conda.py +++ b/easybuild/easyblocks/generic/conda.py @@ -33,7 +33,6 @@ from easybuild.easyblocks.generic.binary import Binary from easybuild.framework.easyconfig import CUSTOM -import easybuild.tools.environment as env from easybuild.tools.run import run_cmd diff --git a/easybuild/easyblocks/generic/configuremakepythonpackage.py b/easybuild/easyblocks/generic/configuremakepythonpackage.py index 5f8abb0c71..b82bdaaa68 100644 --- a/easybuild/easyblocks/generic/configuremakepythonpackage.py +++ b/easybuild/easyblocks/generic/configuremakepythonpackage.py @@ -23,7 +23,8 @@ # along with EasyBuild. If not, see . ## """ -EasyBuild support for Python packages that are configured with 'python configure/make/make install', implemented as an easyblock +EasyBuild support for Python packages that are configured with 'python configure/make/make install', +implemented as an easyblock @author: Bart Verleye (Centre for eResearch, Auckland) @author: Kenneth Hoste (Ghent University) diff --git a/easybuild/easyblocks/generic/craytoolchain.py b/easybuild/easyblocks/generic/craytoolchain.py index a57f5ed74f..32734cb1bb 100644 --- a/easybuild/easyblocks/generic/craytoolchain.py +++ b/easybuild/easyblocks/generic/craytoolchain.py @@ -41,6 +41,7 @@ class CrayToolchain(Bundle): """ Compiler toolchain: generate module file only, nothing to build/install """ + def prepare_step(self, *args, **kwargs): """Prepare build environment (skip loaded of dependencies).""" diff --git a/easybuild/easyblocks/generic/packedbinary.py b/easybuild/easyblocks/generic/packedbinary.py index 6eaa0f8e52..27f05d94a3 100644 --- a/easybuild/easyblocks/generic/packedbinary.py +++ b/easybuild/easyblocks/generic/packedbinary.py @@ -60,4 +60,3 @@ def install_step(self): raise EasyBuildError("Path %s is not a file nor a directory?", srcpath) except OSError as err: raise EasyBuildError("Failed to copy unpacked sources to install directory: %s", err) - diff --git a/easybuild/easyblocks/generic/pythonbundle.py b/easybuild/easyblocks/generic/pythonbundle.py index ee7daf3f29..e036e6ad17 100644 --- a/easybuild/easyblocks/generic/pythonbundle.py +++ b/easybuild/easyblocks/generic/pythonbundle.py @@ -141,7 +141,10 @@ def make_module_extra(self, *args, **kwargs): if self.current_step == 'extensions': new_pylibdirs = self.all_pylibdirs else: - new_pylibdirs = [l for l in self.all_pylibdirs if os.path.exists(os.path.join(self.installdir, l))] + new_pylibdirs = [ + lib_dir for lib_dir in self.all_pylibdirs + if os.path.exists(os.path.join(self.installdir, lib_dir)) + ] for pylibdir in new_pylibdirs: txt += self.module_generator.prepend_paths('PYTHONPATH', pylibdir) diff --git a/easybuild/easyblocks/generic/pythonpackage.py b/easybuild/easyblocks/generic/pythonpackage.py index 06d2ced725..d16ab6d450 100644 --- a/easybuild/easyblocks/generic/pythonpackage.py +++ b/easybuild/easyblocks/generic/pythonpackage.py @@ -663,7 +663,7 @@ def sanity_check_step(self, *args, **kwargs): self.log.info("Detection of downloaded depenencies enabled, checking output of installation command...") patterns = [ 'Downloading .*/packages/.*', # setuptools - 'Collecting .* \(from.*', # pip + r'Collecting .* \(from.*', # pip ] downloaded_deps = [] for pattern in patterns: diff --git a/easybuild/easyblocks/generic/rpm.py b/easybuild/easyblocks/generic/rpm.py index 39762d99a2..cf893e0e30 100644 --- a/easybuild/easyblocks/generic/rpm.py +++ b/easybuild/easyblocks/generic/rpm.py @@ -127,7 +127,7 @@ def configure_step(self): cmd = "rpm --version" (out, _) = run_cmd(cmd, log_all=True, simple=False) - rpmver_re = re.compile("^RPM\s+version\s+(?P[0-9.]+).*") + rpmver_re = re.compile(r"^RPM\s+version\s+(?P[0-9.]+).*") res = rpmver_re.match(out) self.log.debug("RPM version found: %s" % res.group()) @@ -220,9 +220,9 @@ def make_module_req_guess(self): guesses = super(Rpm, self).make_module_req_guess() guesses.update({ - 'PATH': guesses.get('PATH', []) + ['usr/bin', 'sbin', 'usr/sbin'], - 'LD_LIBRARY_PATH': guesses.get('LD_LIBRARY_PATH', []) + ['usr/lib', 'usr/lib64'], - 'MANPATH': guesses.get('MANPATH', []) + ['usr/share/man'], - }) + 'PATH': guesses.get('PATH', []) + ['usr/bin', 'sbin', 'usr/sbin'], + 'LD_LIBRARY_PATH': guesses.get('LD_LIBRARY_PATH', []) + ['usr/lib', 'usr/lib64'], + 'MANPATH': guesses.get('MANPATH', []) + ['usr/share/man'], + }) return guesses