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Created March 26, 2020 11:09
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pep8 diff
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pep8.diff
diff --git a/contrib/hooks/hpc2n_hooks.py b/contrib/hooks/hpc2n_hooks.py
index ad93fe88e..4e00513ba 100644
--- a/contrib/hooks/hpc2n_hooks.py
+++ b/contrib/hooks/hpc2n_hooks.py
@@ -13,6 +13,8 @@ from easybuild.tools.systemtools import get_shared_lib_ext
# Add/remove dependencies and/or patches
# Access to the raw values before templating and such.
+
+
def parse_hook(ec, *args, **kwargs):
# Internal helper function
@@ -58,7 +60,7 @@ def parse_hook(ec, *args, **kwargs):
if LooseVersion(ec.version) >= LooseVersion('3'):
pmix_version = '2.2.1'
if LooseVersion(ec.version) >= LooseVersion('4'):
- pmix_version = '3.0.2' # OpenMPI 4.0.0 is not compatible with PMIx 3.1.x
+ pmix_version = '3.0.2' # OpenMPI 4.0.0 is not compatible with PMIx 3.1.x
extra_deps.append(('PMIx', pmix_version))
# Use of external PMIx requires external libevent
diff --git a/easybuild/base/fancylogger.py b/easybuild/base/fancylogger.py
index f24b336b7..a6103705e 100644
--- a/easybuild/base/fancylogger.py
+++ b/easybuild/base/fancylogger.py
@@ -224,6 +224,7 @@ def getLevelInt(level_name):
class FancyStreamHandler(logging.StreamHandler):
"""The logging StreamHandler with uniform named arg in __init__ for selecting the stream."""
+
def __init__(self, stream=None, stdout=None):
"""Initialize the stream (default is sys.stderr)
- stream : a specific stream to use
@@ -245,6 +246,7 @@ class FancyLogRecord(logging.LogRecord):
This class defines a custom log record.
Adding extra specifiers is as simple as adding attributes to the log record
"""
+
def __init__(self, *args, **kwargs):
logging.LogRecord.__init__(self, *args, **kwargs)
# modify custom specifiers here
@@ -782,7 +784,7 @@ def getAllExistingLoggers():
"""
# not-so-well documented manager (in 2.6 and later)
# return list of (name,logger) tuple
- return [x for x in logging.Logger.manager.loggerDict.items()]+[(logging.root.name, logging.root)]
+ return [x for x in logging.Logger.manager.loggerDict.items()] + [(logging.root.name, logging.root)]
def getAllNonFancyloggers():
diff --git a/easybuild/base/generaloption.py b/easybuild/base/generaloption.py
index 0a301137a..07a5f1ad5 100644
--- a/easybuild/base/generaloption.py
+++ b/easybuild/base/generaloption.py
@@ -307,7 +307,7 @@ class ExtOption(CompleterOption):
empty = get_empty_add_flex(lvalue, self=self)
if empty in value:
ind = value.index(empty)
- lvalue = value[:ind] + default + value[ind+1:]
+ lvalue = value[:ind] + default + value[ind + 1:]
else:
lvalue = value
elif action == "regex":
@@ -1573,7 +1573,7 @@ class GeneralOption(object):
(opt_name, default, action))
else:
if opt_value == default and ((action in ('store_true',) +
- ExtOption.EXTOPTION_LOG and default is False) or
+ ExtOption.EXTOPTION_LOG and default is False) or
(action in ('store_false',) and default is True)):
if hasattr(self.parser.option_class, 'ENABLE') and \
hasattr(self.parser.option_class, 'DISABLE'):
@@ -1588,10 +1588,10 @@ class GeneralOption(object):
if default is not None:
if action == 'add_flex' and default:
for ind, elem in enumerate(opt_value):
- if elem == default[0] and opt_value[ind:ind+len(default)] == default:
+ if elem == default[0] and opt_value[ind:ind + len(default)] == default:
empty = get_empty_add_flex(opt_value, self=self)
# TODO: this will only work for tuples and lists
- opt_value = opt_value[:ind] + type(opt_value)([empty]) + opt_value[ind+len(default):]
+ opt_value = opt_value[:ind] + type(opt_value)([empty]) + opt_value[ind + len(default):]
# only the first occurence
break
elif hasattr(opt_value, '__neg__'):
diff --git a/easybuild/base/optcomplete.py b/easybuild/base/optcomplete.py
index c7a5e0e1a..f0c172d9f 100644
--- a/easybuild/base/optcomplete.py
+++ b/easybuild/base/optcomplete.py
@@ -186,6 +186,7 @@ class NoneCompleter(Completer):
class ListCompleter(Completer):
"""Completes by filtering using a fixed list of strings."""
+
def __init__(self, stringlist):
self.olist = stringlist
@@ -263,6 +264,7 @@ class DirCompleter(Completer):
class KnownHostsCompleter(Completer):
"""Completes a list of known hostnames"""
+
def _call(self, **kwargs):
if SHELL == BASH:
return "_known_hosts"
@@ -310,6 +312,7 @@ class RegexCompleter(Completer):
class CompleterOption(OPTION_CLASS):
"""optparse Option class with completer attribute"""
+
def __init__(self, *args, **kwargs):
completer = kwargs.pop('completer', None)
OPTION_CLASS.__init__(self, *args, **kwargs)
@@ -587,7 +590,7 @@ def autocomplete(parser, arg_completer=None, opt_completer=None, subcmd_complete
'completer_kwargs%s' % str(completer_kwargs),
# 'completer_completions %s' % completer_completions,
'completions %s' % completions,
- ])
+ ])
if isinstance(debugfn, logging.Logger):
debugfn.debug(txt)
else:
diff --git a/easybuild/base/rest.py b/easybuild/base/rest.py
index 842c0bd3c..7e5ed6bc2 100644
--- a/easybuild/base/rest.py
+++ b/easybuild/base/rest.py
@@ -228,6 +228,7 @@ class RequestBuilder(object):
To understand the method(...) calls, check out github.client.Client.
'''
+
def __init__(self, client):
"""Constructor"""
self.client = client
@@ -288,6 +289,7 @@ class RestClient(object):
try to validate the url you feed it. On the other hand, it
automatically supports the full API--so why should you care?
"""
+
def __init__(self, *args, **kwargs):
"""We create a client with the given arguments"""
self.client = Client(*args, **kwargs)
diff --git a/easybuild/base/testing.py b/easybuild/base/testing.py
index e7d75b25a..c78e11818 100644
--- a/easybuild/base/testing.py
+++ b/easybuild/base/testing.py
@@ -60,7 +60,7 @@ def nicediff(txta, txtb, offset=5):
res_idx = []
# very bruteforce
for didx in different_idx:
- for idx in range(max(didx-offset, 0), min(didx+offset, len(diff)-1)):
+ for idx in range(max(didx - offset, 0), min(didx + offset, len(diff) - 1)):
if idx not in res_idx:
res_idx.append(idx)
res_idx.sort()
diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 8ba572464..67cede96b 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -416,7 +416,7 @@ class EasyBlock(object):
# this *must* be of typ int, nothing else
# no 'isinstance(..., int)', since that would make True/False also acceptable
- if type(patch_spec[1]) == int:
+ if isinstance(patch_spec[1], int):
level = patch_spec[1]
elif isinstance(patch_spec[1], string_type):
# non-patch files are assumed to be files to copy
@@ -2161,7 +2161,7 @@ class EasyBlock(object):
# always go back to original work dir to avoid running stuff from a dir that no longer exists
change_dir(self.orig_workdir)
- tup = (ext.name, ext.version or '', idx+1, exts_cnt)
+ tup = (ext.name, ext.version or '', idx + 1, exts_cnt)
print_msg("installing extension %s %s (%d/%d)..." % tup, silent=self.silent)
if self.dry_run:
diff --git a/easybuild/framework/easyconfig/__init__.py b/easybuild/framework/easyconfig/__init__.py
index cf6a11c4e..8fc93cd78 100644
--- a/easybuild/framework/easyconfig/__init__.py
+++ b/easybuild/framework/easyconfig/__init__.py
@@ -28,6 +28,7 @@
# TODO cleanup to be evaluated for 2.0 release
# is used (esp CUSTOM) in some easyblocks
+from easybuild.framework.easyconfig.easyconfig import EasyConfig
from easybuild.framework.easyconfig.default import ALL_CATEGORIES
globals().update(ALL_CATEGORIES)
@@ -35,4 +36,3 @@ globals().update(ALL_CATEGORIES)
EASYCONFIGS_PKG_SUBDIR = 'easyconfigs'
# is used in some tools
-from easybuild.framework.easyconfig.easyconfig import EasyConfig
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index d6033eb7c..75220b33f 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -106,6 +106,7 @@ _easyconfigs_cache = {}
def handle_deprecated_or_replaced_easyconfig_parameters(ec_method):
"""Decorator to handle deprecated/replaced easyconfig parameters."""
+
def new_ec_method(self, key, *args, **kwargs):
"""Check whether any replace easyconfig parameters are still used"""
# map deprecated parameters to their replacements, issue deprecation warning(/error)
@@ -1345,7 +1346,7 @@ class EasyConfig(object):
# (true) boolean value simply indicates that a system toolchain is used
elif isinstance(tc_spec, bool) and tc_spec:
- tc = {'name': SYSTEM_TOOLCHAIN_NAME, 'version': ''}
+ tc = {'name': SYSTEM_TOOLCHAIN_NAME, 'version': ''}
# two-element list/tuple value indicates custom toolchain specification
elif isinstance(tc_spec, (list, tuple,)):
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index 0ac6c380f..61da07d20 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -95,6 +95,7 @@ def get_format_version(txt):
class NestedDict(dict):
"""A nested dictionary, with tracking of depth and parent"""
+
def __init__(self, parent, depth):
"""Initialise NestedDict instance"""
dict.__init__(self)
@@ -121,6 +122,7 @@ class NestedDict(dict):
class TopNestedDict(NestedDict):
"""The top level nested dictionary (depth 0, parent is itself)"""
+
def __init__(self, parent=None, depth=None):
"""Initialise TopNestedDict instance"""
# parent and depth are ignored; just to support same init for copier
@@ -129,6 +131,7 @@ class TopNestedDict(NestedDict):
class Squashed(object):
"""Class to ease the squashing of OrderedVersionOperators and OrderedToolchainVersionOperators"""
+
def __init__(self):
"""Initialise Squashed instance"""
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 853449729..7287ab0ed 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -346,7 +346,7 @@ class FormatOneZero(EasyConfigFormatConfigObj):
'iterabove': {}, # comment above elements of iterable values
'iterinline': {}, # inline comments on elements of iterable values
'tail': [], # comment at the end of the easyconfig file
- }
+ }
parsed_ec = self.get_config_dict()
@@ -514,7 +514,7 @@ def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
dep_block = reg_dep_block.search(block_contents)
if dep_block:
dependencies = eval(dep_block.group(1))
- if type(dependencies) == list:
+ if isinstance(dependencies, list):
block['dependencies'] = dependencies
else:
block['dependencies'] = [dependencies]
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 5f002de6f..1a3c86d1b 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -128,8 +128,8 @@ class EasyConfigFormatConfigObj(EasyConfigFormat):
else:
start_section = reg.start()
last_n = 100
- pre_section_tail = txt[start_section-last_n:start_section]
- sections_head = txt[start_section:start_section+last_n]
+ pre_section_tail = txt[start_section - last_n:start_section]
+ sections_head = txt[start_section:start_section + last_n]
self.log.debug('Sections start at index %s, %d-chars context:\n"""%s""""\n<split>\n"""%s..."""',
start_section, last_n, pre_section_tail, sections_head)
@@ -199,7 +199,7 @@ class EasyConfigFormatConfigObj(EasyConfigFormat):
exc_tb = sys.exc_info()[2]
if exc_tb.tb_next is not None:
err_msg += " (line %d)" % exc_tb.tb_next.tb_lineno
- raise EasyBuildError("Parsing easyconfig file failed: %s", err_msg)
+ raise EasyBuildError("Parsing easyconfig file failed: %s", err_msg)
self.log.debug("pyheader parsed cfg: %s", cfg)
diff --git a/easybuild/framework/easyconfig/format/yeb.py b/easybuild/framework/easyconfig/format/yeb.py
index 6215500f8..e75e136cd 100644
--- a/easybuild/framework/easyconfig/format/yeb.py
+++ b/easybuild/framework/easyconfig/format/yeb.py
@@ -115,7 +115,7 @@ class FormatYeb(EasyConfigFormat):
yaml_header = []
for i, line in enumerate(lines):
if line.startswith(YAML_DIR):
- if lines[i+1].startswith(YAML_SEP):
+ if lines[i + 1].startswith(YAML_SEP):
yaml_header.extend([lines.pop(i), lines.pop(i)])
injected_constants = ['__CONSTANTS__: ']
diff --git a/easybuild/framework/easyconfig/style.py b/easybuild/framework/easyconfig/style.py
index 8adc85594..b4dc2c7d6 100644
--- a/easybuild/framework/easyconfig/style.py
+++ b/easybuild/framework/easyconfig/style.py
@@ -82,7 +82,7 @@ def _eb_check_trailing_whitespace(physical_line, lines, line_number, checker_sta
https://pycodestyle.readthedocs.io/en/latest/developer.html#contribute
"""
# apparently this is not the same as physical_line line?!
- line = lines[line_number-1]
+ line = lines[line_number - 1]
if COMMENT_REGEX.match(line):
return None
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 37403b352..34b1a9829 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -264,6 +264,7 @@ def tweak_one(orig_ec, tweaked_ec, tweaks, targetdir=None):
class TcDict(dict):
"""A special dict class that represents trivial toolchains properly."""
+
def __repr__(self):
return "{'name': '%(name)s', 'version': '%(version)s'}" % self
@@ -612,7 +613,7 @@ def select_or_generate_ec(fp, paths, specs):
# if a value is specified, use that, even if it's not available yet
selected_val = val
# promote value to list if deemed appropriate
- if vals and type(vals[0]) == list and not type(val) == list:
+ if vals and isinstance(vals[0], list) and not isinstance(val, list):
_log.debug("Promoting type of %s value to list, since original value was." % param)
specs[param] = [val]
_log.debug("%s is specified, so using it (even though it's not available yet): %s" % (param, selected_val))
diff --git a/easybuild/framework/extension.py b/easybuild/framework/extension.py
index b44d5759f..f99af4070 100644
--- a/easybuild/framework/extension.py
+++ b/easybuild/framework/extension.py
@@ -85,6 +85,7 @@ class Extension(object):
"""
Support for installing extensions.
"""
+
def __init__(self, mself, ext, extra_params=None):
"""
Constructor for Extension class
diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 2e8c487a2..f2140cd80 100644
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -625,7 +625,8 @@ def stage1(tmpdir, sourcepath, distribute_egg_dir, forcedversion):
# figure out EasyBuild version via eb command line
# note: EasyBuild uses some magic to determine the EasyBuild version based on the versions of the individual pkgs
- pattern = "This is EasyBuild (?P<version>%(v)s) \(framework: %(v)s, easyblocks: %(v)s\)" % {'v': '[0-9.]*[a-z0-9]*'}
+ pattern = r"This is EasyBuild (?P<version>%(v)s) \(framework: %(v)s, easyblocks: %(v)s\)" % {
+ 'v': '[0-9.]*[a-z0-9]*'}
version_re = re.compile(pattern)
version_out_file = os.path.join(tmpdir, 'eb_version.out')
eb_version_cmd = 'from easybuild.tools.version import this_is_easybuild; print(this_is_easybuild())'
diff --git a/easybuild/scripts/mk_tmpl_easyblock_for.py b/easybuild/scripts/mk_tmpl_easyblock_for.py
index 65a0bc13f..32ff59833 100644
--- a/easybuild/scripts/mk_tmpl_easyblock_for.py
+++ b/easybuild/scripts/mk_tmpl_easyblock_for.py
@@ -46,7 +46,7 @@ parser.add_option("--parent", default="EasyBlock",
help="Name of parent easyblock for this easyblock (default: 'EasyBlock').")
parser.add_option("--letter-prefix", default=False, action="store_true",
help="Whether or not to prefix the easyblock path with a letter directory (default: False)")
-
+
(options, args) = parser.parse_args()
@@ -68,7 +68,7 @@ if not os.path.isdir(easyblocks_repo_path):
# determine path for easyblock
if options.letter_prefix:
letter = name.lower()[0]
- if not ord(letter) in range(ord('a'),ord('z')+1):
+ if not ord(letter) in range(ord('a'), ord('z') + 1):
letter = '0'
easyblock_path = os.path.join(easyblocks_repo_path, letter, "%s.py" % name.lower())
else:
@@ -147,8 +147,8 @@ class %(class_name)s(%(parent)s):
# always use env.setvar instead of os.putenv or os.environ for defining environment variables
env.setvar('CUSTOM_ENV_VAR', 'foo')
-
- cmd = "configure command"
+
+ cmd = "configure command"
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
# complete configuration with configure_method of parent
@@ -172,13 +172,13 @@ class %(class_name)s(%(parent)s):
\"\"\"Custom built-in test procedure for %(name)s.\"\"\"
if self.cfg['runtest']:
- cmd = "test-command"
+ cmd = "test-command"
run_cmd(cmd, simple=True, log_all=True, log_ok=True)
def install_step(self):
\"\"\"Custom install procedure for %(name)s.\"\"\"
-
- cmd = "install command"
+
+ cmd = "install command"
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
def sanity_check_step(self):
diff --git a/easybuild/toolchains/cgmpolf.py b/easybuild/toolchains/cgmpolf.py
index d0615734c..556e4efe9 100644
--- a/easybuild/toolchains/cgmpolf.py
+++ b/easybuild/toolchains/cgmpolf.py
@@ -41,4 +41,3 @@ class Cgmpolf(Cgmpich, OpenBLAS, ScaLAPACK, Fftw):
"""Compiler toolchain with Clang, GFortran, MPICH, OpenBLAS, ScaLAPACK and FFTW."""
NAME = 'cgmpolf'
SUBTOOLCHAIN = Cgmpich.NAME
-
diff --git a/easybuild/toolchains/compiler/clang.py b/easybuild/toolchains/compiler/clang.py
index cbf5aaa5a..97aa22b95 100644
--- a/easybuild/toolchains/compiler/clang.py
+++ b/easybuild/toolchains/compiler/clang.py
@@ -43,7 +43,7 @@ class Clang(Compiler):
"""Clang compiler class"""
COMPILER_MODULE_NAME = ['Clang']
-
+
COMPILER_FAMILY = TC_CONSTANT_CLANG
# Don't set COMPILER_FAMILY in this class because Clang does not have
@@ -58,10 +58,10 @@ class Clang(Compiler):
'unroll': 'funroll-loops',
'loop-vectorize': ['fvectorize'],
'basic-block-vectorize': ['fslp-vectorize'],
- 'optarch':'march=native',
+ 'optarch': 'march=native',
# Clang's options do not map well onto these precision modes. The flags enable and disable certain classes of
# optimizations.
- #
+ #
# -fassociative-math: allow re-association of operands in series of floating-point operations, violates the
# ISO C and C++ language standard by possibly changing computation result.
# -freciprocal-math: allow optimizations to use the reciprocal of an argument rather than perform division.
@@ -114,4 +114,3 @@ class Clang(Compiler):
if self.options.get('32bit', None):
raise EasyBuildError("_set_compiler_vars: 32bit set, but no support yet for 32bit Clang in EasyBuild")
-
diff --git a/easybuild/toolchains/compiler/cuda.py b/easybuild/toolchains/compiler/cuda.py
index 6bfcdfa14..2fc19459f 100644
--- a/easybuild/toolchains/compiler/cuda.py
+++ b/easybuild/toolchains/compiler/cuda.py
@@ -45,7 +45,7 @@ class Cuda(Compiler):
COMPILER_CUDA_FAMILY = TC_CONSTANT_CUDA
COMPILER_CUDA_UNIQUE_OPTS = {
- # handle '-gencode arch=X,code=Y' nvcc options (also -arch, -code)
+ # handle '-gencode arch=X,code=Y' nvcc options (also -arch, -code)
# -arch always needs to be specified, -code is optional (defaults to -arch if missing)
# -gencode is syntactic sugar for combining -arch/-code
# multiple values can be specified
@@ -87,7 +87,7 @@ class Cuda(Compiler):
# always C++ compiler flags, even for C!
# note: using $LIBS will yield the use of -lcudart in Xlinker, which is silly, but fine
-
+
cuda_flags = [
'Xcompiler="%s"' % str(self.variables['CXXFLAGS']),
'Xlinker="%s %s"' % (str(self.variables['LDFLAGS']), str(self.variables['LIBS'])),
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index dacecd3b1..8ec1ce2af 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -50,7 +50,7 @@ class Gcc(Compiler):
COMPILER_UNIQUE_OPTS = {
'loop': (False, "Automatic loop parallellisation"),
'f2c': (False, "Generate code compatible with f2c and f77"),
- 'lto':(False, "Enable Link Time Optimization"),
+ 'lto': (False, "Enable Link Time Optimization"),
}
COMPILER_UNIQUE_OPTION_MAP = {
'i8': 'fdefault-integer-8',
@@ -71,16 +71,17 @@ class Gcc(Compiler):
# used when 'optarch' toolchain option is enabled (and --optarch is not specified)
COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
- (systemtools.AARCH32, systemtools.ARM): 'mcpu=native', # implies -march=native and -mtune=native
- (systemtools.AARCH64, systemtools.ARM): 'mcpu=native', # since GCC 6; implies -march=native and -mtune=native
+ (systemtools.AARCH32, systemtools.ARM): 'mcpu=native', # implies -march=native and -mtune=native
+ (systemtools.AARCH64, systemtools.ARM): 'mcpu=native', # since GCC 6; implies -march=native and -mtune=native
(systemtools.POWER, systemtools.POWER): 'mcpu=native', # no support for -march on POWER; implies -mtune=native
- (systemtools.POWER, systemtools.POWER_LE): 'mcpu=native', # no support for -march on POWER; implies -mtune=native
- (systemtools.X86_64, systemtools.AMD): 'march=native', # implies -mtune=native
- (systemtools.X86_64, systemtools.INTEL): 'march=native', # implies -mtune=native
+ # no support for -march on POWER; implies -mtune=native
+ (systemtools.POWER, systemtools.POWER_LE): 'mcpu=native',
+ (systemtools.X86_64, systemtools.AMD): 'march=native', # implies -mtune=native
+ (systemtools.X86_64, systemtools.INTEL): 'march=native', # implies -mtune=native
}
# used with --optarch=GENERIC
COMPILER_GENERIC_OPTION = {
- (systemtools.AARCH32, systemtools.ARM): 'mcpu=generic-armv7', # implies -march=armv7 and -mtune=generic-armv7
+ (systemtools.AARCH32, systemtools.ARM): 'mcpu=generic-armv7', # implies -march=armv7 and -mtune=generic-armv7
(systemtools.AARCH64, systemtools.ARM): 'mcpu=generic', # implies -march=armv8-a and -mtune=generic
(systemtools.POWER, systemtools.POWER): 'mcpu=powerpc64', # no support for -march on POWER
(systemtools.POWER, systemtools.POWER_LE): 'mcpu=powerpc64le', # no support for -march on POWER
@@ -157,7 +158,7 @@ class Gcc(Compiler):
core_types = []
for core_type in [ct.strip().lower() for ct in cpu_model[4:].split('+')]:
# Determine numeric ID for each core type, since we need to sort them later numerically
- res = re.search('\d+$', core_type) # note: numeric ID is expected at the end
+ res = re.search(r'\d+$', core_type) # note: numeric ID is expected at the end
if res:
core_id = int(res.group(0))
core_types.append((core_id, core_type))
diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index 9978bd729..7ab1b7868 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -92,7 +92,7 @@ class IntelIccIfort(Compiler):
LINKER_TOGGLE_STATIC_DYNAMIC = {
'static': '-Bstatic',
- 'dynamic':'-Bdynamic',
+ 'dynamic': '-Bdynamic',
}
LIB_MULTITHREAD = ['iomp5', 'pthread'] # iomp5 is OpenMP related
diff --git a/easybuild/toolchains/compiler/pgi.py b/easybuild/toolchains/compiler/pgi.py
index 38b51f274..06b2efa95 100644
--- a/easybuild/toolchains/compiler/pgi.py
+++ b/easybuild/toolchains/compiler/pgi.py
@@ -58,10 +58,10 @@ class Pgi(Compiler):
COMPILER_UNIQUE_OPTION_MAP = {
'i8': 'i8',
'r8': 'r8',
- 'optarch': '', # PGI by default generates code for the arch it is running on!
+ 'optarch': '', # PGI by default generates code for the arch it is running on!
'openmp': 'mp',
'ieee': 'Kieee',
- 'strict': ['Mnoflushz','Kieee'],
+ 'strict': ['Mnoflushz', 'Kieee'],
'precise': ['Mnoflushz'],
'defaultprec': ['Mflushz'],
'loose': ['Mfprelaxed'],
@@ -90,7 +90,7 @@ class Pgi(Compiler):
LINKER_TOGGLE_STATIC_DYNAMIC = {
'static': '-Bstatic',
- 'dynamic':'-Bdynamic',
+ 'dynamic': '-Bdynamic',
}
def _set_compiler_flags(self):
diff --git a/easybuild/toolchains/fft/fftw.py b/easybuild/toolchains/fft/fftw.py
index cbaa36f8b..6b2523895 100644
--- a/easybuild/toolchains/fft/fftw.py
+++ b/easybuild/toolchains/fft/fftw.py
@@ -65,7 +65,7 @@ class Fftw(Fft):
super(Fftw, self)._set_fft_variables()
- ## TODO can these be replaced with the FFT ones?
+ # TODO can these be replaced with the FFT ones?
self.variables.join('FFTW_INC_DIR', 'FFT_INC_DIR')
self.variables.join('FFTW_LIB_DIR', 'FFT_LIB_DIR')
if 'FFT_STATIC_LIBS' in self.variables:
diff --git a/easybuild/toolchains/giolfc.py b/easybuild/toolchains/giolfc.py
index d367136ca..a7fae239f 100644
--- a/easybuild/toolchains/giolfc.py
+++ b/easybuild/toolchains/giolfc.py
@@ -35,8 +35,8 @@ from easybuild.toolchains.fft.fftw import Fftw
from easybuild.toolchains.linalg.openblas import OpenBLAS
from easybuild.toolchains.linalg.scalapack import ScaLAPACK
+
class Giolfc(Gimpic, OpenBLAS, ScaLAPACK, Fftw):
"""Compiler toolchain with GCC+CUDA, IntelMPI, OpenBLAS, ScaLAPACK and FFTW."""
NAME = 'giolfc'
SUBTOOLCHAIN = [Gimpic.NAME, Golfc.NAME]
-
diff --git a/easybuild/toolchains/gmacml.py b/easybuild/toolchains/gmacml.py
index 0aa383607..29ebd846f 100644
--- a/easybuild/toolchains/gmacml.py
+++ b/easybuild/toolchains/gmacml.py
@@ -34,7 +34,6 @@ from easybuild.toolchains.linalg.acml import Acml
from easybuild.toolchains.linalg.scalapack import ScaLAPACK
-
class Gmacml(Gmvapich2, Acml, ScaLAPACK, Fftw):
"""Compiler toolchain with GCC, MVAPICH2, ACML, ScaLAPACK and FFTW."""
NAME = 'gmacml'
diff --git a/easybuild/toolchains/gsolf.py b/easybuild/toolchains/gsolf.py
index 342ead223..7b0703f57 100644
--- a/easybuild/toolchains/gsolf.py
+++ b/easybuild/toolchains/gsolf.py
@@ -35,6 +35,7 @@ from easybuild.toolchains.fft.fftw import Fftw
from easybuild.toolchains.linalg.openblas import OpenBLAS
from easybuild.toolchains.linalg.scalapack import ScaLAPACK
+
class Gsolf(Gsmpi, OpenBLAS, ScaLAPACK, Fftw):
"""Compiler toolchain with GCC, SpectrumMPI, OpenBLAS, ScaLAPACK and FFTW."""
NAME = 'gsolf'
diff --git a/easybuild/toolchains/impmkl.py b/easybuild/toolchains/impmkl.py
index dd6a150da..d82aa7f2d 100644
--- a/easybuild/toolchains/impmkl.py
+++ b/easybuild/toolchains/impmkl.py
@@ -34,6 +34,7 @@ from easybuild.toolchains.iimkl import Iimkl
from easybuild.toolchains.fft.intelfftw import IntelFFTW
from easybuild.toolchains.linalg.intelmkl import IntelMKL
+
class Impmkl(Impich, IntelMKL, IntelFFTW):
"""
Compiler toolchain with Intel compilers (icc/ifort), MPICH,
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index 6d3f682da..c34498f47 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -80,7 +80,7 @@ class Acml(LinAlg):
self.variables.append_exists('LDFLAGS', root, self.BLAS_LIB_DIR, append_all=True)
incdirs = [os.path.join(x, 'include') for x in subdirs]
self.variables.append_exists('CPPFLAGS', root, incdirs, append_all=True)
- except:
+ except BaseException:
raise EasyBuildError("_set_blas_variables: ACML set LDFLAGS/CPPFLAGS unknown entry in ACML_SUBDIRS_MAP "
"with compiler family %s", self.COMPILER_FAMILY)
@@ -91,4 +91,3 @@ class Acml(LinAlg):
self.BLAS_LIB_MT.insert(0, "acml_mv")
super(Acml, self)._set_blas_variables()
-
diff --git a/easybuild/toolchains/linalg/blacs.py b/easybuild/toolchains/linalg/blacs.py
index 599cede4e..2aca00295 100644
--- a/easybuild/toolchains/linalg/blacs.py
+++ b/easybuild/toolchains/linalg/blacs.py
@@ -44,4 +44,3 @@ class Blacs(LinAlg):
"""Skip setting BLACS variables if it is not required (e.g., with recent ScaLAPACK versions)."""
if self.is_required(self.BLACS_MODULE_NAME[0]):
super(Blacs, self)._set_blacs_variables()
-
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index ed1129688..7877cbf11 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -55,8 +55,8 @@ class IntelMKL(LinAlg):
"interface": None,
"interface_mt": None,
}
- BLAS_LIB = ["mkl_%(interface)s%(lp64)s" , "mkl_sequential", "mkl_core"]
- BLAS_LIB_MT = ["mkl_%(interface)s%(lp64)s" , "mkl_%(interface_mt)s_thread", "mkl_core"]
+ BLAS_LIB = ["mkl_%(interface)s%(lp64)s", "mkl_sequential", "mkl_core"]
+ BLAS_LIB_MT = ["mkl_%(interface)s%(lp64)s", "mkl_%(interface_mt)s_thread", "mkl_core"]
BLAS_LIB_GROUP = True
BLAS_LIB_STATIC = True
BLAS_FAMILY = TC_CONSTANT_INTELMKL
@@ -67,7 +67,7 @@ class IntelMKL(LinAlg):
BLACS_MODULE_NAME = ['imkl']
BLACS_LIB = ["mkl_blacs%(mpi)s%(lp64)s"]
- BLACS_LIB_MAP = {'mpi':None}
+ BLACS_LIB_MAP = {'mpi': None}
BLACS_LIB_GROUP = True
BLACS_LIB_STATIC = True
@@ -114,7 +114,7 @@ class IntelMKL(LinAlg):
self.BLAS_LIB_MAP.update({
"interface": interfacemap[self.COMPILER_FAMILY],
})
- except:
+ except BaseException:
raise EasyBuildError("_set_blas_variables: interface unsupported combination with MPI family %s",
self.COMPILER_FAMILY)
@@ -124,18 +124,17 @@ class IntelMKL(LinAlg):
TC_CONSTANT_PGI: 'pgi',
}
try:
- self.BLAS_LIB_MAP.update({"interface_mt":interfacemap_mt[self.COMPILER_FAMILY]})
- except:
+ self.BLAS_LIB_MAP.update({"interface_mt": interfacemap_mt[self.COMPILER_FAMILY]})
+ except BaseException:
raise EasyBuildError("_set_blas_variables: interface_mt unsupported combination with compiler family %s",
self.COMPILER_FAMILY)
-
if self.options.get('32bit', None):
# 32bit
- self.BLAS_LIB_MAP.update({"lp64":''})
+ self.BLAS_LIB_MAP.update({"lp64": ''})
if self.options.get('i8', None):
# ilp64/i8
- self.BLAS_LIB_MAP.update({"lp64":'_ilp64'})
+ self.BLAS_LIB_MAP.update({"lp64": '_ilp64'})
# CPP / CFLAGS
self.variables.nappend_el('CFLAGS', 'DMKL_ILP64')
@@ -176,7 +175,7 @@ class IntelMKL(LinAlg):
}
try:
self.BLACS_LIB_MAP.update({'mpi': mpimap[self.MPI_FAMILY]})
- except:
+ except BaseException:
raise EasyBuildError("_set_blacs_variables: mpi unsupported combination with MPI family %s",
self.MPI_FAMILY)
@@ -193,11 +192,11 @@ class IntelMKL(LinAlg):
if self.options.get('32bit', None):
# 32 bit
- self.SCALAPACK_LIB_MAP.update({"lp64_sc":'_core'})
+ self.SCALAPACK_LIB_MAP.update({"lp64_sc": '_core'})
elif self.options.get('i8', None):
# ilp64/i8
- self.SCALAPACK_LIB_MAP.update({"lp64_sc":'_ilp64'})
+ self.SCALAPACK_LIB_MAP.update({"lp64_sc": '_ilp64'})
self.SCALAPACK_LIB_DIR = self.BLAS_LIB_DIR
self.SCALAPACK_INCLUDE_DIR = self.BLAS_INCLUDE_DIR
diff --git a/easybuild/toolchains/mpi/craympich.py b/easybuild/toolchains/mpi/craympich.py
index cf3223745..eea99f495 100644
--- a/easybuild/toolchains/mpi/craympich.py
+++ b/easybuild/toolchains/mpi/craympich.py
@@ -57,7 +57,7 @@ class CrayMPICH(Mpi):
"""Set the MPI compiler variables"""
for var_tuple in COMPILER_VARIABLES:
c_var = var_tuple[0] # [1] is the description
- var = MPI_COMPILER_TEMPLATE % {'c_var':c_var}
+ var = MPI_COMPILER_TEMPLATE % {'c_var': c_var}
value = getattr(self, 'MPI_COMPILER_%s' % var.upper(), None)
if value is None:
diff --git a/easybuild/toolchains/mpi/mpich2.py b/easybuild/toolchains/mpi/mpich2.py
index 113d859fb..ae1cceaf2 100644
--- a/easybuild/toolchains/mpi/mpich2.py
+++ b/easybuild/toolchains/mpi/mpich2.py
@@ -45,7 +45,7 @@ class Mpich2(Mpich):
def _set_mpi_compiler_variables(self):
"""Set the MPICH_{CC, CXX, F77, F90, FC} variables."""
- # C/CXX commands are set by the parent or child classes
+ # C/CXX commands are set by the parent or child classes
if self.MPI_COMPILER_MPIF77 is None and self.MPI_COMPILER_MPIF90 is None and self.MPI_COMPILER_MPIFC is None:
# hardwire MPI wrapper commands (otherwise Mpich parent class sets them based on MPICH version)
diff --git a/easybuild/tools/asyncprocess.py b/easybuild/tools/asyncprocess.py
index 17e7e132e..bcab27bc8 100644
--- a/easybuild/tools/asyncprocess.py
+++ b/easybuild/tools/asyncprocess.py
@@ -65,6 +65,8 @@ and the methods will return None.
:author: Jens Timmerman (Ghent University)
"""
+import fcntl # @UnresolvedImport
+import select # @UnresolvedImport
import errno
import os
import subprocess
@@ -73,9 +75,6 @@ import time
PIPE = subprocess.PIPE
STDOUT = subprocess.STDOUT
-import select #@UnresolvedImport
-import fcntl #@UnresolvedImport
-
class Popen(subprocess.Popen):
@@ -117,7 +116,7 @@ class Popen(subprocess.Popen):
try:
written = os.write(self.stdin.fileno(), inp.encode())
except OSError as why:
- if why[0] == errno.EPIPE: #broken pipe
+ if why[0] == errno.EPIPE: # broken pipe
return self._close('stdin')
raise
@@ -147,8 +146,10 @@ class Popen(subprocess.Popen):
if not conn.closed:
fcntl.fcntl(conn, fcntl.F_SETFL, flags)
+
message = "Other end disconnected!"
+
def recv_some(p, t=.2, e=1, tr=5, stderr=0):
if tr < 1:
tr = 1
@@ -171,6 +172,7 @@ def recv_some(p, t=.2, e=1, tr=5, stderr=0):
time.sleep(max((x - time.time()) / tr, 0))
return b''.join(y)
+
def send_all(p, data):
while len(data):
sent = p.send(data)
diff --git a/easybuild/tools/configobj.py b/easybuild/tools/configobj.py
index f96c404ac..e29b698be 100644
--- a/easybuild/tools/configobj.py
+++ b/easybuild/tools/configobj.py
@@ -41,7 +41,7 @@ BOMS = {
BOM_UTF16_BE: ('utf16_be', 'utf_16'),
BOM_UTF16_LE: ('utf16_le', 'utf_16'),
BOM_UTF16: ('utf_16', 'utf_16'),
- }
+}
# All legal variants of the BOM codecs.
# TODO: the list of aliases is not meant to be exhaustive, is there a
# better way ?
@@ -61,7 +61,7 @@ BOM_LIST = {
'utf': 'utf_8',
'utf8': 'utf_8',
'utf-8': 'utf_8',
- }
+}
# Map of encodings to the BOM to write.
BOM_SET = {
@@ -70,7 +70,7 @@ BOM_SET = {
'utf16_be': BOM_UTF16_BE,
'utf16_le': BOM_UTF16_LE,
None: BOM_UTF8
- }
+}
def match_utf8(encoding):
@@ -143,7 +143,6 @@ OPTION_DEFAULTS = {
}
-
def getObj(s):
global compiler
if compiler is None:
@@ -222,12 +221,12 @@ def unrepr(s):
return _builder.build(getObj(s))
-
class ConfigObjError(SyntaxError):
"""
This is the base class for all errors that ConfigObj raises.
It is a subclass of SyntaxError.
"""
+
def __init__(self, message='', line_number=None, line=''):
self.line = line
self.line_number = line_number
@@ -253,6 +252,7 @@ class ReloadError(IOError):
A 'reload' operation failed.
This exception is a subclass of ``IOError``.
"""
+
def __init__(self):
IOError.__init__(self, 'reload failed, filename is not set.')
@@ -291,6 +291,7 @@ class RepeatSectionError(ConfigObjError):
class MissingInterpolationOption(InterpolationError):
"""A value specified for interpolation was missing."""
+
def __init__(self, option):
msg = 'missing option "%s" in interpolation.' % option
InterpolationError.__init__(self, msg)
@@ -300,7 +301,6 @@ class UnreprError(ConfigObjError):
"""An error parsing in unrepr mode."""
-
class InterpolationEngine(object):
"""
A helper class to help perform string interpolation.
@@ -317,10 +317,9 @@ class InterpolationEngine(object):
# the Section instance that "owns" this engine
self.section = section
-
def interpolate(self, key, value):
# short-cut
- if not self._cookie in value:
+ if self._cookie not in value:
return value
def recursive_interpolate(key, value, section, backtrail):
@@ -370,7 +369,6 @@ class InterpolationEngine(object):
value = recursive_interpolate(key, value, self.section, {})
return value
-
def _fetch(self, key):
"""Helper function to fetch values from owning section.
@@ -404,7 +402,6 @@ class InterpolationEngine(object):
raise MissingInterpolationOption(key)
return val, current_section
-
def _parse_match(self, match):
"""Implementation-dependent helper function.
@@ -424,7 +421,6 @@ class InterpolationEngine(object):
raise NotImplementedError()
-
class ConfigParserInterpolation(InterpolationEngine):
"""Behaves like ConfigParser."""
_cookie = '%'
@@ -436,7 +432,6 @@ class ConfigParserInterpolation(InterpolationEngine):
return key, value, section
-
class TemplateInterpolation(InterpolationEngine):
"""Behaves like string.Template."""
_cookie = '$'
@@ -473,6 +468,7 @@ def __newobj__(cls, *args):
# Hack for pickle
return cls.__new__(cls, *args)
+
class Section(dict):
"""
A dictionary-like object that represents a section in a config file.
@@ -491,7 +487,6 @@ class Section(dict):
Iteration follows the order: scalars, then sections.
"""
-
def __setstate__(self, state):
dict.update(self, state[0])
self.__dict__.update(state[1])
@@ -500,7 +495,6 @@ class Section(dict):
state = (dict(self), self.__dict__)
return (__newobj__, (self.__class__,), state)
-
def __init__(self, parent, depth, main, indict=None, name=None):
"""
* parent is the section above
@@ -542,7 +536,6 @@ class Section(dict):
self.extra_values = []
self._created = False
-
def _interpolate(self, key, value):
try:
# do we already have an interpolation engine?
@@ -550,7 +543,7 @@ class Section(dict):
except AttributeError:
# not yet: first time running _interpolate(), so pick the engine
name = self.main.interpolation
- if name == True: # note that "if name:" would be incorrect here
+ if name: # note that "if name:" would be incorrect here
# backwards-compatibility: interpolation=True means use default
name = DEFAULT_INTERPOLATION
name = name.lower() # so that "Template", "template", etc. all work
@@ -565,7 +558,6 @@ class Section(dict):
# let the engine do the actual work
return engine.interpolate(key, value)
-
def __getitem__(self, key):
"""Fetch the item and do string interpolation."""
val = dict.__getitem__(self, key)
@@ -582,7 +574,6 @@ class Section(dict):
return new
return val
-
def __setitem__(self, key, value, unrepr=False):
"""
Correctly set a value.
@@ -641,7 +632,6 @@ class Section(dict):
raise TypeError('Value is not a string "%s".' % value)
dict.__setitem__(self, key, value)
-
def __delitem__(self, key):
"""Remove items from the sequence when deleting."""
dict. __delitem__(self, key)
@@ -652,7 +642,6 @@ class Section(dict):
del self.comments[key]
del self.inline_comments[key]
-
def get(self, key, default=None):
"""A version of ``get`` that doesn't bypass string interpolation."""
try:
@@ -660,7 +649,6 @@ class Section(dict):
except KeyError:
return default
-
def update(self, indict):
"""
A version of update that uses our ``__setitem__``.
@@ -668,7 +656,6 @@ class Section(dict):
for entry in indict:
self[entry] = indict[entry]
-
def pop(self, key, default=MISSING):
"""
'D.pop(k[,d]) -> v, remove specified key and return the corresponding value.
@@ -684,7 +671,6 @@ class Section(dict):
del self[key]
return val
-
def popitem(self):
"""Pops the first (key,val)"""
sequence = (self.scalars + self.sections)
@@ -695,7 +681,6 @@ class Section(dict):
del self[key]
return key, val
-
def clear(self):
"""
A version of clear that also affects scalars/sections
@@ -713,7 +698,6 @@ class Section(dict):
self.defaults = []
self.extra_values = []
-
def setdefault(self, key, default=None):
"""A version of setdefault that sets sequence if appropriate."""
try:
@@ -722,39 +706,32 @@ class Section(dict):
self[key] = default
return self[key]
-
def items(self):
"""D.items() -> list of D's (key, value) pairs, as 2-tuples"""
return zip((self.scalars + self.sections), self.values())
-
def keys(self):
"""D.keys() -> list of D's keys"""
return (self.scalars + self.sections)
-
def values(self):
"""D.values() -> list of D's values"""
return [self[key] for key in (self.scalars + self.sections)]
-
def iteritems(self):
"""D.iteritems() -> an iterator over the (key, value) items of D"""
return iter(self.items())
-
def iterkeys(self):
"""D.iterkeys() -> an iterator over the keys of D"""
return iter((self.scalars + self.sections))
__iter__ = iterkeys
-
def itervalues(self):
"""D.itervalues() -> an iterator over the values of D"""
return iter(self.values())
-
def __repr__(self):
"""x.__repr__() <==> repr(x)"""
def _getval(key):
@@ -763,12 +740,11 @@ class Section(dict):
except MissingInterpolationOption:
return dict.__getitem__(self, key)
return '{%s}' % ', '.join([('%s: %s' % (repr(key), repr(_getval(key))))
- for key in (self.scalars + self.sections)])
+ for key in (self.scalars + self.sections)])
__str__ = __repr__
__str__.__doc__ = "x.__str__() <==> str(x)"
-
# Extra methods - not in a normal dictionary
def dict(self):
@@ -798,7 +774,6 @@ class Section(dict):
newdict[entry] = this_entry
return newdict
-
def merge(self, indict):
"""
A recursive update - useful for merging config files.
@@ -820,12 +795,11 @@ class Section(dict):
"""
for key, val in indict.items():
if (key in self and isinstance(self[key], dict) and
- isinstance(val, dict)):
+ isinstance(val, dict)):
self[key].merge(val)
else:
self[key] = val
-
def rename(self, oldkey, newkey):
"""
Change a keyname to another, without changing position in sequence.
@@ -855,9 +829,8 @@ class Section(dict):
self.comments[newkey] = comm
self.inline_comments[newkey] = inline_comment
-
def walk(self, function, raise_errors=True,
- call_on_sections=False, **keywargs):
+ call_on_sections=False, **keywargs):
"""
Walk every member and call a function on the keyword and value.
@@ -940,7 +913,6 @@ class Section(dict):
**keywargs)
return out
-
def as_bool(self, key):
"""
Accepts a key as input. The corresponding value must be a string or
@@ -970,7 +942,7 @@ class Section(dict):
0
"""
val = self[key]
- if val == True:
+ if val:
return True
elif val == False:
return False
@@ -984,7 +956,6 @@ class Section(dict):
except KeyError:
raise ValueError('Value "%s" is neither True nor False' % val)
-
def as_int(self, key):
"""
A convenience method which coerces the specified value to an integer.
@@ -1007,7 +978,6 @@ class Section(dict):
"""
return int(self[key])
-
def as_float(self, key):
"""
A convenience method which coerces the specified value to a float.
@@ -1029,7 +999,6 @@ class Section(dict):
"""
return float(self[key])
-
def as_list(self, key):
"""
A convenience method which fetches the specified value, guaranteeing
@@ -1051,7 +1020,6 @@ class Section(dict):
return list(result)
return [result]
-
def restore_default(self, key):
"""
Restore (and return) default value for the specified key.
@@ -1067,7 +1035,6 @@ class Section(dict):
self.defaults.append(key)
return default
-
def restore_defaults(self):
"""
Recursively restore default values to all members
@@ -1099,7 +1066,7 @@ class ConfigObj(Section):
(.*) # value (including list values and comments)
$ # line end
''',
- re.VERBOSE)
+ re.VERBOSE)
_sectionmarker = re.compile(r'''^
(\s*) # 1: indentation
@@ -1112,7 +1079,7 @@ class ConfigObj(Section):
((?:\s*\])+) # 4: section marker close
\s*(\#.*)? # 5: optional comment
$''',
- re.VERBOSE)
+ re.VERBOSE)
# this regexp pulls list values out as a single string
# or single values and comments
@@ -1142,7 +1109,7 @@ class ConfigObj(Section):
)
\s*(\#.*)? # optional comment
$''',
- re.VERBOSE)
+ re.VERBOSE)
# use findall to get the members of a list value
_listvalueexp = re.compile(r'''
@@ -1153,7 +1120,7 @@ class ConfigObj(Section):
)
\s*,\s* # comma
''',
- re.VERBOSE)
+ re.VERBOSE)
# this regexp is used for the value
# when lists are switched off
@@ -1166,7 +1133,7 @@ class ConfigObj(Section):
)
\s*(\#.*)? # optional comment
$''',
- re.VERBOSE)
+ re.VERBOSE)
# regexes for finding triple quoted values on one line
_single_line_single = re.compile(r"^'''(.*?)'''\s*(#.*)?$")
@@ -1185,8 +1152,7 @@ class ConfigObj(Section):
'on': True, 'off': False,
'1': True, '0': False,
'true': True, 'false': False,
- }
-
+ }
def __init__(self, infile=None, options=None, configspec=None, encoding=None,
interpolation=True, raise_errors=False, list_values=True,
@@ -1245,7 +1211,6 @@ class ConfigObj(Section):
self._original_configspec = configspec
self._load(infile, configspec)
-
def _load(self, infile, configspec):
if isinstance(infile, string_type):
self.filename = infile
@@ -1342,7 +1307,6 @@ class ConfigObj(Section):
else:
self._handle_configspec(configspec)
-
def _initialise(self, options=None):
if options is None:
options = OPTION_DEFAULTS
@@ -1374,7 +1338,6 @@ class ConfigObj(Section):
# Clear section attributes as well
Section._initialise(self)
-
def __repr__(self):
def _getval(key):
try:
@@ -1383,8 +1346,7 @@ class ConfigObj(Section):
return dict.__getitem__(self, key)
return ('ConfigObj({%s})' %
', '.join([('%s: %s' % (repr(key), repr(_getval(key))))
- for key in (self.scalars + self.sections)]))
-
+ for key in (self.scalars + self.sections)]))
def _handle_bom(self, infile):
"""
@@ -1409,7 +1371,7 @@ class ConfigObj(Section):
passed in as a single string.
"""
if ((self.encoding is not None) and
- (self.encoding.lower() not in BOM_LIST)):
+ (self.encoding.lower() not in BOM_LIST)):
# No need to check for a BOM
# the encoding specified doesn't have one
# just decode
@@ -1486,7 +1448,6 @@ class ConfigObj(Section):
return infile.splitlines(True)
return infile
-
def _a_to_u(self, aString):
"""Decode ASCII strings to unicode if a self.encoding is specified."""
if self.encoding:
@@ -1494,7 +1455,6 @@ class ConfigObj(Section):
else:
return aString
-
def _decode(self, infile, encoding):
"""
Decode infile to unicode. Using the specified encoding.
@@ -1513,7 +1473,6 @@ class ConfigObj(Section):
infile[i] = line.decode(encoding)
return infile
-
def _decode_element(self, line):
"""Decode element to unicode if necessary."""
if not self.encoding:
@@ -1522,7 +1481,6 @@ class ConfigObj(Section):
return line.decode(self.default_encoding)
return line
-
def _str(self, value):
"""
Used by ``stringify`` within validate, to turn non-string values
@@ -1533,7 +1491,6 @@ class ConfigObj(Section):
else:
return value
-
def _parse(self, infile):
"""Actually parse the config file."""
temp_list_values = self.list_values
@@ -1646,12 +1603,12 @@ class ConfigObj(Section):
try:
value = unrepr(value)
except Exception as e:
- if type(e) == UnknownType:
+ if isinstance(e, UnknownType):
msg = 'Unknown name or type in value at line %s.'
else:
msg = 'Parse error in value at line %s.'
self._handle_error(msg, UnreprError, infile,
- cur_index)
+ cur_index)
continue
else:
if self.unrepr:
@@ -1664,7 +1621,7 @@ class ConfigObj(Section):
else:
msg = 'Parse error in value at line %s.'
self._handle_error(msg, UnreprError, infile,
- cur_index)
+ cur_index)
continue
else:
# extract comment and lists
@@ -1701,7 +1658,6 @@ class ConfigObj(Section):
self.final_comment = comment_list
self.list_values = temp_list_values
-
def _match_depth(self, sect, depth):
"""
Given a section and a depth level, walk back through the sections
@@ -1720,7 +1676,6 @@ class ConfigObj(Section):
# shouldn't get here
raise SyntaxError()
-
def _handle_error(self, text, ErrorClass, infile, cur_index):
"""
Handle an error according to the error settings.
@@ -1739,7 +1694,6 @@ class ConfigObj(Section):
# reraise when parsing has finished
self._errors.append(error)
-
def _unquote(self, value):
"""Return an unquoted version of a value"""
if not value:
@@ -1749,7 +1703,6 @@ class ConfigObj(Section):
value = value[1:-1]
return value
-
def _quote(self, value, multiline=True):
"""
Return a safely quoted version of a value.
@@ -1780,7 +1733,7 @@ class ConfigObj(Section):
elif len(value) == 1:
return self._quote(value[0], multiline=False) + ','
return ', '.join([self._quote(val, multiline=False)
- for val in value])
+ for val in value])
if not isinstance(value, string_type):
if self.stringify:
value = str(value)
@@ -1818,7 +1771,6 @@ class ConfigObj(Section):
return quot % value
-
def _get_single_quote(self, value):
if ("'" in value) and ('"' in value):
raise ConfigObjError('Value "%s" cannot be safely quoted.' % value)
@@ -1828,7 +1780,6 @@ class ConfigObj(Section):
quot = dquot
return quot
-
def _get_triple_quote(self, value):
if (value.find('"""') != -1) and (value.find("'''") != -1):
raise ConfigObjError('Value "%s" cannot be safely quoted.' % value)
@@ -1838,7 +1789,6 @@ class ConfigObj(Section):
quot = tsquot
return quot
-
def _handle_value(self, value):
"""
Given a value string, unquote, remove comment,
@@ -1887,7 +1837,6 @@ class ConfigObj(Section):
the_list += [single]
return (the_list, comment)
-
def _multiline(self, value, infile, cur_index, maxline):
"""Extract the value, where we are in a multiline situation."""
quot = value[:3]
@@ -1922,7 +1871,6 @@ class ConfigObj(Section):
(value, comment) = mat.groups()
return (newvalue + value, comment, cur_index)
-
def _handle_configspec(self, configspec):
"""Parse the configspec."""
# FIXME: Should we check that the configspec was created with the
@@ -1942,8 +1890,6 @@ class ConfigObj(Section):
self.configspec = configspec
-
-
def _set_configspec(self, section, copy):
"""
Called by validate. Handles setting the configspec on subsections
@@ -1971,7 +1917,6 @@ class ConfigObj(Section):
if isinstance(section[entry], Section):
section[entry].configspec = configspec[entry]
-
def _write_line(self, indent_string, entry, this_entry, comment):
"""Write an individual line, for the write method"""
# NOTE: the calls to self._quote here handles non-StringType values.
@@ -1985,7 +1930,6 @@ class ConfigObj(Section):
val,
self._decode_element(comment))
-
def _write_marker(self, indent_string, depth, entry, comment):
"""Write a section marker line"""
return '%s%s%s%s%s' % (indent_string,
@@ -1994,7 +1938,6 @@ class ConfigObj(Section):
self._a_to_u(']' * depth),
self._decode_element(comment))
-
def _handle_comment(self, comment):
"""Deal with a comment."""
if not comment:
@@ -2004,7 +1947,6 @@ class ConfigObj(Section):
start += self._a_to_u(' # ')
return (start + comment)
-
# Public methods
def write(self, outfile=None, section=None):
@@ -2087,7 +2029,7 @@ class ConfigObj(Section):
if self.encoding:
out = [l.encode(self.encoding) for l in out]
if (self.BOM and ((self.encoding is None) or
- (BOM_LIST.get(self.encoding.lower()) == 'utf_8'))):
+ (BOM_LIST.get(self.encoding.lower()) == 'utf_8'))):
# Add the UTF8 BOM
if not out:
out.append('')
@@ -2097,7 +2039,7 @@ class ConfigObj(Section):
# Turn the list to a string, joined with correct newlines
newline = self.newlines or os.linesep
if (getattr(outfile, 'mode', None) is not None and outfile.mode == 'w'
- and sys.platform == 'win32' and newline == '\r\n'):
+ and sys.platform == 'win32' and newline == '\r\n'):
# Windows specific hack to avoid writing '\r\r\n'
newline = '\n'
output = self._a_to_u(newline).join(out)
@@ -2116,7 +2058,6 @@ class ConfigObj(Section):
h.write(output)
h.close()
-
def validate(self, validator, preserve_errors=False, copy=False,
section=None):
"""
@@ -2177,7 +2118,6 @@ class ConfigObj(Section):
configspec = section.configspec
self._set_configspec(section, copy)
-
def validate_entry(entry, spec, val, missing, ret_true, ret_false):
section.default_values.pop(entry, None)
@@ -2235,7 +2175,7 @@ class ConfigObj(Section):
if entry in ('__many__', '___many___'):
# reserved names
continue
- if (not entry in section.scalars) or (entry in section.defaults):
+ if (entry not in section.scalars) or (entry in section.defaults):
# missing entries
# or entries from defaults
missing = True
@@ -2298,9 +2238,9 @@ class ConfigObj(Section):
section.inline_comments[entry] = configspec.inline_comments.get(entry, '')
check = self.validate(validator, preserve_errors=preserve_errors, copy=copy, section=section[entry])
out[entry] = check
- if check == False:
+ if not check:
ret_true = False
- elif check == True:
+ elif check:
ret_false = False
else:
ret_true = False
@@ -2323,7 +2263,6 @@ class ConfigObj(Section):
return False
return out
-
def reset(self):
"""Clear ConfigObj instance and restore to 'freshly created' state."""
self.clear()
@@ -2334,7 +2273,6 @@ class ConfigObj(Section):
# Just to be sure ;-)
self._original_configspec = None
-
def reload(self):
"""
Reload a ConfigObj from file.
@@ -2360,7 +2298,6 @@ class ConfigObj(Section):
self._load(filename, configspec)
-
class SimpleVal(object):
"""
A simple validator.
@@ -2419,7 +2356,7 @@ def flatten_errors(cfg, res, levels=None, results=None):
# first time called
levels = []
results = []
- if res == True:
+ if res:
return results
if res == False or isinstance(res, Exception):
results.append((levels[:], None, res))
@@ -2427,7 +2364,7 @@ def flatten_errors(cfg, res, levels=None, results=None):
levels.pop()
return results
for (key, val) in res.items():
- if val == True:
+ if val:
continue
if isinstance(cfg.get(key), dict):
# Go down one level
diff --git a/easybuild/tools/containers/utils.py b/easybuild/tools/containers/utils.py
index b259763d5..4902d2c11 100644
--- a/easybuild/tools/containers/utils.py
+++ b/easybuild/tools/containers/utils.py
@@ -78,7 +78,7 @@ def check_tool(tool_name, min_tool_version=None):
out, ec = run_cmd(version_cmd, simple=False, trace=False, force_in_dry_run=True)
if ec:
raise EasyBuildError("Error running '{0}' for tool {1} with output: {2}".format(version_cmd, tool_name, out))
- res = re.search("\d+\.\d+(\.\d+)?", out.strip())
+ res = re.search(r"\d+\.\d+(\.\d+)?", out.strip())
if not res:
raise EasyBuildError("Error parsing version for tool {0}".format(tool_name))
tool_version = res.group(0)
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 1d1342e2c..f00e237b2 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -490,7 +490,7 @@ def gen_list_easyblocks(list_easyblocks, format_strings):
txt.append(format_strings['root_templ'] % root)
if format_strings.get('newline') is not None:
- txt.append(format_strings['newline'])
+ txt.append(format_strings['newline'])
if 'children' in classes[root]:
txt.extend(avail_classes_tree(classes, classes[root]['children'], locations, detailed, format_strings))
if format_strings.get('newline') is not None:
@@ -522,7 +522,7 @@ def list_software(output_format=FORMAT_TXT, detailed=False, only_installed=False
ecs.append(ec)
print_msg('\r', prefix=False, newline=False, silent=silent)
- print_msg("Processed %d/%d easyconfigs..." % (idx+1, cnt), newline=False, silent=silent)
+ print_msg("Processed %d/%d easyconfigs..." % (idx + 1, cnt), newline=False, silent=silent)
print_msg('', prefix=False, silent=silent)
software = {}
@@ -871,7 +871,7 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
'.. _' + classname + ':',
'',
'``' + classname + '``',
- '=' * (len(classname)+4),
+ '=' * (len(classname) + 4),
'',
]
@@ -936,7 +936,7 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
if os.path.exists(os.path.join(path_to_examples, '%s.eb' % classname)):
title = 'Example easyconfig for ``' + classname + '`` easyblock'
doc.extend([title, '-' * len(title), '', '.. code::', ''])
- for line in read_file(os.path.join(path_to_examples, classname+'.eb')).split('\n'):
+ for line in read_file(os.path.join(path_to_examples, classname + '.eb')).split('\n'):
doc.append(INDENT_4SPACES + line)
doc.append('') # empty line after literal block
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 6ce5ebb5a..4649bd8f2 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -128,28 +128,28 @@ CHECKSUM_TYPES = sorted(CHECKSUM_FUNCTIONS.keys())
EXTRACT_CMDS = {
# gzipped or gzipped tarball
- '.gtgz': "tar xzf %(filepath)s",
- '.gz': "gunzip -c %(filepath)s > %(target)s",
- '.tar.gz': "tar xzf %(filepath)s",
- '.tgz': "tar xzf %(filepath)s",
+ '.gtgz': "tar xzf %(filepath)s",
+ '.gz': "gunzip -c %(filepath)s > %(target)s",
+ '.tar.gz': "tar xzf %(filepath)s",
+ '.tgz': "tar xzf %(filepath)s",
# bzipped or bzipped tarball
- '.bz2': "bunzip2 -c %(filepath)s > %(target)s",
+ '.bz2': "bunzip2 -c %(filepath)s > %(target)s",
'.tar.bz2': "tar xjf %(filepath)s",
- '.tb2': "tar xjf %(filepath)s",
- '.tbz': "tar xjf %(filepath)s",
- '.tbz2': "tar xjf %(filepath)s",
+ '.tb2': "tar xjf %(filepath)s",
+ '.tbz': "tar xjf %(filepath)s",
+ '.tbz2': "tar xjf %(filepath)s",
# xzipped or xzipped tarball
- '.tar.xz': "unxz %(filepath)s --stdout | tar x",
- '.txz': "unxz %(filepath)s --stdout | tar x",
- '.xz': "unxz %(filepath)s",
+ '.tar.xz': "unxz %(filepath)s --stdout | tar x",
+ '.txz': "unxz %(filepath)s --stdout | tar x",
+ '.xz': "unxz %(filepath)s",
# tarball
- '.tar': "tar xf %(filepath)s",
+ '.tar': "tar xf %(filepath)s",
# zip file
- '.zip': "unzip -qq %(filepath)s",
+ '.zip': "unzip -qq %(filepath)s",
# iso file
- '.iso': "7z x %(filepath)s",
+ '.iso': "7z x %(filepath)s",
# tar.Z: using compress (LZW), but can be handled with gzip so use 'z'
- '.tar.z': "tar xzf %(filepath)s",
+ '.tar.z': "tar xzf %(filepath)s",
}
@@ -158,6 +158,7 @@ class ZlibChecksum(object):
wrapper class for adler32 and crc32 checksums to
match the interface of the hashlib module
"""
+
def __init__(self, algorithm):
self.algorithm = algorithm
self.checksum = algorithm(b'') # use the same starting point as the module
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index dd6eccc15..83918a8e8 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -967,7 +967,7 @@ def find_software_name_for_patch(patch_name, ec_dirs):
break
except EasyBuildError as err:
_log.debug("Ignoring easyconfig %s that fails to parse: %s", path, err)
- sys.stdout.write('\r%s of %s easyconfigs checked' % (idx+1, nr_of_ecs))
+ sys.stdout.write('\r%s of %s easyconfigs checked' % (idx + 1, nr_of_ecs))
sys.stdout.flush()
sys.stdout.write('\n')
diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
index 90b971528..9d85402cc 100644
--- a/easybuild/tools/include.py
+++ b/easybuild/tools/include.py
@@ -142,7 +142,7 @@ def verify_imports(pymods, pypkg, from_path):
def is_software_specific_easyblock(module):
"""Determine whether Python module at specified location is a software-specific easyblock."""
- return bool(re.search('^class EB_.*\(.*\):\s*$', read_file(module), re.M))
+ return bool(re.search(r'^class EB_.*\(.*\):\s*$', read_file(module), re.M))
def include_easyblocks(tmpdir, paths):
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 80593a037..4b7927407 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -168,7 +168,7 @@ class GC3Pie(JobBackend):
"""
named_args = {
'jobname': name, # job name in GC3Pie
- 'name': name, # job name in EasyBuild
+ 'name': name, # job name in EasyBuild
}
# environment
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 6e427b6e2..f1f7dd4cd 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -171,7 +171,9 @@ class PbsPython(JobBackend):
# return most frequent
freq_count, freq_np = max([(j, i) for i, j in res.items()])
- self.log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
+ self.log.debug(
+ "Found most frequent np %s (%s times) in interesting nodes %s" %
+ (freq_np, freq_count, interesting_nodes))
self._ppn = freq_np
@@ -453,7 +455,7 @@ class PbsJob(object):
return None
# convert single type into list
- if type(types) is str:
+ if isinstance(types, str):
types = [types]
self.log.debug("Return info types %s" % types)
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index e3859880e..ef9caa760 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -735,7 +735,7 @@ class ModuleGeneratorTcl(ModuleGenerator):
"""
txt = '\n'.join([
"proc ModulesHelp { } {",
- " puts stderr {%s" % re.sub('([{}\[\]])', r'\\\1', self._generate_help_text()),
+ " puts stderr {%s" % re.sub(r'([{}\[\]])', r'\\\1', self._generate_help_text()),
" }",
'}',
'',
diff --git a/easybuild/tools/module_naming_scheme/categorized_mns.py b/easybuild/tools/module_naming_scheme/categorized_mns.py
index 46f0b0e86..3cc0ae174 100644
--- a/easybuild/tools/module_naming_scheme/categorized_mns.py
+++ b/easybuild/tools/module_naming_scheme/categorized_mns.py
@@ -35,6 +35,7 @@ import re
from easybuild.tools.module_naming_scheme.mns import ModuleNamingScheme
from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+
class CategorizedModuleNamingScheme(ModuleNamingScheme):
"""Class implementing the categorized module naming scheme."""
@@ -55,11 +56,10 @@ class CategorizedModuleNamingScheme(ModuleNamingScheme):
Default implementation checks via a strict regex pattern, and assumes short module names are of the form:
<name>/<version>[-<toolchain>]
"""
- modname_regex = re.compile('^[^/]+/%s/\S+$' % re.escape(name))
+ modname_regex = re.compile(r'^[^/]+/%s/\S+$' % re.escape(name))
res = bool(modname_regex.match(short_modname))
tup = (short_modname, name, modname_regex.pattern, res)
self.log.debug("Checking whether '%s' is a module name for software with name '%s' via regex %s: %s" % tup)
return res
-
diff --git a/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py b/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
index 7dfdfc38e..70629b762 100644
--- a/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
+++ b/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
@@ -30,6 +30,7 @@ Implementation of a module naming scheme that can be used to migrate from EasyBu
from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
from easybuild.tools.module_naming_scheme.hierarchical_mns import HierarchicalMNS
+
class MigrateFromEBToHMNS(HierarchicalMNS, EasyBuildMNS):
def det_install_subdir(self, ec):
diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index d18055177..b4c854d58 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -162,7 +162,7 @@ class ModuleNamingScheme(BaseModuleNamingScheme):
Default implementation checks via a strict regex pattern, and assumes short module names are of the form:
<name>/<version>[-<toolchain>]
"""
- modname_regex = re.compile('^%s(/\S+)?$' % re.escape(name))
+ modname_regex = re.compile(r'^%s(/\S+)?$' % re.escape(name))
res = bool(modname_regex.match(short_modname))
self.log.debug("Checking whether '%s' is a module name for software with name '%s' via regex %s: %s",
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 8bfc737bc..a21838697 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -444,9 +444,9 @@ class ModulesTool(object):
idx = 1
while(curr_mod_paths[-idx:] == self.mod_paths[-idx:]):
idx += 1
- self.log.debug("Not prepending %d last entries of %s", idx-1, self.mod_paths)
+ self.log.debug("Not prepending %d last entries of %s", idx - 1, self.mod_paths)
- for mod_path in self.mod_paths[::-1][idx-1:]:
+ for mod_path in self.mod_paths[::-1][idx - 1:]:
self.prepend_module_path(mod_path)
self.log.info("$MODULEPATH set via list of module paths (w/ 'module use'): %s" % os.environ['MODULEPATH'])
@@ -1054,7 +1054,7 @@ class ModulesTool(object):
if path_matches(full_mod_subdir, full_modpath_exts):
# full path to module subdir of dependency is simply path to module file without (short) module name
- dep_full_mod_subdir = self.modulefile_path(dep, strip_ext=True)[:-len(dep)-1]
+ dep_full_mod_subdir = self.modulefile_path(dep, strip_ext=True)[:-len(dep) - 1]
full_mod_subdirs.append(dep_full_mod_subdir)
mods_to_top.append(dep)
@@ -1545,6 +1545,7 @@ def invalidate_module_caches_for(path):
class Modules(EnvironmentModulesC):
"""NO LONGER SUPPORTED: interface to modules tool, use modules_tool from easybuild.tools.modules instead"""
+
def __init__(self, *args, **kwargs):
_log.nosupport("modules.Modules class is now an abstract interface, use modules.modules_tool instead", '2.0')
@@ -1557,7 +1558,7 @@ class NoModulesTool(ModulesTool):
def exist(self, mod_names, *args, **kwargs):
"""No modules, so nothing exists"""
- return [False]*len(mod_names)
+ return [False] * len(mod_names)
def check_loaded_modules(self):
"""Nothing to do since no modules"""
diff --git a/easybuild/tools/multidiff.py b/easybuild/tools/multidiff.py
index 63967244e..a102a3de7 100644
--- a/easybuild/tools/multidiff.py
+++ b/easybuild/tools/multidiff.py
@@ -69,6 +69,7 @@ class MultiDiff(object):
"""
Class representing a multi-diff.
"""
+
def __init__(self, base_fn, base_lines, files, colored=True):
"""
MultiDiff constructor
diff --git a/easybuild/tools/ordereddict.py b/easybuild/tools/ordereddict.py
index 5cdd3da4f..34b2a771f 100644
--- a/easybuild/tools/ordereddict.py
+++ b/easybuild/tools/ordereddict.py
@@ -1,4 +1,4 @@
-## http://code.activestate.com/recipes/576693/ (r9)
+# http://code.activestate.com/recipes/576693/ (r9)
# Backport of OrderedDict() class that runs on Python 2.4, 2.5, 2.6, 2.7 and pypy.
# Passes Python2.7's test suite and incorporates all the latest updates.
@@ -170,7 +170,7 @@ class OrderedDict(dict):
'''
if len(args) > 1:
raise TypeError('update() takes at most 2 positional '
- 'arguments (%d given)' % (1+len(args),))
+ 'arguments (%d given)' % (1 + len(args),))
# Make progressively weaker assumptions about "other"
other = ()
if len(args) == 1:
@@ -255,7 +255,7 @@ class OrderedDict(dict):
'''
if isinstance(other, OrderedDict):
- return len(self)==len(other) and self.items() == other.items()
+ return len(self) == len(other) and self.items() == other.items()
return dict.__eq__(self, other)
def __ne__(self, other):
@@ -274,4 +274,3 @@ class OrderedDict(dict):
def viewitems(self):
"od.viewitems() -> a set-like object providing a view on od's items"
return ItemsView(self)
-
diff --git a/easybuild/tools/py2vs3/py3.py b/easybuild/tools/py2vs3/py3.py
index 3ff66d680..3b5076694 100644
--- a/easybuild/tools/py2vs3/py3.py
+++ b/easybuild/tools/py2vs3/py3.py
@@ -94,7 +94,7 @@ def mk_wrapper_baseclass(metaclass):
def safe_cmp_looseversions(v1, v2):
"""Safe comparison function for two (values containing) LooseVersion instances."""
- if type(v1) != type(v2):
+ if not isinstance(v1, type(v2)):
raise TypeError("Can't compare values of different types: %s (%s) vs %s (%s)" % (v1, type(v1), v2, type(v2)))
# if we receive two iterative values, we need to recurse
@@ -123,7 +123,7 @@ def safe_cmp_looseversions(v1, v2):
# implementation based on '14894.patch' patch file provided in https://bugs.python.org/issue14894
for ver1_part, ver2_part in zip_longest(v1.version, v2.version, fillvalue=''):
# use string comparison if version parts have different type
- if type(ver1_part) != type(ver2_part):
+ if not isinstance(ver1_part, type(ver2_part)):
ver1_part = str(ver1_part)
ver2_part = str(ver2_part)
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 9bf941eda..849b94909 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -219,7 +219,7 @@ def check_conflicts(easyconfigs, modtool, check_inter_ec_conflicts=True):
for runtime_deps in lists_of_runtime_deps:
# also check whether module itself clashes with any of its dependencies
for i, dep1 in enumerate(build_deps + runtime_deps + [key]):
- for dep2 in (build_deps + runtime_deps)[i+1:]:
+ for dep2 in (build_deps + runtime_deps)[i + 1:]:
# don't worry about conflicts between module itself and any of its build deps
if dep1 != key or dep2 not in build_deps:
res |= check_conflict(key, dep1, dep2)
diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index a3471abc0..ed6be6e04 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -338,7 +338,7 @@ def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, re
def escape_special(string):
return re.sub(r"([\+\?\(\)\[\]\*\.\\\$])", r"\\\1", string)
- split = '[\s\n]+'
+ split = r'[\s\n]+'
regSplit = re.compile(r"" + split)
def process_QA(q, a_s):
@@ -569,10 +569,10 @@ def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
"""
global errors_found_in_log
- if regExp and type(regExp) == bool:
+ if regExp and isinstance(regExp, bool):
regExp = r"(?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)"
_log.debug('Using default regular expression: %s' % regExp)
- elif type(regExp) == str:
+ elif isinstance(regExp, str):
pass
else:
raise EasyBuildError("parse_log_for_error no valid regExp used: %s", regExp)
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 0e114cb0d..b2a9eb425 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -333,7 +333,7 @@ def get_cpu_family():
# Distinguish POWER running in little-endian mode
system, node, release, version, machine, processor = platform.uname()
- powerle_regex = re.compile("^ppc(\d*)le")
+ powerle_regex = re.compile(r"^ppc(\d*)le")
if powerle_regex.search(machine):
family = POWER_LE
@@ -457,11 +457,11 @@ def get_cpu_features():
_log.debug("Found CPU features using regex '%s': %s", flags_regex.pattern, cpu_feat)
elif get_cpu_architecture() == POWER:
# for Linux@POWER systems, no flags/features are listed, but we can check for Altivec
- cpu_altivec_regex = re.compile("^cpu\s*:.*altivec supported", re.M)
+ cpu_altivec_regex = re.compile(r"^cpu\s*:.*altivec supported", re.M)
if cpu_altivec_regex.search(proc_cpuinfo):
cpu_feat.append('altivec')
# VSX is supported since POWER7
- cpu_power7_regex = re.compile("^cpu\s*:.*POWER(7|8|9)", re.M)
+ cpu_power7_regex = re.compile(r"^cpu\s*:.*POWER(7|8|9)", re.M)
if cpu_power7_regex.search(proc_cpuinfo):
cpu_feat.append('vsx')
else:
@@ -700,7 +700,7 @@ def get_gcc_version():
# Fedora: gcc (GCC) 5.1.1 20150618 (Red Hat 5.1.1-4)
# Debian: gcc (Debian 4.9.2-10) 4.9.2
- find_version = re.search("^gcc\s+\([^)]+\)\s+(?P<version>[^\s]+)\s+", out)
+ find_version = re.search(r"^gcc\s+\([^)]+\)\s+(?P<version>[^\s]+)\s+", out)
if find_version:
res = find_version.group('version')
_log.debug("Found GCC version: %s from %s", res, out)
diff --git a/easybuild/tools/toolchain/constants.py b/easybuild/tools/toolchain/constants.py
index 0ddd41de7..423154e6b 100644
--- a/easybuild/tools/toolchain/constants.py
+++ b/easybuild/tools/toolchain/constants.py
@@ -203,5 +203,3 @@ ALL_MAP_CLASSES = [
BLAS_MAP_CLASS, LAPACK_MAP_CLASS, BLACS_MAP_CLASS, SCALAPACK_MAP_CLASS,
FFT_MAP_CLASS, FFTW_MAP_CLASS, CO_COMPILER_MAP_CLASS,
]
-
-
diff --git a/easybuild/tools/toolchain/linalg.py b/easybuild/tools/toolchain/linalg.py
index 8edafd839..411b055f2 100644
--- a/easybuild/tools/toolchain/linalg.py
+++ b/easybuild/tools/toolchain/linalg.py
@@ -87,7 +87,7 @@ class LinAlg(Toolchain):
def set_variables(self):
"""Set the variables"""
- ## TODO is link order fully preserved with this order ?
+ # TODO is link order fully preserved with this order ?
self._set_blas_variables()
self._set_lapack_variables()
if getattr(self, 'MPI_MODULE_NAME', None):
@@ -110,7 +110,7 @@ class LinAlg(Toolchain):
if 'FLIBS' in self.variables:
self.variables.join('LIBBLAS', 'FLIBS')
- ## multi-threaded
+ # multi-threaded
if self.BLAS_LIB_MT is None:
self.variables.join('LIBBLAS_MT', 'LIBBLAS')
else:
@@ -133,7 +133,7 @@ class LinAlg(Toolchain):
self.variables.append_exists('BLAS_LIB_DIR', root, self.BLAS_LIB_DIR)
self.variables.append_exists('BLAS_INC_DIR', root, self.BLAS_INCLUDE_DIR)
- ## add general dependency variables
+ # add general dependency variables
self._add_dependency_variables(self.BLAS_MODULE_NAME, ld=self.BLAS_LIB_DIR, cpp=self.BLAS_INCLUDE_DIR)
def _set_lapack_variables(self):
@@ -160,14 +160,14 @@ class LinAlg(Toolchain):
toggle_staticdynamic=self.LAPACK_LIB_STATIC)
if self.LAPACK_LIB_MT is None:
- ## reuse LAPACK variables
+ # reuse LAPACK variables
self.variables.join('LIBLAPACK_MT_ONLY', 'LIBLAPACK_ONLY')
else:
self.variables.nappend('LIBLAPACK_MT_ONLY', self.LAPACK_LIB_MT)
if getattr(self, 'LIB_MULTITHREAD', None) is not None:
self.variables.nappend('LIBLAPACK_MT_ONLY', self.LIB_MULTITHREAD)
- ## need BLAS for LAPACK ?
+ # need BLAS for LAPACK ?
if self.LAPACK_REQUIRES is not None:
self.variables.join('LIBLAPACK', 'LIBLAPACK_ONLY', *self.LAPACK_REQUIRES)
lapack_mt = ["%s_MT" % x for x in self.LAPACK_REQUIRES]
@@ -195,7 +195,7 @@ class LinAlg(Toolchain):
self.variables.join('BLAS_LAPACK_STATIC_LIBS', 'LAPACK_STATIC_LIBS', 'BLAS_STATIC_LIBS')
self.variables.join('BLAS_LAPACK_MT_STATIC_LIBS', 'LAPACK_MT_STATIC_LIBS', 'BLAS_MT_STATIC_LIBS')
- ## add general dependency variables
+ # add general dependency variables
self._add_dependency_variables(self.LAPACK_MODULE_NAME, ld=self.LAPACK_LIB_DIR, cpp=self.LAPACK_INCLUDE_DIR)
def _set_blacs_variables(self):
@@ -207,8 +207,7 @@ class LinAlg(Toolchain):
if hasattr(self, 'BLACS_LIB_MAP') and self.BLACS_LIB_MAP is not None:
lib_map.update(self.BLACS_LIB_MAP)
-
- ## BLACS
+ # BLACS
self.BLACS_LIB = self.variables.nappend('LIBBLACS', [x % lib_map for x in self.BLACS_LIB])
if self.BLACS_LIB is not None:
self.variables.add_begin_end_linkerflags(self.BLACS_LIB,
@@ -218,7 +217,10 @@ class LinAlg(Toolchain):
if self.BLACS_LIB_MT is None:
self.variables.join('LIBBLACS_MT', 'LIBBLACS')
else:
- self.BLACS_LIB_MT = self.variables.nappend('LIBBLACS_MT', [x % self.BLACS_LIB_MAP for x in self.BLACS_LIB_MT])
+ self.BLACS_LIB_MT = self.variables.nappend(
+ 'LIBBLACS_MT', [
+ x %
+ self.BLACS_LIB_MAP for x in self.BLACS_LIB_MT])
if self.BLACS_LIB_MT is not None:
self.variables.add_begin_end_linkerflags(self.BLACS_LIB_MT,
toggle_startstopgroup=self.BLACS_LIB_GROUP,
@@ -234,7 +236,7 @@ class LinAlg(Toolchain):
self.variables.append_exists('BLACS_LIB_DIR', root, self.BLACS_LIB_DIR)
self.variables.append_exists('BLACS_INC_DIR', root, self.BLACS_INCLUDE_DIR)
- ## add general dependency variables
+ # add general dependency variables
self._add_dependency_variables(self.BLACS_MODULE_NAME, ld=self.BLACS_LIB_DIR, cpp=self.BLACS_INCLUDE_DIR)
def _set_scalapack_variables(self):
@@ -259,13 +261,13 @@ class LinAlg(Toolchain):
if 'FLIBS' in self.variables:
self.variables.join('LIBSCALAPACK_ONLY', 'FLIBS')
- ## multi-threaded
+ # multi-threaded
if self.SCALAPACK_LIB_MT is None:
- ## reuse BLAS variables
+ # reuse BLAS variables
self.variables.join('LIBSCALAPACK_MT_ONLY', 'LIBSCALAPACK_ONLY')
else:
self.SCALAPACK_LIB_MT = self.variables.nappend('LIBSCALAPACK_MT_ONLY',
- [x % lib_map for x in self.SCALAPACK_LIB_MT])
+ [x % lib_map for x in self.SCALAPACK_LIB_MT])
self.variables.add_begin_end_linkerflags(self.SCALAPACK_LIB_MT,
toggle_startstopgroup=self.SCALAPACK_LIB_GROUP,
toggle_staticdynamic=self.SCALAPACK_LIB_STATIC)
diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 9a30baa33..d381de99c 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -60,10 +60,10 @@ class Mpi(Toolchain):
MPI_UNIQUE_OPTION_MAP = None
MPI_SHARED_OPTION_MAP = {
'_opt_MPICC': 'cc=%(CC_base)s',
- '_opt_MPICXX':'cxx=%(CXX_base)s',
- '_opt_MPIF77':'fc=%(F77_base)s',
- '_opt_MPIF90':'f90=%(F90_base)s',
- '_opt_MPIFC':'fc=%(FC_base)s',
+ '_opt_MPICXX': 'cxx=%(CXX_base)s',
+ '_opt_MPIF77': 'fc=%(F77_base)s',
+ '_opt_MPIF90': 'f90=%(F90_base)s',
+ '_opt_MPIFC': 'fc=%(FC_base)s',
}
MPI_COMPILER_MPICC = 'mpicc'
@@ -82,7 +82,6 @@ class Mpi(Toolchain):
super(Mpi, self).__init__(*args, **kwargs)
-
def _set_mpi_options(self):
self.options.add_options(self.MPI_SHARED_OPTS, self.MPI_SHARED_OPTION_MAP)
@@ -90,7 +89,6 @@ class Mpi(Toolchain):
self.log.devel('_set_mpi_options: all current options %s', self.options)
-
def set_variables(self):
"""Set the variables"""
self._set_mpi_compiler_variables()
@@ -107,7 +105,7 @@ class Mpi(Toolchain):
for var_tuple in COMPILER_VARIABLES:
c_var = var_tuple[0] # [1] is the description
- var = MPI_COMPILER_TEMPLATE % {'c_var':c_var}
+ var = MPI_COMPILER_TEMPLATE % {'c_var': c_var}
value = getattr(self, 'MPI_COMPILER_%s' % var.upper(), None)
if value is None:
@@ -116,7 +114,7 @@ class Mpi(Toolchain):
# complete compiler variable template to produce e.g. 'mpicc -cc=icc -X -Y' from 'mpicc -cc=%(CC_base)'
templatedict = {
- c_var:str(self.variables[c_var]),
+ c_var: str(self.variables[c_var]),
'%s_base' % c_var: str(self.variables[c_var].get_first()),
}
@@ -133,7 +131,6 @@ class Mpi(Toolchain):
c_var, self.variables[c_var], var, self.variables[var])
self.variables[c_var] = self.variables[var]
-
if self.options.get('cciscxx', None):
self.log.debug("_set_mpi_compiler_variables: cciscxx set: switching MPICXX %s for MPICC value %s",
self.variables['MPICXX'], self.variables['MPICC'])
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index d05fb4a03..9043676b4 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -331,8 +331,7 @@ class Toolchain(object):
if self.vars is None:
self.generate_vars()
- var_names = self.variables.keys()
- var_names.sort()
+ var_names = sorted(self.variables.keys())
res = []
for v in var_names:
res.append("%s=%s" % (v, self.variables[v]))
@@ -661,8 +660,8 @@ class Toolchain(object):
raise EasyBuildError("No module found for toolchain: %s", self.mod_short_name)
if self.is_system_toolchain():
- self.log.info("Loading dependencies using system toolchain...")
- self._load_dependencies_modules(silent=silent)
+ self.log.info("Loading dependencies using system toolchain...")
+ self._load_dependencies_modules(silent=silent)
else:
# load the toolchain and dependencies modules
self.log.debug("Loading toolchain module and dependencies...")
@@ -675,7 +674,7 @@ class Toolchain(object):
dry_run_msg("\nFull list of loaded modules:", silent=silent)
if loaded_mods:
for i, mod_name in enumerate([m['mod_name'] for m in loaded_mods]):
- dry_run_msg(" %d) %s" % (i+1, mod_name), silent=silent)
+ dry_run_msg(" %d) %s" % (i + 1, mod_name), silent=silent)
else:
dry_run_msg(" (none)", silent=silent)
dry_run_msg('', silent=silent)
diff --git a/easybuild/tools/toolchain/variables.py b/easybuild/tools/toolchain/variables.py
index 39d2d0f13..204b6f9e0 100644
--- a/easybuild/tools/toolchain/variables.py
+++ b/easybuild/tools/toolchain/variables.py
@@ -54,6 +54,7 @@ class CommandFlagList(FlagList):
First of the list has no prefix (i.e. the executable)
The remainder of the options are considered flags
"""
+
def _str_self(self):
"""Like a regular flag list, but set first element to original value"""
tmp_str = [self.str_convert(x) for x in self if self._str_ok(x)]
@@ -66,7 +67,7 @@ class LibraryList(StrList):
"""Link library list"""
PREFIX = "-l"
- SANITIZE_REMOVE_DUPLICATE_KEEP = -1 # sanitize from end
+ SANITIZE_REMOVE_DUPLICATE_KEEP = -1 # sanitize from end
JOIN_BEGIN_END = True
@@ -174,5 +175,3 @@ class LinkerFlagList(StrList):
self.IS_BEGIN, self.PREFIX, self.BEGIN)
super(LinkerFlagList, self).sanitize()
-
-
diff --git a/easybuild/tools/variables.py b/easybuild/tools/variables.py
index d1bdab930..210290a17 100644
--- a/easybuild/tools/variables.py
+++ b/easybuild/tools/variables.py
@@ -52,7 +52,7 @@ def get_class(name, default_class, map_class=None):
if name is not None:
try:
klass = map_class[name]
- except:
+ except BaseException:
for k, v in map_class.items():
if type(k) in (type,) and name in v:
klass = k
@@ -154,7 +154,7 @@ class CommaList(StrList):
class AbsPathList(StrList):
"""Absolute paths (eg -L or -I)"""
- SANITIZE_REMOVE_DUPLICATE_KEEP = -1 # sanitize from end
+ SANITIZE_REMOVE_DUPLICATE_KEEP = -1 # sanitize from end
def append_exists(self, prefix, paths, suffix=None, filename=None, append_all=False):
"""
@@ -225,11 +225,11 @@ class ListOfLists(list):
self.protected_classes = self.PROTECTED_CLASSES[:]
if self.PROTECT_CLASS_SELF:
- if not self.DEFAULT_CLASS in self.protected_classes:
+ if self.DEFAULT_CLASS not in self.protected_classes:
self.protected_classes.append(self.DEFAULT_CLASS)
self.protected_instances = self.PROTECTED_INSTANCES[:]
if self.PROTECT_INSTANCE_SELF:
- if not self.DEFAULT_CLASS in self.protected_instances:
+ if self.DEFAULT_CLASS not in self.protected_instances:
self.protected_instances.append(self.DEFAULT_CLASS)
def append_empty(self):
@@ -287,11 +287,11 @@ class ListOfLists(list):
try:
# this might work, but probably not
newvalue = klass(value, **kwargs)
- except:
+ except BaseException:
newvalue = klass(**kwargs)
if value is not None:
newvalue.append(value)
- if not position is None:
+ if position is not None:
newvalue.POSITION = position
if self._str_ok(newvalue) or append_empty:
self.append(newvalue)
@@ -328,7 +328,7 @@ class ListOfLists(list):
try:
# this might work, but probably not
newvalue = klass(el)
- except:
+ except BaseException:
newvalue = klass()
if value is not None:
newvalue.append(el)
@@ -378,7 +378,8 @@ class ListOfLists(list):
to_remove = []
# work in reversed order; don't check last one (ie real el 0), it has no next element
for idx in range(1, len(self))[::-1]:
- if self[idx].BEGIN is None or self[idx].END is None: continue
+ if self[idx].BEGIN is None or self[idx].END is None:
+ continue
self.log.devel("idx %s len %s", idx, len(self))
# do check POSITION, sorting already done
if self[idx].BEGIN == self[idx - 1].BEGIN and self[idx].END == self[idx - 1].END:
@@ -564,4 +565,3 @@ class Variables(dict):
return _passthrough
else:
return super(Variables, self).__getattribute__(attr_name)
-
diff --git a/test/framework/config.py b/test/framework/config.py
index 63ce53700..71fac496e 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -190,7 +190,7 @@ class EasyBuildConfigTest(EnhancedTestCase):
os.environ['EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION'] = 'whatever'
error = r"Found 2 environment variable\(s\) that are prefixed with %s " % CONFIG_ENV_VAR_PREFIX
- error += "but do not match valid option\(s\): "
+ error += r"but do not match valid option\(s\): "
error += ','.join(['EASYBUILD_FOO', 'EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION'])
self.assertErrorRegex(EasyBuildError, error, init_config)
@@ -365,7 +365,7 @@ class EasyBuildConfigTest(EnhancedTestCase):
# only valid keys can be set
BuildOptions.__class__._instances.clear()
- msg = "Encountered unknown keys .* \(known keys: .*"
+ msg = r"Encountered unknown keys .* \(known keys: .*"
self.assertErrorRegex(KeyError, msg, BuildOptions, {'thisisclearlynotavalidbuildoption': 'FAIL'})
# test init_build_options and build_option functions
diff --git a/test/framework/containers.py b/test/framework/containers.py
index b89d5882e..73d0df22e 100644
--- a/test/framework/containers.py
+++ b/test/framework/containers.py
@@ -362,7 +362,7 @@ class ContainersTest(EnhancedTestCase):
args.append('--container-tmpdir=%s' % self.test_prefix)
stdout, stderr = self.run_main(args)
self.assertFalse(stderr)
- regexs[-3] = "^== Running 'sudo\s*SINGULARITY_TMPDIR=%s \S*/singularity build .*" % self.test_prefix
+ regexs[-3] = r"^== Running 'sudo\s*SINGULARITY_TMPDIR=%s \S*/singularity build .*" % self.test_prefix
self.check_regexs(regexs, stdout)
def test_end2end_dockerfile(self):
@@ -460,8 +460,8 @@ class ContainersTest(EnhancedTestCase):
self.assertFalse(stderr)
regexs = [
"^== docker tool found at %s/bin/docker" % self.test_prefix,
- "^== Dockerfile definition file created at %s/containers/Dockerfile\.toy-0.0" % self.test_prefix,
- "^== Running 'sudo docker build -f .* -t .* \.', you may need to enter your 'sudo' password...",
+ r"^== Dockerfile definition file created at %s/containers/Dockerfile\.toy-0.0" % self.test_prefix,
+ r"^== Running 'sudo docker build -f .* -t .* \.', you may need to enter your 'sudo' password...",
"^== Docker image created at toy-0.0:latest",
]
self.check_regexs(regexs, stdout)
diff --git a/test/framework/docs.py b/test/framework/docs.py
index 7a12ed04d..f6716ea17 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -109,7 +109,7 @@ class DocsTest(EnhancedTestCase):
self.assertTrue(gplv3 in lic_docs, "%s found in: %s" % (gplv3, lic_docs))
lic_docs = avail_easyconfig_licenses(output_format='rst')
- regex = re.compile("^``GPLv3``\s*The GNU General Public License", re.M)
+ regex = re.compile(r"^``GPLv3``\s*The GNU General Public License", re.M)
self.assertTrue(regex.search(lic_docs), "%s found in: %s" % (regex.pattern, lic_docs))
def test_list_software(self):
@@ -260,7 +260,7 @@ class DocsTest(EnhancedTestCase):
]
txt = list_software(output_format='txt', detailed=True)
lines = txt.split('\n')
- expected_found = any([lines[i:i+len(expected)] == expected for i in range(len(lines))])
+ expected_found = any([lines[i:i + len(expected)] == expected for i in range(len(lines))])
self.assertTrue(expected_found, "%s found in: %s" % (expected, lines))
expected = [
@@ -283,7 +283,7 @@ class DocsTest(EnhancedTestCase):
]
txt = list_software(output_format='rst', detailed=True)
lines = txt.split('\n')
- expected_found = any([lines[i:i+len(expected)] == expected for i in range(len(lines))])
+ expected_found = any([lines[i:i + len(expected)] == expected for i in range(len(lines))])
self.assertTrue(expected_found, "%s found in: %s" % (expected, lines))
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 057bcfb56..3dc2c68cc 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -53,6 +53,7 @@ from easybuild.tools.utilities import time2str
from easybuild.tools.version import get_git_revision, this_is_easybuild
from easybuild.tools.py2vs3 import string_type
+
class EasyBlockTest(EnhancedTestCase):
""" Baseclass for easyblock testcases """
@@ -287,7 +288,7 @@ class EasyBlockTest(EnhancedTestCase):
elif get_module_syntax() == 'Lua':
regexs = [r'^prepend_path\("MODULEPATH", ".*/modules/funky/Compiler/pi/3.14/%s"\)$' % c for c in modclasses]
home = r'os.getenv\("HOME"\)'
- pj_usermodsdir = 'pathJoin\("%s", "funky", "Compiler/pi/3.14"\)' % usermodsdir
+ pj_usermodsdir = r'pathJoin\("%s", "funky", "Compiler/pi/3.14"\)' % usermodsdir
regexs.extend([
# extension for user modules is guarded
r'if isDir\(pathJoin\(%s, %s\)\) then' % (home, pj_usermodsdir),
@@ -993,7 +994,7 @@ class EasyBlockTest(EnhancedTestCase):
# [==[ or ]==] in description is fatal
if get_module_syntax() == 'Lua':
- error_pattern = "Found unwanted '\[==\[' or '\]==\]' in: .*"
+ error_pattern = r"Found unwanted '\[==\[' or '\]==\]' in: .*"
for descr in ["test [==[", "]==] foo"]:
ectxt = read_file(self.eb_file)
write_file(self.eb_file, re.sub('description.*', 'description = "%s"' % descr, ectxt))
@@ -1195,7 +1196,7 @@ class EasyBlockTest(EnhancedTestCase):
# old format for specifying source with custom extract command is deprecated
eb.src = []
- error_msg = "DEPRECATED \(since v4.0\).*Using a 2-element list/tuple.*"
+ error_msg = r"DEPRECATED \(since v4.0\).*Using a 2-element list/tuple.*"
self.assertErrorRegex(EasyBuildError, error_msg, eb.fetch_sources,
[('toy-0.0_gzip.patch.gz', "gunzip %s")], checksums=[])
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 0f45797bc..f3239de88 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -558,12 +558,12 @@ class EasyConfigTest(EnhancedTestCase):
homepage = "http://www.justatest.com"
tweaks = {
- 'version': ver,
- 'versionprefix': verpref,
- 'versionsuffix': versuff,
- 'toolchain_version': tcver,
- 'patches': new_patches
- }
+ 'version': ver,
+ 'versionprefix': verpref,
+ 'versionsuffix': versuff,
+ 'toolchain_version': tcver,
+ 'patches': new_patches
+ }
tweak_one(self.eb_file, tweaked_fn, tweaks)
eb = EasyConfig(tweaked_fn)
@@ -939,11 +939,11 @@ class EasyConfigTest(EnhancedTestCase):
def test_templating(self):
""" test easyconfig templating """
inp = {
- 'name': 'PI',
- # purposely using minor version that starts with a 0, to check for correct version_minor value
- 'version': '3.04',
- 'namelower': 'pi',
- 'cmd': 'tar xfvz %s',
+ 'name': 'PI',
+ # purposely using minor version that starts with a 0, to check for correct version_minor value
+ 'version': '3.04',
+ 'namelower': 'pi',
+ 'cmd': 'tar xfvz %s',
}
# don't use any escaping insanity here, since it is templated itself
self.contents = '\n'.join([
@@ -1028,8 +1028,8 @@ class EasyConfigTest(EnhancedTestCase):
doc = avail_easyconfig_constants()
# expected length: 1 per constant and 1 extra per constantgroup
temps = [
- easyconfig.constants.EASYCONFIG_CONSTANTS,
- ]
+ easyconfig.constants.EASYCONFIG_CONSTANTS,
+ ]
self.assertEqual(len(doc.split('\n')), sum([len(temps)] + [len(x) for x in temps]))
def test_build_options(self):
@@ -1987,17 +1987,17 @@ class EasyConfigTest(EnhancedTestCase):
# check internal structure to keep track of comments
self.assertEqual(ec.parser._formatter.comments['above'], {
- 'dependencies': [
- '# this is a multiline comment above dependencies',
- '# I said multiline',
- '# multi > 3',
- ],
- 'sanity_check_paths': ['# how about comments above and in a dict value?'],
- 'source_urls': ['# how about # a comment with # multple additional hashes'],
- 'sources': ['# after toolchain, before sources comment',
- '',
- '# this comment contains another #, uh-oh...'],
- 'version': ["# the version doesn't matter much here"],
+ 'dependencies': [
+ '# this is a multiline comment above dependencies',
+ '# I said multiline',
+ '# multi > 3',
+ ],
+ 'sanity_check_paths': ['# how about comments above and in a dict value?'],
+ 'source_urls': ['# how about # a comment with # multple additional hashes'],
+ 'sources': ['# after toolchain, before sources comment',
+ '',
+ '# this comment contains another #, uh-oh...'],
+ 'version': ["# the version doesn't matter much here"],
})
self.assertEqual(ec.parser._formatter.comments['header'], [
'# this is a header',
diff --git a/test/framework/easyconfigversion.py b/test/framework/easyconfigversion.py
index 2fc9b0c60..8547b2ce6 100644
--- a/test/framework/easyconfigversion.py
+++ b/test/framework/easyconfigversion.py
@@ -215,7 +215,7 @@ class EasyConfigVersion(EnhancedTestCase):
(tc, '1.2.2', False), # version not ok, name ok
('x' + tc, '1.2.3', False), # version ok, name not ok
('x' + tc, '1.2.2', False), # version not ok, name not ok
- )),
+ )),
]
for txt, subtests in tests:
tcversop = ToolchainVersionOperator(txt)
diff --git a/test/framework/general.py b/test/framework/general.py
index 0f2227226..07e8c3601 100644
--- a/test/framework/general.py
+++ b/test/framework/general.py
@@ -49,9 +49,9 @@ class GeneralTest(EnhancedTestCase):
easybuild_loc = os.path.dirname(os.path.dirname(os.path.abspath(easybuild.framework.__file__)))
log_method_regexes = [
- re.compile("log\.error\("),
- re.compile("log\.exception\("),
- re.compile("log\.raiseException\("),
+ re.compile(r"log\.error\("),
+ re.compile(r"log\.exception\("),
+ re.compile(r"log\.raiseException\("),
]
for dirpath, _, filenames in os.walk(easybuild_loc):
diff --git a/test/framework/github.py b/test/framework/github.py
index bb1e4be68..fe5cf22c8 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -87,7 +87,7 @@ class GithubTest(EnhancedTestCase):
try:
expected = [(None, ['a_directory', 'second_dir'], ['README.md']),
('a_directory', ['a_subdirectory'], ['a_file.txt']), ('a_directory/a_subdirectory', [],
- ['a_file.txt']), ('second_dir', [], ['a_file.txt'])]
+ ['a_file.txt']), ('second_dir', [], ['a_file.txt'])]
self.assertEqual([x for x in self.ghfs.walk(None)], expected)
except IOError:
pass
@@ -403,7 +403,7 @@ class GithubTest(EnhancedTestCase):
print("Skipping test_find_easybuild_easyconfig, no GitHub token available?")
return
path = gh.find_easybuild_easyconfig(github_user=GITHUB_TEST_ACCOUNT)
- expected = os.path.join('e', 'EasyBuild', 'EasyBuild-[1-9]+\.[0-9]+\.[0-9]+\.eb')
+ expected = os.path.join('e', 'EasyBuild', r'EasyBuild-[1-9]+\.[0-9]+\.[0-9]+\.eb')
regex = re.compile(expected)
self.assertTrue(regex.search(path), "Pattern '%s' found in '%s'" % (regex.pattern, path))
self.assertTrue(os.path.exists(path), "Path %s exists" % path)
@@ -542,9 +542,9 @@ class GithubTest(EnhancedTestCase):
patch_paths = [os.path.join(self.test_prefix, p) for p in ['1.patch', '2.patch', '3.patch']]
file_info = {'ecs': [
- {'name': 'A', 'patches': ['1.patch'], 'exts_list': []},
- {'name': 'B', 'patches': [], 'exts_list': []},
- ]
+ {'name': 'A', 'patches': ['1.patch'], 'exts_list': []},
+ {'name': 'B', 'patches': [], 'exts_list': []},
+ ]
}
error_pattern = "Failed to determine software name to which patch file .*/2.patch relates"
self.mock_stdout(True)
diff --git a/test/framework/include.py b/test/framework/include.py
index 9bf791e50..16dd73986 100644
--- a/test/framework/include.py
+++ b/test/framework/include.py
@@ -41,7 +41,7 @@ from easybuild.tools.include import is_software_specific_easyblock
def up(path, cnt):
"""Return path N times up."""
if cnt > 0:
- path = up(os.path.dirname(path), cnt-1)
+ path = up(os.path.dirname(path), cnt - 1)
return path
diff --git a/test/framework/lib.py b/test/framework/lib.py
index ae1122582..5bd099ed3 100644
--- a/test/framework/lib.py
+++ b/test/framework/lib.py
@@ -80,7 +80,7 @@ class EasyBuildLibTest(TestCase):
"""Test use of run_cmd function in the context of using EasyBuild framework as a library."""
error_pattern = "Undefined build option: .*"
- error_pattern += " Make sure you have set up the EasyBuild configuration using set_up_configuration\(\)"
+ error_pattern += r" Make sure you have set up the EasyBuild configuration using set_up_configuration\(\)"
self.assertErrorRegex(EasyBuildError, error_pattern, run_cmd, "echo hello")
self.configure()
@@ -96,7 +96,7 @@ class EasyBuildLibTest(TestCase):
test_dir = os.path.join(self.tmpdir, 'test123')
error_pattern = "Undefined build option: .*"
- error_pattern += " Make sure you have set up the EasyBuild configuration using set_up_configuration\(\)"
+ error_pattern += r" Make sure you have set up the EasyBuild configuration using set_up_configuration\(\)"
self.assertErrorRegex(EasyBuildError, error_pattern, mkdir, test_dir)
self.configure()
@@ -110,7 +110,7 @@ class EasyBuildLibTest(TestCase):
"""Test use of modules_tool function in the context of using EasyBuild framework as a library."""
error_pattern = "Undefined build option: .*"
- error_pattern += " Make sure you have set up the EasyBuild configuration using set_up_configuration\(\)"
+ error_pattern += r" Make sure you have set up the EasyBuild configuration using set_up_configuration\(\)"
self.assertErrorRegex(EasyBuildError, error_pattern, modules_tool)
self.configure()
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 81ce79421..1b73ec3f1 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -1322,11 +1322,11 @@ class ModuleGeneratorTest(EnhancedTestCase):
init_config(build_options=build_options)
test_ecs = {
- 'GCC-6.4.0-2.28.eb': ('compiler/GCC/6.4.0-2.28', '', [], [], []),
+ 'GCC-6.4.0-2.28.eb': ('compiler/GCC/6.4.0-2.28', '', [], [], []),
'OpenMPI-2.1.2-GCC-6.4.0-2.28.eb': ('mpi/OpenMPI/2.1.2-GCC-6.4.0-2.28', '', [], [], []),
- 'gzip-1.5-foss-2018a.eb': ('tools/gzip/1.5-foss-2018a', '', [], [], []),
- 'foss-2018a.eb': ('toolchain/foss/2018a', '', [], [], []),
- 'impi-5.1.2.150.eb': ('mpi/impi/5.1.2.150', '', [], [], []),
+ 'gzip-1.5-foss-2018a.eb': ('tools/gzip/1.5-foss-2018a', '', [], [], []),
+ 'foss-2018a.eb': ('toolchain/foss/2018a', '', [], [], []),
+ 'impi-5.1.2.150.eb': ('mpi/impi/5.1.2.150', '', [], [], []),
}
for ecfile, mns_vals in test_ecs.items():
test_ec(ecfile, *mns_vals)
diff --git a/test/framework/modules.py b/test/framework/modules.py
index ca3d826e7..072efe64e 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -890,7 +890,7 @@ class ModulesTest(EnhancedTestCase):
# exact error message depends on Lmod version
load_err_msg = '|'.join([
r'These[\s\sn]*module\(s\)[\s\sn]*exist[\s\sn]*but[\s\sn]*cannot[\s\sn]*be',
- 'The[\s\sn]*following[\s\sn]*module\(s\)[\s\sn]*are[\s\sn]*unknown',
+ r'The[\s\sn]*following[\s\sn]*module\(s\)[\s\sn]*are[\s\sn]*unknown',
])
else:
load_err_msg = "Unable to locate a modulefile"
@@ -1100,7 +1100,7 @@ class ModulesTest(EnhancedTestCase):
r"^\* GCC/6.4.0-2.28",
r"^\* hwloc/1.11.8-GCC-6.4.0-2.28",
r"^\* OpenMPI/2.1.2-GCC-6.4.0-2.28",
- "This is not recommended since it may affect the installation procedure\(s\) performed by EasyBuild.",
+ r"This is not recommended since it may affect the installation procedure\(s\) performed by EasyBuild.",
"To make EasyBuild allow particular loaded modules, use the --allow-loaded-modules configuration option.",
"To specify action to take when loaded modules are detected, use "
"--detect-loaded-modules={error,ignore,purge,unload,warn}",
@@ -1118,7 +1118,7 @@ class ModulesTest(EnhancedTestCase):
# error mentioning 1 non-allowed module (OpenMPI), both GCC and hwloc loaded modules are allowed
error_pattern = r"Found one or more non-allowed loaded .* module.*\n"
- error_pattern += "\* OpenMPI/2.1.2-GCC-6.4.0-2.28\n\nThis is not"
+ error_pattern += r"\* OpenMPI/2.1.2-GCC-6.4.0-2.28\n\nThis is not"
self.assertErrorRegex(EasyBuildError, error_pattern, self.modtool.check_loaded_modules)
# check for warning message when purge is being run on loaded modules
diff --git a/test/framework/options.py b/test/framework/options.py
index e4eed050d..e6c8e557a 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -125,12 +125,12 @@ class CommandLineOptionsTest(EnhancedTestCase):
if txt is None:
topt = EasyBuildOptions(
- go_args=['-h'],
- go_nosystemexit=True, # when printing help, optparse ends with sys.exit
- go_columns=100, # fix col size for reproducible unittest output
- help_to_string=True, # don't print to stdout, but to StingIO fh,
- prog='easybuildoptions_test', # generate as if called from generaloption.py
- )
+ go_args=['-h'],
+ go_nosystemexit=True, # when printing help, optparse ends with sys.exit
+ go_columns=100, # fix col size for reproducible unittest output
+ help_to_string=True, # don't print to stdout, but to StingIO fh,
+ prog='easybuildoptions_test', # generate as if called from generaloption.py
+ )
outtxt = topt.parser.help_to_file.getvalue()
else:
@@ -148,12 +148,12 @@ class CommandLineOptionsTest(EnhancedTestCase):
"""Test long help message."""
topt = EasyBuildOptions(
- go_args=['-H'],
- go_nosystemexit=True, # when printing help, optparse ends with sys.exit
- go_columns=200, # fix col size for reproducible unittest output
- help_to_string=True, # don't print to stdout, but to StingIO fh,
- prog='easybuildoptions_test', # generate as if called from generaloption.py
- )
+ go_args=['-H'],
+ go_nosystemexit=True, # when printing help, optparse ends with sys.exit
+ go_columns=200, # fix col size for reproducible unittest output
+ help_to_string=True, # don't print to stdout, but to StingIO fh,
+ prog='easybuildoptions_test', # generate as if called from generaloption.py
+ )
outtxt = topt.parser.help_to_file.getvalue()
self.assertTrue(re.search("-H OUTPUT_FORMAT, --help=OUTPUT_FORMAT", outtxt),
@@ -198,9 +198,9 @@ class CommandLineOptionsTest(EnhancedTestCase):
for info_arg in ['--info']:
args = [
- 'nosuchfile.eb',
- info_arg,
- ]
+ 'nosuchfile.eb',
+ info_arg,
+ ]
outtxt = self.eb_main(args)
error_tmpl = "%s log messages are included when using %s ( out: %s)"
@@ -236,9 +236,9 @@ class CommandLineOptionsTest(EnhancedTestCase):
# check log message without --force
args = [
- eb_file,
- '--debug',
- ]
+ eb_file,
+ '--debug',
+ ]
outtxt, error_thrown = self.eb_main(args, return_error=True)
error_msg = "No error is thrown if software is already installed (error_thrown: %s)" % error_thrown
@@ -317,7 +317,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
# make sure that sanity check is *NOT* skipped under --skip
test_ec = os.path.join(self.test_prefix, 'test.eb')
test_ec_txt = read_file(toy_ec)
- regex = re.compile("sanity_check_paths = \{(.|\n)*\}", re.M)
+ regex = re.compile(r"sanity_check_paths = \{(.|\n)*\}", re.M)
test_ec_txt = regex.sub("sanity_check_paths = {'files': ['bin/nosuchfile'], 'dirs': []}", test_ec_txt)
write_file(test_ec, test_ec_txt)
args = [
@@ -350,12 +350,12 @@ class CommandLineOptionsTest(EnhancedTestCase):
write_file(self.logfile, '')
args = [
- eb_file,
- '--job',
- ] + job_args
+ eb_file,
+ '--job',
+ ] + job_args
outtxt = self.eb_main(args)
- job_msg = "INFO.* Command template for jobs: .* && eb %%\(spec\)s.* %s.*\n" % ' .*'.join(passed_args)
+ job_msg = r"INFO.* Command template for jobs: .* && eb %%\(spec\)s.* %s.*\n" % ' .*'.join(passed_args)
assertmsg = "Info log msg with job command template for --job (job_msg: %s, outtxt: %s)" % (job_msg, outtxt)
self.assertTrue(re.search(job_msg, outtxt), assertmsg)
@@ -462,7 +462,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
param_start = 0
for param in params:
# regex for parameter name (with optional '*') & description, matches both txt and rst formats
- regex = re.compile("^[`]*%s(?:\*)?[`]*\s+\w+" % param, re.M)
+ regex = re.compile(r"^[`]*%s(?:\*)?[`]*\s+\w+" % param, re.M)
tup = (param, avail_arg, args, regex.pattern, logtxt)
msg = "Parameter %s is listed with help in output of eb %s (args: %s, regex: %s): %s" % tup
res = regex.search(logtxt)
@@ -490,9 +490,9 @@ class CommandLineOptionsTest(EnhancedTestCase):
os.close(fd)
args = [
- '--list-toolchains',
- '--unittest-file=%s' % self.logfile,
- ]
+ '--list-toolchains',
+ '--unittest-file=%s' % self.logfile,
+ ]
self.eb_main(args, logfile=dummylogfn, raise_error=True)
info_msg = r"INFO List of known toolchains \(toolchainname: module\[,module\.\.\.\]\):"
@@ -505,7 +505,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
'intel': ['icc', 'ifort', 'imkl', 'impi'],
}
for tc, tcelems in tcs.items():
- res = re.findall("^\s*%s: .*" % tc, logtxt, re.M)
+ res = re.findall(r"^\s*%s: .*" % tc, logtxt, re.M)
self.assertTrue(res, "Toolchain %s is included in list of known compiler toolchains" % tc)
# every toolchain should only be mentioned once
n = len(res)
@@ -528,9 +528,9 @@ class CommandLineOptionsTest(EnhancedTestCase):
}
for (name, items) in name_items.items():
args = [
- '--avail-%s' % name,
- '--unittest-file=%s' % self.logfile,
- ]
+ '--avail-%s' % name,
+ '--unittest-file=%s' % self.logfile,
+ ]
self.eb_main(args, logfile=dummylogfn)
logtxt = read_file(self.logfile)
@@ -538,7 +538,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
info_msg = r"INFO List of supported %s:" % words
self.assertTrue(re.search(info_msg, logtxt), "Info message with list of available %s" % words)
for item in items:
- res = re.findall("^\s*%s" % item, logtxt, re.M)
+ res = re.findall(r"^\s*%s" % item, logtxt, re.M)
self.assertTrue(res, "%s is included in list of available %s" % (item, words))
# every item should only be mentioned once
n = len(res)
@@ -594,9 +594,9 @@ class CommandLineOptionsTest(EnhancedTestCase):
write_file(self.logfile, '')
args = [
- list_arg,
- '--unittest-file=%s' % self.logfile,
- ]
+ list_arg,
+ '--unittest-file=%s' % self.logfile,
+ ]
self.eb_main(args, logfile=dummylogfn)
logtxt = read_file(self.logfile)
@@ -635,9 +635,9 @@ class CommandLineOptionsTest(EnhancedTestCase):
# detailed view
args = [
- '--list-easyblocks=detailed',
- '--unittest-file=%s' % self.logfile,
- ]
+ '--list-easyblocks=detailed',
+ '--unittest-file=%s' % self.logfile,
+ ]
self.eb_main(args, logfile=dummylogfn)
logtxt = read_file(self.logfile)
@@ -738,7 +738,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
txt = self.get_stdout()
self.mock_stdout(False)
- self.assertTrue(re.search('^CFGS\d+=', txt, re.M), "CFGS line message found in '%s'" % txt)
+ self.assertTrue(re.search(r'^CFGS\d+=', txt, re.M), "CFGS line message found in '%s'" % txt)
for ec in ["toy-0.0.eb", "toy-0.0-multiple.eb"]:
regex = re.compile(r" \* \$CFGS\d+/*%s" % ec, re.M)
self.assertTrue(regex.search(txt), "Found pattern '%s' in: %s" % (regex.pattern, txt))
@@ -1063,7 +1063,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
("FFTW-3.3.7-gompi-2018b.eb", "FFTW/3.3.7-gompi-2018b", 'F'),
]
for ec, mod, mark in ecs_mods:
- regex = re.compile("^ \* \[%s\] \S+%s \(module: %s\)$" % (mark, ec, mod), re.M)
+ regex = re.compile(r"^ \* \[%s\] \S+%s \(module: %s\)$" % (mark, ec, mod), re.M)
self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
def test_try_toolchain_mapping(self):
@@ -1136,7 +1136,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
("gzip-1.5-foss-2018a.eb", "MPI/GCC/6.4.0-2.28/OpenMPI/2.1.2", "gzip/1.5", ' '),
]
for ec, mod_subdir, mod_name, mark in ecs_mods:
- regex = re.compile("^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)
+ regex = re.compile(r"^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)
self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
if os.path.exists(dummylogfn):
@@ -1177,7 +1177,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
("gzip-1.5-foss-2018a.eb", "MPI/GCC/6.4.0-2.28/OpenMPI/2.1.2/tools", "gzip/1.5", ' '),
]
for ec, mod_subdir, mod_name, mark in ecs_mods:
- regex = re.compile("^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)
+ regex = re.compile(r"^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)
self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
if os.path.exists(dummylogfn):
@@ -1370,10 +1370,10 @@ class CommandLineOptionsTest(EnhancedTestCase):
"""Test using no arguments."""
args = [
- '--software-name=nosuchsoftware',
- '--robot=.',
- '--debug',
- ]
+ '--software-name=nosuchsoftware',
+ '--robot=.',
+ '--debug',
+ ]
outtxt = self.eb_main(args)
# error message when template is not found
@@ -1539,7 +1539,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
regex = re.compile("Checking OS dependencies")
self.assertTrue(regex.search(outtxt), "OS dependencies are checked, outtxt: %s" % outtxt)
msg = "One or more OS dependencies were not found: "
- msg += "\[\('nosuchosdependency',\), \('nosuchdep_option1', 'nosuchdep_option2'\)\]"
+ msg += r"\[\('nosuchosdependency',\), \('nosuchdep_option1', 'nosuchdep_option2'\)\]"
regex = re.compile(r'%s' % msg, re.M)
self.assertTrue(regex.search(outtxt), "OS dependencies are honored, outtxt: %s" % outtxt)
@@ -1764,7 +1764,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
for extra_args, mod in test_cases:
outtxt = self.eb_main(args + extra_args, verbose=True, raise_error=True)
- mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+ mod_regex = re.compile(r"\(module: %s\)$" % mod, re.M)
self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
for extra_arg in ['--try-software=foo', '--try-toolchain=gompi', '--try-toolchain=gomp,2018a,-a-suffix']:
@@ -1825,7 +1825,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
outtxt = self.eb_main(args + extra_args, verbose=True, raise_error=True)
# toolchain GCC/4.7.2 (subtoolchain of gompi/2018a) should be listed (and present)
- tc_regex = re.compile("^ \* \[x\] .*/GCC-6.4.0-2.28.eb \(module: .*GCC/6.4.0-2.28\)$", re.M)
+ tc_regex = re.compile(r"^ \* \[x\] .*/GCC-6.4.0-2.28.eb \(module: .*GCC/6.4.0-2.28\)$", re.M)
self.assertTrue(tc_regex.search(outtxt), "Pattern %s found in %s" % (tc_regex.pattern, outtxt))
# both toy and gzip dependency should be listed with new toolchains
@@ -1837,7 +1837,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
mod = ec_name.replace('-', '/')
else:
mod = '%s-GCC-6.4.0-2.28' % ec_name.replace('-', '/')
- mod_regex = re.compile("^ \* \[ \] \S+/eb-\S+/%s \(module: .*%s\)$" % (ec, mod), re.M)
+ mod_regex = re.compile(r"^ \* \[ \] \S+/eb-\S+/%s \(module: .*%s\)$" % (ec, mod), re.M)
self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
# clear fictious dependency
@@ -1849,10 +1849,10 @@ class CommandLineOptionsTest(EnhancedTestCase):
for extra_args in [['--try-software-version=1.2.3'], ['--software-version=1.2.3']]:
outtxt = self.eb_main(args + extra_args, raise_error=True)
for mod in ['toy/1.2.3-gompi-2018a', 'gompi/2018a', 'GCC/6.4.0-2.28']:
- mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+ mod_regex = re.compile(r"\(module: %s\)$" % mod, re.M)
self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
for mod in ['gompi/1.2.3', 'GCC/1.2.3']:
- mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+ mod_regex = re.compile(r"\(module: %s\)$" % mod, re.M)
self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
def test_cleanup_builddir(self):
@@ -2053,8 +2053,8 @@ class CommandLineOptionsTest(EnhancedTestCase):
'--hide-toolchains=GCC',
]
outtxt = self.eb_main(args)
- self.assertTrue(re.search('module: GCC/\.4\.9\.2', outtxt))
- self.assertTrue(re.search('module: gzip/1\.6-GCC-4\.9\.2', outtxt))
+ self.assertTrue(re.search(r'module: GCC/\.4\.9\.2', outtxt))
+ self.assertTrue(re.search(r'module: gzip/1\.6-GCC-4\.9\.2', outtxt))
def test_test_report_env_filter(self):
"""Test use of --test-report-env-filter."""
@@ -2122,7 +2122,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
eb_file,
'--robot-paths=%s' % test_ecs_path,
]
- error_regex = "Missing modules for dependencies .*: toy/\.0.0-deps"
+ error_regex = r"Missing modules for dependencies .*: toy/\.0.0-deps"
self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True, do_build=True)
# enable robot, but without passing path required to resolve toy dependency => FAIL
@@ -2771,7 +2771,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
mytmpdir = set_tmpdir(tmpdir=tmpdir)
- parent = re.sub('[^\w/.-]', 'X', parent)
+ parent = re.sub(r'[^\w/.-]', 'X', parent)
for var in ['TMPDIR', 'TEMP', 'TMP']:
self.assertTrue(os.environ[var].startswith(os.path.join(parent, 'eb-')))
@@ -2837,8 +2837,8 @@ class CommandLineOptionsTest(EnhancedTestCase):
txt = self.get_stdout()
self.mock_stdout(False)
comp = 'Compiler/GCC/6.4.0-2.28'
- sqlite_regex = re.compile("hwloc-1.11.8-GCC-6.4.0-2.28.eb \(module: %s \| hwloc/" % comp, re.M)
- sqlite_regex = re.compile("SQLite-3.8.10.2-GCC-6.4.0-2.28.eb \(module: %s \| SQLite/" % comp, re.M)
+ sqlite_regex = re.compile(r"hwloc-1.11.8-GCC-6.4.0-2.28.eb \(module: %s \| hwloc/" % comp, re.M)
+ sqlite_regex = re.compile(r"SQLite-3.8.10.2-GCC-6.4.0-2.28.eb \(module: %s \| SQLite/" % comp, re.M)
self.assertTrue(sqlite_regex.search(txt), "Pattern '%s' found in: %s" % (sqlite_regex.pattern, txt))
def test_extended_dry_run(self):
@@ -3218,7 +3218,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
args.append('--pr-commit-msg=this is just a test')
txt, _ = self._run_mock_eb(args, do_build=True, raise_error=True, testing=False)
- regex = re.compile('^\* title: "this is just a test"', re.M)
+ regex = re.compile(r'^\* title: "this is just a test"', re.M)
self.assertTrue(regex.search(txt), "Pattern '%s' is found in: %s" % (regex.pattern, txt))
args = [
@@ -3268,7 +3268,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
regexs = [
"# Built with EasyBuild",
"# Build statistics",
- "buildstats\s*=",
+ r"buildstats\s*=",
]
self._assert_regexs(regexs, txt, assert_true=False)
@@ -3658,8 +3658,8 @@ class CommandLineOptionsTest(EnhancedTestCase):
patterns = [
"^# Current EasyBuild configuration",
- "^module-syntax\s*\(C\) = Tcl",
- "^modules-tool\s*\(E\) = EnvironmentModulesC",
+ r"^module-syntax\s*\(C\) = Tcl",
+ r"^modules-tool\s*\(E\) = EnvironmentModulesC",
]
for pattern in patterns:
regex = re.compile(pattern, re.M)
@@ -3680,8 +3680,8 @@ class CommandLineOptionsTest(EnhancedTestCase):
patterns = [
"^# Current EasyBuild configuration",
- "^module-syntax\s*\(C\) = Tcl",
- "^modules-tool\s*\(E\) = EnvironmentModulesC",
+ r"^module-syntax\s*\(C\) = Tcl",
+ r"^modules-tool\s*\(E\) = EnvironmentModulesC",
]
# EnvironmentModulesC modules tool + Tcl module syntax is fine
@@ -3693,7 +3693,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
# default modules tool (Lmod) with Tcl module syntax is also fine
del os.environ['EASYBUILD_MODULES_TOOL']
- patterns[-1] = "^modules-tool\s*\(D\) = Lmod"
+ patterns[-1] = r"^modules-tool\s*\(D\) = Lmod"
stdout, _ = self._run_mock_eb(args, do_build=True, raise_error=True, testing=False, redo_init_config=False)
for pattern in patterns:
regex = re.compile(pattern, re.M)
@@ -3703,7 +3703,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
"""Test which configuration settings are affected by --prefix."""
txt, _ = self._run_mock_eb(['--show-full-config', '--prefix=%s' % self.test_prefix], raise_error=True)
- regex = re.compile("(?P<cfg_opt>\S*).*%s.*" % self.test_prefix, re.M)
+ regex = re.compile(r"(?P<cfg_opt>\S*).*%s.*" % self.test_prefix, re.M)
expected = ['buildpath', 'containerpath', 'installpath', 'packagepath', 'prefix', 'repositorypath']
self.assertEqual(sorted(regex.findall(txt)), expected)
@@ -3789,7 +3789,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
regex = re.compile(pattern, re.M)
self.assertTrue(regex.search(stdout), "Pattern '%s' not found in: %s" % (regex.pattern, stdout))
- regex = re.compile("^== creating build dir, resetting environment\.\.\.$")
+ regex = re.compile(r"^== creating build dir, resetting environment\.\.\.$")
self.assertFalse(regex.search(stdout), "Pattern '%s' found in: %s" % (regex.pattern, stdout))
def test_parse_external_modules_metadata(self):
@@ -3943,19 +3943,19 @@ class CommandLineOptionsTest(EnhancedTestCase):
def test_list_prs(self):
"""Test --list-prs."""
args = ['--list-prs', 'foo']
- error_msg = "must be one of \['open', 'closed', 'all'\]"
+ error_msg = r"must be one of \['open', 'closed', 'all'\]"
self.assertErrorRegex(EasyBuildError, error_msg, self.eb_main, args, raise_error=True)
args = ['--list-prs', 'open,foo']
- error_msg = "must be one of \['created', 'updated', 'popularity', 'long-running'\]"
+ error_msg = r"must be one of \['created', 'updated', 'popularity', 'long-running'\]"
self.assertErrorRegex(EasyBuildError, error_msg, self.eb_main, args, raise_error=True)
args = ['--list-prs', 'open,created,foo']
- error_msg = "must be one of \['asc', 'desc'\]"
+ error_msg = r"must be one of \['asc', 'desc'\]"
self.assertErrorRegex(EasyBuildError, error_msg, self.eb_main, args, raise_error=True)
args = ['--list-prs', 'open,created,asc,foo']
- error_msg = "must be in the format 'state\[,order\[,direction\]\]"
+ error_msg = r"must be in the format 'state\[,order\[,direction\]\]"
self.assertErrorRegex(EasyBuildError, error_msg, self.eb_main, args, raise_error=True)
args = ['--list-prs', 'closed,updated,asc']
@@ -4368,17 +4368,17 @@ class CommandLineOptionsTest(EnhancedTestCase):
bar_patch_bis = 'bar-0.0_fix-very-silly-typo-in-printf-statement.patch'
bar_patch_bis_sha256 = 'd0bf102f9c5878445178c5f49b7cd7546e704c33fe2060c7354b7e473cfeb52b'
patterns = [
- "^== injecting sha256 checksums in .*/test\.eb$",
- "^== fetching sources & patches for test\.eb\.\.\.$",
- "^== backup of easyconfig file saved to .*/test\.eb\.bak_[0-9]+_[0-9]+\.\.\.$",
- "^== injecting sha256 checksums for sources & patches in test\.eb\.\.\.$",
- "^== \* toy-0.0\.tar\.gz: %s$" % toy_source_sha256,
- "^== \* toy-0\.0_fix-silly-typo-in-printf-statement\.patch: %s$" % toy_patch_sha256,
- "^== injecting sha256 checksums for extensions in test\.eb\.\.\.$",
- "^== \* bar-0\.0\.tar\.gz: %s$" % bar_tar_gz_sha256,
- "^== \* %s: %s$" % (bar_patch, bar_patch_sha256),
- "^== \* %s: %s$" % (bar_patch_bis, bar_patch_bis_sha256),
- "^== \* barbar-0\.0\.tar\.gz: a33100d1837d6d54edff7d19f195056c4bd9a4c8d399e72feaf90f0216c4c91c$",
+ r"^== injecting sha256 checksums in .*/test\.eb$",
+ r"^== fetching sources & patches for test\.eb\.\.\.$",
+ r"^== backup of easyconfig file saved to .*/test\.eb\.bak_[0-9]+_[0-9]+\.\.\.$",
+ r"^== injecting sha256 checksums for sources & patches in test\.eb\.\.\.$",
+ r"^== \* toy-0.0\.tar\.gz: %s$" % toy_source_sha256,
+ r"^== \* toy-0\.0_fix-silly-typo-in-printf-statement\.patch: %s$" % toy_patch_sha256,
+ r"^== injecting sha256 checksums for extensions in test\.eb\.\.\.$",
+ r"^== \* bar-0\.0\.tar\.gz: %s$" % bar_tar_gz_sha256,
+ r"^== \* %s: %s$" % (bar_patch, bar_patch_sha256),
+ r"^== \* %s: %s$" % (bar_patch_bis, bar_patch_bis_sha256),
+ r"^== \* barbar-0\.0\.tar\.gz: a33100d1837d6d54edff7d19f195056c4bd9a4c8d399e72feaf90f0216c4c91c$",
]
for pattern in patterns:
regex = re.compile(pattern, re.M)
@@ -4481,7 +4481,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
toy_ec_txt = read_file(toy_ec)
# get rid of existing checksums
- regex = re.compile('^checksums(?:.|\n)*?\]\s*$', re.M)
+ regex = re.compile(r'^checksums(?:.|\n)*?\]\s*$', re.M)
toy_ec_txt = regex.sub('', toy_ec_txt)
self.assertFalse('checksums = ' in toy_ec_txt)
@@ -4491,13 +4491,13 @@ class CommandLineOptionsTest(EnhancedTestCase):
stdout, stderr = self._run_mock_eb(args, raise_error=True, strip=True)
patterns = [
- "^== injecting md5 checksums in .*/test\.eb$",
- "^== fetching sources & patches for test\.eb\.\.\.$",
- "^== backup of easyconfig file saved to .*/test\.eb\.bak_[0-9]+_[0-9]+\.\.\.$",
- "^== injecting md5 checksums for sources & patches in test\.eb\.\.\.$",
- "^== \* toy-0.0\.tar\.gz: be662daa971a640e40be5c804d9d7d10$",
- "^== \* toy-0\.0_fix-silly-typo-in-printf-statement\.patch: e6785e1a721fc8bf79892e3ef41557c0$",
- "^== \* toy-extra\.txt: 3b0787b3bf36603ae1398c4a49097893$",
+ r"^== injecting md5 checksums in .*/test\.eb$",
+ r"^== fetching sources & patches for test\.eb\.\.\.$",
+ r"^== backup of easyconfig file saved to .*/test\.eb\.bak_[0-9]+_[0-9]+\.\.\.$",
+ r"^== injecting md5 checksums for sources & patches in test\.eb\.\.\.$",
+ r"^== \* toy-0.0\.tar\.gz: be662daa971a640e40be5c804d9d7d10$",
+ r"^== \* toy-0\.0_fix-silly-typo-in-printf-statement\.patch: e6785e1a721fc8bf79892e3ef41557c0$",
+ r"^== \* toy-extra\.txt: 3b0787b3bf36603ae1398c4a49097893$",
]
for pattern in patterns:
regex = re.compile(pattern, re.M)
@@ -4552,7 +4552,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
]
stdout, stderr = self._run_mock_eb(args, do_build=True, raise_error=True, verbose=True, strip=True)
self.assertEqual(stdout, '')
- regex = re.compile("^WARNING: Found file toy-0.0.tar.gz at .*, but re-downloading it anyway\.\.\.$")
+ regex = re.compile(r"^WARNING: Found file toy-0.0.tar.gz at .*, but re-downloading it anyway\.\.\.$")
self.assertTrue(regex.match(stderr), "Pattern '%s' matches: %s" % (regex.pattern, stderr))
# check that existing source tarball was backed up
@@ -4574,7 +4574,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
# checksum is missing for patch of 'bar' extension, so --enforce-checksums should result in an error
copy_file(toy_ec, test_ec)
- error_pattern = "Missing checksum for bar-0.0[^ ]*\.patch"
+ error_pattern = r"Missing checksum for bar-0.0[^ ]*\.patch"
self.assertErrorRegex(EasyBuildError, error_pattern, self.eb_main, args, do_build=True, raise_error=True)
# get rid of checksums for extensions, should result in different error message
@@ -4583,13 +4583,13 @@ class CommandLineOptionsTest(EnhancedTestCase):
test_ec_txt = regex.sub('', read_file(test_ec))
self.assertFalse("'checksums':" in test_ec_txt)
write_file(test_ec, test_ec_txt)
- error_pattern = "Missing checksum for bar-0\.0\.tar\.gz"
+ error_pattern = r"Missing checksum for bar-0\.0\.tar\.gz"
self.assertErrorRegex(EasyBuildError, error_pattern, self.eb_main, args, do_build=True, raise_error=True)
# wipe both exts_list and checksums, so we can check whether missing checksum for main source is caught
test_ec_txt = read_file(test_ec)
for param in ['checksums', 'exts_list']:
- regex = re.compile('^%s(?:.|\n)*?\]\s*$' % param, re.M)
+ regex = re.compile(r'^%s(?:.|\n)*?\]\s*$' % param, re.M)
test_ec_txt = regex.sub('', test_ec_txt)
self.assertFalse('%s = ' % param in test_ec_txt)
@@ -4601,13 +4601,13 @@ class CommandLineOptionsTest(EnhancedTestCase):
"""Test for --show-system-info."""
txt, _ = self._run_mock_eb(['--show-system-info'], raise_error=True)
patterns = [
- "^System information \(.*\):$",
- "^\* OS:$",
+ r"^System information \(.*\):$",
+ r"^\* OS:$",
"^ -> name: ",
"^ -> type: ",
"^ -> version: ",
"^ -> platform name: ",
- "^\* CPU:$",
+ r"^\* CPU:$",
"^ -> vendor: ",
"^ -> architecture: ",
"^ -> family: ",
@@ -4615,7 +4615,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
"^ -> speed: [0-9.]+",
"^ -> cores: [0-9]+",
"^ -> features: ",
- "^\* software:$",
+ r"^\* software:$",
"^ -> glibc version: ",
"^ -> Python binary: .*/[pP]ython[0-9]?",
"^ -> Python version: [0-9.]+",
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 9487b63e8..ed1eb04f2 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -86,6 +86,7 @@ def mock(*args, **kwargs):
class MockPbsJob(object):
"""Mocking class for PbsJob."""
+
def __init__(self, *args, **kwargs):
self.deps = []
self.jobid = None
@@ -173,7 +174,7 @@ class ParallelBuildTest(EnhancedTestCase):
# dependencies for gzip/1.4-GCC-4.6.3: GCC/4.6.3 (toolchain) + toy/.0.0-deps
self.assertTrue('gzip-1.4-GCC-4.6.3.eb' in jobs[3].script)
self.assertEqual(len(jobs[3].deps), 2)
- regex = re.compile('toy-0.0-deps.eb\s* --hidden')
+ regex = re.compile(r'toy-0.0-deps.eb\s* --hidden')
self.assertTrue(regex.search(jobs[3].deps[0].script))
self.assertTrue('GCC-4.6.3.eb' in jobs[3].deps[1].script)
@@ -303,9 +304,9 @@ class ParallelBuildTest(EnhancedTestCase):
# (unparsed) optarch value got wrapped in single quotes, double quotes got stripped
" --optarch='GCC:O3 -mtune=generic;Intel:O3 -xHost' ",
# templates to be completed via build_easyconfigs_in_parallel -> create_job
- ' eb %\(spec\)s ',
- ' %\(add_opts\)s ',
- ' --testoutput=%\(output_dir\)s',
+ r' eb %\(spec\)s ',
+ r' %\(add_opts\)s ',
+ r' --testoutput=%\(output_dir\)s',
]
for regex in regexs:
regex = re.compile(regex)
diff --git a/test/framework/robot.py b/test/framework/robot.py
index fc94a8485..129684b42 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -574,7 +574,7 @@ class RobotTest(EnhancedTestCase):
}],
}
- error = "Missing dependencies: somedep/4.5.6 \(no easyconfig file or existing module found\)"
+ error = r"Missing dependencies: somedep/4.5.6 \(no easyconfig file or existing module found\)"
self.assertErrorRegex(EasyBuildError, error, resolve_dependencies, [ec], self.modtool)
# check behaviour if only module file is available
@@ -583,7 +583,7 @@ class RobotTest(EnhancedTestCase):
self.assertEqual(len(res), 1)
self.assertEqual(res[0]['full_mod_name'], 'test/123')
- error = "Missing dependencies: somedep/4.5.6 \(no easyconfig file found in robot search path\)"
+ error = r"Missing dependencies: somedep/4.5.6 \(no easyconfig file found in robot search path\)"
self.assertErrorRegex(EasyBuildError, error, resolve_dependencies, [ec], self.modtool, retain_all_deps=True)
res = resolve_dependencies([ec], self.modtool, retain_all_deps=True, raise_error_missing_ecs=False)
diff --git a/test/framework/run.py b/test/framework/run.py
index e7d608c7b..f0c7db6e5 100644
--- a/test/framework/run.py
+++ b/test/framework/run.py
@@ -228,7 +228,7 @@ class RunTest(EnhancedTestCase):
# a more 'complex' command to run, make sure all required output is there
(out, ec) = run_cmd("for j in `seq 1 3`; do for i in `seq 1 100`; do echo hello; done; sleep 1.4; done")
self.assertTrue(out.startswith('hello\nhello\n'))
- self.assertEqual(len(out), len("hello\n"*300))
+ self.assertEqual(len(out), len("hello\n" * 300))
self.assertEqual(ec, 0)
def test_run_cmd_log_output(self):
diff --git a/test/framework/sandbox/easybuild/easyblocks/g/gcc.py b/test/framework/sandbox/easybuild/easyblocks/g/gcc.py
index 02d96ef2d..232489178 100644
--- a/test/framework/sandbox/easybuild/easyblocks/g/gcc.py
+++ b/test/framework/sandbox/easybuild/easyblocks/g/gcc.py
@@ -29,5 +29,6 @@ Dummy easyblock for GCC
"""
from easybuild.framework.easyblock import EasyBlock
+
class EB_GCC(EasyBlock):
pass
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py b/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py
index ae580258a..099e2e3e1 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py
@@ -31,6 +31,7 @@ i.e. configure/make/make install.
from easybuild.framework.easyblock import EasyBlock
from easybuild.framework.easyconfig import CUSTOM
+
class ConfigureMake(EasyBlock):
"""Dummy support for building and installing applications with configure/make/make install."""
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py b/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
index af97c3f25..88591809f 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
@@ -30,6 +30,7 @@ EasyBuild support for building and installing dummy extensions, implemented as a
from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
+
class DummyExtension(ExtensionEasyBlock):
"""Support for building/installing dummy extensions."""
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py b/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
index fd1de3a89..d31635817 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
@@ -29,13 +29,18 @@ Dummy easyblock for toolchains.
"""
from easybuild.framework.easyblock import EasyBlock
+
class Toolchain(EasyBlock):
"""Dummy support for toolchains."""
+
def configure_step(self):
pass
+
def build_step(self):
pass
+
def install_step(self):
pass
+
def sanity_check_step(self):
pass
diff --git a/test/framework/sandbox/easybuild/easyblocks/h/hpl.py b/test/framework/sandbox/easybuild/easyblocks/h/hpl.py
index 0b89ba202..db4e66065 100644
--- a/test/framework/sandbox/easybuild/easyblocks/h/hpl.py
+++ b/test/framework/sandbox/easybuild/easyblocks/h/hpl.py
@@ -29,5 +29,6 @@ Dummy easyblock for HPL
"""
from easybuild.framework.easyblock import EasyBlock
+
class EB_HPL(EasyBlock):
pass
diff --git a/test/framework/sandbox/easybuild/easyblocks/s/scalapack.py b/test/framework/sandbox/easybuild/easyblocks/s/scalapack.py
index 1dcef0a54..3cf433cb3 100644
--- a/test/framework/sandbox/easybuild/easyblocks/s/scalapack.py
+++ b/test/framework/sandbox/easybuild/easyblocks/s/scalapack.py
@@ -29,5 +29,6 @@ Dummy easyblock for ScaLAPACK
"""
from easybuild.framework.easyblock import EasyBlock
+
class EB_ScaLAPACK(EasyBlock):
pass
diff --git a/test/framework/sandbox/easybuild/easyblocks/t/toy_buggy.py b/test/framework/sandbox/easybuild/easyblocks/t/toy_buggy.py
index 959ff5b92..731713883 100644
--- a/test/framework/sandbox/easybuild/easyblocks/t/toy_buggy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/t/toy_buggy.py
@@ -30,6 +30,7 @@
from easybuild.framework.easyblock import EasyBlock
+
class EB_toy_buggy(EasyBlock):
"""Support for building/installing toy."""
diff --git a/test/framework/sandbox/easybuild/easyblocks/t/toytoy.py b/test/framework/sandbox/easybuild/easyblocks/t/toytoy.py
index 3ebbfe724..ee700251a 100644
--- a/test/framework/sandbox/easybuild/easyblocks/t/toytoy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/t/toytoy.py
@@ -40,5 +40,5 @@ class EB_toytoy(EB_toy):
"""Custom easyconfig parameters for toytoy."""
extra_vars = {
'toytoy_extra1': [None, "first toytoy-specific easyconfig parameter", CUSTOM],
- }
+ }
return EB_toy.extra_options(extra_vars)
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index fa1f1331c..acb9b3893 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -280,7 +280,7 @@ MACHINE_NAME = None
def mocked_read_file(fp):
"""Mocked version of read_file, with specified contents for known filenames."""
known_fps = {
- MAX_FREQ_FP: '2850000',
+ MAX_FREQ_FP: '2850000',
PROC_CPUINFO_FP: PROC_CPUINFO_TXT,
PROC_MEMINFO_FP: PROC_MEMINFO_TXT,
}
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 909bb2f07..11e5eb94f 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -1304,7 +1304,7 @@ class ToolchainTest(EnhancedTestCase):
ccache = which('ccache')
if ccache is None:
- msg = "ccache binary not found in \$PATH, required by --use-compiler-cache"
+ msg = r"ccache binary not found in \$PATH, required by --use-compiler-cache"
self.assertErrorRegex(EasyBuildError, msg, self.eb_main, args, raise_error=True, do_build=True)
# generate shell script to mock ccache/f90cache
diff --git a/test/framework/toolchainvariables.py b/test/framework/toolchainvariables.py
index 890417c35..7edbdde91 100644
--- a/test/framework/toolchainvariables.py
+++ b/test/framework/toolchainvariables.py
@@ -125,11 +125,11 @@ class ToolchainVariablesTest(EnhancedTestCase):
# e.g. numpy and mkl blas
# -Wl:-Bstatic,-Wl:--start-group,mkl_intel_lp64,mkl_intel_thread,mkl_core,-Wl:--end-group,-Wl:-Bdynamic,iomp5
kwargs = {
- 'prefix': '',
- 'prefix_begin_end': '-Wl:',
- 'separator': ',',
- 'separator_begin_end': ',',
- }
+ 'prefix': '',
+ 'prefix_begin_end': '-Wl:',
+ 'separator': ',',
+ 'separator_begin_end': ',',
+ }
copy_blas_2.try_function_on_element('change', kwargs=kwargs)
copy_blas_2.SEPARATOR = ','
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index d4a285e7f..e70fbac20 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -229,8 +229,8 @@ class ToyBuildTest(EnhancedTestCase):
shutil.copy2(os.path.join(test_ecs_dir, 'test_ecs', 't', 'toy', 'toy-0.0.eb'), ec_file)
modloadmsg = 'THANKS FOR LOADING ME\\nI AM %(name)s v%(version)s'
- modloadmsg_regex_tcl = 'THANKS.*\n\s*I AM toy v0.0\n\s*"'
- modloadmsg_regex_lua = '\[==\[THANKS.*\n\s*I AM toy v0.0\n\s*\]==\]'
+ modloadmsg_regex_tcl = r'THANKS.*\n\s*I AM toy v0.0\n\s*"'
+ modloadmsg_regex_lua = r'\[==\[THANKS.*\n\s*I AM toy v0.0\n\s*\]==\]'
# tweak easyconfig by appending to it
ec_extra = '\n'.join([
@@ -357,14 +357,14 @@ class ToyBuildTest(EnhancedTestCase):
sys.path.append(tmpdir)
args = [
- 'toy-0.0-multiple.eb',
- '--sourcepath=%s' % self.test_sourcepath,
- '--buildpath=%s' % self.test_buildpath,
- '--installpath=%s' % self.test_installpath,
- '--debug',
- '--unittest-file=%s' % self.logfile,
- '--force',
- ]
+ 'toy-0.0-multiple.eb',
+ '--sourcepath=%s' % self.test_sourcepath,
+ '--buildpath=%s' % self.test_buildpath,
+ '--installpath=%s' % self.test_installpath,
+ '--debug',
+ '--unittest-file=%s' % self.logfile,
+ '--force',
+ ]
outtxt = self.eb_main(args, logfile=self.dummylogfn, do_build=True, verbose=True)
for toy_prefix, toy_version, toy_suffix in [
@@ -700,7 +700,7 @@ class ToyBuildTest(EnhancedTestCase):
self.assertTrue(regex.search(outtxt), "Pattern '%s' found in: %s" % (regex.pattern, toy_mod_txt))
else:
pattern = "Can't generate robust check in Lua modules for users belonging to group %s. "
- pattern += "Lmod version not recent enough \(%s\), should be >= 6.0.8" % lmod_version
+ pattern += r"Lmod version not recent enough \(%s\), should be >= 6.0.8" % lmod_version
regex = re.compile(pattern % group_name, re.M)
self.assertTrue(regex.search(outtxt), "Pattern '%s' found in: %s" % (regex.pattern, outtxt))
else:
@@ -807,7 +807,7 @@ class ToyBuildTest(EnhancedTestCase):
modtxt = read_file(toy_module_path)
modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '6.4.0-2.28', 'toy', '0.0')
if get_module_syntax() == 'Tcl':
- self.assertTrue(re.search('^module\s*use\s*"%s"' % modpath_extension, modtxt, re.M))
+ self.assertTrue(re.search(r'^module\s*use\s*"%s"' % modpath_extension, modtxt, re.M))
elif get_module_syntax() == 'Lua':
fullmodpath_extension = os.path.join(self.test_installpath, modpath_extension)
regex = re.compile(r'^prepend_path\("MODULEPATH", "%s"\)' % fullmodpath_extension, re.M)
@@ -822,7 +822,7 @@ class ToyBuildTest(EnhancedTestCase):
modtxt = read_file(toy_module_path)
modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '6.4.0-2.28', 'toy', '0.0')
if get_module_syntax() == 'Tcl':
- self.assertFalse(re.search('^module\s*use\s*"%s"' % modpath_extension, modtxt, re.M))
+ self.assertFalse(re.search(r'^module\s*use\s*"%s"' % modpath_extension, modtxt, re.M))
elif get_module_syntax() == 'Lua':
fullmodpath_extension = os.path.join(self.test_installpath, modpath_extension)
regex = re.compile(r'^prepend_path\("MODULEPATH", "%s"\)' % fullmodpath_extension, re.M)
@@ -1185,7 +1185,7 @@ class ToyBuildTest(EnhancedTestCase):
modloadmsg_lua = [
r'io.stderr:write\(\[==\[THANKS FOR LOADING ME',
r'I AM toy v0.0',
- '\]==\]\)',
+ r'\]==\]\)',
]
help_txt = '\n'.join([
@@ -1827,7 +1827,7 @@ class ToyBuildTest(EnhancedTestCase):
ectxt = read_file(ec_file)
# modify test easyconfig: move lib/libtoy.a to lib64/libtoy.a
- ectxt = re.sub("\s*'files'.*", "'files': ['bin/toy', ('lib/libtoy.a', 'lib/libfoo.a')],", ectxt)
+ ectxt = re.sub(r"\s*'files'.*", "'files': ['bin/toy', ('lib/libtoy.a', 'lib/libfoo.a')],", ectxt)
postinstallcmd = "mkdir %(installdir)s/lib64 && mv %(installdir)s/lib/libtoy.a %(installdir)s/lib64/libtoy.a"
ectxt = re.sub("postinstallcmds.*", "postinstallcmds = ['%s']" % postinstallcmd, ectxt)
@@ -1843,8 +1843,8 @@ class ToyBuildTest(EnhancedTestCase):
self.test_toy_build(ec_file=test_ec, raise_error=True)
# also check with 'lib' in sanity check dirs (special case)
- ectxt = re.sub("\s*'files'.*", "'files': ['bin/toy'],", ectxt)
- ectxt = re.sub("\s*'dirs'.*", "'dirs': ['lib'],", ectxt)
+ ectxt = re.sub(r"\s*'files'.*", "'files': ['bin/toy'],", ectxt)
+ ectxt = re.sub(r"\s*'dirs'.*", "'dirs': ['lib'],", ectxt)
write_file(test_ec, ectxt)
error_pattern = r"Sanity check failed: no \(non-empty\) directory found at 'lib' in "
@@ -1855,7 +1855,7 @@ class ToyBuildTest(EnhancedTestCase):
# also check other way around (lib64 -> lib)
ectxt = read_file(ec_file)
- ectxt = re.sub("\s*'files'.*", "'files': ['bin/toy', 'lib64/libtoy.a'],", ectxt)
+ ectxt = re.sub(r"\s*'files'.*", "'files': ['bin/toy', 'lib64/libtoy.a'],", ectxt)
write_file(test_ec, ectxt)
# sanity check fails if lib64 fallback in sanity check is disabled, since lib64/libtoy.a is not there
@@ -1867,8 +1867,8 @@ class ToyBuildTest(EnhancedTestCase):
self.test_toy_build(ec_file=test_ec, raise_error=True)
# also check with 'lib64' in sanity check dirs (special case)
- ectxt = re.sub("\s*'files'.*", "'files': ['bin/toy'],", ectxt)
- ectxt = re.sub("\s*'dirs'.*", "'dirs': ['lib64'],", ectxt)
+ ectxt = re.sub(r"\s*'files'.*", "'files': ['bin/toy'],", ectxt)
+ ectxt = re.sub(r"\s*'dirs'.*", "'dirs': ['lib64'],", ectxt)
write_file(test_ec, ectxt)
error_pattern = r"Sanity check failed: no \(non-empty\) directory found at 'lib64' in "
@@ -1879,7 +1879,7 @@ class ToyBuildTest(EnhancedTestCase):
# check whether fallback works for files that's more than 1 subdir deep
ectxt = read_file(ec_file)
- ectxt = re.sub("\s*'files'.*", "'files': ['bin/toy', 'lib/test/libtoy.a'],", ectxt)
+ ectxt = re.sub(r"\s*'files'.*", "'files': ['bin/toy', 'lib/test/libtoy.a'],", ectxt)
postinstallcmd = "mkdir -p %(installdir)s/lib64/test && "
postinstallcmd += "mv %(installdir)s/lib/libtoy.a %(installdir)s/lib64/test/libtoy.a"
ectxt = re.sub("postinstallcmds.*", "postinstallcmds = ['%s']" % postinstallcmd, ectxt)
diff --git a/test/framework/type_checking.py b/test/framework/type_checking.py
index b1247832c..df75c4940 100644
--- a/test/framework/type_checking.py
+++ b/test/framework/type_checking.py
@@ -356,7 +356,7 @@ class TypeCheckingTest(EnhancedTestCase):
# extra keys ruin it
foo_dict.update({'extra_key': 'bogus'})
- self.assertErrorRegex(EasyBuildError, "Found unexpected \(key, value\) pair: .*", to_dependency, foo_dict)
+ self.assertErrorRegex(EasyBuildError, r"Found unexpected \(key, value\) pair: .*", to_dependency, foo_dict)
# no name/version
self.assertErrorRegex(EasyBuildError, "Can not parse dependency without name and version: .*",
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