diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index f67103570c7cb63593b26443782ad5c73c29970e..6117934b1001b49bf41e90e7b9f7794f2f5aad33 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -52,17 +52,16 @@ class FSLNotPresent(Exception):
"""Error raised by the :func:`runfsl` function when ``$FSLDIR`` cannot
be found.
"""
- pass
@contextlib.contextmanager
-def dryrun(*args):
+def dryrun(*_):
"""Context manager which causes all calls to :func:`run` to be logged but
not executed. See the :data:`DRY_RUN` flag.
The returned standard output will be equal to ``' '.join(args)``.
"""
- global DRY_RUN
+ global DRY_RUN # pylint: disable=global-statement
oldval = DRY_RUN
DRY_RUN = True
@@ -184,16 +183,16 @@ def run(*args, **kwargs):
returnExitcode = kwargs.pop('exitcode', False)
submit = kwargs.pop('submit', {})
cmdonly = kwargs.pop('cmdonly', False)
- log = kwargs.pop('log', None)
+ logg = kwargs.pop('log', None)
args = prepareArgs(args)
- if log is None:
- log = {}
+ if logg is None:
+ logg = {}
- tee = log.get('tee', False)
- logStdout = log.get('stdout', None)
- logStderr = log.get('stderr', None)
- logCmd = log.get('cmd', None)
+ tee = logg.get('tee', False)
+ logStdout = logg.get('stdout', None)
+ logStderr = logg.get('stderr', None)
+ logCmd = logg.get('cmd', None)
if not bool(submit):
submit = None
@@ -394,25 +393,32 @@ def runfsl(*args, **kwargs):
def wslcmd(cmdpath, *args):
+ """Convert a command + arguments into an equivalent set of arguments that
+ will run the command under Windows Subsystem for Linux
+
+ :param cmdpath: Fully qualified path to the command. This is essentially
+ a WSL path not a Windows one since FSLDIR is specified
+ as a WSL path, however it may have backslashes as path
+ separators due to previous use of ``os.path.join``
+
+ :param args: Sequence of command arguments (the first of which is the
+ unqualified command name)
+
+ :return: If ``cmdpath`` exists and is executable in WSL, return a
+ sequence of command arguments which when executed will run the
+ command in WSL. Windows paths in the argument list will be
+ converted to WSL paths. If ``cmdpath`` was not executable in
+ WSL, returns None
"""
- Convert a command + arguments into an equivalent set of arguments that will run the command
- under Windows Subsystem for Linux
-
- :param cmdpath: Fully qualified path to the command. This is essentially a WSL path not a Windows
- one since FSLDIR is specified as a WSL path, however it may have backslashes
- as path separators due to previous use of ``os.path.join``
- :param args: Sequence of command arguments (the first of which is the unqualified command name)
-
- :return: If ``cmdpath`` exists and is executable in WSL, return a sequence of command arguments
- which when executed will run the command in WSL. Windows paths in the argument list will
- be converted to WSL paths. If ``cmdpath`` was not executable in WSL, returns None
- """
- # Check if command exists in WSL (remembering that the command path may include FSLDIR which
- # is a Windows path)
+ # Check if command exists in WSL (remembering
+ # that the command path may include FSLDIR
+ # which is a Windows path)
cmdpath = fslpath.wslpath(cmdpath)
- _stdout, _stderr, retcode = _realrun(False, None, None, None, "wsl", "test", "-x", cmdpath)
+ _stdout, _stderr, retcode = _realrun(
+ False, None, None, None, "wsl", "test", "-x", cmdpath)
if retcode == 0:
- # Form a new argument list and convert any Windows paths in it into WSL paths
+ # Form a new argument list and convert
+ # any Windows paths in it into WSL paths
wslargs = [fslpath.wslpath(arg) for arg in args]
wslargs[0] = cmdpath
local_fsldir = fslpath.wslpath(fslplatform.fsldir)
@@ -420,8 +426,10 @@ def wslcmd(cmdpath, *args):
local_fsldevdir = fslpath.wslpath(fslplatform.fsldevdir)
else:
local_fsldevdir = None
- # Prepend important environment variables - note that it seems we cannot
- # use WSLENV for this due to its insistance on path mapping. FIXME FSLDEVDIR?
+ # Prepend important environment variables -
+ # note that it seems we cannot use WSLENV
+ # for this due to its insistance on path
+ # mapping. FIXME FSLDEVDIR?
local_path = "$PATH"
if local_fsldevdir:
local_path += ":%s/bin" % local_fsldevdir
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 638587cea739e18229f6ca9d26508c9146117738..2f1d97d6726fa930fecdb9fbf97da1d5280c5ea0 100755
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -1,5 +1,8 @@
#!/usr/bin/env python
#
+# pylint: disable=unused-import
+# flake8: noqa: F401
+#
# __init__.py - Wrappers for FSL command-line tools.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
@@ -79,37 +82,37 @@ decorators.
"""
-from .wrapperutils import (LOAD,) # noqa
-from .bet import (bet, # noqa
- robustfov)
-from .eddy import (eddy_cuda, # noqa
- topup,
- applytopup)
-from .fast import (fast,) # noqa
-from .fsl_anat import (fsl_anat,) # noqa
-from .fsl_sub import (fsl_sub,) # noqa
-from .flirt import (flirt, # noqa
- invxfm,
- applyxfm,
- applyxfm4D,
- concatxfm,
- mcflirt)
-from .fnirt import (fnirt, # noqa
- applywarp,
- invwarp,
- convertwarp)
-from .fslmaths import (fslmaths,) # noqa
-from .fslstats import (fslstats,) # noqa
-from .fugue import (fugue, # noqa
- prelude,
- sigloss,
- fsl_prepare_fieldmap)
-from .melodic import (melodic, # noqa
- fsl_regfilt)
-from .misc import (fslreorient2std, # noqa
- fslroi,
- slicer,
- cluster,
- gps)
-from .epi_reg import epi_reg
-from . import tbss # noqa
+from fsl.wrappers.wrapperutils import (LOAD,)
+from fsl.wrappers.bet import (bet,
+ robustfov)
+from fsl.wrappers.eddy import (eddy_cuda,
+ topup,
+ applytopup)
+from fsl.wrappers.fast import (fast,)
+from fsl.wrappers.fsl_anat import (fsl_anat,)
+from fsl.wrappers.fsl_sub import (fsl_sub,)
+from fsl.wrappers.flirt import (flirt,
+ invxfm,
+ applyxfm,
+ applyxfm4D,
+ concatxfm,
+ mcflirt)
+from fsl.wrappers.fnirt import (fnirt,
+ applywarp,
+ invwarp,
+ convertwarp)
+from fsl.wrappers.fslmaths import (fslmaths,)
+from fsl.wrappers.fslstats import (fslstats,)
+from fsl.wrappers.fugue import (fugue,
+ prelude,
+ sigloss,
+ fsl_prepare_fieldmap)
+from fsl.wrappers.melodic import (melodic,
+ fsl_regfilt)
+from fsl.wrappers.misc import (fslreorient2std,
+ fslroi,
+ slicer,
+ cluster,
+ gps)
+from fsl.wrappers.epi_reg import epi_reg
+from fsl.wrappers import tbss
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 60413b866bee6100c3e9be198ac14abb42e221fd..ac647674bfa4c1161f8b5e8ed62e8268a9940518 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -441,7 +441,7 @@ file should be loaded into memory and returned as a Python object.
"""
-class FileOrThing(object):
+class FileOrThing:
"""Decorator which ensures that certain arguments which are passed into the
decorated function are always passed as file names. Both positional and
keyword arguments can be specified.