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Commit d211ea51 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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STY: Address/suppress lint

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fsl/utils/run.py
+ 36
− 28
View file @ d211ea51
......@@ -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
......
fsl/wrappers/__init__.py
+ 37
− 34
View file @ d211ea51
#!/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
fsl/wrappers/wrapperutils.py
+ 1
− 1
View file @ d211ea51
......@@ -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.
......
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