diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 7f7f80cf0b3ad541ac3206ee84630320eaad58cd..0a0859528945a7b944482442b0ffc658d0dc05f9 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -23,6 +23,8 @@ paths.
removeDuplicates
uniquePrefix
commonBase
+ wslpath
+ winpath
"""
@@ -30,10 +32,11 @@ import os.path as op
import os
import glob
import operator
-import re
+import re
from fsl.utils.platform import platform
+
class PathError(Exception):
"""``Exception`` class raised by the functions defined in this module
when something goes wrong.
@@ -527,17 +530,18 @@ def commonBase(paths):
raise PathError('No common base')
+
def wslpath(winpath):
"""
- Convert Windows path (or a command line argument containing a Windows path)
+ Convert Windows path (or a command line argument containing a Windows path)
to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``). Also supports
paths in the form ``\\wsl$\\(distro)\\users\\...``
- :param winpath: Command line argument which may (or may not) contain a Windows path. It is assumed to be
- either of the form <windows path> or --<arg>=<windows path>. Note that we don't need to
- handle --arg <windows path> or -a <windows path> since in these cases the argument
- and the path will be parsed as separate entities.
- :return: If ``winpath`` matches a Windows path, the converted argument (including the --<arg>= portion).
+ :param winpath: Command line argument which may (or may not) contain a Windows path. It is assumed to be
+ either of the form <windows path> or --<arg>=<windows path>. Note that we don't need to
+ handle --arg <windows path> or -a <windows path> since in these cases the argument
+ and the path will be parsed as separate entities.
+ :return: If ``winpath`` matches a Windows path, the converted argument (including the --<arg>= portion).
Otherwise returns ``winpath`` unchanged.
"""
match = re.match(r"^(--[\w-]+=)?\\\\wsl\$[\\\/][^\\^\/]+(.*)$", winpath)
@@ -552,10 +556,11 @@ def wslpath(winpath):
arg, drive, path = match.group(1, 2, 3)
if arg is None:
arg = ""
- return arg + "/mnt/" + drive.lower() + path.replace("\\", "/")
+ return arg + "/mnt/" + drive.lower() + path.replace("\\", "/")
return winpath
+
def winpath(wslpath):
"""
Convert a WSL-local filepath (for example ``/usr/local/fsl/``) into a path that can be used from
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 73d0937d264a1a88396d25deb837d34ba6130d56..ebd9478cb79f3d11d5cda0d4bf8a3eeb00c534f7 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -285,16 +285,19 @@ class Platform(notifier.Notifier):
"""
return os.environ.get('FSLDIR', None)
+
@property
def fsldevdir(self):
"""The FSL development directory location. """
return os.environ.get('FSLDEVDIR', None)
+
@property
def fslwsl(self):
"""Boolean flag indicating whether FSL is installed in Windows Subsystem for Linux """
return self.fsldir is not None and self.fsldir.startswith("\\\\wsl$")
+
@fsldir.setter
def fsldir(self, value):
"""Changes the value of the :attr:`fsldir` property, and notifies any
@@ -404,6 +407,7 @@ class Platform(notifier.Notifier):
"""
return self.__glIsSoftware
+
platform = Platform()
"""An instance of the :class:`Platform` class. Feel free to create your own
instance, but be aware that if you do so you will not be updated of changes
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index acb77c741e2bb1f329d67833de7e53459bff4697..e2adbeb8de7d39006b28eac3497573fd281cd8d9 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -20,17 +20,17 @@
"""
-import sys
-import shlex
-import logging
-import threading
-import contextlib
-import collections
-import subprocess as sp
-import os.path as op
-import os
-
-import six
+import sys
+import shlex
+import logging
+import threading
+import contextlib
+import collections.abc as abc
+import subprocess as sp
+import os.path as op
+import os
+
+import six
from fsl.utils.platform import platform as fslplatform
import fsl.utils.fslsub as fslsub
@@ -203,7 +203,7 @@ def run(*args, **kwargs):
if submit is True:
submit = dict()
- if submit is not None and not isinstance(submit, collections.Mapping):
+ if submit is not None and not isinstance(submit, abc.Mapping):
raise ValueError('submit must be a mapping containing '
'options for fsl.utils.fslsub.submit')
@@ -377,16 +377,17 @@ def runfsl(*args, **kwargs):
return run(*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
@@ -423,6 +424,7 @@ def wslcmd(cmdpath, *args):
# Command was not found in WSL with this path
return None
+
def wait(job_ids):
"""Proxy for :func:`.fslsub.wait`. """
return fslsub.wait(job_ids)