MNT: Avoid collections.abc warning, minor formatting

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

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

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)