Fix merge issues: 'fsl_checkfirst_function' to 'dev'

Also solves issues of inconsistent return statements reported by newer versions of pylint, reverting 8bb9eb9 merged in #1211.

lib/mrtrix3/_5ttgen/fsl.py

@@ -35,7 +35,7 @@ def getInputs(): #pylint: disable=unused-variable
 
 def execute(): #pylint: disable=unused-variable
   import math, os
-  from mrtrix3 import app, file, fsl, image, path, run #pylint: disable=redefined-builtin
+  from mrtrix3 import app, fsl, image, run
 
   if app.isWindows():
     app.error('\'fsl\' algorithm of 5ttgen script cannot be run on Windows: FSL not available on Windows')

lib/mrtrix3/app.py

@@ -867,7 +867,6 @@ def done(self):
     import sys
     global verbosity
     global clearLine, colourConsole, colourClear, colourExec
-    self.counter = self.target
     self.iscomplete = True
     self.value = 100
     if self.isatty:

lib/mrtrix3/fsl.py

@@ -89,7 +89,7 @@ def exeName(name): #pylint: disable=unused-variable
 #   FSL commands will generate based on the suffix() function, the FSL binaries themselves
 #   ignore the FSLOUTPUTTYPE environment variable. Therefore, the safest approach is:
 # Whenever receiving an output image from an FSL command, explicitly search for the path
-def findImage(name): #pylint: disable=unused-variable,inconsistent-return-statements
+def findImage(name): #pylint: disable=unused-variable
   import os
   from mrtrix3 import app
   prefix = os.path.join(os.path.dirname(name), os.path.basename(name).split('.')[0])
@@ -101,6 +101,7 @@ def findImage(name): #pylint: disable=unused-variable,inconsistent-return-statem
       app.debug('Expected image at \"' + prefix + suffix() + '\", but found at \"' + prefix + suf + '\"')
       return prefix + suf
   app.error('Unable to find FSL output file for path \"' + name + '\"')
+  return ''
 
 
 

lib/mrtrix3/run.py

@@ -23,7 +23,7 @@ def setContinue(filename): #pylint: disable=unused-variable
 
 
 
-def command(cmd, exitOnError=True): #pylint: disable=unused-variable,inconsistent-return-statements
+def command(cmd, exitOnError=True): #pylint: disable=unused-variable
 
   import inspect, itertools, shlex, signal, string, subprocess, sys, tempfile
   from distutils.spawn import find_executable
@@ -41,7 +41,7 @@ def command(cmd, exitOnError=True): #pylint: disable=unused-variable,inconsisten
     if app.verbosity:
       sys.stderr.write(app.colourExec + 'Skipping command:' + app.colourClear + ' ' + cmd + '\n')
       sys.stderr.flush()
-    return
+    return ('', '')
 
   # This splits the command string based on the piping character '|', such that each
   #   individual executable (along with its arguments) appears as its own list
@@ -235,7 +235,7 @@ def command(cmd, exitOnError=True): #pylint: disable=unused-variable,inconsisten
 
 
 
-def function(fn, *args): #pylint: disable=unused-variable,inconsistent-return-statements
+def function(fn, *args): #pylint: disable=unused-variable
 
   import inspect, sys
   from mrtrix3 import app
@@ -248,7 +248,7 @@ def function(fn, *args): #pylint: disable=unused-variable,inconsistent-return-st
     if app.verbosity:
       sys.stderr.write(app.colourExec + 'Skipping function:' + app.colourClear + ' ' + fnstring + '\n')
       sys.stderr.flush()
-    return
+    return None
 
   if app.verbosity:
     sys.stderr.write(app.colourExec + 'Function:' + app.colourClear + ' ' + fnstring + '\n')
@@ -327,7 +327,7 @@ def exeName(item):
 #   or a non-MRtrix3 command with the same name as an MRtrix3 command
 #   (e.g. C:\Windows\system32\mrinfo.exe; On Windows, subprocess uses CreateProcess(),
 #   which checks system32\ before PATH)
-def versionMatch(item): #pylint: disable=inconsistent-return-statements
+def versionMatch(item):
   from distutils.spawn import find_executable
   from mrtrix3 import app
   global _mrtrix_bin_path, _mrtrix_exe_list
@@ -347,6 +347,7 @@ def versionMatch(item): #pylint: disable=inconsistent-return-statements
     return exe_path_sys
 
   app.error('Unable to find executable for MRtrix3 command ' + item)
+  return ''