Drop python2 support

.github/workflows/checks.yml

@@ -160,40 +160,21 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install pylint pylint3 python3-sphinx sphinx-rtd-theme-common python3-recommonmark python3-sphinx-rtd-theme python3-pip
-         pip3 install sphinx-notfound-page
+         sudo apt-get install python3-sphinx sphinx-rtd-theme-common python3-recommonmark python3-sphinx-rtd-theme python3-pip python3-setuptools
+         pip3 install pylint sphinx-notfound-page
 
 
     - name: check syntax
       run: ./check_syntax || { cat syntax.log; false; }
 
-    - name: pylint (Python 2)
+    - name: pylint
       run: |
          echo "__version__ = 'pylint testing' #pylint: disable=unused-variable" > ./lib/mrtrix3/_version.py
-         PYTHON=python2 ./run_pylint || { cat pylint.log; false; }
-
-    - name: pylint (Python 3)
-      run: |
-         echo "__version__ = 'pylint testing' #pylint: disable=unused-variable" > ./lib/mrtrix3/_version.py
-         PYTHON=python3 ./run_pylint || { cat pylint.log; false; }
+         ./run_pylint || { cat pylint.log; false; }
 
     - name: check copyright headers
       run: ./update_copyright && git diff --exit-code
 
     - name: check building of documentation
       run: python3 -m sphinx -n -N -W -w sphinx.log docs/ tmp/
 
-    - name: install build dependencies
-      run: sudo apt-get install clang-8 libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev
-
-    - name: check configure with Python 2
-      run: python2 ./configure || { cat configure.log; false; }
-
-    - name: check build with Python 2
-      run: python2 ./build -dryrun || { cat build.log; false; }
-
-    - name: check configure with Python 3
-      run: python3 ./configure || { cat configure.log; false; }
-
-    - name: check build with Python 3
-      run: python3 ./build -dryrun || { cat build.log; false; }

bin/5ttgen

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -15,14 +15,6 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-# Script that generates a five-tissue-type (5TT) segmented image: the format appropriate for ACT
-#
-# In this script, major stages of processing can be performed in one of two ways:
-#   - Using FSL tools: BET for brain extraction, FAST for tissue segmentation, FIRST for sub-cortical grey matter segmentation
-#   - Using segmentations from FreeSurfer
-# Alternative algorithms for performing this conversion can be added by creating a new file in lib/mrtrix3/_5ttgen/ and
-#   defining the appropriate functions; 5ttgen will automatically make that algorithm available at the command-line
-
 
 
 def usage(cmdline): #pylint: disable=unused-variable
@@ -66,5 +58,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/blend

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #

bin/convert_bruker

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -83,13 +83,13 @@ def main():
       try:
         nslices #pylint: disable=pointless-statement
         file_out.write (',' + str(nslices))
-      except:
+      except NameError:
         pass
 
     try:
       nacq #pylint: disable=pointless-statement
       file_out.write (',' + str(nacq))
-    except:
+    except NameError:
       pass
 
     file_out.write ('\nvox: ' + str(res[0]) + ',' + str(res[1]))
@@ -99,12 +99,12 @@ def main():
       try:
         slicethick #pylint: disable=pointless-statement
         file_out.write (',' + str(slicethick))
-      except:
+      except NameError:
         pass
     try:
       nacq #pylint: disable=pointless-statement
       file_out.write (',')
-    except:
+    except NameError:
       pass
 
     file_out.write ('\ndatatype: ')
@@ -122,12 +122,12 @@ def main():
     try:
       nslices #pylint: disable=pointless-statement
       file_out.write (',+2')
-    except:
+    except NameError:
       pass
     try:
       nacq #pylint: disable=pointless-statement
       file_out.write (',+3')
-    except:
+    except NameError:
       pass
 
     file_out.write ('\nfile: ' + sys.argv[1] + '\n')
@@ -137,7 +137,7 @@ def main():
       bvec = [ bvec[n:n+3] for n in range(0,len(bvec),3) ]
       for direction, value in zip(bvec, bval):
         file_out.write ('dw_scheme: ' + direction[0] + ',' + direction[1] + ',' + str(-float(direction[2])) + ',' + value + '\n')
-    except:
+    except AssertionError:
       pass
 
 main()

bin/dwi2response

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -15,9 +15,6 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-# Script for estimating response functions for spherical deconvolution
-# A number of different approaches are available within this script for performing response function estimation.
-
 
 
 def usage(cmdline): #pylint: disable=unused-variable
@@ -62,16 +59,16 @@ def execute(): #pylint: disable=unused-variable
       lmax = [ int(x) for x in app.ARGS.lmax.split(',') ]
       if any([lmax_value%2 for lmax_value in lmax]):
         raise MRtrixError('Value of lmax must be even')
-    except:
-      raise MRtrixError('Parameter lmax must be a number')
+    except ValueError as exception:
+      raise MRtrixError('Parameter lmax must be a number') from exception
     if alg.needs_single_shell() and not len(lmax) == 1:
       raise MRtrixError('Can only specify a single lmax value for single-shell algorithms')
   shells_option = ''
   if app.ARGS.shells:
     try:
       shells_values = [ int(round(float(x))) for x in app.ARGS.shells.split(',') ]
-    except:
-      raise MRtrixError('-shells option should provide a comma-separated list of b-values')
+    except ValueError as exception:
+      raise MRtrixError('-shells option should provide a comma-separated list of b-values') from exception
     if alg.needs_single_shell() and not len(shells_values) == 1:
       raise MRtrixError('Can only specify a single b-value shell for single-shell algorithms')
     shells_option = ' -shells ' + app.ARGS.shells
@@ -123,5 +120,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/dwibiascorrect

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -15,8 +15,6 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-# Script that performs B1 field inhomogeneity correction for a DWI volume series
-# Bias field is typically estimated using the mean b=0 image, and subsequently used to correct all volumes
 
 
 def usage(cmdline): #pylint: disable=unused-variable
@@ -79,5 +77,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/dwicat

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -109,8 +109,8 @@ def execute(): #pylint: disable=unused-variable
       if 'Estimated scale factor is' in line:
         try:
           scaling_factor = float(line.split()[-1])
-        except ValueError:
-          raise MRtrixError('Unable to convert scaling factor from mrhistmatch output to floating-point number')
+        except ValueError as exception:
+          raise MRtrixError('Unable to convert scaling factor from mrhistmatch output to floating-point number') from exception
         break
     if scaling_factor is None:
       raise MRtrixError('Unable to extract scaling factor from mrhistmatch output')
@@ -137,5 +137,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/dwifslpreproc

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -18,7 +18,6 @@
 
 
 import glob, itertools, json, math, os, shutil, sys
-from distutils.spawn import find_executable
 
 
 
@@ -306,10 +305,10 @@ def execute(): #pylint: disable=unused-variable
                    'contents of file \"' + app.ARGS.eddy_slspec + '\" appears to instead be slice timings; '
                    'these data have been imported and will be converted to the appropriate format')
           if len(slice_timing) != dwi_num_slices:
-            raise MRtrixError('Cannot use slice timing information from file \"' + app.ARGS.eddy_slspec + '\" for slice-to-volume correction: ' + \
+            raise MRtrixError('Cannot use slice timing information from file \"' + app.ARGS.eddy_slspec + '\" for slice-to-volume correction: ' # pylint: disable=raise-missing-from
                               'number of entries (' + str(len(slice_timing)) + ') does not match number of slices (' + str(dwi_num_slices) + ')')
         except ValueError:
-          raise MRtrixError('Error parsing eddy \"slspec\" file \"' + app.ARGS.eddy_slspec + '\" '
+          raise MRtrixError('Error parsing eddy \"slspec\" file \"' + app.ARGS.eddy_slspec + '\" ' # pylint: disable=raise-missing-from
                             '(please see FSL eddy help page, specifically the --slspec option)')
     else:
       if 'SliceTiming' not in dwi_header.keyval():
@@ -323,7 +322,7 @@ def execute(): #pylint: disable=unused-variable
       # Fudges necessary to maniupulate nature of slice timing data in cases where
       #   bad JSON formatting has led to the data not being simply a list of floats
       #   (whether from MRtrix3 DICOM conversion or from anything else)
-      if isinstance(slice_timing, utils.STRING_TYPES):
+      if isinstance(slice_timing, str):
         slice_timing = slice_timing.split()
       if not isinstance(slice_timing, list):
         raise MRtrixError('Cannot use slice timing information in image header for slice-to-volume correction: '
@@ -341,9 +340,9 @@ def execute(): #pylint: disable=unused-variable
       if not all( [ isinstance(entry, float) for entry in slice_timing ] ):
         try:
           slice_timing = [ float(entry) for entry in slice_timing ]
-        except ValueError:
+        except ValueError as exception:
           raise MRtrixError('Cannot use slice timing information in image header for slice-to-volume correction: '
-                            'data are not numeric')
+                            'data are not numeric') from exception
       app.debug('Re-formatted slice timing contents from header: ' + str(slice_timing))
       if len(slice_timing) != dwi_num_slices:
         raise MRtrixError('Cannot use slice timing information in image header for slice-to-volume correction: '
@@ -1040,7 +1039,7 @@ def execute(): #pylint: disable=unused-variable
 
   # Run eddy qc tool QUAD if installed and one of -eddyqc_text or -eddyqc_all is specified
   if eddyqc_path:
-    if find_executable('eddy_quad'):
+    if shutil.which('eddy_quad'):
       eddyqc_options = ' -idx eddy_indices.txt -par eddy_config.txt -m eddy_mask.nii -b bvals'
       if os.path.isfile('dwi_post_eddy.eddy_residuals'):
         eddyqc_options += ' -g ' + bvecs_path
@@ -1309,5 +1308,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/dwigradcheck

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -202,5 +202,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/dwinormalise

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -15,8 +15,6 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-# Script that performs intensity normalisation of DWIs in various ways
-
 
 def usage(cmdline): #pylint: disable=unused-variable
   from mrtrix3 import algorithm #pylint: disable=no-name-in-module, import-outside-toplevel
@@ -46,5 +44,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/dwishellmath

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -61,5 +61,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/for_each

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -81,7 +81,7 @@ def usage(cmdline): #pylint: disable=unused-variable
 
 
 # These need to be globals in order to be accessible from execute_parallel()
-class Shared(object):
+class Shared:
   def __init__(self):
     self._job_index = 0
     self.lock = threading.Lock()
@@ -132,7 +132,7 @@ def execute(): #pylint: disable=unused-variable
             to_exclude.extend(regex_hits)
           else:
             exclude_unmatched.append(exclude)
-        except Exception:
+        except re.error:
           exclude_unmatched.append(exclude)
     if exclude_unmatched:
       app.warn('Item' + ('s' if len(exclude_unmatched) > 1 else '') + ' specified via -exclude did not appear in input list: ' + str('\'' + exclude_unmatched[0] + '\'' if len(exclude_unmatched) == 1 else exclude_unmatched))
@@ -154,10 +154,10 @@ def execute(): #pylint: disable=unused-variable
 
   try:
     next(entry for entry in CMDSPLIT if any(key for key in KEYLIST if key in entry))
-  except StopIteration:
-    raise MRtrixError('None of the unique for_each keys ' + str(KEYLIST) + ' appear in command string "' + app.ARGS.command + '"; no substitution can occur')
+  except StopIteration as exception:
+    raise MRtrixError('None of the unique for_each keys ' + str(KEYLIST) + ' appear in command string "' + app.ARGS.command + '"; no substitution can occur') from exception
 
-  class Entry(object):
+  class Entry:
     def __init__(self, input_text):
       self.input_text = input_text
       self.sub_in = input_text
@@ -297,5 +297,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member

bin/labelsgmfix

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Copyright (c) 2008-2020 the MRtrix3 contributors.
 #
@@ -171,5 +171,5 @@ def execute(): #pylint: disable=unused-variable
 
 
 # Execute the script
-import mrtrix3
+import mrtrix3 #pylint: disable=wrong-import-position
 mrtrix3.execute() #pylint: disable=no-member