Pylint fixes for master branch

.github/workflows/checks.yml

@@ -27,7 +27,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev python3-distutils
+         sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev libpng-dev
 
     - name: configure
       run: ./configure -assert || { cat configure.log; false; }
@@ -182,13 +182,7 @@ jobs:
       run: python3 -m sphinx -n -N -W -w sphinx.log docs/ tmp/
 
     - name: install build dependencies
-      run: sudo apt-get install python2 clang 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; }
+      run: sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev
 
     - name: check configure with Python 3
       run: python3 ./configure || { cat configure.log; false; }

bin/5ttgen

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/blend

@@ -1,6 +1,6 @@
 #!/usr/bin/env python2
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/convert_bruker

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/dwi2response

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/dwibiascorrect

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/dwicat

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/dwifslpreproc

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -23,7 +23,10 @@
 
 
 import itertools, json, math, os, shutil, sys
-from distutils.spawn import find_executable
+try:
+  from shutil import which as find_executable
+except ImportError:
+  from distutils.spawn import find_executable # pylint: disable=deprecated-module
 
 
 
@@ -115,7 +118,11 @@ def execute(): #pylint: disable=unused-variable
   if not fsl_path:
     raise MRtrixError('Environment variable FSLDIR is not set; please run appropriate FSL configuration script')
 
-  if not pe_design == 'None':
+  if pe_design == 'None':
+    topup_config_path = None
+    topup_cmd = None
+    applytopup_cmd = None
+  else:
     topup_config_path = os.path.join(fsl_path, 'etc', 'flirtsch', 'b02b0.cnf')
     if not os.path.isfile(topup_config_path):
       raise MRtrixError('Could not find necessary default config file for FSL topup command (expected location: ' + topup_config_path + ')')
@@ -513,7 +520,7 @@ def execute(): #pylint: disable=unused-variable
 
 
   # Deal with the phase-encoding of the images to be fed to topup (if applicable)
-  do_topup = (not pe_design == 'None')
+  do_topup = pe_design != 'None'
   overwrite_se_epi_pe_scheme = False
   se_epi_path = 'se_epi.mif'
   dwi_permvols_preeddy_option = ''

bin/dwigradcheck

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -163,6 +163,9 @@ def execute(): #pylint: disable=unused-variable
 
           grad_option = ' -fslgrad ' + grad_path + ' bvals'
 
+        else:
+          assert False
+
         # Run the tracking experiment
         run.command('tckgen -algorithm tensor_det data.mif' + grad_option + ' -seed_image mask.mif -mask mask.mif' + number_option + ' -minlength 0 -downsample 5 tracks' + suffix + '.tck')
 
@@ -202,6 +205,8 @@ def execute(): #pylint: disable=unused-variable
       grad_import_option = ' -grad grad' + suffix + '.b'
     elif best[3] == 'image':
       grad_import_option = ' -fslgrad bvecs' + suffix + ' bvals'
+    else:
+      assert False
     run.command('mrinfo data.mif' + grad_import_option + grad_export_option, force=app.FORCE_OVERWRITE)
 
 

bin/dwinormalise

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/dwishellmath

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/for_each

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/gen_scheme

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/labelsgmfix

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/mrtrix_cleanup

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/notfound

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

bin/population_template

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -119,7 +119,7 @@ def copy(src, dst, follow_symlinks=True):
   return dst
 
 
-def check_linear_transformation(transformation, cmd, max_scaling=0.5, max_shear=0.2, max_rot=None, pause_on_warn=True):
+def check_linear_transformation(transformation, cmd, max_scaling=0.5, max_shear=0.2, max_rot=None, pause_on_warn=True): #pylint: disable=too-many-positional-arguments
   from mrtrix3 import app, run, utils #pylint: disable=no-name-in-module, import-outside-toplevel
   if max_rot is None:
     max_rot = 2 * math.pi
@@ -385,7 +385,7 @@ class Input(object):
         copy files into folders in current working directory. modifies _local_ims and  _local_msk
 
       """
-  def __init__(self, uid, filenames, directories, contrasts, mask_filename='', mask_directory=''):
+  def __init__(self, uid, filenames, directories, contrasts, mask_filename='', mask_directory=''): #pylint: disable=too-many-positional-arguments
     self.contrasts = contrasts
 
     self.uid = uid
@@ -923,7 +923,7 @@ def execute(): #pylint: disable=unused-variable
 
   if use_masks:
     path.make_dir('mask_transformed')
-  write_log = (app.VERBOSITY >= 2)
+  write_log = app.VERBOSITY >= 2
   if write_log:
     path.make_dir('log')
 

bin/responsemean

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

build

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -868,7 +868,10 @@ class Entry(object):
     return self.timestamp == float("inf") or self.timestamp < self.dep_timestamp
 
   def display (self, indent=''):
-    show_rebuild = lambda x: x+' [REBUILD]' if todo[x].need_rebuild() else x
+    def show_rebuild(x):
+      if not todo[x].need_rebuild():
+        return x
+      return x+' [REBUILD]'
     msg = indent + '[' + self.action + '] ' + show_rebuild (self.name) + ':\n'
     msg += indent + '  timestamp: ' + str(self.timestamp)
     if self.deps:

check_syntax

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5tt2gmwmi.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5tt2vis.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5ttcheck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5ttedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/afdconnectivity.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/amp2response.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/amp2sh.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/connectome2tck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/connectomeedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/connectomestats.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dcmedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dcminfo.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dirflip.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dirgen.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dirmerge.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dirorder.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dirsplit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dirstat.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dwi2adc.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dwi2fod.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dwi2mask.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/dwi2tensor.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this