Merge pull request #762 from Remi-Gau/ci

[MNT] update CI and fix tests

Author: Remi-Gau

.github/workflows/check_md_links.yml

@@ -23,4 +23,4 @@ jobs:
       with:
         use-quiet-mode: 'yes'
         use-verbose-mode: 'yes'
-        config-file: 'mlc_config.json'
+        config-file: '.github/workflows/mlc_config.json'

.github/workflows/miss_hit.yml

@@ -28,7 +28,7 @@ jobs:
 
     - uses: actions/checkout@v3
       with:
-        fetch-depth: 1
+        fetch-depth: 0
 
     - name: Set up Python
       uses: actions/setup-python@v4

mlc_config.json renamed to .github/workflows/mlc_config.json

@@ -44,7 +44,7 @@ jobs:
     # only trigger update on upstream repo
     if: github.repository_owner == 'cpp-lln-lab'
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -67,7 +67,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           submodules: true
-          fetch-depth: 2
+          fetch-depth: 0
 
       - name: Get moae fmriprep data from OSF
         run: |

.github/workflows/run_system_tests_matlab.yml

@@ -1,4 +1,4 @@
-name: "system tests with octave: failure expected"
+name: "system tests with octave"
 
 # Uses the cron schedule for github actions
 #
@@ -44,7 +44,7 @@ jobs:
     # only trigger update on upstream repo
     if: github.repository_owner == 'cpp-lln-lab'
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -58,11 +58,15 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install octave liboctave-dev
 
+    - name: Info
+      run: |
+        octave --version
+
     - name: Clone bidspm
       uses: actions/checkout@v3
       with:
         submodules: true
-        fetch-depth: 2
+        fetch-depth: 0
 
     - name: Get moae fmriprep data from OSF
       run: |

.github/workflows/run_system_tests_octave.yml

@@ -28,7 +28,7 @@ jobs:
 
   tests_matlab:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
       - name: Install MATLAB
@@ -41,7 +41,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           submodules: true
-          fetch-depth: 2
+          fetch-depth: 0
 
       - name: Install SPM
         run: |
@@ -66,15 +66,15 @@ jobs:
         with:
           command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
 
-      - name: Run tests
+      - name: Check tests
         run: |
           cat test_report.log | grep 0
-          bash <(curl -s https://codecov.io/bash)
 
       - name: Code coverage
         uses: codecov/codecov-action@v3
         with:
-          file: coverage.xml # optional
-          flags: unittests # optional
-          name: codecov-umbrella # optional
-          fail_ci_if_error: true # optional (default = false)
+          file: coverage.xml
+          flags: matlab
+          name: codecov-matlab
+          fail_ci_if_error: false
+        # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits

.github/workflows/run_tests_matlab.yml

@@ -1,4 +1,4 @@
-name: "tests with octave: failure expected"
+name: "tests with octave"
 
 on:
 
@@ -23,7 +23,7 @@ env:
 jobs:
   tests_octave:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     # only trigger update on upstream repo
     if: github.repository_owner == 'cpp-lln-lab'
@@ -35,11 +35,15 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install octave liboctave-dev
 
+    - name: Info
+      run: |
+        octave --version
+
     - name: Clone bidspm
       uses: actions/checkout@v3
       with:
         submodules: true
-        fetch-depth: 2
+        fetch-depth: 0
 
     - name: Install SPM
       run: |
@@ -67,4 +71,15 @@ jobs:
         octave $OCTFLAGS --eval "bidspm(); cd demos/MoAE; download_moae_ds(true);"
         cd .github/workflows
         octave $OCTFLAGS --eval "tests_octave;"
-        cat test_report.log | grep 0
+
+    - name: Check tests
+      run: cat test_report.log | grep 0
+
+    - name: Code coverage
+      uses: codecov/codecov-action@v3
+      with:
+        file: coverage.xml
+        flags: octave
+        name: codecov-octave
+        fail_ci_if_error: false
+        # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits

.github/workflows/run_tests_octave.yml

@@ -13,38 +13,42 @@ function bidspm(varargin)
 
   defaultAction = 'init';
 
-  isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);
+  isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
   isFileOrStruct = @(x) isstruct(x) || exist(x, 'file') == 2;
 
-  isLogical = @(x) validateattributes(x, {'logical'}, {'numel', 1});
-  isChar = @(x) validateattributes(x, {'char'}, {'row'});
-  isPositiveScalar = @(x) validateattributes(x, {'numeric'}, {'nonnegative', 'numel', 1});
+  isLogical = @(x) islogial(x) && numel(x) == 1;
+  isChar = @(x) ischar(x);
+  isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
 
-  isLowLevelActionOrDir = @(x) (ismember(x, low_level_actions()) || isdir(x));
+  isFolder = @(x) isfolder(x);
+
+  isCellStr = @(x) iscellstr(x);
+
+  isLowLevelActionOrDir = @(x) (ismember(x, low_level_actions()) || isfolder(x));
 
   addOptional(args, 'bids_dir', pwd, isLowLevelActionOrDir);
 
   addOptional(args, 'output_dir', '', isChar);
   addOptional(args, 'analysis_level', 'subject', @(x) ismember(x, {'subject', 'dataset'}));
 
   addParameter(args, 'action', defaultAction, isChar);
-  addParameter(args, 'participant_label', {}, @iscellstr);
-  addParameter(args, 'task', {}, @iscellstr);
+  addParameter(args, 'participant_label', {}, isCellStr);
+  addParameter(args, 'task', {}, isCellStr);
   addParameter(args, 'dry_run', false, isLogical);
   addParameter(args, 'bids_filter_file', struct([]), isFileOrStruct);
   addParameter(args, 'options', struct([]), isFileOrStruct);
   addParameter(args, 'verbosity', 2, isPositiveScalar);
 
   addParameter(args, 'fwhm', 6, isPositiveScalar);
-  addParameter(args, 'space', {}, @iscellstr);
+  addParameter(args, 'space', {}, isCellStr);
 
   % preproc only
   addParameter(args, 'dummy_scans', 0, isPositiveScalar);
   addParameter(args, 'anat_only', false, isLogical);
   addParameter(args, 'ignore', {}, isEmptyOrCellstr);
 
   % stats only
-  addParameter(args, 'preproc_dir', pwd, @isdir);
+  addParameter(args, 'preproc_dir', pwd, isFolder);
   addParameter(args, 'model_file', struct([]), isFileOrStruct);
   addParameter(args, 'roi_based', false, isLogical);
   % group level stats only
@@ -178,6 +182,11 @@ function bidspm(varargin)
     if ismember('fieldmaps', args.Results.ignore)
       opt.useFieldmaps = false;
     end
+    if ismember('qa', lower(args.Results.ignore))
+      opt.QA.func.do = false;
+      opt.QA.anat.do = false;
+      opt.QA.glm.do = false;
+    end
 
     opt.dummy_scans = args.Results.dummy_scans;
 
@@ -375,11 +384,12 @@ function initBidspm(dev)
   opt.verbosity = 2;
   opt.msg.color = '';
 
-  octaveVersion = '4.0.3';
+  octaveVersion = '6.4.0';
   matlabVersion = '8.6.0';
 
   % octave packages
-  installlist = {'io', 'statistics', 'image'};
+  installlist = {};
+  % installlist = {'io', 'statistics', 'image'};
 
   thisDirectory = fileparts(mfilename('fullpath'));
 
@@ -440,6 +450,10 @@ function initBidspm(dev)
 
     addpath(BIDSPM_PATHS, '-begin');
 
+    if isOctave
+      warning('off', 'Octave:shadowed-function');
+    end
+
     checkDependencies(opt);
     printCredits(opt);
 
@@ -533,6 +547,11 @@ function run_tests()
 
   bidspm('action', 'dev');
 
+  % to reduce noise in the output
+  if isOctave
+    warning('off', 'setGraphicWindow:noGraphicWindow');
+  end
+
   cd(fileparts(mfilename('fullpath')));
 
   if isGithubCi
@@ -552,8 +571,7 @@ function run_tests()
   folderToCover = fullfile(pwd, 'src');
   testFolder = fullfile(pwd, 'tests', subfolder);
 
-  success = moxunit_runtests( ...
-                             testFolder, ...
+  success = moxunit_runtests(testFolder, ...
                              '-verbose', '-recursive', '-with_coverage', ...
                              '-cover', folderToCover, ...
                              '-cover_xml_file', 'coverage.xml', ...

bidspm.m

@@ -22,6 +22,10 @@
 addpath(fullfile(pwd, '..', '..'));
 bidspm();
 
+if isOctave
+  warning('off', 'setGraphicWindow:noGraphicWindow');
+end
+
 % Getting the raw dataset
 download_data = true;
 download_moae_ds(download_data);

demos/MoAE/moae_fmriprep.m

@@ -22,26 +22,29 @@
 
 addpath(fullfile(WD, '..', '..'));
 
+bidspm();
 if download_data
-  bidspm();
   download_moae_ds(download_data, clean);
 end
 
+warning('off', 'SPM:noDisplay');
+if isOctave
+  warning('off', 'setGraphicWindow:noGraphicWindow');
+end
+
 optionsFile = fullfile(WD, 'options', 'options_task-auditory.json');
 
-space = { 'IXI549Space'
+space = {'IXI549Space'
          'IXI549Space'
          'individual'
          'individual'};
-ignore = {
-          {''}
-          {'unwarp'}
+ignore = {{''}
+          {'unwarp', 'qa'}
           {'unwarp'}
           {''}
          };
 
-models = {
-          fullfile(WD, 'models', 'model-MoAE_smdl.json')
+models = {fullfile(WD, 'models', 'model-MoAE_smdl.json')
           fullfile(WD, 'models', 'model-MoAE_smdl.json')
           fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
           fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
@@ -77,4 +80,14 @@
 
   rmdir(fullfile(WD, 'outputs', 'derivatives'), 's');
 
+  % with Octave running more n-1 loop in CI is fine
+  % but not running crashes with a segmentation fault
+  % /home/runner/work/_temp/fb8e9d58-fa9f-4f93-8c96-387973f3632e.sh: line 2:
+  % 7487 Segmentation fault      (core dumped) octave $OCTFLAGS --eval "run system_tests_facerep;"
+  %
+  % not sure why
+  if isOctave
+    break
+  end
+
 end