[MAINT] try not indexing dependencies for a speed up (#1129)

* try not indexing dependencies for a speed up

* fix

* speed up layout indexing during tests

* fix concatenation

* separate slow tests

* fewer subjects in bms

* update flags coverage

* fix octave bug

.github/workflows/tests.yml

@@ -43,16 +43,27 @@ jobs:
         os: [ubuntu-latest, macos-latest]
         matlab: [R2022b]
         include:
+        # only run bms on ubuntu because of datalad setup
         - test_type: system
+          os: ubuntu-latest
+          matlab: R2022b
           script: bms
+        - test_type: unit
           os: ubuntu-latest
           matlab: R2022b
+          mode: fast
+        - test_type: unit
+          os: macos-latest
+          matlab: R2022b
+          mode: fast
         - test_type: unit
           os: ubuntu-latest
           matlab: R2022b
+          mode: slow
         - test_type: unit
           os: macos-latest
           matlab: R2022b
+          mode: slow
       fail-fast: false
 
     runs-on: ${{ matrix.os }}
@@ -124,18 +135,24 @@ jobs:
       with:
         release: ${{ matrix.matlab }}
 
-    - name: Run unit tests MATLAB
-      if: matrix.test_type == 'unit'
+    - name: Run fast unit tests MATLAB
+      if: matrix.test_type == 'unit' && matrix.mode == 'fast'
       uses: matlab-actions/[email protected]
       with:
         command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
 
+    - name: Run slow unit tests MATLAB
+      if: matrix.test_type == 'unit' && matrix.mode == 'slow'
+      uses: matlab-actions/[email protected]
+      with:
+        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab;
+
     - name: Code coverage matlab
       if: matrix.test_type == 'unit'
       uses: codecov/codecov-action@v3
       with:
         file: coverage.xml
-        flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}
+        flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }}
         name: codecov-matlab
         fail_ci_if_error: false
       # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits

.github/workflows/tests_octave.m

@@ -11,8 +11,6 @@ function tests_octave()
 
   cd(fullfile(fileparts(mfilename('fullpath')), '..', '..'));
 
-  bidspm('action', 'dev');
-
   success = bidspm('action', 'run_tests');
 
   toc;

.github/workflows/tests_octave.yml

@@ -47,6 +47,9 @@ jobs:
         script: [moae, facerep, fmriprep]
         include:
         - test_type: unit
+          mode: fast
+        - test_type: unit
+          mode: slow
       fail-fast: false
 
     steps:
@@ -125,21 +128,29 @@ jobs:
         make -C spm12/src PLATFORM=octave install
         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
 
-    - name: Run unit tests Octave
-      if: matrix.test_type == 'unit'
+    - name: Run fast unit tests Octave
+      if: matrix.test_type == 'unit' && matrix.mode == 'fast'
       run: |
         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"
         octave $OCTFLAGS --eval "bidspm(); cd demos/MoAE; download_moae_ds(true);"
         cd .github/workflows
         octave $OCTFLAGS --eval "tests_octave;"
 
+    - name: Run fast unit tests Octave
+      if: matrix.test_type == 'unit' && matrix.mode == 'slow'
+      run: |
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"
+        octave $OCTFLAGS --eval "bidspm(); cd demos/MoAE; download_moae_ds(true);"
+        cd .github/workflows
+        octave $OCTFLAGS --eval " global SLOW; SLOW=true; tests_octave;"
+
     - name: Code coverage
       if: matrix.test_type == 'unit'
       uses: codecov/codecov-action@v3
       with:
         file: coverage.xml
         flags: octave
-        name: codecov-octave
+        name: codecov-octave_${{ matrix.mode }}
         fail_ci_if_error: false
       # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
 

.github/workflows/tests_windows.yml

@@ -46,6 +46,11 @@ jobs:
         - test_type: unit
           os: windows-latest
           matlab: R2022b
+          mode: fast
+        - test_type: unit
+          os: windows-latest
+          matlab: R2022b
+          mode: slow
       fail-fast: false
 
     runs-on: ${{ matrix.os }}
@@ -109,18 +114,24 @@ jobs:
       with:
         release: ${{ matrix.matlab }}
 
-    - name: Run unit tests MATLAB
-      if: matrix.test_type == 'unit'
+    - name: Run fast unit tests MATLAB
+      if: matrix.test_type == 'unit' && matrix.mode == 'fast'
       uses: matlab-actions/[email protected]
       with:
         command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
 
+    - name: Run slow unit tests MATLAB
+      if: matrix.test_type == 'unit' && matrix.mode == 'slow'
+      uses: matlab-actions/[email protected]
+      with:
+        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab;
+
     - name: Code coverage matlab
       if: matrix.test_type == 'unit'
       uses: codecov/codecov-action@v3
       with:
         file: coverage.xml
-        flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}
+        flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }}
         name: codecov-matlab
         fail_ci_if_error: false
       # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits

bidspm.m

@@ -316,9 +316,13 @@ function uninitBidspm()
 
   spm('defaults', 'fMRI');
 
-  subfolder = '';
-
   folderToCover = fullfile(pwd, 'src');
+
+  subfolder = '';
+  if usingSlowTestMode()
+    fprintf(1, 'Running in slow tests only.\n');
+    subfolder = 'tests_slow';
+  end
   testFolder = fullfile(pwd, 'tests', subfolder);
 
   returnCode = moxunit_runtests(testFolder, ...

demos/bayes/ds000114_run.m

@@ -11,7 +11,7 @@
 FWHM = 8;
 
 % set to false to not re run the smoothing
-SMOOTH = false;
+SMOOTH = true;
 
 % set to false to not re run the model specification
 FIRST_LEVEL = true;
@@ -30,7 +30,6 @@
 participant_label = {'[0-9]*'}; %#ok<*NASGU>
 if TESTING
   participant_label = {'^0[12]$'};
-  participant_label = {'[0-9]*'};
 end
 
 %% Smooth

src/IO/getData.m

@@ -6,7 +6,7 @@
   %
   %   [BIDS, opt] = getData(opt, bidsDir)
   %
-  % :type opt:  structure
+  % :type  opt:  structure
   % :param opt: Options chosen for the analysis.
   %             See checkOptions.
   %
@@ -27,6 +27,7 @@
 
   addRequired(args, 'opt', @isstruct);
   addRequired(args, 'bidsDir', isFolder);
+  addOptional(args, 'index_dependencies', true, @islogical);
 
   try
     parse(args, varargin{:});
@@ -44,6 +45,11 @@
   opt = args.Results.opt;
   bidsDir = args.Results.bidsDir;
 
+  index_dependencies = args.Results.index_dependencies;
+  if strcmp(opt.pipeline.type, 'stats')
+    index_dependencies = false;
+  end
+
   if isfield(opt, 'taskName')
     msg = sprintf('FOR TASK(s): %s', strjoin(opt.taskName, ' '));
     logger('INFO', msg, 'options', opt, 'filename', mfilename());
@@ -59,16 +65,20 @@
   BIDS = bids.layout(bidsDir, ...
                      'use_schema', opt.useBidsSchema, ...
                      'verbose', opt.verbosity > 1, ...
-                     'filter', layout_filter);
+                     'filter', layout_filter, ...
+                     'index_dependencies', index_dependencies);
 
   if strcmp(opt.pipeline.type, 'stats') && ~opt.pipeline.isBms
     if exist(fullfile(opt.dir.raw, 'layout.mat'), 'file') == 2
       msg = sprintf('Loading BIDS raw layout from:\n\t%s', ...
                     bids.internal.format_path(fullfile(opt.dir.raw, 'layout.mat')));
       logger('INFO', msg, 'options', opt, 'filename', mfilename());
       tmp = load(fullfile(opt.dir.raw, 'layout.mat'), 'BIDS');
+
       if isempty(fieldnames(tmp))
-        BIDS.raw = bids.layout(opt.dir.raw, 'filter', layout_filter);
+        BIDS.raw = bids.layout(opt.dir.raw, ...
+                               'filter', layout_filter, ...
+                               'index_dependencies', index_dependencies);
       else
         BIDS.raw = tmp.BIDS;
       end

src/bids/initBids.m

@@ -35,6 +35,7 @@ function initBids(varargin)
     BIDS = bids.layout(opt.dir.output, ...
                        'use_schema', false, ...
                        'index_derivatives', false, ...
+                       'index_dependencies', false, ...
                        'tolerant', true, ...
                        'verbose', opt.verbosity > 0);
 

src/bids_model/addConfoundsToDesignMatrix.m

@@ -182,14 +182,16 @@
   toClean = cellfun(@(x) isempty(x), designMatrix);
   designMatrix(toClean) = [];
 
-  numeric = cellfun(@(x) isnumeric(x), designMatrix);
-  tmp = unique(designMatrix(~numeric));
-  if size(tmp, 1) > 1
-    tmp = tmp';
+  if isempty(designMatrix)
+    return
   end
   if size(designMatrix, 1) > 1
     designMatrix = designMatrix';
   end
+
+  numeric = cellfun(@(x) isnumeric(x), designMatrix);
+  tmp = unique(designMatrix(~numeric));
+
   designMatrix = cat(2, tmp, designMatrix(numeric));
 end
 

src/workflows/stats/bidsResults.m

@@ -544,7 +544,9 @@
       if ismember(lower(node.Level), {'run', 'session', 'subject'})
 
         if isempty(BIDS)
-          BIDS =  bids.layout(opt.dir.preproc, 'use_schema', false, ...
+          BIDS =  bids.layout(opt.dir.preproc, ...
+                              'use_schema', false, ...
+                              'index_dependencies', false, ...
                               'filter', struct('sub', {opt.subjects}));
         end
 

tests/tests_QA/test_computeDesignEfficiency.m

@@ -15,7 +15,9 @@ function test_computeDesignEfficiency_vislocalizer()
 
   opt = setOptions('vismotion', '01');
 
-  BIDS = bids.layout(opt.dir.input);
+  BIDS = bids.layout(opt.dir.input, ...
+                     'use_schema', false, ...
+                     'index_dependencies', false);
 
   metadata = bids.query(BIDS, 'metadata', ...
                         'sub', opt.subjects, ...

tests/tests_bids/test_getAnatFilename.m

@@ -119,7 +119,9 @@ function test_getAnatFilename_no_session()
   subLabel = '01';
   opt = setOptions('MoAE-preproc');
 
-  BIDS = bids.layout(opt.dir.input);
+  BIDS = bids.layout(opt.dir.input, ...
+                     'use_schema', false, ...
+                     'index_dependencies', false);
 
   [anatImage, anatDataDir] = getAnatFilename(BIDS, opt, subLabel);
 

tests/tests_bids/unit_tests/test_getInfo.m

@@ -93,7 +93,9 @@ function test_getInfo_no_session_no_run()
   opt = setOptions('MoAE-preproc', subLabel);
   opt.dir.input = opt.dir.preproc;
 
-  BIDS = bids.layout(opt.dir.input);
+  BIDS = bids.layout(opt.dir.input, ...
+                     'use_schema', false, ...
+                     'index_dependencies', false);
 
   sessions = getInfo(BIDS, subLabel, opt, 'sessions');
   assertEqual(sessions, {''});

tests/tests_cli/test_bidspm_smooth.m

@@ -35,7 +35,8 @@ function test_smooth()
 
   BIDS = bids.layout(fullfile(outputPath, 'derivatives', 'bidspm-preproc'), ...
                      'verbose', false, ...
-                     'use_schema', false);
+                     'use_schema', false, ...
+                     'index_dependencies', false);
 
   assertEqual(numel(bids.query(BIDS, 'data', 'desc', 'smth6')), 2);
 
@@ -65,7 +66,8 @@ function test_smooth_anat_only()
 
   BIDS = bids.layout(fullfile(outputPath, 'derivatives', 'bidspm-preproc'), ...
                      'verbose', false, ...
-                     'use_schema', false);
+                     'use_schema', false, ...
+                     'index_dependencies', false);
 
   assertEqual(numel(bids.query(BIDS, 'data', 'desc', 'smth6')), 2);
 

tests/tests_slow/README.md

@@ -0,0 +1,11 @@
+# Slow tests folders
+
+Move files in this folder if they are too slow.
+
+Add the following at the beginning of each test.
+
+```matlab
+  if ~usingSlowTestMode()
+    moxunit_throw_test_skipped_exception('slow test only');
+  end
+```

tests/tests_workflows/preproc/test_bidsGenerateT1map.m → tests/tests_slow/tests_workflows/preproc/test_bidsGenerateT1map.m

@@ -10,6 +10,10 @@
 
 function test_bidsGenerateT1map_basic()
 
+  if ~usingSlowTestMode()
+    moxunit_throw_test_skipped_exception('slow test only');
+  end
+
   opt = setOptions('vismotion');
 
   matlabbatch = bidsGenerateT1map(opt);

tests/tests_workflows/preproc/test_bidsRealignReslice.m → tests/tests_slow/tests_workflows/preproc/test_bidsRealignReslice.m

@@ -10,6 +10,10 @@
 
 function test_bidsRealignReslice_basic()
 
+  if ~usingSlowTestMode()
+    moxunit_throw_test_skipped_exception('slow test only');
+  end
+
   opt = setOptions('vislocalizer', '');
 
   opt.funcVoxelDims = [2 2 2];

tests/tests_workflows/preproc/test_bidsRealignUnwarp.m → tests/tests_slow/tests_workflows/preproc/test_bidsRealignUnwarp.m

@@ -10,6 +10,10 @@
 
 function test_bidsRealignUnwarp_basic()
 
+  if ~usingSlowTestMode()
+    moxunit_throw_test_skipped_exception('slow test only');
+  end
+
   opt = setOptions('vislocalizer', '');
   opt.bidsFilterFile.bold.part = 'mag';
   opt.funcVoxelDims = [2 2 2];

tests/tests_workflows/preproc/test_bidsRemoveDummies.m → tests/tests_slow/tests_workflows/preproc/test_bidsRemoveDummies.m

@@ -10,6 +10,10 @@
 
 function test_bidsRemoveDummies_basic()
 
+  if ~usingSlowTestMode()
+    moxunit_throw_test_skipped_exception('slow test only');
+  end
+
   if bids.internal.is_octave()
     tmpDir = fullfile(tempname);
   else