[MAINT] remove test pollution

.github/workflows/run_tests_notebooks.yml

@@ -33,7 +33,7 @@ jobs:
       uses: matlab-actions/setup-matlab@v1.2.4
       with:
           # MATLAB release to set up R2020a
-        release: R2020a
+        release: R2023a
 
     - name: Clone bidspm
       uses: actions/checkout@v3

.github/workflows/tests.yml

@@ -41,28 +41,28 @@ jobs:
         test_type: [system]
         script: [moae, facerep, fmriprep]
         os: [ubuntu-latest, macos-latest]
-        matlab: [R2022b]
+        matlab: [R2023a]
         include:
         # only run bms on ubuntu because of datalad setup
         - test_type: system
           os: ubuntu-latest
-          matlab: R2022b
+          matlab: R2023a
           script: bms
         - test_type: unit
           os: ubuntu-latest
-          matlab: R2022b
+          matlab: R2023a
           mode: fast
         - test_type: unit
           os: macos-latest
-          matlab: R2022b
+          matlab: R2023a
           mode: fast
         - test_type: unit
           os: ubuntu-latest
-          matlab: R2022b
+          matlab: R2023a
           mode: slow
         - test_type: unit
           os: macos-latest
-          matlab: R2022b
+          matlab: R2023a
           mode: slow
       fail-fast: false
 

.github/workflows/tests_windows.yml

@@ -39,17 +39,17 @@ jobs:
     strategy:
       matrix:
         test_type: [system]
-        script: [moae, facerep, fmriprep]
+        script: [moae, fmriprep]
         os: [windows-latest]
-        matlab: [R2022b]
+        matlab: [R2023a]
         include:
         - test_type: unit
           os: windows-latest
-          matlab: R2022b
+          matlab: R2023a
           mode: fast
         - test_type: unit
           os: windows-latest
-          matlab: R2022b
+          matlab: R2023a
           mode: slow
       fail-fast: false
 

bidspm.m

@@ -325,6 +325,8 @@ function uninitBidspm()
   end
   testFolder = fullfile(pwd, 'tests', subfolder);
 
+  generateLayoutMat();
+
   returnCode = moxunit_runtests(testFolder, ...
                                 '-verbose', '-recursive', '-randomize_order', ...
                                 '-with_coverage', ...

demos/face_repetition/test_face_rep.m

@@ -9,12 +9,10 @@
 clc;
 close all;
 
-% skipping validation for now
-% as raw data is not 100% valid
-skip_validation = true;
-
 download_data = true;
 
+VERBOSITY = 0;
+
 WD = fileparts(mfilename('fullpath'));
 
 addpath(fullfile(WD, '..', '..'));
@@ -69,8 +67,8 @@
          'task', 'facerepetition', ...
          'space', {'IXI549Space'}, ...
          'ignore', ignore, ...
-         'options', opt, ...
-         'skip_validation', skip_validation);
+         'verbosity', VERBOSITY, ...
+         'options', opt);
 
   %% stats
 
@@ -106,7 +104,7 @@
          'preproc_dir', [preproc_dir '-preproc'], ...
          'model_file', newModel, ...
          'options', opt, ...
-         'skip_validation', skip_validation, ...
+         'verbosity', VERBOSITY, ...
          'concatenate', true);
 
 end

src/IO/saveSpmScript.m

@@ -8,8 +8,9 @@
   %
   % :param input: a ``matlabbatch`` variable (cell) or the fullpath to a ``.mat`` file
   %               containing such ``matlabbatch`` variable.
+  %
   % :param outputFilename: optional. Path to output file
-  % :type outputFilename: path
+  % :type  outputFilename: path
   %
   % :returns: - :outputFilename: (path)
   %

src/stats/subject_level/getConfoundsRegressorFilename.m

@@ -37,13 +37,13 @@
 
   if numel(filenames) > 1
     msg = ['Found several confounds files:', ...
-           bids.internal.create_unordered_list(filenames)];
+           bids.internal.create_unordered_list(bids.internal.format_path(filenames))];
     id = 'tooManyFiles';
     logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
 
   elseif isempty(filenames)
     msg = sprintf('No TSV file found in:\n\t%s\nfor query:%s\n', ...
-                  BIDS.pth, ...
+                  bids.internal.format_path(BIDS.pth), ...
                   bids.internal.create_unordered_list(opt.query));
     id = 'noFileFound';
     logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);

src/workflows/bidsQApreproc.m

@@ -34,6 +34,7 @@
 
   [BIDS, opt] = setUpWorkflow(opt, 'preprocessing quality control');
 
+  visible = 'off';
   if opt.verbosity > 1
     visible = 'on';
   end

tests/tests_batches/preproc/test_setBatchSTC.m

@@ -5,9 +5,7 @@
     test_functions = localfunctions(); %#ok<*NASGU>
   catch % no problem; early Matlab versions can use initTestSuite fine
   end
-
   initTestSuite;
-
 end
 
 function test_setBatchSTC_dual_task()

tests/tests_batches/stats/test_setBatchSubjectLevelContrasts.m

@@ -10,9 +10,6 @@
 
 function test_setBatchSubjectLevelContrasts_F_contrast()
 
-  % TODO: fixturize
-  createDummyData();
-
   subLabel = '01';
 
   opt = setOptions('vismotion', subLabel, 'pipelineType', 'stats');
@@ -46,9 +43,6 @@ function test_setBatchSubjectLevelContrasts_F_contrast()
 
 function test_setBatchSubjectLevelContrasts_basic()
 
-  % TODO: fixturize
-  createDummyData();
-
   subLabel = '01';
 
   opt = setOptions('vismotion', subLabel, 'pipelineType', 'stats');
@@ -106,9 +100,6 @@ function test_setBatchSubjectLevelContrasts_basic()
 
 function test_setBatchSubjectLevelContrasts_select_node()
 
-  % TODO: fixturize
-  createDummyData();
-
   subLabel = '01';
 
   opt = setOptions('vismotion', subLabel, 'pipelineType', 'stats');

tests/tests_batches/stats/test_setBatchSubjectLevelGLMSpec.m

@@ -5,9 +5,7 @@
     test_functions = localfunctions(); %#ok<*NASGU>
   catch % no problem; early Matlab versions can use initTestSuite fine
   end
-
   initTestSuite;
-
 end
 
 % TODO add test to better cover setScans
@@ -17,7 +15,9 @@ function test_setBatchSubjectLevelGLMSpec_slicetiming_metadata()
   %% GIVEN
   subLabel = '^01';
 
-  opt = setOptions('vismotion', subLabel, 'pipelineType', 'stats');
+  opt = setOptions('vismotion', subLabel, ...
+                   'pipelineType', 'stats', ...
+                   'useTempDir', true);
 
   % needed to update the options with the content of the model
   opt = checkOptions(opt);
@@ -40,7 +40,9 @@ function test_setBatchSubjectLevelGLMSpec_vismotion_acq_1pt6acq()
   %% GIVEN
   subLabel = '^01';
 
-  opt = setOptions('vismotion', subLabel, 'pipelineType', 'stats');
+  opt = setOptions('vismotion', subLabel, ...
+                   'pipelineType', 'stats', ...
+                   'useTempDir', true);
 
   opt.model.file = spm_file(opt.model.file, 'basename', 'model-vismotion-desc-1pt6acq_smdl');
   opt.model.bm = BidsModel('file', opt.model.file);
@@ -65,7 +67,9 @@ function test_setBatchSubjectLevelGLMSpec_brain_mask()
   %% GIVEN
   subLabel = '^01';
 
-  opt = setOptions('vislocalizer', subLabel, 'pipelineType', 'stats');
+  opt = setOptions('vislocalizer', subLabel, ...
+                   'pipelineType', 'stats', ...
+                   'useTempDir', true);
 
   opt.model.bm.Nodes{1}.Model.Options.Mask = struct('desc', 'brain', 'suffix', 'mask');
 
@@ -120,7 +124,9 @@ function test_setBatchSubjectLevelGLMSpec_basic()
   %% GIVEN
   subLabel = '^01';
 
-  opt = setOptions('vislocalizer', subLabel, 'pipelineType', 'stats');
+  opt = setOptions('vislocalizer', subLabel, ...
+                   'pipelineType', 'stats', ...
+                   'useTempDir', true);
 
   opt.model.bm.Nodes{1}.Model.Options = rmfield(opt.model.bm.Nodes{1}.Model.Options, ...
                                                 'Mask');

tests/tests_batches/stats/test_setBatchSubjectLevelResults.m

@@ -10,9 +10,6 @@
 
 function test_setBatchSubjectLevelResults_basic()
 
-  % TODO: fixturize
-  createDummyData();
-
   % IF
   contrast_name = 'VisMot';
   [subLabel, opt, result] = setUp('vismotion', contrast_name);
@@ -55,9 +52,6 @@ function test_setBatchSubjectLevelResults_basic()
 
 function test_setBatchSubjectLevelResults_missing_contrast_name()
 
-  % TODO: fixturize
-  createDummyData();
-
   if bids.internal.is_octave()
     moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
   end
@@ -77,9 +71,6 @@ function test_setBatchSubjectLevelResults_missing_contrast_name()
 
 function test_setBatchSubjectLevelResults_error_no_matching_contrast()
 
-  % TODO: fixturize
-  createDummyData();
-
   if bids.internal.is_octave()
     moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
   end

tests/tests_batches/test_saveMatlabBatch.m

@@ -41,11 +41,10 @@ function test_saveMatlabBatch_group()
   matlabbatch = struct('test', 1);
 
   expectedOutput = fullfile(opt.dir.jobs, 'group', ...
-                            ['batch_groupTest_' datestr(now, 'yyyy-mm-ddTHH-MM') '.mat']);
+                            ['batch_groupTest_' datestr(now, 'yyyy_mm_ddTHH_MM') '.m']);
 
   saveMatlabBatch(matlabbatch, 'groupTest', opt);
 
-  assertEqual(exist(expectedOutput, 'file'), 0);
-  assertEqual(exist(spm_file(strrep(expectedOutput, '-', '_'), 'ext', '.m'), 'file'), 2);
+  assertEqual(exist(expectedOutput, 'file'), 2);
 
 end

tests/tests_batches/test_setBachRename.m

@@ -1,52 +1,32 @@
 function test_suite = test_setBachRename %#ok<*STOUT>
-  %
-
   % (C) Copyright 2022 bidspm developers
-
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
     test_functions = localfunctions(); %#ok<*NASGU>
   catch % no problem; early Matlab versions can use initTestSuite fine
   end
-
   initTestSuite;
-
 end
 
 function test_setBachRename_basic()
 
   % GIVEN
-  filename = 'sub-01_T1w_seg8.mat';
-  setUp(filename);
+  moveTo = tempName();
+  files = fullfile(moveTo, 'sub-01_T1w_seg8.mat');
+  touch(files);
 
-  files = {fullfile(pwd, filename)};
-  moveTo = {pwd};
   patternReplace(1).pattern = 'T1w';
   patternReplace(1).repl = 'label-T1w';
   patternReplace(2).pattern = 'seg8';
   patternReplace(2).repl = 'segparam';
 
   % WHEN
   matlabbatch = {};
-  matlabbatch = setBachRename(matlabbatch, files, moveTo, patternReplace);
+  matlabbatch = setBachRename(matlabbatch, {files}, {moveTo}, patternReplace);
 
   spm_jobman('run', matlabbatch);
 
   % THEN
   expectedFile = 'sub-01_label-T1w_segparam.mat';
-  assert(exist(fullfile(pwd, expectedFile), 'file') == 2);
-
-  cleanUp(expectedFile);
-
-end
-
-function setUp(filename)
-
-  system(sprintf('touch %s', filename));
-
-end
-
-function cleanUp(filename)
-
-  delete(fullfile(pwd, filename));
+  assert(exist(fullfile(moveTo, expectedFile), 'file') == 2);
 
 end

tests/tests_batches/test_setBatchInverseNormalize.m

@@ -7,6 +7,29 @@
   initTestSuite;
 end
 
+function test_setBatchInverseNormalize_basic()
+
+  subLabel = '^01';
+
+  opt = setOptions('vismotion', subLabel);
+
+  BIDS = getLayout(opt);
+
+  imgToResample = {'foo'};
+
+  matlabbatch = {};
+  matlabbatch = setBatchInverseNormalize(matlabbatch, BIDS, opt, subLabel, imgToResample);
+
+  deformationField = fullfile(BIDS.pth, 'sub-01', 'ses-01', 'anat', ...
+                              'sub-01_ses-01_from-IXI549Space_to-T1w_mode-image_xfm.nii');
+
+  assertEqual(matlabbatch{1}.spm.spatial.normalise.write.subj.def(1), {deformationField});
+  assertEqual(matlabbatch{1}.spm.spatial.normalise.write.woptions.vox, nan(1, 3));
+  assertEqual(matlabbatch{1}.spm.spatial.normalise.write.subj.resample(1), {'foo'});
+  assertEqual(matlabbatch{1}.spm.spatial.normalise.write.woptions.bb, nan(2, 3));
+
+end
+
 function test_setBatchInverseNormalize_warning()
 
   opt = setOptions('vismotion');

tests/tests_bids/test_fileFilterForBold.m

@@ -7,9 +7,7 @@
     test_functions = localfunctions(); %#ok<*NASGU>
   catch % no problem; early Matlab versions can use initTestSuite fine
   end
-
   initTestSuite;
-
 end
 
 function test_fileFilterForBold_events()

tests/tests_bids/test_getROIs.m

@@ -7,9 +7,7 @@
     test_functions = localfunctions(); %#ok<*NASGU>
   catch % no problem; early Matlab versions can use initTestSuite fine
   end
-
   initTestSuite;
-
 end
 
 function test_getROIs_individual_space_no_subject()