fix test pollution in test batches

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/mlc_config.json

@@ -0,0 +1,7 @@
+{
+    "ignorePatterns": [
+        {
+            "pattern": "^https://www.fil.ion.ucl.ac.uk/spm"
+        }
+    ]
+}

tests/tests_batches/stats/test_setBatchFactorialDesign.m

@@ -10,8 +10,6 @@
 
 function test_setBatchFactorialDesign_within_group()
 
-  % createDummyData();
-
   opt = setOptions('vislocalizer', '', 'pipelineType', 'stats');
 
   opt.model.file = spm_file(opt.model.file, ...
@@ -33,8 +31,6 @@ function test_setBatchFactorialDesign_within_group()
 
 function test_setBatchFactorialDesign_complex()
 
-  % createDummyData();
-
   opt = setOptions('vismotion', {'01' 'ctrl01'}, 'pipelineType', 'stats');
 
   opt.model.file = spm_file(opt.model.file, ...
@@ -79,8 +75,6 @@ function test_setBatchFactorialDesign_complex()
 
 function test_setBatchFactorialDesign_basic()
 
-  % createDummyData();
-
   opt = setOptions('vismotion', {'01' 'ctrl01'}, 'pipelineType', 'stats');
 
   datasetNode = opt.model.bm.get_nodes('Level', 'dataset');

tests/tests_batches/stats/test_setBatchSubjectLevelGLMSpec.m

@@ -35,8 +35,6 @@ function test_setBatchSubjectLevelGLMSpec_vismotion_acq_1pt6acq()
   [~, dir] = fileparts(matlabbatch{1}.spm.stats.fmri_spec.dir{1});
   assertEqual(dir, 'task-vismotion_acq-1p60mm_space-IXI549Space_FWHM-6');
 
-  cleanUp(fullfile(pwd, 'derivatives'));
-
 end
 
 function test_setBatchSubjectLevelGLMSpec_brain_mask()
@@ -58,8 +56,6 @@ function test_setBatchSubjectLevelGLMSpec_brain_mask()
   assertEqual(spm_file(matlabbatch{1}.spm.stats.fmri_spec.mask, 'filename'), ...
               {'sub-01_ses-01_space-IXI549Space_desc-brain_mask.nii'});
 
-  cleanUp(fullfile(pwd, 'derivatives'));
-
 end
 
 function test_setBatchSubjectLevelGLMSpec_missing_raw_data()
@@ -136,8 +132,6 @@ function test_setBatchSubjectLevelGLMSpec_basic()
   assertEqual(matlabbatch{1}.spm.stats.fmri_spec.timing.units, 'secs');
   assertEqual(matlabbatch{1}.spm.stats.fmri_spec.timing.RT, 1.55);
 
-  cleanUp(fullfile(pwd, 'derivatives'));
-
 end
 
 function test_setBatchSubjectLevelGLMSpec_slicetiming_metadata()
@@ -161,8 +155,6 @@ function test_setBatchSubjectLevelGLMSpec_slicetiming_metadata()
   assertEqual(matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t,  14);
   assertEqual(matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t0, 7);
 
-  cleanUp(fullfile(pwd, 'derivatives'));
-
 end
 
 function test_setBatchSubjectLevelGLMSpec_inconsistent_metadata()
@@ -214,6 +206,6 @@ function test_setBatchSubjectLevelGLMSpec_design_only()
   assertEqual(matlabbatch{1}.spm.stats.fmri_design.cvi, 'FAST');
   assertEqual(matlabbatch{1}.spm.stats.fmri_design.bases.hrf.derivs, [1 0]);
 
-  cleanUp(fullfile(pwd, 'derivatives'));
+  createDummyData();
 
 end

tests/tests_batches/stats/test_setBatchSubjectLevelResults.m

@@ -10,8 +10,6 @@
 
 function test_setBatchSubjectLevelResults_basic()
 
-  % createDummyData();
-
   % IF
   contrast_name = 'VisMot';
   [subLabel, opt, result] = setUp('vismotion', contrast_name);