try speed up test by not indexing dependencies

Remi-Gau · Aug 17, 2023 · 49ba5e1 · 49ba5e1
1 parent 990ed3a
commit 49ba5e1
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Showing 23 changed files with 130 additions and 93 deletions.
diff --git a/+bids/+internal/list_all_trial_types.m b/+bids/+internal/list_all_trial_types.m
@@ -54,6 +54,8 @@
 
   trial_type_list = {};
 
+  BIDS = bids.layout(BIDS, 'index_dependencies', false);
+
   event_files = bids.query(BIDS, 'data', ...
                            'suffix', 'events', ...
                            'extension', '.tsv', ...

diff --git a/+bids/diagnostic.m b/+bids/diagnostic.m
@@ -78,7 +78,8 @@
   parse(args, varargin{:});
 
   %%
-  BIDS = bids.layout(args.Results.BIDS, 'use_schema', args.Results.use_schema);
+  BIDS = bids.layout(args.Results.BIDS, 'use_schema', args.Results.use_schema, ...
+                     'index_dependencies', false);
 
   output_path = args.Results.output_path;
 

diff --git a/tests/test_diagnostic.m b/tests/test_diagnostic.m
@@ -19,7 +19,7 @@ function test_diagnostic_basic()
 
   for i = 1:size(examples, 1)
 
-    BIDS = bids.layout(deblank(examples(i, :)));
+    BIDS = bids.layout(deblank(examples(i, :)), 'index_dependencies', false);
 
     diagnostic_table = bids.diagnostic(BIDS, 'output_path', pwd);
     diagnostic_table = bids.diagnostic(BIDS, 'split_by', {'suffix'}, 'output_path', pwd);

diff --git a/tests/test_report.m b/tests/test_report.m
@@ -14,7 +14,7 @@ function test_report_asl()
 
   BIDS = fullfile(cfg.pth_bids_example, datasets);
 
-  BIDS = bids.layout(BIDS, 'use_schema', true);
+  BIDS = bids.layout(BIDS, 'use_schema', true, 'index_dependencies', false);
 
   filter.modality = 'perf';
 
@@ -46,7 +46,7 @@ function test_report_basic()
   for i = 1:numel(datasets)
 
     BIDS = fullfile(cfg.pth_bids_example, datasets{i});
-    BIDS = bids.layout(BIDS, 'use_schema', true);
+    BIDS = bids.layout(BIDS, 'use_schema', true, 'index_dependencies', false);
 
     for j = 1:numel(modalities)
 
@@ -81,7 +81,7 @@ function test_report_pet()
 
   BIDS = fullfile(cfg.pth_bids_example, datasets);
 
-  BIDS = bids.layout(BIDS, 'use_schema', true);
+  BIDS = bids.layout(BIDS, 'use_schema', true, 'index_dependencies', false);
 
   filter.modality = 'pet';
 
@@ -120,7 +120,7 @@ function test_report_moae_data()
                               'verbose', true, ...
                               'delete_previous', false);
 
-  BIDS = bids.layout(pth, 'use_schema', true);
+  BIDS = bids.layout(pth, 'use_schema', true, 'index_dependencies', false);
 
   report = bids.report(BIDS, ...
                        'output_path', cfg.output_path, ...

diff --git a/tests/tests_layout/test_layout.m b/tests/tests_layout/test_layout.m
@@ -61,6 +61,7 @@ function test_layout_filter()
 
   BIDS = bids.layout(fullfile(get_test_data_dir(), '7t_trt'), ...
                      'verbose', verbose, ...
+                     'index_dependencies', false, ...
                      'filter', struct('sub', {{'01', '02'}}, ...
                                       'modality', {{'anat', 'func'}}, ...
                                       'ses', {{'1', '2'}}));
@@ -82,6 +83,7 @@ function test_layout_filter_regex()
 
   BIDS = bids.layout(fullfile(get_test_data_dir(), '7t_trt'), ...
                      'verbose', verbose, ...
+                     'index_dependencies', false, ...
                      'filter', struct('sub', {{'^.*0[12]'}}, ...
                                       'modality', {{'anat', 'func'}}, ...
                                       'ses', {{'[1]'}}));
@@ -96,13 +98,3 @@ function test_layout_filter_regex()
   assertEqual(subjects, {'1'});
 
 end
-
-function test_layout_smoke_test()
-
-  verbose = false;
-
-  BIDS = bids.layout(fullfile(get_test_data_dir(), 'genetics_ukbb'), 'verbose', verbose);
-
-  BIDS = bids.layout(fullfile(get_test_data_dir(), 'ds210'), 'verbose', verbose);
-
-end
diff --git a/tests/tests_layout/test_layout_derivatives.m b/tests/tests_layout/test_layout_derivatives.m
@@ -6,24 +6,6 @@
   initTestSuite;
 end
 
-function test_layout_warning_invalid_subfolder_struct_fieldname()
-
-  % https://github.com/bids-standard/bids-matlab/issues/332
-
-  invalid_subfolder = fullfile(get_test_data_dir(), '..', ...
-                               'data', 'synthetic', 'derivatives', 'invalid_subfolder');
-
-  if bids.internal.is_octave()
-    moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
-  end
-
-  assertWarning(@()bids.layout(invalid_subfolder, ...
-                               'use_schema', false, ...
-                               'verbose', true), ...
-                'layout:invalidSubfolderName');
-
-end
-
 function test_layout_nested()
 
   pth_bids_example = get_test_data_dir();
@@ -41,7 +23,8 @@ function test_layout_nested()
   for i = 1:numel(dataset_to_test)
     BIDS = bids.layout(fullfile(pth_bids_example, dataset_to_test{i}), ...
                        'use_schema', true, 'tolerant', false, ...
-                       'index_derivatives', true);
+                       'index_derivatives', true, ...
+                       'index_dependencies', false);
     fprintf(1, '.');
   end
 
@@ -55,7 +38,8 @@ function test_layout_meg_derivatives()
                               'ds000117', ...
                               'derivatives', ...
                               'meg_derivatives'), ...
-                     'use_schema', false);
+                     'use_schema', false, ...
+                     'index_dependencies', false);
 
   modalities = {'meg'};
   assertEqual(bids.query(BIDS, 'modalities'), modalities);
@@ -80,6 +64,7 @@ function test_layout_prefix()
                     'swuasub-01_acq-anat_TB1TFL.nii.gz'));
 
   BIDS = bids.layout(fullfile(pth_bids_example, 'qmri_tb1tfl'), ...
+                     'index_dependencies', false, ...
                      'use_schema', false);
 
   data = bids.query(BIDS, 'data', ...
@@ -99,8 +84,8 @@ function test_layout_schemaless()
 
   pth_bids_example = get_test_data_dir();
 
-  BIDS = bids.layout(fullfile(pth_bids_example, ...
-                              'ds000001-fmriprep'), ...
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds000001-fmriprep'), ...
+                     'index_dependencies', false, ...
                      'use_schema', false);
 
   modalities = {'anat', 'figures', 'func'};
@@ -132,3 +117,21 @@ function test_layout_schemaless()
                           '_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii']
                         });
 end
+
+function test_layout_warning_invalid_subfolder_struct_fieldname()
+
+  % https://github.com/bids-standard/bids-matlab/issues/332
+
+  invalid_subfolder = fullfile(get_test_data_dir(), '..', ...
+                               'data', 'synthetic', 'derivatives', 'invalid_subfolder');
+
+  if bids.internal.is_octave()
+    moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
+  end
+
+  assertWarning(@()bids.layout(invalid_subfolder, ...
+                               'use_schema', false, ...
+                               'verbose', true), ...
+                'layout:invalidSubfolderName');
+
+end
diff --git a/tests/tests_layout/test_layout_schemaless.m b/tests/tests_layout/test_layout_schemaless.m
@@ -23,6 +23,7 @@ function test_layout_no_schema_no_ses_in_filename()
 
   BIDS = bids.layout(bids_dir, ...
                      'verbose', verbose, ...
+                     'index_dependencies', false, ...
                      'use_schema', true, ...
                      'filter', filter);
 
@@ -31,6 +32,7 @@ function test_layout_no_schema_no_ses_in_filename()
 
   BIDS = bids.layout(bids_dir, ...
                      'verbose', verbose, ...
+                     'index_dependencies', false, ...
                      'use_schema', false, ...
                      'filter', filter);
 

diff --git a/tests/tests_private/test_append_to_layout.m b/tests/tests_private/test_append_to_layout.m
@@ -32,8 +32,7 @@ function test_append_to_layout_schema_unknown_entity()
 
   file = 'sub-16_task-bar_foo-bar_meg.ds';
 
-  assertWarning( ...
-                @()bids.internal.append_to_layout(file, subject, modality, schema, previous), ...
+  assertWarning(@()bids.internal.append_to_layout(file, subject, modality, schema, previous), ...
                 'append_to_layout:unknownEntity');
 
 end
@@ -61,8 +60,7 @@ function test_append_to_layout_basic()
   file = 'sub-16_ses-mri_run-1_acq-hd_T1w.nii.gz';
   subject = bids.internal.append_to_layout(file, subject, modality, schema, previous);
 
-  expected.anat = struct( ...
-                         'filename', 'sub-16_ses-mri_run-1_acq-hd_T1w.nii.gz', ...
+  expected.anat = struct('filename', 'sub-16_ses-mri_run-1_acq-hd_T1w.nii.gz', ...
                          'suffix', 'T1w', ...
                          'ext', '.nii.gz', ...
                          'prefix', '', ...
@@ -114,8 +112,7 @@ function test_append_to_structure_basic_test()
   subject = bids.internal.append_to_layout(file, subject, ...
                                            modality, schema, previous);
 
-  expected.anat(1, 1) = struct( ...
-                               'filename', 'sub-16_ses-mri_run-1_acq-hd_T1w.nii.gz', ...
+  expected.anat(1, 1) = struct('filename', 'sub-16_ses-mri_run-1_acq-hd_T1w.nii.gz', ...
                                'suffix', 'T1w', ...
                                'ext', '.nii.gz', ...
                                'prefix', '', ...
@@ -203,8 +200,7 @@ function test_append_to_layout_schemaless()
   schema = bids.Schema(use_schema);
   schema.verbose = true;
 
-  subject = struct( ...
-                   modality, struct([]), ...
+  subject = struct(modality, struct([]), ...
                    'path', fullfile(pwd, 'sub-01'));
 
   previous = struct('group', struct('index', 0, 'base', '', 'len', 1), ...