[MAINT] merge main in dev (#644)

* BIDS schema update (#628) Co-authored-by: Remi-Gau <[email protected]> * Bump actions/checkout from 3 to 4 (#629) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * BIDS schema update (#633) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#634) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#635) Co-authored-by: Remi-Gau <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#636) updates: - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BIDS schema update (#637) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#639) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#640) Co-authored-by: Remi-Gau <[email protected]> * Bump matlab-actions/setup-matlab from 1.2.4 to 1.2.5 (#641) Bumps [matlab-actions/setup-matlab](https://github.com/matlab-actions/setup-matlab) from 1.2.4 to 1.2.5. - [Release notes](https://github.com/matlab-actions/setup-matlab/releases) - [Commits](matlab-actions/setup-matlab@v1.2.4...v1.2.5) --- updated-dependencies: - dependency-name: matlab-actions/setup-matlab dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump matlab-actions/run-command from 1.2.1 to 1.2.2 (#642) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.1 to 1.2.2. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.2.1...v1.2.2) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [FIX] update test after schema update (#643) * fix test after schema update * set os version for doc * update schema * fix typos * update tests --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
bids-standard · Nov 6, 2023 · 2b8ba88 · 2b8ba88
1 parent 8bbabd6
commit 2b8ba88
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Showing 13 changed files with 84 additions and 34 deletions.
diff --git a/+bids/+transformers_list/Merge_identical_rows.m b/+bids/+transformers_list/Merge_identical_rows.m
@@ -26,7 +26,7 @@
   %    - If a variable is found, but is empty, it is ignored
   %    - The content of the other columns corresponds to the last row being merged:
   %      this means that the content from other columns but the one specified in will be deleted
-  %      execpt for the last one
+  %      except for the last one
   %
   % CODE EXAMPLE
   % ------------

diff --git a/+bids/transformers.m b/+bids/transformers.m
@@ -39,10 +39,10 @@
 
   % (C) Copyright 2022 BIDS-MATLAB developers
 
-  SUPPORTED_TRANSFORMERS = lower(cat(1, basic_transfomers, ...
-                                     munge_transfomers, ...
-                                     logical_transfomers, ...
-                                     compute_transfomers));
+  SUPPORTED_TRANSFORMERS = lower(cat(1, basic_transformers, ...
+                                     munge_transformers, ...
+                                     logical_transformers, ...
+                                     compute_transformers));
 
   p = inputParser;
 
@@ -98,16 +98,16 @@
 
   switch transformerName
 
-    case lower(basic_transfomers)
+    case lower(basic_transformers)
       output = bids.transformers_list.Basic(trans, data);
 
-    case lower(logical_transfomers)
+    case lower(logical_transformers)
       output = bids.transformers_list.Logical(trans, data);
 
-    case lower(munge_transfomers)
+    case lower(munge_transformers)
       output = apply_munge(trans, data);
 
-    case lower(compute_transfomers)
+    case lower(compute_transformers)
       output = apply_compute(trans, data);
 
     otherwise
@@ -211,21 +211,21 @@ function not_implemented(name)
                                false);
 end
 
-function BASIC = basic_transfomers()
+function BASIC = basic_transformers()
   BASIC = {'Add'
            'Divide'
            'Multiply'
            'Power'
            'Subtract'};
 end
 
-function LOGICAL = logical_transfomers()
+function LOGICAL = logical_transformers()
   LOGICAL = {'And'
              'Or'
              'Not'};
 end
 
-function MUNGE = munge_transfomers()
+function MUNGE = munge_transformers()
   MUNGE = {'Assign'
            'Concatenate'
            'Constant'
@@ -242,7 +242,7 @@ function not_implemented(name)
            'Split'};
 end
 
-function COMPUTE = compute_transfomers()
+function COMPUTE = compute_transformers()
   COMPUTE = {'Mean'
              'Product'
              'Scale'

diff --git a/.github/workflows/run_tests_matlab.yml b/.github/workflows/run_tests_matlab.yml
@@ -50,6 +50,7 @@ jobs:
     - name: Install bids validator
       run: npm install -g bids-validator
 
+
     - name: Install bids example
       run: |
         cd tests

diff --git a/.github/workflows/run_tests_octave.yml b/.github/workflows/run_tests_octave.yml
@@ -31,7 +31,7 @@ jobs:
     steps:
 
     - name: Clone bids-matlab
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: true
         fetch-depth: 1

diff --git a/.github/workflows/update_schema.yml b/.github/workflows/update_schema.yml
@@ -49,7 +49,7 @@ jobs:
     steps:
 
     - name: Clone bids-matlab
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Get BIDS schema
       run: make update_schema

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ exclude: schema.json
 repos:
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -12,7 +12,6 @@ repos:
   - id: check-json
 
 - repo: local
-
   hooks:
   - id: mh_style
     name: mh_style

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -6,6 +6,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: '3.12'
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
@@ -22,6 +27,5 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: '3.8'
   install:
   - requirements: requirements.txt
diff --git a/demos/spm/facerep/code/convert_facerep_ds.m b/demos/spm/facerep/code/convert_facerep_ds.m
@@ -302,7 +302,7 @@ function create_readme(output_dir)
          '- 2 presentations of 26 Famous and 26 Nonfamous Greyscale photographs, '
          '  for 0.5s, randomly intermixed, for fame judgment task '
          '  (one of two right finger key presses).'
-         '- Parameteric factor "lag" = number of faces intervening '
+         '- Parametric factor "lag" = number of faces intervening '
          '  between repetition of a specific face + 1'
          '- Minimal SOA=4.5s, with probability 2/3 (ie 1/3 null events)'
          ''

diff --git a/schema.json b/schema.json
diff --git a/tests/test_bids_file.m b/tests/test_bids_file.m
@@ -372,7 +372,8 @@ function test_reorder()
                                   'dir'; ...
                                   'run'; ...
                                   'echo'; ...
-                                  'part'});
+                                  'part'; ...
+                                  'chunk'});
   assertEqual(file.json_filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.json');
 
 end
@@ -406,7 +407,7 @@ function test_reorder_schemaless()
                                   'split'
                                   'recording'
                                   'chunk'
-                                  'atlas'
+                                  'seg'
                                   'res'
                                   'den'
                                   'label'
@@ -435,7 +436,8 @@ function test_reorder_with_schema()
                                   'dir'
                                   'run'
                                   'echo'
-                                  'part'});
+                                  'part'
+                                  'chunk'});
   assertEqual(file.json_filename, 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.json');
 end
 
@@ -540,7 +542,8 @@ function test_bids_file_parsing_filename_schema_based()
                'dir'
                'run'
                'echo'
-               'part'});
+               'part'
+               'chunk'});
 
   assertEqual(file.prefix, '');
   assertEqual(file.suffix, 'bold');

diff --git a/tests/test_bids_schema.m b/tests/test_bids_schema.m
@@ -65,7 +65,17 @@ function test_return_entities()
   entities = schema.return_entities('datatype', 'func', ...
                                     'suffix', 'bold', ...
                                     'required_only', false);
-  expected_entities = {'sub', 'ses', 'task', 'acq', 'ce', 'rec', 'dir', 'run', 'echo', 'part'};
+  expected_entities = {'sub', ...
+                       'ses', ...
+                       'task', ...
+                       'acq', ...
+                       'ce', ...
+                       'rec', ...
+                       'dir', ...
+                       'run', ...
+                       'echo', ...
+                       'part', ...
+                       'chunk'};
   assertEqual(entities, expected_entities);
 
   schema = bids.Schema();
@@ -79,7 +89,17 @@ function test_return_entities()
   entities = schema.return_entities('datatype', 'func', ...
                                     'suffix', {'bold', 'cbv'}, ...
                                     'required_only', false);
-  expected_entities = {'sub', 'ses', 'task', 'acq', 'ce', 'rec', 'dir', 'run', 'echo', 'part'};
+  expected_entities = {'sub', ...
+                       'ses',  ...
+                       'task',  ...
+                       'acq',  ...
+                       'ce',  ...
+                       'rec',  ...
+                       'dir',  ...
+                       'run',  ...
+                       'echo',  ...
+                       'part', ...
+                       'chunk'};
   assertEqual(entities, expected_entities);
 
   % smoke test
@@ -100,7 +120,7 @@ function test_return_entities_with_only_datatype_as_argument()
   entities = schema.return_entities('datatype', 'func', ...
                                     'required_only', false);
   expected_entities = {'sub', 'ses', 'task', 'acq', 'ce', 'rec', ...
-                       'dir', 'run', 'echo', 'part', 'recording'};
+                       'dir', 'run', 'echo', 'part', 'recording', 'chunk'};
   assertEqual(entities, expected_entities);
 
 end
@@ -127,7 +147,17 @@ function test_return_entities_for_suffix_modality()
   schema = bids.Schema();
   [entities, required] = schema.return_entities_for_suffix_modality('bold', 'func');
 
-  expected_entities = {'sub', 'ses', 'task', 'acq', 'ce', 'rec', 'dir', 'run', 'echo', 'part'};
+  expected_entities = {'sub', ...
+                       'ses', ...
+                       'task', ...
+                       'acq', ...
+                       'ce', ...
+                       'rec',  ...
+                       'dir',  ...
+                       'run',  ...
+                       'echo',  ...
+                       'part',  ...
+                       'chunk'};
   assertEqual(entities, expected_entities);
 
   expected_required = {'sub', 'task'};
@@ -265,7 +295,17 @@ function test_schemaless()
   suffix_group = schema.content.rules.datatypes.func.func;
   entities = schema.return_entities_for_suffix_group(suffix_group);
 
-  expected_output = {'sub', 'ses', 'task', 'acq', 'ce', 'rec', 'dir', 'run', 'echo', 'part'};
+  expected_output = {'sub', ...
+                     'ses', ...
+                     'task', ...
+                     'acq', ...
+                     'ce', ...
+                     'rec',  ...
+                     'dir',  ...
+                     'run',  ...
+                     'echo',  ...
+                     'part',  ...
+                     'chunk'};
 
   assertEqual(entities, expected_output);
 
@@ -301,7 +341,7 @@ function test_schemaless()
               'split'; ...
               'recording'; ...
               'chunk'; ...
-              'atlas'; ...
+              'segmentation'; ...
               'resolution'; ...
               'density'; ...
               'label'; ...

diff --git a/tests/test_transformers/test_transformers_side_functions.m b/tests/test_transformers/test_transformers_side_functions.m
@@ -53,7 +53,7 @@ function test_get_input()
 function status = test_is_run_level()
 
   data = struct('onset', [], 'duration', [], 'foo', 'bar');
-  assert(bids.transfomers.is_run_level(data));
+  assert(bids.transformers.is_run_level(data));
 
 end
 

diff --git a/tests/tests_private/test_append_to_layout.m b/tests/tests_private/test_append_to_layout.m
@@ -72,7 +72,8 @@ function test_append_to_layout_basic()
                                             'ce', '', ...
                                             'rec', '', ...
                                             'echo', '', ...
-                                            'part', ''));
+                                            'part', '', ...
+                                            'chunk', ''));
 
   expected.anat.metafile = {};
 
@@ -129,7 +130,8 @@ function test_append_to_structure_basic_test()
                                                   'ce', '', ...
                                                   'rec', '', ...
                                                   'echo', '', ...
-                                                  'part', ''));
+                                                  'part', '', ...
+                                                  'chunk', ''));
   expected.anat(1, 1).metafile = {};
 
   expected.anat(1, 1).dependencies.explicit = {};
@@ -147,7 +149,8 @@ function test_append_to_structure_basic_test()
                                   'run', '1', ...
                                   'acq', '', ...
                                   'ce', '', ...
-                                  'rec', ''));     %#ok<*STRNU>
+                                  'rec', '', ...
+                                  'chunk', ''));     %#ok<*STRNU>
 
   tmp.metafile = {};