Merge branch 'master' into dev

bids-standard · Nov 6, 2023 · 7a2c518 · 7a2c518
2 parents 85a01a1 + 4dc20a3
commit 7a2c518
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Showing 8 changed files with 41 additions and 12 deletions.
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/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
@@ -540,7 +541,8 @@ 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
@@ -127,7 +127,17 @@ 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 +275,17 @@ 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);
 

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 = {};