Merge branch 'bids-standard:main' into main

+bids/+internal/list_all_trial_types.m

@@ -111,4 +111,10 @@
     trial_type_list{idx} = [];
   end
 
+  % n/a not included as trial type
+  idx = ismember(trial_type_list, 'n/a');
+  if any(idx)
+    trial_type_list(idx) = [];
+  end
+
 end

+bids/Model.m

@@ -926,6 +926,45 @@ function write(obj, filename)
 
     end
 
+    function validate_constrasts(obj, node)
+
+      if ~isfield(node, 'Contrasts')
+        return
+      end
+
+      for iCon = 1:numel(node.Contrasts)
+
+        if ~isfield(node.Contrasts{iCon}, 'Weights')
+          msg = sprintf('No weights specified for Contrast %s of Node %s', ...
+                        node.Contrasts{iCon}.Name, node.Name);
+          bids.internal.error_handling(mfilename(), ...
+                                       'weightsRequired', ...
+                                       msg, ...
+                                       obj.tolerant, ...
+                                       obj.verbose);
+        end
+
+        switch node.Contrasts{iCon}.Test
+          case 't'
+            nb_weights = numel(node.Contrasts{iCon}.Weights);
+          case 'F'
+            nb_weights = size(node.Contrasts{iCon}.Weights, 2);
+        end
+
+        if nb_weights ~= numel(node.Contrasts{iCon}.ConditionList)
+          msg = sprintf('Number of Weights and Conditions unequal for Contrast %s of Node %s', ...
+                        node.Contrasts{iCon}.Name, node.Name);
+          bids.internal.error_handling(mfilename(), ...
+                                       'numelWeightsConditionMismatch', ...
+                                       msg, ...
+                                       obj.tolerant, ...
+                                       obj.verbose);
+        end
+
+      end
+
+    end
+
   end
 
   methods (Static)
@@ -996,39 +1035,6 @@ function write(obj, filename)
       end
     end
 
-    % could be made static
-    function validate_constrasts(node)
-
-      if ~isfield(node, 'Contrasts')
-        return
-      end
-
-      for iCon = 1:numel(node.Contrasts)
-
-        if ~isfield(node.Contrasts{iCon}, 'Weights')
-          msg = sprintf('No weights specified for Contrast %s of Node %s', ...
-                        node.Contrasts{iCon}.Name, node.Name);
-          bids.internal.error_handling(mfilename(), ...
-                                       'weightsRequired', ...
-                                       msg, ...
-                                       obj.tolerant, ...
-                                       obj.verbose);
-        end
-
-        if numel(node.Contrasts{iCon}.Weights) ~= numel(node.Contrasts{iCon}.ConditionList)
-          msg = sprintf('Number of Weights and Conditions unequal for Contrast %s of Node %s', ...
-                        node.Contrasts{iCon}.Name, node.Name);
-          bids.internal.error_handling(mfilename(), ...
-                                       'numelWeightsConditionMismatch', ...
-                                       msg, ...
-                                       obj.tolerant, ...
-                                       obj.verbose);
-        end
-
-      end
-
-    end
-
   end
 
   methods (Access = protected)

+bids/layout.m

@@ -239,7 +239,7 @@ function handle_invalid_input(ME, root)
     bids.internal.is_octave
     if ischar(root)
       msg = sprintf(['First input argument must be an existing directory.'...
-                     '\nGot: ''%s.'''], root);
+                     '\nGot: "%s".'], root);
       bids.internal.error_handling(mfilename(), 'InvalidInput', ...
                                    msg, false);
     end
@@ -395,6 +395,12 @@ function handle_invalid_input(ME, root)
     % so the parsing is unconstrained
     for iModality = 1:numel(modalities)
 
+      % when we go schemaless session level folder
+      % may get indexed as modality
+      if bids.internal.starts_with(modalities{iModality}, 'ses-')
+        continue
+      end
+
       if isfield(filter, 'modality') && ...
           ~ismember(modalities{iModality}, filter.modality)
         continue
@@ -836,6 +842,9 @@ function handle_invalid_input(ME, root)
     % other is present to help with analysis.
     intended = {};
     if isfield(metadata, 'IntendedFor')
+      if isempty(metadata.IntendedFor)
+        continue
+      end
       intended = cellstr(metadata.IntendedFor);
     end
 

.github/workflows/run_tests_matlab.yml

@@ -46,9 +46,12 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install unzip wget
 
+    - name: Install Deno
+      uses: denoland/setup-deno@v1
+      with:
+        deno-version: v1.x
     - name: Install bids validator
-      run: npm install -g bids-validator
-
+      run: deno install -Agf -n bids-validator jsr:@bids/validator
 
     - name: Install bids example
       run: |

.github/workflows/run_tests_octave.yml

@@ -40,8 +40,12 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install unzip wget
 
+    - name: Install Deno
+      uses: denoland/setup-deno@v1
+      with:
+        deno-version: v1.x
     - name: Install bids validator
-      run: npm install -g bids-validator
+      run: deno install -Agf -n bids-validator jsr:@bids/validator
 
     - name: Install bids-example
       run: |

.github/workflows/validate.yml

@@ -22,12 +22,6 @@ jobs:
       with:
         args: --validate
 
-  codespell:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: codespell-project/actions-codespell@master
-
   markdown_link_check:
     runs-on: ubuntu-latest
     steps:
@@ -37,26 +31,3 @@ jobs:
         use-quiet-mode: yes
         use-verbose-mode: yes
         config-file: .github/workflows/mlc_config.json
-
-  miss_hit:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        command: [mh_style, mh_metric --ci, mh_lint]
-      fail-fast: false
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: true
-        fetch-depth: 1
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.11
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip3 install -r requirements.txt
-    - name: ${{ matrix.command }}
-      run: |
-        ${{ matrix.command }}

.pre-commit-config.yaml

@@ -46,4 +46,3 @@ repos:
   rev: v2.3.0
   hooks:
   - id: codespell
-    args: [--config=setup.cfg]

CITATION.cff

@@ -4,7 +4,7 @@ cff-version: 1.2.0
 
 title: bids-matlab
 
-version: 0.2.0
+version: 0.3.0
 
 license: MIT