Merge branch 'tmp' into bmc

.github/workflows/system_tests_bms.m

@@ -0,0 +1,12 @@
+%
+% (C) Copyright 2023 bidspm developers
+
+root_dir = getenv('GITHUB_WORKSPACE');
+
+fprintf('\nroot dir is %s\n', root_dir);
+
+addpath(fullfile(root_dir, 'spm12'));
+
+cd(fullfile(root_dir, 'demos', 'bayes'));
+
+run ds000114_run;

.github/workflows/tests_bayes.yml

@@ -0,0 +1,87 @@
+---
+name: tests bayesian model selection
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+# ┌───────────── minute (0 - 59)
+# │ ┌───────────── hour (0 - 23)
+# │ │ ┌───────────── day of the month (1 - 31)
+# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+# │ │ │ │ │
+# │ │ │ │ │
+# │ │ │ │ │
+# * * * * *
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+  - cron: 0 0 1,15 * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+
+  tests:
+
+    if: github.repository_owner == 'cpp-lln-lab'
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Install Node
+      uses: actions/setup-node@v3
+      with:
+        node-version: 18
+
+    - name: Install python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get install -y git-annex
+        python -m pip install --upgrade pip setuptools
+        pip install datalad
+
+    - name: Get data
+      run: make -C demos/bayes data_ds000114 
+
+    - name: Clone bidspm
+      uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        fetch-depth: 0
+
+    - name: Install validators
+      run: make install
+
+    - name: Install SPM
+      run: |
+        git clone https://github.com/spm/spm12.git --depth 1
+
+    - name: Copy Macs toolbox to SPM inputs_folder
+      run: cp -rv lib/MACS spm12/toolbox/MACS
+
+    - name: Install MATLAB
+      uses: matlab-actions/setup-matlab@v1.2.4
+      with:
+        release: R2022b
+
+    - name: Run system tests MATLAB BMS
+      uses: matlab-actions/run-command@v1.2.1
+      with:
+        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_bms};

demos/bayes/ds000114_run.m

@@ -17,7 +17,7 @@
 FWHM = 8;
 
 % to run on fewer subjects
-TESTING = false;
+TESTING = true;
 
 % The directory where the data are located
 root_dir = fileparts(mfilename('fullpath'));

src/cli/cliCreateRoi.m

@@ -18,7 +18,7 @@ function cliCreateRoi(varargin)
               'pipelineType', 'create_roi', ...
               'verbosity', 0);
 
-  if opt.boilerplate_only
+  if opt.boilerplateOnly
     return
   end
 

src/cli/cliPreprocess.m

@@ -37,7 +37,7 @@ function cliPreprocess(varargin)
               'outputPath', fullfile(opt.dir.output, 'reports'), ...
               'pipelineType', 'preprocess', ...
               'verbosity', 0);
-  if opt.boilerplate_only
+  if opt.boilerplateOnly
     return
   end
 

src/cli/cliStats.m

@@ -58,7 +58,7 @@ function cliStats(varargin)
                 'outputPath', fullfile(opt.dir.output, 'reports'), ...
                 'pipelineType', 'stats', ...
                 'verbosity', 0);
-    if opt.boilerplate_only
+    if opt.boilerplateOnly
       continue
     end
 

src/cli/getOptionsFromCliArgument.m

@@ -40,7 +40,7 @@
   end
 
   if isfield(args.Results, 'boilerplate_only')
-    opt.boilerplate_only = args.Results.boilerplate_only;
+    opt.boilerplateOnly = args.Results.boilerplate_only;
   end
 
   if isfield(args.Results, 'dry_run')
@@ -198,6 +198,9 @@
 end
 
 function opt = overrideSpace(opt, args)
+  if ~isfield(args.Results, 'space')
+    return
+  end
   if ~isempty(args.Results.space)
     if isfield(opt, 'space') && ~all(ismember(args.Results.space, opt.space))
       overrideMsg('space', convertToString(args.Results.space), ...

src/cli/inputParserForCreateModel.m

@@ -8,6 +8,7 @@
   args = baseInputParser();
 
   isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
+  isCellStr = @(x) iscellstr(x);
 
   addParameter(args, 'space', {}, isCellStr);
   addParameter(args, 'task', {}, isEmptyOrCellstr);

src/cli/inputParserForStats.m

@@ -29,6 +29,7 @@
   addParameter(args, 'design_only', false, isLogical);
   addParameter(args, 'concatenate', false, isLogical);
   addParameter(args, 'keep_residuals', false, isLogical);
+  addParameter(args, 'use_dummy_regressor', false, isLogical);
 
   addParameter(args, 'roi_atlas', 'neuromorphometrics', isInAvailableAtlas);
 

src/defaults/checkOptions.m

@@ -65,7 +65,7 @@
   %     - ``opt.pipeline.isBms`` whether this is a bayesion model selection
   %       pipeline
   %
-  %     - ``opt.boilerplate_only = false`` -
+  %     - ``opt.boilerplateOnly = false`` -
   %       If set to ``true`` only creates dataset description reports and methods description.
   %       Overwrites previous versions.
   %
@@ -267,7 +267,7 @@
   fieldsToSet.pipeline.name = 'bidspm';
   fieldsToSet.pipeline.isBms = false;
 
-  fieldsToSet.boilerplate_only = false;
+  fieldsToSet.boilerplateOnly = false;
 
   fieldsToSet.useBidsSchema = false;
 

src/messages/bidspmHelp.m

@@ -306,6 +306,7 @@ function bidspmHelp()
   %          'design_only', false, ...
   %          'ignore', {}, ...
   %          'concatenate', false, ...
+  %          'use_dummy_regressor', false)
   %          'skip_validation', false)
   %
   %
@@ -359,9 +360,14 @@ function bidspmHelp()
   % :param roi_name:      Names or regex expression of the ROI to use.
   % :type  roi_name:      cell string
   %
-  % :param boilerplate_only:  Only creates dataset description reports.
-  %                           and methods description. Defaults to ``false``.
-  % :type  boilerplate_only:  logical
+  % :param boilerplate_only:       Only creates dataset description reports.
+  %                                and methods description. Defaults to ``false``.
+  % :type  boilerplate_only:       logical
+  %
+  % :param use_dummy_regressor:    If true any missing condition will be modelled
+  %                                by a dummy regressor of ``NaN``.
+  %                                Defaults to ``false``.
+  % :type  use_dummy_regressor:    logical
   %
   %
   %
@@ -393,19 +399,19 @@ function bidspmHelp()
   %
   %   For the bayesian model selection to function
   %   you must first specify all your models using the ``'specify_only'`` action
-  %   with the options ``useDummyRegressor = true``.
+  %   with the options ``'use_dummy_regressor', true``.
   %
   %   .. code-block:: matlab
   %
   %          opt.glm.useDummyRegressor = true;
   %
   %          bidspm(bids_dir, output_dir, 'subject', ...
   %                'participant_label', participant_label, ...
-  %                'action', 'specify_only', ...
   %                'preproc_dir', preproc_dir, ...
+  %                'action', 'specify_only', ...
   %                'model_file', models_dir, ...
-  %                'fwhm', FWHM, ...
-  %                'options', opt);
+  %                'use_dummy_regressor', true
+  %                'fwhm', FWHM);
   %
   %
   % **low level calls**

src/workflows/bidsReport.m

@@ -22,7 +22,7 @@ function bidsReport(opt)
 
   opt.pipeline.type = 'preproc';
 
-  if ~opt.boilerplate_only && ...
+  if ~opt.boilerplateOnly && ...
       isdir(fullfile(opt.dir.output, 'reports'))
     logger('INFO', 'Dataset reports already exist.', ...
            'options', opt, ...