[INFRA] run matlab CI on all OS

.github/dependabot.yml

@@ -1,13 +1,14 @@
+---
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
-  - package-ecosystem: 'github-actions'
-    directory: '/'
-    schedule:
-      interval: 'monthly'
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: monthly
 
-  - package-ecosystem: 'gitsubmodule'
-    directory: '/'
-    schedule:
-      interval: 'monthly'
+- package-ecosystem: gitsubmodule
+  directory: /
+  schedule:
+    interval: monthly

.github/release-drafter.yml

@@ -1,3 +1,4 @@
+---
 template: |
   ## Release Notes
 

.github/workflows/run_tests_matlab.yml

@@ -1,57 +1,73 @@
+---
 name: tests and coverage with matlab
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
 
   push:
     branches:
-      - master
-      - dev
+    - master
+    - dev
 
   pull_request:
-    branches: ["*"]
+    branches: ['*']
 
 jobs:
 
   build:
 
-    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        version: [R2021a, R2021b, R2022a, R2022b]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+      fail-fast: false  # Don't cancel all jobs if one fails
+
+    runs-on: ${{ matrix.os }}
 
     steps:
 
-      - name: Install MATLAB
-        uses: matlab-actions/setup-matlab@v1.2.4
-        with:
-          # MATLAB release to set up R2020a
-          release: R2020a
-
-      - name: Clone spm_2_bids
-        uses: actions/checkout@v3
-        with:
-          submodules: true
-          fetch-depth: 2
-
-      - name: Install Moxunit and MOcov
-        run: |
-          git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
-          git clone https://github.com/MOcov/MOcov.git --depth 1
-
-      - name: get bids-matlab and JSONio
-        run: make install_dev
-
-      - name: Run commands
-        uses: matlab-actions/run-command@v1.1.3
-        with:
-          command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
-
-      - name: Run tests
-        run: |
-          cat test_report.log | grep 0
-          bash <(curl -s https://codecov.io/bash)
-
-      - name: Code coverage
-        uses: codecov/codecov-action@v3
-        with:
-          file: coverage.xml # optional
-          flags: unittests # optional
-          name: codecov-umbrella # optional
-          fail_ci_if_error: false # optional (default = false)
+    - name: Install MATLAB
+      uses: matlab-actions/setup-matlab@v1.2.4
+      with:
+        release: ${{ matrix.version }}
+
+    - name: Clone spm_2_bids
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+        fetch-depth: 2
+
+    - name: Install Moxunit and MOcov
+      run: |
+        git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+        git clone https://github.com/MOcov/MOcov.git --depth 1
+
+    - name: get bids-matlab and JSONio
+      run: make install_dev
+
+    - name: Run commands
+      uses: matlab-actions/run-command@v1.1.3
+      with:
+        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
+
+    - name: Check logs unix
+      if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
+      run: grep -q 0 test_report.log || { echo "Some tests failed. Check the 'Run tests' step to know which ones." >&2; exit 1; }
+    - name: Check logs windows
+      if: matrix.os == 'windows-latest'
+      run: |
+        if (-not (Get-Content test_report.log | Select-String -Pattern "0")) {
+          throw "Some tests failed.  Check the 'Run tests' step to know which ones."
+        }
+
+    - name: Code coverage
+      if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
+      uses: codecov/codecov-action@v3
+      with:
+        file: coverage.xml
+        flags: ${{ matrix.os }}_matlab-${{ matrix.version }}
+        with_coverage: true
+        cover_xml_file: coverage.xml

.github/workflows/run_tests_octave.yml

@@ -1,10 +1,15 @@
+---
 name: tests_octave
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches:
-      - master
-      - dev
+    - master
+    - dev
   pull_request:
     branches: ['*']
 
@@ -35,4 +40,13 @@ jobs:
         tests: tests
         src: src src/defaults src/utils
         ext: lib/JSONio lib/bids-matlab tests/utils
-        with_coverage: false
+        with_coverage: true
+        cover_xml_file: coverage.xml
+
+    - name: Code coverage
+      uses: codecov/codecov-action@v3
+      with:
+        file: coverage.xml
+        flags: ubuntu-latest_octave
+        name: codecov-umbrella
+        fail_ci_if_error: true

.github/workflows/validate_cff.yml

@@ -1,14 +1,15 @@
+---
 name: validate CITATION.cff
 
 on:
   push:
     branches: ['*']
     paths:
-      - 'CITATION.cff'
+    - CITATION.cff
   pull_request:
     branches: ['*']
     paths:
-      - 'CITATION.cff'
+    - CITATION.cff
 
 jobs:
 
@@ -23,4 +24,4 @@ jobs:
     - name: Check whether the citation metadata from CITATION.cff is valid
       uses: citation-file-format/cffconvert-github-action@2.0.0
       with:
-        args: "--validate"
+        args: --validate

.pre-commit-config.yaml

@@ -1,42 +1,54 @@
+---
 repos:
 
--   repo: local
-
-    hooks:
-
-    - id: mh_style
-      name: mh_style
-      entry: mh_style
-      args: [--process-slx, --fix]
-      files: ^(.*\.(m|slx))$
-      language: python
-      additional_dependencies: [miss_hit_core]
-
-    - id: mh_metric
-      name: mh_metric
-      entry: mh_metric
-      args: [--ci]
-      files: ^(.*\.(m|slx))$
-      language: python
-      additional_dependencies: [miss_hit_core]
-
-    - id: mh_lint
-      name: mh_lint
-      entry: mh_lint
-      files: ^(.*\.(m|slx))$
-      language: python
-      additional_dependencies: [miss_hit]
+- repo: local
+
+  hooks:
+
+  - id: mh_style
+    name: mh_style
+    entry: mh_style
+    args: [--process-slx, --fix]
+    files: ^(.*\.(m|slx))$
+    language: python
+    additional_dependencies: [miss_hit_core]
+
+  - id: mh_metric
+    name: mh_metric
+    entry: mh_metric
+    args: [--ci]
+    files: ^(.*\.(m|slx))$
+    language: python
+    additional_dependencies: [miss_hit_core]
+
+  - id: mh_lint
+    name: mh_lint
+    entry: mh_lint
+    files: ^(.*\.(m|slx))$
+    language: python
+    additional_dependencies: [miss_hit]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
-    - id: trailing-whitespace
-    - id: end-of-file-fixer
-    - id: check-yaml
-    - id: check-added-large-files
-
--   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-    -   id: rst-backticks # Detect common mistake of using single backticks when writing rst
-    -   id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.10.0
+  hooks:
+  - id: rst-backticks     # Detect common mistake of using single backticks when writing rst
+  - id: rst-inline-touching-normal     # Detect mistake of inline code touching normal text in rst
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+
+- repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+  rev: 0.2.2
+  hooks:
+  - id: yamlfmt
+    args: [--mapping, '2', --sequence, '2', --offset, '0']

binder/environment.yml

@@ -1,2 +1,3 @@
+---
 dependencies:
 - octave_kernel

run_tests.m

@@ -2,26 +2,35 @@
 
 thisDir = fullfile(fileparts(mfilename('fullpath')));
 
+folderToCover = fullfile(thisDir, 'src');
+addpath(genpath(folderToCover));
+
 if isdir(fullfile(thisDir, 'lib', 'bids-matlab'))
     addpath(fullfile(thisDir, 'lib', 'bids-matlab'));
 end
 if isdir(fullfile(thisDir, 'lib', 'JSONio'))
     addpath(fullfile(thisDir, 'lib', 'JSONio'));
 end
 
-folderToCover = fullfile(thisDir, 'src');
 testFolder = fullfile(thisDir, 'tests');
 
 addpath(fullfile(testFolder, 'utils'));
 
-success = moxunit_runtests(testFolder, ...
-                           '-verbose', '-recursive', '-with_coverage', ...
-                           '-cover', folderToCover, ...
-                           '-cover_xml_file', 'coverage.xml', ...
-                           '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+if ispc
+    success = moxunit_runtests(testFolder, '-verbose');
+
+else
+    success = moxunit_runtests(testFolder, ...
+                               '-verbose', '-recursive', '-with_coverage', ...
+                               '-cover', folderToCover, ...
+                               '-cover_xml_file', 'coverage.xml', ...
+                               '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+end
 
+fileID = fopen('test_report.log', 'w');
 if success
-    system('echo 0 > test_report.log');
+    fprintf(fileID, '0');
 else
-    system('echo 1 > test_report.log');
+    fprintf(fileID, '1');
 end
+fclose(fileID);