update MACS (#1142) #680
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| name: tests matlab | |
| # 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' | |
| strategy: | |
| matrix: | |
| test_type: [system] | |
| script: [moae, facerep, fmriprep] | |
| os: [ubuntu-latest, macos-latest] | |
| matlab: [R2023a] | |
| include: | |
| # only run bms on ubuntu because of datalad setup | |
| - test_type: system | |
| os: ubuntu-latest | |
| matlab: R2023a | |
| script: bms | |
| - test_type: unit | |
| os: ubuntu-latest | |
| matlab: R2023a | |
| mode: fast | |
| - test_type: unit | |
| os: macos-latest | |
| matlab: R2023a | |
| mode: fast | |
| - test_type: unit | |
| os: ubuntu-latest | |
| matlab: R2023a | |
| mode: slow | |
| - test_type: unit | |
| os: macos-latest | |
| matlab: R2023a | |
| mode: slow | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: ${{ matrix.test_type }} test | |
| if: matrix.test_type == 'system' | |
| run: echo ${{ matrix.test_type }} test ${{ matrix.script }} | |
| - 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 | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get -y -qq update | |
| sudo apt-get -y install unzip wget git-annex | |
| python -m pip install --upgrade pip setuptools | |
| pip install datalad | |
| - 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: Get moae fmriprep data from OSF | |
| run: | | |
| mkdir -p demos/MoAE/inputs/ | |
| cd demos/MoAE/inputs/ | |
| wget https://osf.io/vufjs/download | |
| unzip download | |
| mv moae_fmriprep fmriprep | |
| - name: Prepare test data unix | |
| run: | | |
| cd tests | |
| make data | |
| - name: Get data for BMS | |
| if: matrix.script == 'bms' | |
| run: make -C demos/bayes data_ds000114 | |
| - 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: Install MATLAB | |
| uses: matlab-actions/setup-matlab@v1.2.4 | |
| with: | |
| release: ${{ matrix.matlab }} | |
| - name: Run fast unit tests MATLAB | |
| if: matrix.test_type == 'unit' && matrix.mode == 'fast' | |
| uses: matlab-actions/run-command@v1.2.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab; | |
| - name: Run slow unit tests MATLAB | |
| if: matrix.test_type == 'unit' && matrix.mode == 'slow' | |
| uses: matlab-actions/run-command@v1.2.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab; | |
| - name: Code coverage matlab | |
| if: matrix.test_type == 'unit' | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: coverage.xml | |
| flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }} | |
| name: codecov-matlab | |
| fail_ci_if_error: false | |
| # token: ${{ secrets.CODECOV_TOKEN }} # not required but might help API rate limits | |
| - name: Run system tests MATLAB ${{ matrix.script }} | |
| if: matrix.test_type == 'system' | |
| uses: matlab-actions/run-command@v1.2.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }}; |