[pre-commit.ci] pre-commit autoupdate #1130
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| --- | |
| 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: | |
| fast_tests: | |
| if: github.repository_owner == 'cpp-lln-lab' | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-13] | |
| matlab: [R2023b] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Install Deno | |
| uses: denoland/setup-deno@v1 | |
| with: | |
| deno-version: v1.x | |
| - name: Install python | |
| uses: actions/setup-python@v5 | |
| 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@v4 | |
| 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: 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: Get data for testing QA | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| cd demos/openneuro/ | |
| make data_ds000114_mriqc | |
| make data_ds000114_fmriprep | |
| - name: Prepare test data unix | |
| run: | | |
| cd tests | |
| make data | |
| - 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@v2.2.0 | |
| with: | |
| release: ${{ matrix.matlab }} | |
| - name: Run fast unit tests MATLAB | |
| uses: matlab-actions/run-command@v2.1.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab; | |
| - name: Code coverage matlab | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage.xml | |
| flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_fast | |
| name: codecov-matlab | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slow_tests: | |
| needs: [fast_tests] | |
| if: github.repository_owner == 'cpp-lln-lab' | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-13] | |
| matlab: [R2023b] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Install Deno | |
| uses: denoland/setup-deno@v1 | |
| with: | |
| deno-version: v1.x | |
| - name: Install python | |
| uses: actions/setup-python@v5 | |
| 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@v4 | |
| 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: 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: Get data for testing QA | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| cd demos/openneuro/ | |
| make data_ds000114_mriqc | |
| make data_ds000114_fmriprep | |
| - name: Prepare test data unix | |
| run: | | |
| cd tests | |
| make data | |
| - 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@v2.2.0 | |
| with: | |
| release: ${{ matrix.matlab }} | |
| - name: Run slow unit tests MATLAB | |
| uses: matlab-actions/run-command@v2.1.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab; | |
| - name: Code coverage matlab | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage.xml | |
| flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_slow | |
| name: codecov-matlab | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| system_tests: | |
| needs: [fast_tests] | |
| if: github.repository_owner == 'cpp-lln-lab' | |
| strategy: | |
| matrix: | |
| script: [moae, facerep, fmriprep] | |
| os: [ubuntu-latest, macos-13] | |
| matlab: [R2023b] | |
| include: | |
| # only run bms on ubuntu because of datalad setup | |
| - os: ubuntu-latest | |
| matlab: R2023b | |
| script: bms | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: test ${{ matrix.script }} | |
| run: test ${{ matrix.script }} | |
| - name: Install Deno | |
| uses: denoland/setup-deno@v1 | |
| with: | |
| deno-version: v1.x | |
| - name: Install python | |
| uses: actions/setup-python@v5 | |
| 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@v4 | |
| 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: 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 MATLAB | |
| uses: matlab-actions/setup-matlab@v2.2.0 | |
| with: | |
| release: ${{ matrix.matlab }} | |
| - name: Run system tests MATLAB ${{ matrix.script }} | |
| uses: matlab-actions/run-command@v2.1.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }}; |