[ENH] use sub commands for python CLI #642
Workflow file for this run
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| --- | |
| name: tests windows | |
| # 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_windows: | |
| if: github.repository_owner == 'cpp-lln-lab' | |
| strategy: | |
| matrix: | |
| test_type: [system] | |
| script: [moae, fmriprep] | |
| os: [windows-latest] | |
| matlab: [R2023b] | |
| include: | |
| - test_type: unit | |
| os: windows-latest | |
| matlab: R2023b | |
| mode: fast | |
| - test_type: unit | |
| os: windows-latest | |
| matlab: R2023b | |
| 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@v4 | |
| with: | |
| node-version: 18 | |
| - name: Install python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - 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: | | |
| New-Item -ItemType Directory -Path ".\demos\MoAE\inputs\" -Force | |
| Set-Location -Path ".\demos\MoAE\inputs\" | |
| Invoke-WebRequest -Uri "https://osf.io/vufjs/download" -OutFile "download" | |
| Expand-Archive -Path ".\download" -DestinationPath ".\" | |
| Rename-Item -Path ".\moae_fmriprep" -NewName "fmriprep" | |
| - name: Prepare test data | |
| run: | | |
| cd tests | |
| make create_dummy_dataset | |
| make bids_examples | |
| Invoke-WebRequest -Uri "https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=" -OutFile "moae_spm12.zip" | |
| New-Item -ItemType Directory -Path "data/MoAE/derivatives/spm12" -Force | |
| Expand-Archive -Path "./moae_spm12.zip" -DestinationPath "./data/MoAE/derivatives/spm12" | |
| - 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 | |
| if: matrix.test_type == 'unit' && matrix.mode == 'fast' | |
| uses: matlab-actions/run-command@v2.1.1 | |
| 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@v2.1.1 | |
| 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@v4 | |
| 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 ${{ matrix.script }} | |
| if: matrix.test_type == 'system' | |
| uses: matlab-actions/run-command@v2.1.1 | |
| with: | |
| command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }}; |