[MAINT] update bids matlab #288
Workflow file for this run
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 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: [R2023a] | |
| include: | |
| - test_type: unit | |
| os: windows-latest | |
| matlab: R2023a | |
| mode: fast | |
| - test_type: unit | |
| os: windows-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: 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: Copy-Item -Recurse -Verbose -Path ".\lib\MACS" -Destination ".\spm12\toolbox\MACS" | |
| - 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@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 }}; |