fix: Confusion with Overriding input After Snakemake Modularization #8961
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| concurrency: | |
| # Cancel concurrent flows on PRs | |
| group: ci-${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| formatting: | |
| if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main' | |
| permissions: | |
| contents: read # for actions/checkout to fetch code | |
| pull-requests: write # for marocchino/sticky-pull-request-comment to create or update PR comment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| environments: "quality" | |
| pixi-version: v0.42.1 | |
| cache: false # no pixi.lock | |
| locked: false | |
| - name: Run black | |
| run: pixi run -e quality format --check --diff . | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/sticky-pull-request-comment@v2 | |
| with: | |
| message: "Please format your code with [black](https://black.readthedocs.io): `black snakemake tests/*.py`." | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ################################################################################################ | |
| # Testing: Run tests using Pixi | |
| ################################################################################################ | |
| tests: | |
| if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] | |
| # see pyprojec.toml: [tool.pixi.feature.test] for available test types | |
| os: [ubuntu-latest, windows-latest, macos-latest] # , macos-13 not supported yet | |
| env: ["py311", "py312", "py313"] | |
| exclude: | |
| - os: windows-latest | |
| env: "py311" | |
| - os: macos-latest | |
| env: "py311" | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| AWS_AVAILABLE: "${{ secrets.AWS_ACCESS_KEY_ID }}" | |
| GCP_AVAILABLE: "${{ secrets.GCP_SA_KEY }}" | |
| ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}" | |
| CI: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install Pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| environments: ${{ matrix.env }} | |
| pixi-version: v0.42.1 | |
| cache: false # no pixi.lock | |
| locked: false | |
| # See https://github.com/apptainer/apptainer/pull/2262 | |
| - name: Disable apparmor namespace restrictions for apptainer (os='Linux') | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo sh -c 'echo kernel.apparmor_restrict_unprivileged_userns=0 \ | |
| >/etc/sysctl.d/90-disable-userns-restrictions.conf' | |
| sudo sysctl -p /etc/sysctl.d/90-disable-userns-restrictions.conf | |
| - name: Setup MinIO for AWS S3 testing (os='Linux', for AWS S3 testing) | |
| if: runner.os == 'Linux' | |
| uses: comfuture/minio-action@v1 | |
| with: | |
| access_key: minio | |
| secret_key: minio123 | |
| port: 9000 | |
| - name: Test MinIO (os='Linux') | |
| if: runner.os == 'Linux' | |
| run: | | |
| export AWS_ACCESS_KEY_ID=minio | |
| export AWS_SECRET_ACCESS_KEY=minio123 | |
| export AWS_EC2_METADATA_DISABLED=true | |
| aws --endpoint-url http://127.0.0.1:9000/ s3 mb s3://test | |
| - name: Run Tests for Linux (os= 'Linux') | |
| if: runner.os == 'Linux' | |
| run: | | |
| pixi run --environment ${{matrix.env}} test-all \ | |
| --splits 10 \ | |
| --group ${{ matrix.test_group }} \ | |
| --splitting-algorithm=least_duration \ | |
| --showlocals \ | |
| --show-capture=all | |
| cd tests/test_report | |
| pixi run -e ${{ matrix.env }} snakemake \ | |
| --use-conda \ | |
| --cores 1 \ | |
| --report report.zip | |
| - name: Run Tests for MacOS (os='macOS') | |
| if: runner.os == 'macOS' | |
| run: | | |
| pixi run --environment ${{matrix.env}} test-simple \ | |
| --splits 10 \ | |
| --group ${{ matrix.test_group }} \ | |
| --splitting-algorithm=least_duration \ | |
| --showlocals \ | |
| --show-capture=all | |
| - name: Run Tests for Windows (os='Windows') | |
| if: runner.os == 'Windows' | |
| run: | | |
| pixi run --environment ${{matrix.env}} test-simple --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration --showlocals --show-capture=all | |
| build-container-image: | |
| if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main' | |
| runs-on: ubuntu-latest | |
| needs: tests | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build container image | |
| run: docker build . | |
| testing-done: | |
| if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main' | |
| needs: | |
| - tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: echo "All tests passed." |