Fix post-overhaul integration gates #9
Workflow file for this run
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| name: Python wheels | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| release: | |
| types: [published] | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: macos-14 | |
| target: aarch64-apple-darwin | |
| manylinux: 'off' | |
| - os: macos-13 | |
| target: x86_64-apple-darwin | |
| manylinux: 'off' | |
| - os: ubuntu-latest | |
| target: x86_64-unknown-linux-gnu | |
| manylinux: '2_28' | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: '3.11' | |
| - uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1 | |
| with: | |
| target: ${{ matrix.target }} | |
| manylinux: ${{ matrix.manylinux }} | |
| command: build | |
| args: --release --locked --out dist | |
| - name: Fresh wheel smoke | |
| shell: bash | |
| run: | | |
| python -m venv wheel-venv | |
| wheel-venv/bin/pip install dist/*.whl | |
| wheel-venv/bin/python -c 'import rosalind; print(rosalind.__version__)' | |
| wheel-venv/bin/rosalind --version | |
| mkdir -p wheel-smoke | |
| wheel-venv/bin/rosalind sort \ | |
| --input examples/data/illumina_toy/alignments.bam \ | |
| --output wheel-smoke/sorted.bam | |
| wheel-venv/bin/rosalind reference build \ | |
| --fasta examples/data/illumina_toy/reference.fa \ | |
| --output wheel-smoke/reference.rref | |
| wheel-venv/bin/python - <<'PY' | |
| import rosalind | |
| run = rosalind.iter_features( | |
| "wheel-smoke/reference.rref", | |
| "wheel-smoke/sorted.bam", | |
| workdir="wheel-smoke/python", | |
| ) | |
| rows = sum(batch.num_rows for batch in run.batches()) | |
| assert rows > 0 | |
| assert run.result is not None and run.result.returncode == 0 | |
| receipt = rosalind.inspect_receipt(run.result.manifest_path) | |
| assert receipt.params["feature.schema"] == "1" | |
| PY | |
| - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 | |
| with: | |
| name: wheel-${{ matrix.target }} | |
| path: dist/*.whl | |
| if-no-files-found: error | |
| publish-testpypi: | |
| if: github.event_name == 'release' && github.event.release.prerelease | |
| needs: build | |
| runs-on: ubuntu-latest | |
| environment: release | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4 | |
| with: | |
| pattern: wheel-* | |
| path: dist | |
| merge-multiple: true | |
| - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # release/v1 | |
| with: | |
| repository-url: https://test.pypi.org/legacy/ | |
| packages-dir: dist | |
| publish-pypi: | |
| if: github.event_name == 'release' && !github.event.release.prerelease | |
| needs: build | |
| runs-on: ubuntu-latest | |
| environment: release | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4 | |
| with: | |
| pattern: wheel-* | |
| path: dist | |
| merge-multiple: true | |
| - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # release/v1 | |
| with: | |
| packages-dir: dist |