Add description about integration and "fix" one normalizaiton issue. #12
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| name: test-python-package | |
| on: [push, pull_request] | |
| jobs: | |
| build-and-test: | |
| outputs: | |
| VERSION: ${{ steps.get-version.outputs.VERSION }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: nschloe/action-cached-lfs-checkout@v1 | |
| - uses: actions/setup-python@v4 | |
| name: Install Python | |
| with: | |
| python-version: '3.10' | |
| - uses: ./.github/actions/setup-rust | |
| with: | |
| cache: true | |
| - name: Install dependencies | |
| run: | | |
| sudo pip install --upgrade pip | |
| pip install --user coverage pytest hypothesis==6.72.4 wheel | |
| - name: Build wheel files | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/snapatac2-python | |
| mkdir ${GITHUB_WORKSPACE}/wheel_files | |
| pip wheel . --wheel-dir ${GITHUB_WORKSPACE}/wheel_files | |
| - name: Test Python package | |
| run: | | |
| pip install --user ${GITHUB_WORKSPACE}/wheel_files/*.whl | |
| coverage run -m pytest ${GITHUB_WORKSPACE}/snapatac2-python/tests | |
| - name: Get SnapATAC2 version | |
| id: get-version | |
| run: | | |
| VERSION_NUMBER=$(python -c "import snapatac2;print(snapatac2.__version__)") | |
| echo $VERSION_NUMBER | |
| echo "VERSION=$VERSION_NUMBER" >> $GITHUB_OUTPUT | |
| - name: Upload Coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| - name: Upload wheel files as artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheel-files | |
| path: ./wheel_files/snapatac2*.whl | |
| build-wheel: | |
| needs: build-and-test | |
| if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, '[wheel]') }} | |
| uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main | |
| publish: | |
| needs: build-wheel | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write | |
| if: ${{ startsWith(github.ref, 'refs/tags') }} | |
| steps: | |
| - name: Download wheel files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: dist | |
| pattern: snapatac2-* | |
| merge-multiple: true | |
| - name: Publish to PyPI | |
| uses: pypa/[email protected] | |
| # build-docker: | |
| # needs: [build-and-test, build-wheel] | |
| # if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, '[docker]') }} | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Docker | |
| # uses: ./.github/actions/build-docker-image | |
| # with: | |
| # snapatac2-version: ${{ needs.build-and-test.outputs.VERSION }} | |
| # python-version: 3.11 | |
| # username: ${{ secrets.dockerhub_username }} | |
| # password: ${{ secrets.dockerhub_token }} |