Improved singleton counting (#170) #53
Workflow file for this run
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| name: Upload Release Tarball and Container | |
| on: | |
| push: | |
| tags: | |
| - '*' # Push events of any tag created | |
| jobs: | |
| build_versioned_container: | |
| name: Build and Push versioned container | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Setup mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| init-shell: bash | |
| generate-run-shell: true | |
| environment-file: resources/harpy.yaml | |
| cache-environment: false | |
| post-cleanup: 'all' | |
| - name: Install harpy | |
| shell: micromamba-shell {0} | |
| run: | | |
| python3 -m pip install --upgrade build && python3 -m build | |
| pip install dist/*.whl | |
| resources/buildforCI.sh | |
| - name: Clear space | |
| run: rm -rf /opt/hostedtoolcache | |
| - name: Recreate container | |
| shell: micromamba-shell {0} | |
| run: harpy containerize | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| push: true | |
| tags: pdimens/harpy:${{ github.ref_name }} | |
| build_tarball: | |
| name: Upload Release Tarball | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| repository-projects: write | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Version the Container | |
| # this removes the :latest tag and replaces with versioned container | |
| run: | | |
| for i in harpy/snakefiles/*.smk; do | |
| sed -i "s/harpy\:latest/harpy\:${{ github.ref_name }}/g" $i | |
| done | |
| - name: Bump Harpy Version | |
| # this removes the :latest tag and replaces with versioned container | |
| run: | | |
| sed -i "s/0\.0\.0/${{ github.ref_name }}/g" harpy/__main__.py | |
| sed -i "s/0\.0\.0/${{ github.ref_name }}/g" pyproject.toml | |
| - name: Build project | |
| # This builds the release tarball, stripped of unneccessary things | |
| run: | | |
| mkdir artifacts | |
| tar --exclude="test" --exclude=".deprecated" --exclude="artifacts" --exclude=".git" --exclude=".github" -zcvf artifacts/harpy.${{ github.ref_name }}.tar.gz . | |
| - name: Create Release with Assets | |
| uses: softprops/action-gh-release@v2 | |
| with: | |
| files: ./artifacts/harpy.${{ github.ref_name }}.tar.gz |