Fixed how overlapping genes are identified during training (#15) #294
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| name: Package | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| sdist: | |
| runs-on: ubuntu-latest | |
| name: Build source distribution | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: List project dependencies | |
| run: python setup.py list_requirements | |
| - name: Install project dependencies | |
| run: python -m pip install -r requirements.txt | |
| - name: Build wheel distribution | |
| run: python setup.py sdist | |
| - name: Store built archive | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: dist | |
| path: dist/* | |
| wheel: | |
| runs-on: ubuntu-latest | |
| name: Build wheel distribution | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: List project dependencies | |
| run: python setup.py list_requirements | |
| - name: Install project dependencies | |
| run: python -m pip install -r requirements.txt | |
| - name: Build wheel distribution | |
| run: python setup.py bdist_wheel | |
| - name: Store built wheel | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: dist | |
| path: dist/* | |
| upload: | |
| environment: PyPI | |
| runs-on: ubuntu-latest | |
| name: Upload to PyPI | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| needs: | |
| - sdist | |
| - wheel | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v1 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.9 | |
| - name: Download built distributions | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: dist | |
| path: dist | |
| - name: Publish distributions to PyPI | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| skip_existing: false | |
| changelog: | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| name: Update GitHub release notes | |
| needs: upload | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v1 | |
| - name: Release a Changelog | |
| uses: rasmus-saks/[email protected] | |
| with: | |
| github-token: '${{ secrets.GITHUB_TOKEN }}' | |
| attach: | |
| runs-on: ubuntu-latest | |
| name: Attach artifacts to GitHub release | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| needs: changelog | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: List project dependencies | |
| run: python setup.py list_requirements | |
| - name: Install project dependencies | |
| run: python -m pip install -r requirements.txt | |
| - name: Build new HMM artifacts | |
| run: python setup.py build_data -f -r | |
| - name: Compress Pfam HMM | |
| run: gzip -c build/lib/gecco/hmmer/Pfam.h3m > Pfam.h3m.gz | |
| - name: Upload HMM | |
| uses: softprops/action-gh-release@v1 | |
| if: startsWith(github.ref, 'refs/tags/') | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| files: Pfam.h3m.gz |