Fix issue with gecco convert when given a relative path
#301
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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') | |
| permissions: | |
| id-token: write | |
| 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@release/v1 | |
| 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/release-a-changelog-action@v1.0.1 | |
| 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 |