added cpu support for renaming fasta entries #342
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| name: CI | |
| on: push | |
| jobs: | |
| test: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@master | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| # make phykit CLI available for tests | |
| make install | |
| # install test dependencies | |
| pip install -r tests/requirements.txt | |
| - name: Generate coverage report | |
| if: ${{ matrix.python-version == '3.10' }} | |
| run: | | |
| make test.coverage | |
| - name: Upload unit test coverage to Codecov | |
| if: ${{ matrix.python-version == '3.10' }} | |
| uses: codecov/codecov-action@v1.0.7 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./unit.coverage.xml | |
| flags: unit | |
| env_vars: PYTHON | |
| name: codecov-unit | |
| fail_ci_if_error: false | |
| - name: Upload integration test coverage to Codecov | |
| if: ${{ matrix.python-version == '3.10' }} | |
| uses: codecov/codecov-action@v1.0.7 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./integration.coverage.xml | |
| flags: integration | |
| env_vars: PYTHON | |
| name: codecov-integration | |
| fail_ci_if_error: false | |
| docs: | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@master | |
| with: | |
| persist-credentials: false | |
| - name: Setup Python | |
| uses: actions/setup-python@master | |
| with: | |
| python-version: 3.9 | |
| - name: Install pipenv | |
| uses: dschep/install-pipenv-action@v1 | |
| - name: Build docs | |
| run: | | |
| cd docs | |
| pipenv install | |
| pipenv run make html | |
| cd .. | |
| - name: Deploy | |
| uses: JamesIves/github-pages-deploy-action@releases/v3 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages | |
| FOLDER: docs/_build/html |