115 download cif files if pdb are not available #321
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Testing | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install black flake8 isort mypy pylint pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8, pylint, isort and black | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| # check also with pylint | |
| pylint $(git ls-files '*.py') --ignore=conf.py | |
| # mypy | |
| mypy src | |
| # isort | |
| isort --check-only --recursive --quiet . | |
| # black | |
| black --check -q . | |
| - name: Test with pytest | |
| run: | | |
| tree tests | |
| pytest --cov --cov-report=xml | |
| - name: Test & publish code coverage | |
| # https://github.com/marketplace/actions/code-climate-coverage-action | |
| uses: paambaati/codeclimate-action@v3.0.0 | |
| env: | |
| CC_TEST_REPORTER_ID: 495554b5189c33d77f3404148524a617700107caa4fb990963753099aa3fc86c | |
| # Codecov: https://app.codecov.io/gh/iacopy/RCSB-Sync/new | |
| - name: Upload coverage reports to Codecov | |
| run: | | |
| curl -Os https://uploader.codecov.io/latest/linux/codecov | |
| chmod +x codecov | |
| ./codecov | |
| - name: Coverage comment | |
| id: coverage_comment | |
| uses: py-cov-action/python-coverage-comment-action@v3 | |
| with: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| - name: Store Pull Request comment to be posted | |
| uses: actions/upload-artifact@v3 | |
| if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true' | |
| with: | |
| # If you use a different name, update COMMENT_ARTIFACT_NAME accordingly | |
| name: python-coverage-comment-action | |
| # If you use a different name, update COMMENT_FILENAME accordingly | |
| path: python-coverage-comment-action.txt |