Attempt to fix pytest and generate badge #10
Workflow file for this run
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| # See the NOTICE file distributed with this work for additional information | |
| # regarding copyright ownership. | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| name: "Python CI" | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| permissions: write-all | |
| defaults: | |
| run: | |
| working-directory: ./ | |
| jobs: | |
| pylint: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/actions/python_build | |
| - name: Run pylint | |
| run: | | |
| pylint --rcfile pyproject.toml mevolib | |
| pylint --rcfile pyproject.toml tests | |
| mypy: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/actions/python_build | |
| - name: Run mypy | |
| run: | | |
| mypy --config-file pyproject.toml mevolib | |
| mypy --config-file pyproject.toml tests | |
| black: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/actions/python_build | |
| - name: Run black | |
| run: | | |
| black --config pyproject.toml --check . | |
| pytest: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/actions/python_build | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y fasttree raxml mafft muscle clustalo | |
| - name: Run pytest with coverage | |
| continue-on-error: true | |
| run: | | |
| coverage run -m pytest --junitxml=./reports/test-results-${{ matrix.python-version }}.xml | |
| coverage xml -o ./reports/coverage/coverage.xml | |
| genbadge coverage -i ./reports/coverage/coverage.xml -o ./reports/coverage/coverage-badge.svg | |
| coverage report -m | |
| - name: Archive code coverage results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: code-coverage-report | |
| path: ./tests/inference_init_tmp_dir | |
| - name: Add coverage reports | |
| uses: xportation/junit-coverage-report@main | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| junit-path: ./reports/unit/test-results-${{ matrix.python-version }}.xml | |
| coverage-path: ./reports/coverage/coverage.xml | |
| - name: Upload badge as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: badge | |
| path: ./reports/coverage/coverage-badge.svg | |
| if-no-files-found: error | |
| - name: Commit badge | |
| continue-on-error: true | |
| env: | |
| BADGE: ./reports/coverage/coverage-badge.svg | |
| run: | | |
| git config --local user.email "action@github.com" | |
| git config --local user.name "GitHub Action" | |
| git add "${BADGE}" | |
| git commit -m "Add/Update badge" | |
| - name: Push badge commit | |
| uses: ad-m/github-push-action@master | |
| if: ${{ success() }} | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: badges |