fix: decimer to work on low res images #284
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| name: test | |
| on: | |
| pull_request: | |
| branches: [main, development] | |
| paths-ignore: | |
| - 'CHANGELOG.md' | |
| - 'package.json' | |
| - 'package-lock.json' | |
| push: | |
| branches: [main, development] | |
| paths-ignore: | |
| - 'CHANGELOG.md' | |
| - 'package.json' | |
| - 'package-lock.json' | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| # Get the source code | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| # Setup Python environment with caching | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| # Debug environment variables | |
| - name: Print all environment variables | |
| run: printenv | |
| # Install all required dependencies | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip3 install --upgrade setuptools pip | |
| pip3 install --no-cache-dir -r requirements.txt | |
| pip install git+https://github.com/Kohulan/DECIMER-Image-Segmentation.git@bbox --no-deps | |
| pip3 install --no-deps decimer | |
| pip install flake8 pytest | |
| pip install pytest-cov | |
| wget -O surge "https://github.com/StructureGenerator/surge/releases/download/v1.0/surge-linux-v1.0" | |
| chmod +x surge | |
| sudo mv surge /usr/bin | |
| # Run code quality checks | |
| - name: Analysing the code with pylint | |
| run: | | |
| flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files '*.py') . | |
| # Execute tests with coverage | |
| - name: Run tests and collect coverage | |
| run: | | |
| python3 -m pytest --cov=./ --cov-report=xml | |
| # Upload coverage data to Codecov | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/[email protected] | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| with: | |
| file: ./coverage.xml | |
| fail_ci_if_error: true | |
| flags: service | |
| name: codecov-umbrella | |
| verbose: true |