🆕 Use Annotations as a Filter for Patch Extraction #3827
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ develop, pre-release, master, main ] | |
| tags: v* | |
| pull_request: | |
| branches: [ develop, pre-release, master, main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-24.04 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools | |
| python -m pip install --upgrade pip | |
| python -m pip install ruff==0.6.5 pytest pytest-cov pytest-runner | |
| pip install -r requirements/requirements.txt | |
| - name: Cache tiatoolbox static assets | |
| uses: actions/cache@v3 | |
| with: | |
| key: tiatoolbox-home-static | |
| path: ~/.tiatoolbox | |
| - name: Print Version Information | |
| run: | | |
| echo "---SQlite---" | |
| sqlite3 --version | |
| sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit" | |
| echo "---Openslide---" | |
| openslide-quickhash1sum --version | |
| echo "---OpenJPEG---" | |
| opj_dump -h | head -n 5 | |
| echo "---Python---" | |
| python -c "import sys; print('Python %s' % sys.version)" | |
| python -c "import sqlite3; print('SQLite %s' % sqlite3.sqlite_version)" | |
| python -c "import numpy; print('Numpy %s' % numpy.__version__)" | |
| python -c "import openslide; print('OpenSlide %s' % openslide.__version__)" | |
| - name: Lint with ruff | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| ruff check . | |
| - name: Test with pytest | |
| run: | | |
| pytest --basetemp={envtmpdir} \ | |
| --cov=tiatoolbox --cov-report=term --cov-report=xml \ | |
| --capture=sys \ | |
| --durations=10 --durations-min=1.0 \ | |
| --maxfail=1 | |
| - name: Report test coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| with: | |
| files: coverage.xml | |
| fail_ci_if_error: false | |
| verbose: true | |
| - name: Report test coverage to DeepSource | |
| uses: deepsourcelabs/test-coverage-action@master | |
| with: | |
| key: python | |
| coverage-file: coverage.xml | |
| dsn: ${{ secrets.DEEPSOURCE_DSN }} | |
| fail-ci-on-error: false | |
| release: | |
| runs-on: ubuntu-24.04 | |
| timeout-minutes: 15 | |
| needs: build | |
| if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/pre-release' || startsWith(github.ref, 'refs/tags/v') | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install -y libopenslide-dev libopenjp2-7 | |
| python -m pip install --upgrade pip | |
| pip install -r requirements/requirements.txt | |
| pip install build | |
| - name: Build package | |
| run: python -m build | |
| - name: Publish package to Test PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| skip_existing: true # Ignore errors if the current version exists already | |
| - name: Publish package to PyPI | |
| if: startsWith(github.ref, 'refs/tags/v') # Only run on tags starting with v | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |