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Cellfinder merge #713
Workflow file for this run
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| name: tests | |
| on: | |
| # Only run on pushes to main, or when version tags are pushed | |
| push: | |
| branches: | |
| - "main" | |
| tags: | |
| - "v**" | |
| # Run on all pull-requests | |
| pull_request: | |
| # Allow workflow dispatch from GitHub | |
| workflow_dispatch: | |
| concurrency: | |
| # Cancel this workflow if it is running, | |
| # and then changes are applied on top of the HEAD of the branch, | |
| # triggering another run of the workflow | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: neuroinformatics-unit/actions/lint@v2 | |
| manifest: | |
| name: Check Manifest | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: neuroinformatics-unit/actions/check_manifest@v2 | |
| test: | |
| needs: [linting, manifest] | |
| name: Run package tests | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| # Run all supported Python versions on linux | |
| os: [ubuntu-latest] | |
| python-version: ["3.8", "3.9", "3.10"] | |
| # Include one windows, one macos run | |
| include: | |
| - os: macos-latest | |
| python-version: "3.10" | |
| - os: windows-latest | |
| python-version: "3.10" | |
| steps: | |
| # Cache the tensorflow model so we don't have to remake it every time | |
| - name: Cache tensorflow model | |
| uses: actions/cache@v3 | |
| with: | |
| path: "~/.cellfinder" | |
| key: models-${{ hashFiles('~/.cellfinder/**') }} | |
| # Setup pyqt libraries | |
| - name: Setup qtpy libraries | |
| uses: tlambert03/setup-qt-libs@v1 | |
| # Run all tests | |
| - uses: neuroinformatics-unit/actions/test@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| use-xvfb: true | |
| # Run cellfinder tests to make sure cellfinder is still compatible | |
| # with cellfinder-core | |
| test_cellfinder: | |
| needs: [linting, manifest] | |
| name: Run cellfinder tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cache tensorflow model | |
| uses: actions/cache@v3 | |
| with: | |
| path: "~/.cellfinder" | |
| key: models-${{ hashFiles('~/.cellfinder/**') }} | |
| - name: Checkout cellfinder | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'brainglobe/cellfinder' | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| # Install latest SHA on this cellfinder-core branch | |
| python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA | |
| # Install checked out copy of cellfinder | |
| python -m pip install .[dev] | |
| - name: Run cellfinder tests | |
| run: | | |
| python -m pytest --color=yes -v | |
| build_sdist_wheel: | |
| name: Build source distribution and wheel | |
| needs: [test, test_cellfinder] | |
| if: github.event_name == 'push' && github.ref_type == 'tag' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 | |
| upload_all: | |
| name: Publish build distributions | |
| needs: [build_sdist_wheel] | |
| if: github.event_name == 'push' && github.ref_type == 'tag' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: artifact | |
| path: dist | |
| - uses: pypa/[email protected] | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.TWINE_API_KEY }} |