feat: add write_tiff export to OME-TIFF, include full metadata as StructuredAnnotation
#507
Workflow file for this run
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| name: CI | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - "v*" | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| jobs: | |
| check-manifest: | |
| name: Check Manifest | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: pipx run check-manifest | |
| test: | |
| name: ${{ matrix.platform }} (${{ matrix.python-version }}) | |
| runs-on: ${{ matrix.platform }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [macos-latest, windows-latest, "ubuntu-latest"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: tests/data | |
| key: ${{ hashFiles('scripts/download_samples.py') }} | |
| - name: Download Samples | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| pip install requests | |
| python scripts/download_samples.py | |
| - name: Build | |
| # -e seems necessary for coverage to work | |
| run: pip install -e .[test] | |
| - name: Test | |
| run: pytest -v --cov=nd2 --cov-report=xml --cov-report=term | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| benchmarks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: tests/data | |
| key: ${{ hashFiles('scripts/download_samples.py') }} | |
| - name: Download Samples | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| pip install requests | |
| python scripts/download_samples.py | |
| - name: install | |
| run: python -m pip install .[test] | |
| - name: Run benchmarks | |
| uses: CodSpeedHQ/action@v2 | |
| with: | |
| run: pytest --codspeed -v --color=yes | |
| deploy: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.x" | |
| - name: 👷 Build | |
| run: | | |
| python -m pip install build | |
| python -m build | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.TWINE_API_KEY }} | |
| - uses: softprops/action-gh-release@v2 | |
| with: | |
| generate_release_notes: true |