Move detection (2d/3d filtering, structure splitting) to PyTorch (#440) #702
Workflow file for this run
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| name: Test (and Deploy to PyPI on tag) | |
| 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: | |
| schedule: | |
| # Runs at 6:10am UTC on Monday | |
| - cron: '10 6 * * 1' | |
| # 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 | |
| name: Check Linting | |
| 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 | |
| timeout-minutes: 120 | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| KERAS_BACKEND: torch | |
| CELLFINDER_TEST_DEVICE: cpu | |
| # pooch cache dir | |
| BRAINGLOBE_TEST_DATA_DIR: "~/.pooch_cache" | |
| strategy: | |
| matrix: | |
| # Run all supported Python versions on linux | |
| os: [ubuntu-latest] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| # Include one windows and one macOS (arm based) run | |
| include: | |
| - os: macos-latest | |
| python-version: "3.12" | |
| - os: windows-latest | |
| python-version: "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache pooch data | |
| uses: actions/cache@v4 | |
| with: | |
| path: "~/.pooch_cache" | |
| # hash on conftest in case url changes | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pooch_registry.txt') }} | |
| # Cache the tensorflow model so we don't have to remake it every time | |
| - name: Cache brainglobe directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
| ~/.brainglobe | |
| !~/.brainglobe/atlas.tar.gz | |
| key: brainglobe | |
| # Setup pyqt libraries | |
| - name: Setup qtpy libraries | |
| uses: tlambert03/setup-qt-libs@v1 | |
| # Setup VTK with headless display | |
| - uses: pyvista/setup-headless-display-action@v2 | |
| # Run all tests | |
| - uses: neuroinformatics-unit/actions/test@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| secret-codecov-token: ${{ secrets.CODECOV_TOKEN }} | |
| use-xvfb: true | |
| test_numba_disabled: | |
| needs: [linting, manifest] | |
| name: Run tests with numba disabled | |
| timeout-minutes: 120 | |
| runs-on: ubuntu-latest | |
| env: | |
| NUMBA_DISABLE_JIT: "1" | |
| PYTORCH_JIT: "0" | |
| # pooch cache dir | |
| BRAINGLOBE_TEST_DATA_DIR: "~/.pooch_cache" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache brainglobe directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
| ~/.brainglobe | |
| !~/.brainglobe/atlas.tar.gz | |
| key: brainglobe | |
| - name: Cache pooch data | |
| uses: actions/cache@v4 | |
| with: | |
| path: "~/.pooch_cache" | |
| key: ${{ runner.os }}-3.10-${{ hashFiles('**/pooch_registry.txt') }} | |
| # Setup pyqt libraries | |
| - name: Setup qtpy libraries | |
| uses: tlambert03/setup-qt-libs@v1 | |
| # Setup VTK with headless display | |
| - uses: pyvista/setup-headless-display-action@v2 | |
| # Run test suite with numba disabled | |
| - uses: neuroinformatics-unit/actions/test@v2 | |
| with: | |
| python-version: "3.12" | |
| secret-codecov-token: ${{ secrets.CODECOV_TOKEN }} | |
| codecov-flags: "numba" | |
| # Run brainglobe-workflows brainmapper-CLI tests to check for | |
| # breakages | |
| test_brainmapper_cli: | |
| needs: [linting, manifest] | |
| name: Run brainmapper tests to check for breakages | |
| timeout-minutes: 120 | |
| runs-on: ubuntu-latest | |
| env: | |
| KERAS_BACKEND: torch | |
| CELLFINDER_TEST_DEVICE: cpu | |
| steps: | |
| - name: Cache brainglobe directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
| ~/.brainglobe | |
| !~/.brainglobe/atlas.tar.gz | |
| key: brainglobe | |
| - name: Checkout brainglobe-workflows | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'brainglobe/brainglobe-workflows' | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.12" | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| # Install cellfinder from the latest SHA on this branch | |
| python -m pip install "cellfinder @ git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA" | |
| # Install checked out copy of brainglobe-workflows | |
| python -m pip install .[dev] | |
| - name: Run brainmapper tests in brainglobe-workflows | |
| run: | | |
| python -m pytest --color=yes -v tests/brainmapper | |
| build_sdist_wheel: | |
| name: Build source distribution and wheel | |
| needs: [test, test_numba_disabled] | |
| 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: neuroinformatics-unit/actions/upload_pypi@v2 | |
| with: | |
| secret-pypi-key: ${{ secrets.TWINE_API_KEY }} |