fix(zarr): correctly handle fill value for uint64 data type #1379
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| name: Build | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - v** | |
| pull_request: | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| type: boolean | |
| description: "Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)" | |
| required: false | |
| default: false | |
| jobs: | |
| client: | |
| strategy: | |
| matrix: | |
| os: | |
| - "ubuntu-latest" | |
| - "windows-latest" | |
| - "macos-latest" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # Need full history to determine version number. | |
| fetch-depth: 0 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22.x | |
| cache: "npm" | |
| cache-dependency-path: | | |
| package-lock.json | |
| # uv required for javascript tests | |
| - uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: false | |
| # go needed for fake_gcs_server used by the javascript tests | |
| - name: Setup go | |
| uses: actions/setup-go@v5 | |
| with: | |
| go-version: "stable" | |
| - run: npm ci | |
| - run: npm run format:fix | |
| - name: Check for dirty working directory | |
| run: git diff --exit-code | |
| - run: npm run lint:check | |
| - name: Typecheck with TypeScript | |
| run: npm run typecheck | |
| - name: Build client bundles | |
| run: | | |
| build_info="{'tag':'$(git describe --always --tags)', 'url':'https://github.com/google/neuroglancer/commit/$(git rev-parse HEAD)', 'timestamp':'$(date)'}" | |
| npm run build -- --no-typecheck --no-lint --define NEUROGLANCER_BUILD_INFO="${build_info}" | |
| echo $build_info > ./dist/client/version.json | |
| shell: bash | |
| - name: Build Python client bundles | |
| run: npm run build-python -- --no-typecheck --no-lint | |
| - run: npm run build-package | |
| - run: npm publish --dry-run | |
| working-directory: dist/package | |
| - name: Run JavaScript tests (including WebGL) | |
| run: npm test | |
| if: ${{ runner.os != 'macOS' }} | |
| - name: Run JavaScript tests (excluding WebGL) | |
| run: npm test -- --project node | |
| if: ${{ runner.os == 'macOS' }} | |
| - name: Run JavaScript benchmarks | |
| run: npm run benchmark | |
| - name: Upload NPM package as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: npm-package | |
| path: dist/package | |
| if: ${{ runner.os == 'Linux' }} | |
| - name: Upload client as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: client | |
| path: dist/client | |
| if: ${{ runner.os == 'Linux' }} | |
| example-project-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install pnpm | |
| uses: pnpm/action-setup@v4 | |
| with: | |
| version: 10 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22.x | |
| cache: "pnpm" | |
| cache-dependency-path: | | |
| examples/**/pnpm-lock.yaml | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22.x | |
| cache: "npm" | |
| cache-dependency-path: | | |
| package-lock.json | |
| - run: npm ci | |
| - run: npm run example-project-test -- --reporter=html | |
| - name: Upload report and built clients | |
| uses: actions/upload-artifact@v4 | |
| if: ${{ !cancelled() }} | |
| with: | |
| name: example-project-test-results | |
| path: | | |
| playwright-report/ | |
| examples/*/*/dist/ | |
| # Builds Python package and runs Python tests | |
| # | |
| # On ubuntu-latest, this also runs browser-based tests. On Mac OS and | |
| # Windows, this only runs tests that do not require a browser, since a working | |
| # headless WebGL2 implementation is not available on Github actions. | |
| python-tests: | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.9" | |
| - "3.12" | |
| os: | |
| - "ubuntu-latest" | |
| - "windows-latest" | |
| - "macos-latest" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # Need full history to determine version number. | |
| fetch-depth: 0 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22.x | |
| - uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: false | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: ./.github/actions/setup-firefox | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }} | |
| - run: uvx nox -s lint format mypy | |
| - name: Check for dirty working directory | |
| run: git diff --exit-code | |
| - name: Run python tests (skip browser tests) | |
| run: uvx nox -s test -- --skip-browser-tests | |
| if: ${{ runner.os != 'Linux' }} | |
| - name: Run python tests (include browser tests) | |
| run: uvx nox -s test_xvfb -- --browser firefox | |
| if: ${{ runner.os == 'Linux' }} | |
| # Verify that editable install works | |
| - name: Test in editable form | |
| run: uvx nox -s test_editable | |
| python-build-package: | |
| strategy: | |
| matrix: | |
| include: | |
| - os: "ubuntu-latest" | |
| cibw_build: "*" | |
| wheel_identifier: "linux" | |
| - os: "windows-latest" | |
| cibw_build: "*" | |
| wheel_identifier: "windows" | |
| - os: "macos-14" | |
| cibw_build: "*_x86_64" | |
| wheel_identifier: "macos_x86_64" | |
| - os: "macos-14" | |
| cibw_build: "*_arm64" | |
| wheel_identifier: "macos_arm64" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # Need full history to determine version number. | |
| fetch-depth: 0 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22.x | |
| cache: "npm" | |
| - uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: false | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.x | |
| - name: Get uv cache dir | |
| id: uv-cache | |
| run: | | |
| echo "dir=$(uv cache dir)" >> "$GITHUB_OUTPUT" | |
| - run: npm ci | |
| - run: | | |
| build_info="{'tag':'$(git describe --always --tags)', 'url':'https://github.com/google/neuroglancer/commit/$(git rev-parse HEAD)', 'timestamp':'$(date)'}" | |
| npm run build-python -- --no-typecheck --no-lint --define NEUROGLANCER_BUILD_INFO="${build_info}" | |
| shell: bash | |
| - name: Check for dirty working directory | |
| run: git diff --exit-code | |
| - name: Build Python source distribution (sdist) | |
| run: uv build --sdist | |
| if: ${{ runner.os == 'Linux' }} | |
| - name: Build Python wheels | |
| run: uvx nox -s cibuildwheel | |
| env: | |
| # On Linux, share uv cache with manylinux docker containers | |
| CIBW_ENVIRONMENT_LINUX: UV_CACHE_DIR=/host${{ steps.uv-cache.outputs.dir }} | |
| CIBW_BEFORE_ALL_LINUX: /project/python/build_tools/cibuildwheel_linux_cache_setup.sh /host${{ steps.uv-cache.outputs.dir }} | |
| CIBW_BUILD: ${{ matrix.cibw_build }} | |
| - name: Upload wheels as artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: python-wheels-${{ matrix.wheel_identifier }} | |
| path: | | |
| dist/*.whl | |
| dist/*.tar.gz | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: false | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Setup Graphviz | |
| uses: ts-graphviz/setup-graphviz@b1de5da23ed0a6d14e0aeee8ed52fdd87af2363c # v2.0.2 | |
| with: | |
| macos-skip-brew-update: "true" | |
| - name: Build docs | |
| run: uvx nox -s docs | |
| - name: Upload docs as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docs | |
| path: | | |
| dist/docs | |
| publish-package: | |
| # Only publish package on push to tag or default branch. | |
| if: ${{ github.event_name == 'push' && (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/master') }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - "client" | |
| - "python-build-package" | |
| - "docs" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Use Node.js | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22.x | |
| registry-url: "https://registry.npmjs.org" | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: python-wheels-* | |
| path: dist | |
| merge-multiple: true | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: npm-package | |
| path: npm-package | |
| # - name: Publish to PyPI (test server) | |
| # uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806 # 2020-09-25 | |
| # with: | |
| # user: __token__ | |
| # password: ${{ secrets.pypi_test_token }} | |
| - name: Publish to PyPI (main server) | |
| uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806 # 2020-09-25 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.pypi_token }} | |
| if: ${{ startsWith(github.ref, 'refs/tags/v') }} | |
| - name: Publish to NPM registry | |
| if: ${{ startsWith(github.ref, 'refs/tags/v') }} | |
| run: npm publish | |
| working-directory: npm-package | |
| env: | |
| NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }} | |
| # Download dist/client after publishing to PyPI, because PyPI publish | |
| # action fails if dist/client directory is present. | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: client | |
| path: dist/client | |
| - name: Publish client to Firebase hosting | |
| uses: FirebaseExtended/action-hosting-deploy@v0 | |
| with: | |
| firebaseServiceAccount: "${{ secrets.FIREBASE_HOSTING_SERVICE_ACCOUNT_KEY }}" | |
| projectId: neuroglancer-demo | |
| channelId: live | |
| target: app | |
| # Download dist/docs after publishing to PyPI, because PyPI publish | |
| # action fails if dist/docs directory is present. | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: docs | |
| path: dist/docs | |
| - name: Publish docs to Firebase hosting | |
| uses: FirebaseExtended/action-hosting-deploy@v0 | |
| with: | |
| firebaseServiceAccount: "${{ secrets.FIREBASE_HOSTING_SERVICE_ACCOUNT_KEY }}" | |
| projectId: neuroglancer-demo | |
| channelId: live | |
| target: docs | |
| ngauth: | |
| strategy: | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup go | |
| uses: actions/setup-go@v5 | |
| with: | |
| go-version-file: ngauth_server/go.mod | |
| cache-dependency-path: ngauth_server/go.sum | |
| - run: go build . | |
| working-directory: ngauth_server | |
| wasm: | |
| # Ensures that .wasm files are reproducible. | |
| strategy: | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: ./src/mesh/draco/build.sh | |
| - run: ./src/sliceview/compresso/build.sh | |
| - run: ./src/sliceview/png/build.sh | |
| - run: ./src/sliceview/jxl/build.sh | |
| # Check that there are no differences. | |
| - run: git diff --exit-code |