Merge pull request #115 from MetaCell/develop

Develop

Author: filippomc

.eslintignore

@@ -0,0 +1,2 @@
+# Prettier formatting
+b67a299daf9d0366283169d4f1ec15c54f861546

.eslintrc.yml

@@ -7,6 +7,13 @@ on:
     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:
@@ -24,12 +31,20 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-node@v4
         with:
-          node-version: 20.x
+          node-version: 22.x
           cache: "npm"
           cache-dependency-path: |
             package-lock.json
-            examples/**/package-lock.json
-      - run: npm install
+      # 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
@@ -47,7 +62,6 @@ jobs:
       - run: npm run build-package
       - run: npm publish --dry-run
         working-directory: dist/package
-      - uses: ./.github/actions/setup-firefox
       - name: Run JavaScript tests (including WebGL)
         run: npm test
         if: ${{ runner.os != 'macOS' }}
@@ -68,6 +82,36 @@ jobs:
           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
   #
@@ -92,28 +136,30 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-node@v4
         with:
-          node-version: 20.x
+          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 }}
-      # Uncomment the action below for an interactive shell
-      # - name: Setup tmate session
-      #   uses: mxschmitt/action-tmate@v3
-      - name: Install Python packaging/test tools
-        run: pip install --upgrade pip tox nox wheel numpy -r python/requirements-test.txt
       - uses: ./.github/actions/setup-firefox
-      - run: nox -s lint format mypy
+      - 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: Test with tox
-        run: tox -e ${{ fromJSON('["skip-browser-tests","firefox-xvfb"]')[runner.os == 'Linux'] }}
+      - 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: Install in editable form
-        run: pip install -e . --config-settings editable_mode=strict
-      - name: Run Python tests against editable install (excluding WebGL)
-        working-directory: python/tests
-        run: pytest -vv --skip-browser-tests
+      - name: Test in editable form
+        run: uvx nox -s test_editable
 
   python-build-package:
     strategy:
@@ -139,36 +185,35 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-node@v4
         with:
-          node-version: 20.x
+          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 pip cache dir
-        id: pip-cache
+      - name: Get uv cache dir
+        id: uv-cache
         run: |
-          echo "dir=$(pip cache dir)" >> "$GITHUB_OUTPUT"
-      - run: npm install
+          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: Install setuptools
-        run: pip install setuptools
       - name: Build Python source distribution (sdist)
-        run: python setup.py sdist --format gztar
+        run: uv build --sdist
         if: ${{ runner.os == 'Linux' }}
-      - name: Install cibuildwheel
-        run: pip install cibuildwheel
       - name: Build Python wheels
-        run: bash -xve ./python/build_tools/cibuildwheel.sh
+        run: uvx nox -s cibuildwheel
         env:
-          # On Linux, share pip cache with manylinux docker containers
-          CIBW_ENVIRONMENT_LINUX: PIP_CACHE_DIR=/host${{ steps.pip-cache.outputs.dir }}
-          CIBW_BEFORE_ALL_LINUX: /project/python/build_tools/cibuildwheel_linux_cache_setup.sh /host${{ steps.pip-cache.outputs.dir }}
+          # On Linux, share uv cache with manylinux docker containers
+          CIBW_ENVIRONMENT_LINUX: UV_CACHE_DIR=/host${{ 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
@@ -182,6 +227,9 @@ jobs:
     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:
@@ -190,10 +238,8 @@ jobs:
         uses: ts-graphviz/setup-graphviz@b1de5da23ed0a6d14e0aeee8ed52fdd87af2363c # v2.0.2
         with:
           macos-skip-brew-update: "true"
-      - name: Install nox
-        run: pip install nox
       - name: Build docs
-        run: nox -s docs
+        run: uvx nox -s docs
       - name: Upload docs as artifact
         uses: actions/upload-artifact@v4
         with:
@@ -214,7 +260,7 @@ jobs:
       - name: Use Node.js
         uses: actions/setup-node@v4
         with:
-          node-version: 20.x
+          node-version: 22.x
           registry-url: "https://registry.npmjs.org"
       - uses: actions/download-artifact@v4
         with:
@@ -296,5 +342,6 @@ jobs:
       - 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

.git-blame-ignore-revs

@@ -9,18 +9,19 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+      - 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: 3.12
+          python-version: 3.13
       - name: Setup Graphviz
         uses: ts-graphviz/setup-graphviz@b1de5da23ed0a6d14e0aeee8ed52fdd87af2363c # v2.0.2
         with:
           macos-skip-brew-update: "true"
-      - name: Install nox
-        run: pip install nox
       - name: Build documentation
-        run: nox -s docs
+        run: uvx nox -s docs
       - name: Upload client as artifact
         uses: actions/upload-artifact@v4
         with:

.github/workflows/build.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         node-version:
-          - "20.x"
+          - "22.x"
     runs-on: ubuntu-latest
 
     steps:

.github/workflows/build_docs_preview.yml

@@ -8,6 +8,8 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      statuses: write
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     steps:
       - name: "Create commit status"

.github/workflows/build_preview.yml

@@ -8,6 +8,8 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      statuses: write
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     steps:
       - name: "Create commit status"

.github/workflows/deploy_docs_preview.yml

@@ -21,3 +21,8 @@ tsconfig.tsbuildinfo
 .eslintcache
 /lib
 /.firebase
+/test-results
+/playwright-report
+-/docs/python/api/index.rst
+/docs/python/api/*.rst
+/.vite

.github/workflows/deploy_preview.yml

@@ -0,0 +1,5 @@
+reject:
+  # API break
+  - "gl-matrix"
+  - "@types/gl-matrix"
+  - "codemirror"