Merge branch 'master' into feature/hide-cross-section-opaque

.github/workflows/build.yml

@@ -31,11 +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
+      # uv required for javascript tests
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      # 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 install
       - run: npm run format:fix
       - name: Check for dirty working directory
@@ -54,7 +63,6 @@ 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' }}
@@ -99,7 +107,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-node@v4
         with:
-          node-version: 20.x
+          node-version: 22.x
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -146,7 +154,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-node@v4
         with:
-          node-version: 20.x
+          node-version: 22.x
           cache: "npm"
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -221,7 +229,7 @@ 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:

.github/workflows/build_preview.yml

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

.oxlintrc.json

@@ -0,0 +1,61 @@
+{
+  "$schema": "./node_modules/oxlint/configuration_schema.json",
+  "plugins": ["import", "typescript", "oxc", "unicorn", "promise", "vitest"],
+  "env": {
+    "browser": true
+  },
+  "settings": {},
+  "rules": {
+    // Seems to be buggy
+    "no-loss-of-precision": "off",
+    "import/no-cycle": "error",
+    "import/first": "error",
+    "no-unsafe-finally": "off",
+    "require-yield": "off",
+    "@typescript-eslint/no-explicit-any": "off",
+    "@typescript-eslint/no-non-null-assertion": "off",
+    "@typescript-eslint/no-inferrable-types": "off",
+    "@typescript-eslint/no-this-alias": "off",
+    "@typescript-eslint/no-empty-function": "off",
+    "@typescript-eslint/no-empty-interface": "off",
+    "erasing-op": "off",
+    "no-unused-vars": [
+      "error",
+      {
+        "argsIgnorePattern": "^_",
+        "varsIgnorePattern": "^_",
+        "ignoreRestSiblings": true
+      }
+    ],
+    "no-new-array": "off",
+    "no-document-cookie": "off",
+    "@typescript-eslint/consistent-type-imports": "error"
+  },
+  "overrides": [
+    {
+      "files": ["*.test.ts", "*.spec.ts"],
+      "rules": {
+        "@typescript-eslint/no-explicit-any": "off"
+      }
+    }
+  ],
+  "ignorePatterns": [
+    "**/node_modules",
+    "**/dist",
+    "**/python",
+    "templates/neuroglancer/sliceview",
+    "src/third_party/jpgjs/jpg.js",
+    "**/templates",
+    "**/build",
+    "**/.tox",
+    "**/.nox",
+    "**/.venv",
+    "lib",
+    "**/python",
+    "**/config",
+    "**/typings",
+    "src/mesh/draco/stub.js",
+    "**/tsconfig.tsbuildinfo",
+    "examples"
+  ]
+}

.prettierignore

@@ -1,9 +1,13 @@
 /templates/
 /python/
 /third_party/jpgjs/jpg.js
-/testdata/*.json
+/testdata/
+zarr.json
 .parcel-cache
 dist
 /lib
 /docs/_build/
 /.ruff_cache
+package.json
+package-lock.json
+.venv

README.md

@@ -7,6 +7,8 @@
 
 Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).
 
+Refer to the documentation website at https://neuroglancer-docs.web.app for more details.
+
 This is not an official Google product.
 
 # Examples
@@ -157,6 +159,7 @@ There is a Google Group/mailing list for discussion related to Neuroglancer:
 
 # Related Projects
 
+- [Panel-Neuroglancer](https://github.com/panel-extensions/panel-neuroglancer) - Integrate Neuroglancer into Jupyter notebook workflows and Python web apps with this HoloViz Panel extension.
 - [TensorStore](https://github.com/google/tensorstore) - C++ and Python library for efficiently
   reading and writing multi-dimensional arrays in formats supported by Neuroglancer.
 - [4Quant/neuroglancer-docker](https://github.com/4Quant/neuroglancer-docker) - Example setup for

build_tools/after-version-change.ts

@@ -28,8 +28,17 @@ await Promise.all(
       await execFileAsync("npm", ["install", "--no-audit", "--no-fund"], {
         cwd: exampleDir,
       });
-      await execFileAsync("git", ["add", "package-lock.json"], {
-        cwd: exampleDir,
-      });
     }),
 );
+
+await execFileAsync(
+  "git",
+  [
+    "add",
+    ...(await glob("examples/*/*/package-lock.json", {
+      absolute: false,
+      cwd: rootDir,
+    })),
+  ],
+  { cwd: rootDir },
+);

build_tools/build-package.ts

@@ -71,6 +71,7 @@ async function buildPackage(options: {
     outbase: srcDir,
     bundle: false,
     outdir: libDir,
+    target: "es2022",
   });
 
   let compilerOptionsFromConfigFile: ts.CompilerOptions = {};
@@ -122,6 +123,7 @@ async function buildPackage(options: {
     const { postpack } = packageJson["scripts"];
     delete packageJson["scripts"];
     packageJson["scripts"] = { postpack };
+    packageJson["files"] = ["lib/**/*"];
   } else {
     delete packageJson["private"];
     packageJson["scripts"] = {};

build_tools/update-conditions.ts

@@ -17,70 +17,100 @@ const imports: Record<string, any> = {};
 imports["#src/third_party/jpgjs/jpg.js"] = "./src/third_party/jpgjs/jpg.js";
 imports["#src/*.js"] = "./src/*.ts";
 imports["#src/*"] = "./src/*";
+imports["#tests/fixtures/msw"] = {
+  node: "./tests/fixtures/msw_node.ts",
+  default: "./tests/fixtures/msw_browser.ts",
+};
+imports["#tests/fixtures/gl"] = {
+  node: "./tests/fixtures/gl_node.ts",
+  default: "./tests/fixtures/gl_browser.ts",
+};
+imports["#tests/*.js"] = "./tests/*.ts";
 imports["#testdata/*"] = "./testdata/*";
 
-const datasourceDir = path.resolve(rootDir, "src", "datasource");
-const layerDir = path.resolve(rootDir, "src", "layer");
-
-const datasources = (
-  await fs.promises.readdir(datasourceDir, { withFileTypes: true })
-)
-  .filter((e) => e.isDirectory())
-  .map((e) => e.name);
-
-const layers = (await fs.promises.readdir(layerDir, { withFileTypes: true }))
-  .filter((e) => e.isDirectory())
-  .map((e) => e.name);
-
-const datasourceKeys = {
-  backend: "backend",
-  async_computation: "async_computation",
-  register_default: "frontend",
-  register_credentials_provider: "frontend",
-} as const;
+async function listSubdirs(dir: string): Promise<string[]> {
+  return (await fs.promises.readdir(dir, { withFileTypes: true }))
+    .filter((e) => e.isDirectory())
+    .map((e) => e.name);
+}
 
-const datasourceModules = Object.fromEntries(
-  Object.values(datasourceKeys).map((key) => [key, new Array<string>()]),
-);
+async function writeModule(modulePath: string, imports: string[]) {
+  await fs.promises.writeFile(
+    modulePath,
+    "// DO NOT EDIT: Generated by config/update_conditions.ts\n" +
+      imports.map((name) => `import ${JSON.stringify(name)};\n`).join(""),
+    { encoding: "utf-8" },
+  );
+}
 
-for (const datasource of datasources) {
-  for (const [filePrefix, moduleKind] of Object.entries(datasourceKeys)) {
-    const sourcePrefix = `./src/datasource/${datasource}/${filePrefix}`;
-    if (
-      await fs.promises
-        .stat(path.resolve(rootDir, `${sourcePrefix}.ts`))
-        .catch(() => undefined)
-    ) {
-      const source = sourcePrefix + JS_EXT;
-      const conditions: Record<string, string> = {};
-      if (datasource === "python") {
-        conditions["neuroglancer/python"] = source;
-        conditions.default = NOOP;
-      } else {
-        if (filePrefix === "register_credentials_provider") {
-          conditions["neuroglancer/python"] = NOOP;
+async function handleDrivers(
+  kind: string,
+  moduleMap: Record<string, string[]>,
+) {
+  const driverDir = path.resolve(rootDir, "src", kind);
+  const drivers = await listSubdirs(driverDir);
+  const modules: Record<string, string[]> = {};
+  for (const driver of drivers) {
+    for (const [filePrefix, moduleKinds] of Object.entries(moduleMap)) {
+      const sourcePrefix = `./src/${kind}/${driver}/${filePrefix}`;
+      if (
+        await fs.promises
+          .stat(path.resolve(rootDir, `${sourcePrefix}.ts`))
+          .catch(() => undefined)
+      ) {
+        const source = sourcePrefix + JS_EXT;
+        const conditions: Record<string, string> = {};
+        if (driver === "python") {
+          conditions["neuroglancer/python"] = source;
+          conditions.default = NOOP;
+        } else {
+          if (filePrefix === "register_credentials_provider") {
+            conditions["neuroglancer/python"] = NOOP;
+          }
+          conditions[`neuroglancer/${kind}/${driver}:enabled`] = source;
+          conditions[`neuroglancer/${kind}:none_by_default`] = NOOP;
+          conditions[`neuroglancer/${kind}/${driver}:disabled`] = NOOP;
+          conditions.default = source;
+        }
+        let moduleId = `#${kind}/${driver}`;
+        if (filePrefix !== "index") {
+          moduleId += `/${filePrefix}`;
+        }
+        imports[moduleId] = conditions;
+        for (const moduleKind of moduleKinds) {
+          if (modules[moduleKind] === undefined) {
+            modules[moduleKind] = [];
+          }
+          modules[moduleKind].push(moduleId);
         }
-        conditions[`neuroglancer/datasource/${datasource}:enabled`] = source;
-        conditions["neuroglancer/datasource:none_by_default"] = NOOP;
-        conditions[`neuroglancer/datasource/${datasource}:disabled`] = source;
-        conditions.default = source;
       }
-      const moduleId = `#datasource/${datasource}/${filePrefix}`;
-      imports[moduleId] = conditions;
-      datasourceModules[moduleKind].push(moduleId);
     }
   }
+  for (const [moduleKind, moduleIds] of Object.entries(modules)) {
+    await writeModule(
+      path.resolve(driverDir, `enabled_${moduleKind}_modules.ts`),
+      moduleIds,
+    );
+  }
 }
 
-for (const layer of layers) {
-  const source = `./src/layer/${layer}/index` + JS_EXT;
-  imports[`#layer/${layer}`] = {
-    [`neuroglancer/layer/${layer}:enabled`]: source,
-    "neuroglancer/layer:none_by_default": NOOP,
-    [`neuroglancer/layer/${layer}:enabled`]: source,
-    default: source,
-  };
-}
+await handleDrivers("datasource", {
+  backend: ["backend"],
+  async_computation: ["async_computation"],
+  register_default: ["frontend"],
+  register_credentials_provider: ["frontend"],
+});
+
+await handleDrivers("kvstore", {
+  register: ["frontend", "backend"],
+  register_frontend: ["frontend"],
+  register_backend: ["backend"],
+  register_credentials_provider: ["frontend"],
+});
+
+await handleDrivers("layer", {
+  index: ["frontend"],
+});
 
 // main entrypoint.
 imports["#main"] = {
@@ -94,32 +124,6 @@ imports["#python_integration_build"] = {
   default: NOOP,
 };
 
-async function writeModule(modulePath: string, imports: string[]) {
-  await fs.promises.writeFile(
-    modulePath,
-    "// DO NOT EDIT: Generated by config/update_conditions.ts\n" +
-      imports.map((name) => `import ${JSON.stringify(name)};\n`).join(""),
-    { encoding: "utf-8" },
-  );
-}
-
-for (const [moduleKind, moduleIds] of Object.entries(datasourceModules)) {
-  await writeModule(
-    path.resolve(
-      rootDir,
-      "src",
-      "datasource",
-      `enabled_${moduleKind}_modules.ts`,
-    ),
-    moduleIds,
-  );
-}
-
-await writeModule(
-  path.resolve(rootDir, "src", "layer", "enabled_frontend_modules.ts"),
-  layers.map((name) => `#layer/${name}`),
-);
-
 packageJson.imports = imports;
 
 packageJson.exports = {