chore: Apply formatting

.meta-updater/main.mjs

@@ -3,7 +3,6 @@ const LUMAGL_VERSION = '~8.5.21';
 const MATHGL_VERSION = '^3.5.7';
 const REACT_VERSION = '^16.8.0 || ^17.0.0';
 
-
 /** @typedef {import('@pnpm/types').PackageManifest} PackageManifest */
 
 /**
@@ -12,7 +11,11 @@ const REACT_VERSION = '^16.8.0 || ^17.0.0';
  * @param {PackageManifest} manifest
  */
 function pinVersions(manifest) {
-  for (const key of /** @type {const} */ (['dependencies', 'devDependencies', 'peerDependencies'])) {
+  for (const key of /** @type {const} */ ([
+    'dependencies',
+    'devDependencies',
+    'peerDependencies'
+  ])) {
     const deps = manifest[key] ?? {};
     for (const name of Object.keys(deps)) {
       if (name.startsWith('@deck.gl/') || name === 'deck.gl') {

package.json

@@ -16,9 +16,7 @@
     "build": "pnpm -r --parallel build",
     "clean": "pnpm -r exec -- rm -rf node_modules",
     "test": "pnpm -r --parallel test",
-    "check-format": "prettier --check --ignore-path .gitignore tsconfig.json sites/avivator packages/",
-    "lint": "npm run check-format && eslint \"packages/*/src/**/*\" \"sites/avivator/src/**/*\"",
-    "format": "npm run check-format -- --write",
+    "fix": "biome check --apply .",
     "version": "node ./scripts/version.mjs",
     "publish": "pnpm build && pnpm changeset publish"
   },

packages/extensions/prepare.mjs

@@ -29,7 +29,7 @@ for (const file of files) {
   // find colormap name
   const name = contents.match(/^vec4 (.*) \(.*\{$/m)[1];
   const impl = contents
-    .replace(`vec4 ${name}`, "vec4 apply_cmap") // replace colormap fn name
+    .replace(`vec4 ${name}`, 'vec4 apply_cmap') // replace colormap fn name
     .replace(/^#pragma glslify.*\n/gm, ''); // strip off glslify export
 
   await fh.write(`export const ${name} = \`\\\n${impl}\`;\n`);

packages/extensions/src/color-palette-3d-extensions/additive-blend-extension.js

@@ -1,6 +1,6 @@
 import BaseExtension from './base-extension';
 
-const _BEFORE_RENDER = "";
+const _BEFORE_RENDER = '';
 
 const _RENDER = `\
   vec3 rgbCombo = vec3(0.0);
@@ -24,7 +24,7 @@ const _RENDER = `\
   }
 `;
 
-const _AFTER_RENDER = "";
+const _AFTER_RENDER = '';
 
 /**
  * This deck.gl extension allows for a color palette to be used for rendering in 3D with additive blending.

packages/layers/src/utils.js

@@ -46,7 +46,7 @@ export function padContrastLimits({
   domain,
   dtype
 }) {
-  const maxSliderValue = (domain?.[1]) || getDtypeValues(dtype).max;
+  const maxSliderValue = domain?.[1] || getDtypeValues(dtype).max;
   const newContrastLimits = contrastLimits.map((slider, i) =>
     channelsVisible[i]
       ? slider

packages/layers/src/xr-3d-layer/xr-3d-layer.js

@@ -138,7 +138,8 @@ const XR3DLayer = class extends Layer {
     gl.pixelStorei(GL.UNPACK_ALIGNMENT, 1);
     gl.pixelStorei(GL.PACK_ALIGNMENT, 1);
     const programManager = ProgramManager.getDefaultProgramManager(gl);
-    const processStr = "fs:DECKGL_PROCESS_INTENSITY(inout float intensity, vec2 contrastLimits, int channelIndex)";
+    const processStr =
+      'fs:DECKGL_PROCESS_INTENSITY(inout float intensity, vec2 contrastLimits, int channelIndex)';
     if (!programManager._hookFunctions.includes(processStr)) {
       programManager.addShaderHook(processStr);
     }
@@ -151,9 +152,7 @@ const XR3DLayer = class extends Layer {
       if (shaders) {
         const { inject = {}, modules = [] } = shaders;
         const definesInjection = inject[hookName];
-        const moduleDefinesInjection = modules.some(
-          m => m?.inject?.[hookName]
-        );
+        const moduleDefinesInjection = modules.some(m => m?.inject?.[hookName]);
         return definesInjection || moduleDefinesInjection;
       }
       return false;

packages/layers/src/xr-layer/xr-layer.js

@@ -110,7 +110,8 @@ const XRLayer = class extends Layer {
 
     const mutateStr =
       'fs:DECKGL_MUTATE_COLOR(inout vec4 rgba, float intensity0, float intensity1, float intensity2, float intensity3, float intensity4, float intensity5, vec2 vTexCoord)';
-    const processStr = "fs:DECKGL_PROCESS_INTENSITY(inout float intensity, vec2 contrastLimits, int channelIndex)";
+    const processStr =
+      'fs:DECKGL_PROCESS_INTENSITY(inout float intensity, vec2 contrastLimits, int channelIndex)';
     // Only initialize shader hook functions _once globally_
     // Since the program manager is shared across all layers, but many layers
     // might be created, this solves the performance issue of always adding new

packages/layers/tests/utils.spec.js

@@ -110,18 +110,18 @@ test('getRenderingAttrs WebGL1', t => {
         t.equal(
           attrs.sampler,
           'sampler2D',
-          "always return sampler2D as sampler"
+          'always return sampler2D as sampler'
         );
-        t.equal(attrs.type, GL.FLOAT, "always return FLOAT as dtype");
+        t.equal(attrs.type, GL.FLOAT, 'always return FLOAT as dtype');
         t.equal(
           attrs.dataFormat,
           GL.LUMINANCE,
-          "always return LUMINANCE as dataFormat"
+          'always return LUMINANCE as dataFormat'
         );
         t.equal(
           attrs.format,
           GL.LUMINANCE,
-          "always return LUMINANCE as format"
+          'always return LUMINANCE as format'
         );
         t.equal(
           attrs.filter,

packages/loaders/src/tiff/lib/indexers.ts

@@ -16,9 +16,10 @@ export type OmeTiffIndexer = (
  * bioformats case we need to return the GeoTIFF object and the IFD index.
  */
 export type OmeTiffResolver = (
-    sel: OmeTiffSelection) =>
-    | { tiff: GeoTIFF; ifdIndex: number }
-    | Promise<{ tiff: GeoTIFF; ifdIndex: number }>;
+  sel: OmeTiffSelection
+) =>
+  | { tiff: GeoTIFF; ifdIndex: number }
+  | Promise<{ tiff: GeoTIFF; ifdIndex: number }>;
 
 /*
  * An "indexer" for a GeoTIFF-based source is a function that takes a

packages/loaders/src/tiff/multi-tiff.ts

@@ -20,7 +20,7 @@ function assertSameResolution(images: MultiTiffImage[]) {
   const height = images[0].tiff.getHeight();
   for (const image of images) {
     if (image.tiff.getWidth() !== width || image.tiff.getHeight() !== height) {
-      throw new Error("All images must have the same width and height");
+      throw new Error('All images must have the same width and height');
     }
   }
 }

packages/loaders/src/zarr/pixel-source.ts

@@ -111,7 +111,8 @@ class ZarrPixelSource<S extends string[]> implements PixelSource<S> {
     // and ignored by deck.gl.
     if (xStart === xStop || yStart === yStop) {
       throw new BoundsCheckError('Tile slice is zero-sized.');
-    }if (xStart < 0 || yStart < 0 || xStop > width || yStop > height) {
+    }
+    if (xStart < 0 || yStart < 0 || xStop > width || yStop > height) {
       throw new BoundsCheckError('Tile slice is out of bounds.');
     }
 
@@ -121,7 +122,7 @@ class ZarrPixelSource<S extends string[]> implements PixelSource<S> {
   private async _getRaw(
     selection: (null | Slice | number)[],
     // biome-ignore lint/suspicious/noExplicitAny: any is used to pass through storeOptions
-    getOptions?: { storeOptions?: any } 
+    getOptions?: { storeOptions?: any }
   ) {
     const result = await this._data.getRaw(selection, getOptions);
     if (typeof result !== 'object') {

packages/types/src/index.d.ts

@@ -112,7 +112,7 @@ type WithExtensionProps<LayerProps> = LayerProps extends { extensions: unknown }
         LensExtensionProps &
         ColorPalette3DExtensionProps &
         AdditiveColormap3DExtensionProps
-        // biome-ignore lint/suspicious/noExplicitAny: This is a catch-all for any other extension props
+      // biome-ignore lint/suspicious/noExplicitAny: This is a catch-all for any other extension props
     > & { [extensionProp: string]: any }
   : unknown;
 

packages/viewers/src/VivViewer.jsx

@@ -94,13 +94,12 @@ class VivViewerWrapper extends React.PureComponent {
     // Save the view state and trigger rerender.
     const { views, onViewStateChange } = this.props;
     viewState =
-      (onViewStateChange?.({
-          viewId,
-          viewState,
-          interactionState,
-          oldViewState
-        })) ||
-      viewState;
+      onViewStateChange?.({
+        viewId,
+        viewState,
+        interactionState,
+        oldViewState
+      }) || viewState;
     this.setState(prevState => {
       const viewStates = {};
       views.forEach(view => {

packages/views/tests/DetailView.spec.js

@@ -10,7 +10,7 @@ detailViewArguments.initialViewState.id = id;
 
 generateViewTests(DetailView, detailViewArguments);
 
-test("DetailView layer type and props check", t => {
+test('DetailView layer type and props check', t => {
   const view = new DetailView(detailViewArguments);
   const loader = { type: 'loads' };
   const layers = view.getLayers({
@@ -44,7 +44,7 @@ test("DetailView layer type and props check", t => {
   t.end();
 });
 
-test("DetailView does not render scale bar without physical size", t => {
+test('DetailView does not render scale bar without physical size', t => {
   const view = new DetailView(detailViewArguments);
   const loader = { type: 'loads' };
   const layers = view.getLayers({

packages/views/tests/OverviewView.spec.js

@@ -32,7 +32,7 @@ const linkedViewIds = [DETAIL_VIEW_ID];
 
 generateViewTests(OverviewView, overviewViewArguments, linkedViewIds);
 
-test("OverviewView layer type check.", t => {
+test('OverviewView layer type check.', t => {
   const view = new OverviewView(overviewViewArguments);
 
   const viewState = view.filterViewState({ viewState: overviewViewState });
@@ -50,7 +50,7 @@ test("OverviewView layer type check.", t => {
   t.end();
 });
 
-test("OverviewView respects maximumHeight and minimumHeight when height > width.", t => {
+test('OverviewView respects maximumHeight and minimumHeight when height > width.', t => {
   const minimumHeight = 350;
   let view = new OverviewView({ ...overviewViewArguments, minimumHeight });
   t.equal(
@@ -68,7 +68,7 @@ test("OverviewView respects maximumHeight and minimumHeight when height > width.
   t.end();
 });
 
-test("OverviewView respects maximumWidth and minimumWidth when width > height.", t => {
+test('OverviewView respects maximumWidth and minimumWidth when width > height.', t => {
   const minimumWidth = 350;
   const loaderWidth = [
     { type: 'loads', shape: [10000, 20000] },
@@ -99,7 +99,7 @@ test("OverviewView respects maximumWidth and minimumWidth when width > height.",
   t.end();
 });
 
-test("OverviewView maintains viewState.", t => {
+test('OverviewView maintains viewState.', t => {
   const view = new OverviewView(overviewViewArguments);
   const viewState1 = view.filterViewState({
     height: 10,

packages/views/tests/SideBySideView.spec.js

@@ -7,7 +7,7 @@ import { MultiscaleImageLayer, ImageLayer, ScaleBarLayer } from '@vivjs/layers';
 
 generateViewTests(SideBySideView, defaultArguments);
 
-test("SideBySideView layer type and props check", t => {
+test('SideBySideView layer type and props check', t => {
   const view = new SideBySideView(defaultArguments);
   const loader = { type: 'loads' };
   const layers = view.getLayers({
@@ -43,7 +43,7 @@ test("SideBySideView layer type and props check", t => {
   t.end();
 });
 
-test("SideBySideView layer with multiscale", t => {
+test('SideBySideView layer with multiscale', t => {
   const view = new SideBySideView(defaultArguments);
   const loader = { type: 'loads' };
   const layers = view.getLayers({
@@ -80,7 +80,7 @@ test("SideBySideView layer with multiscale", t => {
   t.end();
 });
 
-test("SideBySideView layer does not render scale bar without physical size", t => {
+test('SideBySideView layer does not render scale bar without physical size', t => {
   const view = new SideBySideView(defaultArguments);
   const loader = { type: 'loads' };
   const layers = view.getLayers({

packages/views/tests/VivView.spec.js

@@ -71,12 +71,12 @@ export function generateViewTests(ViewType, args, linkedViewIds = []) {
       viewStates
     });
     layers?.forEach(layer => {
-        layer &&
-          t.ok(
-            layer.id.includes(getVivId(view.id)),
-            "Layer should include view's id as returned by getVivId."
-          );
-      });
+      layer &&
+        t.ok(
+          layer.id.includes(getVivId(view.id)),
+          "Layer should include view's id as returned by getVivId."
+        );
+    });
     t.end();
   });
 }

scripts/bundle-test.mjs

@@ -1,4 +1,4 @@
-import * as esbuild from "esbuild";
+import * as esbuild from 'esbuild';
 
 // These are necessary as long as we use `tape` for tests in the browser.
 // The package relies on many node-isms and must be adapted.
@@ -8,9 +8,6 @@ import { NodeModulesPolyfillPlugin as builtins } from '@esbuild-plugins/node-mod
 esbuild.build({
   entryPoints: [process.argv[2]],
   bundle: true,
-  format: "iife",
-  plugins: [
-    globals({ process: true, buffer: true }),
-    builtins(),
-  ],
+  format: 'iife',
+  plugins: [globals({ process: true, buffer: true }), builtins()]
 });

scripts/bundle.mjs

@@ -1,18 +1,18 @@
-import * as esbuild from "esbuild";
+import * as esbuild from 'esbuild';
 
 esbuild.build({
   entryPoints: [process.argv[2]],
   outfile: './dist/index.js',
   bundle: true,
-  format: "esm",
+  format: 'esm',
   plugins: [
     {
-      name: "make-all-packages-external",
+      name: 'make-all-packages-external',
       setup(build) {
         build.onResolve({ filter: /^[^\.]/ }, ({ path }) => {
           return { path, external: true };
         });
-      },
-    },
-  ],
-})
+      }
+    }
+  ]
+});

scripts/version.mjs

@@ -6,14 +6,16 @@ import * as childProcess from 'node:child_process';
 import matter from 'gray-matter';
 
 const __dirname = path.dirname(url.fileURLToPath(import.meta.url));
-const mainPackage = "@hms-dbmi/viv";
+const mainPackage = '@hms-dbmi/viv';
 
 /**
  * @param {matter.GrayMatterFile<string>} changeset
  */
 function getGreatestBumpType(changeset) {
   const BUMP_TYPES = /** @type {const} */ (['none', 'patch', 'minor', 'major']);
-  const versions = Object.values(changeset.data).map(v => BUMP_TYPES.indexOf(v));
+  const versions = Object.values(changeset.data).map(v =>
+    BUMP_TYPES.indexOf(v)
+  );
   const bumpType = BUMP_TYPES[Math.max(...versions)];
   if (!bumpType) {
     throw new Error(`Invalid bump type: ${bumpType}`);
@@ -27,7 +29,9 @@ function getGreatestBumpType(changeset) {
  */
 function updateContentsWithAffectedPackages(changeset) {
   const contentLines = changeset.content.split('\n');
-  const packageInfo = Object.keys(changeset.data).map(name => `\`${name}\``).join(', ');
+  const packageInfo = Object.keys(changeset.data)
+    .map(name => `\`${name}\``)
+    .join(', ');
   contentLines[1] = `${contentLines[1]} (${packageInfo})`;
   return contentLines.join('\n');
 }
@@ -57,25 +61,28 @@ function updateContentsWithAffectedPackages(changeset) {
  * ```
  *
  */
-function preChangesetsVersion(){
+function preChangesetsVersion() {
   const entries = fs.readdirSync(path.resolve(__dirname, '../.changeset'));
   for (const file of entries) {
-    if (!file.endsWith(".md")) {
+    if (!file.endsWith('.md')) {
       continue;
     }
     const filePath = path.resolve(__dirname, '../.changeset', file);
     const changeset = matter.read(filePath);
     changeset.content = updateContentsWithAffectedPackages(changeset);
     changeset.data = { [mainPackage]: getGreatestBumpType(changeset) };
-    fs.writeFileSync(filePath, matter.stringify(changeset.content, changeset.data));
+    fs.writeFileSync(
+      filePath,
+      matter.stringify(changeset.content, changeset.data)
+    );
   }
 }
 
 function clearChangelogs(pkgDir) {
   for (const pkg of fs.readdirSync(pkgDir)) {
-    if (pkg === "main") continue;
+    if (pkg === 'main') continue;
     try {
-      fs.unlinkSync(path.resolve(pkgDir, pkg, "CHANGELOG.md"));
+      fs.unlinkSync(path.resolve(pkgDir, pkg, 'CHANGELOG.md'));
     } catch {
       // ignore
     }