chore: Replace prettier with biome (#196)

biome.json

@@ -0,0 +1,34 @@
+{
+  "$schema": "https://biomejs.dev/schemas/1.7.3/schema.json",
+  "organizeImports": {
+    "enabled": true
+  },
+  "formatter": {
+    "enabled": true,
+    "indentStyle": "space",
+    "indentWidth": 2,
+    "lineEnding": "lf",
+    "lineWidth": 120
+  },
+  "linter": {
+    "enabled": false,
+    "rules": {
+      "recommended": true,
+      "style": {
+        "useConst": "off",
+        "noParameterAssign": "off"
+      },
+      "suspicious": {
+        "noShadowRestrictedNames": "off"
+      }
+    }
+  },
+  "files": {
+    "ignore": ["python"]
+  },
+  "vcs": {
+    "enabled": true,
+    "clientKind": "git",
+    "useIgnoreFile": true
+  }
+}

main.ts

@@ -1,28 +1,28 @@
-import * as vizarr from './src/index';
-import debounce from 'just-debounce-it';
+import debounce from "just-debounce-it";
+import * as vizarr from "./src/index";
 
 function initStandaloneApp(viewer: vizarr.VizarrViewer) {
   const url = new URL(window.location.href);
 
-  if (!url.searchParams.has('source')) {
+  if (!url.searchParams.has("source")) {
     return;
   }
 
   // see if we have initial viewState
-  if (url.searchParams.has('viewState')) {
-    const viewState = JSON.parse(url.searchParams.get('viewState')!);
+  if (url.searchParams.has("viewState")) {
+    const viewState = JSON.parse(url.searchParams.get("viewState")!);
     viewer.setViewState(viewState);
   }
 
   // Add event listener to sync viewState as query param.
   // Debounce to limit how quickly we are pushing to browser history
   viewer.on(
-    'viewStateChange',
+    "viewStateChange",
     debounce((update: vizarr.ViewState) => {
       const url = new URL(window.location.href);
-      url.searchParams.set('viewState', JSON.stringify(update));
-      window.history.pushState({}, '', decodeURIComponent(url.href));
-    }, 200)
+      url.searchParams.set("viewState", JSON.stringify(update));
+      window.history.pushState({}, "", decodeURIComponent(url.href));
+    }, 200),
   );
 
   // parse image config
@@ -39,13 +39,13 @@ function initStandaloneApp(viewer: vizarr.VizarrViewer) {
 
   // Only update history if the new loacation is different from the current
   if (window.location.href !== newLocation) {
-    window.history.pushState(null, '', newLocation);
+    window.history.pushState(null, "", newLocation);
   }
 }
 
 async function main() {
   console.log(`vizarr v${vizarr.version}: https://github.com/hms-dbmi/vizarr`);
-  const viewer = await vizarr.createViewer(document.querySelector('#root')!);
+  const viewer = await vizarr.createViewer(document.querySelector("#root")!);
   initStandaloneApp(viewer);
 }
 

package.json

@@ -4,16 +4,14 @@
   "type": "module",
   "scripts": {
     "dev": "vite",
-    "build": "vite build",
+    "build": "npm run check && vite build",
     "preview": "vite preview",
-    "export": "npm run check && npm run build",
-    "format": "prettier --write \"{src,types}/**/*.{js,jsx,ts,tsx}\" vite.config.js main.ts",
-    "lint": "prettier --check \"{src,types}/**/*.{js,jsx,ts,tsx}\" vite.config.js main.ts",
+    "lint": "biome ci",
+    "fix": "biome check --write",
     "check": "tsc"
   },
   "dependencies": {
     "@hms-dbmi/viv": "^0.16.0",
-    "@hms-dbmi/vizarr": "link:",
     "@material-ui/core": "^4.11.0",
     "@material-ui/icons": "^4.9.1",
     "@material-ui/styles": "^4.11.5",
@@ -29,19 +27,13 @@
     "react-dom": "^18.2.0",
     "zarrita": "^0.4.0-next.14"
   },
-  "prettier": {
-    "trailingComma": "es5",
-    "printWidth": 120,
-    "semi": true,
-    "singleQuote": true
-  },
   "devDependencies": {
+    "@biomejs/biome": "^1.8.3",
     "@danmarshall/deckgl-typings": "^4.3.10",
     "@types/node": "^20.14.11",
     "@types/react": "^18.2.51",
     "@types/react-dom": "^18.2.18",
     "@vitejs/plugin-react": "^4.3.1",
-    "prettier": "^3.3.3",
     "typescript": "^5.5.3",
     "vite": "^5.3.3"
   },

src/ZarrPixelSource.ts

@@ -1,18 +1,18 @@
-import * as zarr from 'zarrita';
+import * as zarr from "zarrita";
 
-import type * as viv from '@vivjs/types';
-import type { Readable } from '@zarrita/storage';
+import type * as viv from "@vivjs/types";
+import type { Readable } from "@zarrita/storage";
 
-import { assert } from './utils';
-import { getImageSize } from '@hms-dbmi/viv';
+import { getImageSize } from "@hms-dbmi/viv";
+import { assert } from "./utils";
 
 // TODO: Export from top-level zarrita
 type Slice = ReturnType<typeof zarr.slice>;
 
-const X_AXIS_NAME = 'x';
-const Y_AXIS_NAME = 'y';
-const RGBA_CHANNEL_AXIS_NAME = '_c';
-const SUPPORTED_DTYPES = ['Uint8', 'Uint16', 'Uint32', 'Float32', 'Int8', 'Int16', 'Int32', 'Float64'] as const;
+const X_AXIS_NAME = "x";
+const Y_AXIS_NAME = "y";
+const RGBA_CHANNEL_AXIS_NAME = "_c";
+const SUPPORTED_DTYPES = ["Uint8", "Uint16", "Uint32", "Float32", "Int8", "Int16", "Int32", "Float64"] as const;
 
 export class ZarrPixelSource<S extends Array<string> = Array<string>> implements viv.PixelSource<S> {
   #arr: zarr.Array<zarr.DataType, Readable>;
@@ -25,7 +25,7 @@ export class ZarrPixelSource<S extends Array<string> = Array<string>> implements
     options: {
       labels: viv.Labels<S>;
       tileSize: number;
-    }
+    },
   ) {
     this.#arr = arr;
     this.labels = options.labels;
@@ -64,10 +64,10 @@ export class ZarrPixelSource<S extends Array<string> = Array<string>> implements
     // a BoundsCheckError which is picked up in `ZarrPixelSource.onTileError`
     // and ignored by deck.gl.
     if (xStart === xStop || yStart === yStop) {
-      throw new BoundsCheckError('Tile slice is zero-sized.');
+      throw new BoundsCheckError("Tile slice is zero-sized.");
     }
     if (xStart < 0 || yStart < 0 || xStop > width || yStop > height) {
-      throw new BoundsCheckError('Tile slice is out of bounds.');
+      throw new BoundsCheckError("Tile slice is out of bounds.");
     }
 
     sel[this.labels.indexOf(X_AXIS_NAME)] = zarr.slice(xStart, xStop);
@@ -126,8 +126,5 @@ function isSupportedDtype(dtype: string): dtype is viv.SupportedDtype {
 }
 
 class BoundsCheckError extends Error {
-  name = 'BoundsCheckError';
-  constructor(message?: string) {
-    super(message);
-  }
+  name = "BoundsCheckError";
 }

src/codecs/jpeg2k.ts

@@ -2,16 +2,16 @@
 // `deno bundle` since the pdf.js dist does not include ESM source code (only UMD or CJS).
 
 // @ts-ignore
-import { JpxImage } from 'https://cdn.jsdelivr.net/gh/mozilla/pdf.js@30bd5f0/src/core/jpx.js';
+import { JpxImage } from "https://cdn.jsdelivr.net/gh/mozilla/pdf.js@30bd5f0/src/core/jpx.js";
 
 export default class Jpeg2k {
-  kind = 'bytes_to_bytes' as const;
-  static codecId = 'jpeg2k';
+  kind = "bytes_to_bytes" as const;
+  static codecId = "jpeg2k";
   static fromConfig(): Jpeg2k {
     return new Jpeg2k();
   }
   encode(_: Uint8Array): never {
-    throw new Error('encode not implemented');
+    throw new Error("encode not implemented");
   }
   async decode(data: Uint8Array): Promise<Uint8Array> {
     const img = new JpxImage();

src/codecs/register.ts

@@ -1,2 +1,2 @@
-import { registry } from 'zarrita';
-registry.set('jpeg2k', () => import('./jpeg2k').then((m) => m.default));
+import { registry } from "zarrita";
+registry.set("jpeg2k", () => import("./jpeg2k").then((m) => m.default));