Migrate to Biome v2 (#287)

manzt · web-flow · commit c0dd684dc4da · 2025-07-13T18:36:21.000-04:00
diff --git a/biome.json b/biome.json
@@ -1,7 +1,9 @@
 {
-	"$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
-	"organizeImports": {
-		"enabled": true
+	"$schema": "https://biomejs.dev/schemas/2.1.1/schema.json",
+	"assist": {
+		"actions": {
+			"source": { "organizeImports": "on" }
+		}
 	},
 	"linter": {
 		"enabled": true,
@@ -17,7 +19,13 @@
 		}
 	},
 	"files": {
-		"ignore": ["fixtures", ".changeset", "package.json", "jsr.json"]
+		"includes": [
+			"**",
+			"!**/fixtures",
+			"!**/.changeset",
+			"!**/package.json",
+			"!**/jsr.json"
+		]
 	},
 	"vcs": {
 		"enabled": true,
diff --git a/docs/.vitepress/theme/index.ts b/docs/.vitepress/theme/index.ts
@@ -1,6 +1,6 @@
-import { enhanceAppWithTabs } from "vitepress-plugin-tabs/client";
 // https://vitepress.dev/guide/custom-theme
 import Theme from "vitepress/theme";
+import { enhanceAppWithTabs } from "vitepress-plugin-tabs/client";
 
 import "./style.css";
 
diff --git a/package.json b/package.json
@@ -11,7 +11,7 @@
 		"update-fixtures": "uv run scripts/generate-v2.py && uv run scripts/generate-v3.py"
 	},
 	"devDependencies": {
-		"@biomejs/biome": "1.9.4",
+		"@biomejs/biome": "2.1.1",
 		"@changesets/cli": "^2.28.1",
 		"@petamoriken/float16": "^3.9.1",
 		"@svitejs/changesets-changelog-github-compact": "^1.2.0",
diff --git a/packages/@zarrita-ndarray/__tests__/index.test.ts b/packages/@zarrita-ndarray/__tests__/index.test.ts
@@ -1,8 +1,7 @@
 import * as path from "node:path";
 import * as url from "node:url";
-import { describe, expect, it } from "vitest";
-
 import { FileSystemStore } from "@zarrita/storage";
+import { describe, expect, it } from "vitest";
 import * as zarr from "zarrita";
 
 import { get } from "../src/index.js";
diff --git a/packages/@zarrita-ndarray/__tests__/setter.test.ts b/packages/@zarrita-ndarray/__tests__/setter.test.ts
@@ -2,8 +2,8 @@ import ndarray, { type TypedArray } from "ndarray";
 import { assign } from "ndarray-ops";
 import { describe, expect, it } from "vitest";
 import {
-	type Projection,
 	_zarrita_internal_get_strides as get_strides,
+	type Projection,
 	slice,
 	_zarrita_internal_slice_indices as slice_indices,
 } from "zarrita";
diff --git a/packages/@zarrita-ndarray/__tests__/slice.test.ts b/packages/@zarrita-ndarray/__tests__/slice.test.ts
@@ -1,6 +1,6 @@
 import ndarray from "ndarray";
 import { describe, expect, it } from "vitest";
-import { IndexError, create, slice } from "zarrita";
+import { create, IndexError, slice } from "zarrita";
 
 import { get, set } from "../src/index.js";
 
diff --git a/packages/@zarrita-storage/__tests__/fs.test.ts b/packages/@zarrita-storage/__tests__/fs.test.ts
@@ -1,8 +1,7 @@
-import { afterAll, beforeAll, describe, expect, it } from "vitest";
-
 import * as fs from "node:fs/promises";
 import * as path from "node:path";
 import * as url from "node:url";
+import { afterAll, beforeAll, describe, expect, it } from "vitest";
 
 import FileSystemStore from "../src/fs.js";
 
diff --git a/packages/@zarrita-storage/src/index.ts b/packages/@zarrita-storage/src/index.ts
@@ -1,5 +1,5 @@
 export { default as FetchStore } from "./fetch.js";
 export { default as FileSystemStore } from "./fs.js";
 export { default as ReferenceStore } from "./ref.js";
-export { default as ZipFileStore } from "./zip.js";
 export type * from "./types.js";
+export { default as ZipFileStore } from "./zip.js";
diff --git a/packages/@zarrita-storage/src/zip.ts b/packages/@zarrita-storage/src/zip.ts
@@ -1,8 +1,7 @@
-import { unzip } from "unzipit";
-import { assert, fetch_range, strip_prefix } from "./util.js";
-
 import type { Reader, ZipInfo } from "unzipit";
+import { unzip } from "unzipit";
 import type { AbsolutePath, AsyncReadable } from "./types.js";
+import { assert, fetch_range, strip_prefix } from "./util.js";
 
 export class BlobReader implements Reader {
 	constructor(public blob: Blob) {}
diff --git a/packages/zarrita/__tests__/consolidated.test.ts b/packages/zarrita/__tests__/consolidated.test.ts
@@ -1,8 +1,7 @@
 import * as path from "node:path";
 import * as url from "node:url";
-import { assert, describe, expect, it } from "vitest";
-
 import { FileSystemStore } from "@zarrita/storage";
+import { assert, describe, expect, it } from "vitest";
 import { tryWithConsolidated, withConsolidated } from "../src/consolidated.js";
 import { NodeNotFoundError } from "../src/errors.js";
 import { Array as ZarrArray } from "../src/hierarchy.js";
diff --git a/packages/zarrita/__tests__/open.test.ts b/packages/zarrita/__tests__/open.test.ts
@@ -589,7 +589,9 @@ describe("v3", () => {
 					kind: "array",
 				});
 				expect(await arr.getChunk([0])).toStrictEqual({
-					data: new Float16Array([-1000.5, 0, 1000.5, 0]),
+					data: new (globalThis.Float16Array ?? Float16Array)([
+						-1000.5, 0, 1000.5, 0,
+					]),
 					shape: [4],
 					stride: [1],
 				});
diff --git a/packages/zarrita/__tests__/util.test.ts b/packages/zarrita/__tests__/util.test.ts
@@ -1,18 +1,17 @@
 import { afterAll, beforeAll, describe, expect, test, vi } from "vitest";
 import type { DataType } from "../src/metadata.js";
+import {
+	BoolArray,
+	ByteStringArray,
+	UnicodeStringArray,
+} from "../src/typedarray.js";
 import {
 	byteswap_inplace,
 	get_ctr,
 	get_strides,
 	is_dtype,
 } from "../src/util.js";
 
-import {
-	BoolArray,
-	ByteStringArray,
-	UnicodeStringArray,
-} from "../src/typedarray.js";
-
 describe("get_ctr", () => {
 	describe("without Float16Array", () => {
 		beforeAll(() => {
diff --git a/packages/zarrita/src/codecs.ts b/packages/zarrita/src/codecs.ts
@@ -1,6 +1,4 @@
 import type { Codec as _Codec } from "numcodecs";
-import type { Chunk, CodecMetadata, DataType } from "./metadata.js";
-
 import { BitroundCodec } from "./codecs/bitround.js";
 import { BytesCodec } from "./codecs/bytes.js";
 import { Crc32cCodec } from "./codecs/crc32c.js";
@@ -9,6 +7,7 @@ import { JsonCodec } from "./codecs/json2.js";
 import { TransposeCodec } from "./codecs/transpose.js";
 import { VLenUTF8 } from "./codecs/vlen-utf8.js";
 import { ZlibCodec } from "./codecs/zlib.js";
+import type { Chunk, CodecMetadata, DataType } from "./metadata.js";
 import { assert } from "./util.js";
 
 type ChunkMetadata<D extends DataType> = {
diff --git a/packages/zarrita/src/codecs/json2.ts b/packages/zarrita/src/codecs/json2.ts
@@ -139,7 +139,7 @@ export class JsonCodec {
 		items.push("|O");
 		items.push(buf.shape);
 
-		let replacer: ReplacerFunction | undefined = undefined;
+		let replacer: ReplacerFunction | undefined;
 		if (replacer_functions.length) {
 			replacer = (key, value) => {
 				let new_value = value;
diff --git a/packages/zarrita/src/codecs/sharding.ts b/packages/zarrita/src/codecs/sharding.ts
@@ -1,10 +1,9 @@
+import type { Readable } from "@zarrita/storage";
+import { create_codec_pipeline } from "../codecs.js";
 import type { Location } from "../hierarchy.js";
 import type { Chunk } from "../metadata.js";
 import { assert, type ShardingCodecMetadata } from "../util.js";
 
-import type { Readable } from "@zarrita/storage";
-import { create_codec_pipeline } from "../codecs.js";
-
 const MAX_BIG_UINT = 18446744073709551615n;
 
 export function create_sharded_chunk_getter<Store extends Readable>(
diff --git a/packages/zarrita/src/create.ts b/packages/zarrita/src/create.ts
@@ -27,12 +27,12 @@ interface CreateArrayOptions<Dtype extends DataType> {
 
 export async function create<
 	Store extends Mutable,
-	Dtype extends DataType = DataType,
+	_Dtype extends DataType = DataType,
 >(location: Location<Store> | Store): Promise<Group<Store>>;
 
 export async function create<
 	Store extends Mutable,
-	Dtype extends DataType = DataType,
+	_Dtype extends DataType = DataType,
 >(
 	location: Location<Store> | Store,
 	options: CreateGroupOptions,
diff --git a/packages/zarrita/src/hierarchy.ts b/packages/zarrita/src/hierarchy.ts
@@ -1,6 +1,6 @@
 import type { AbsolutePath, Readable } from "@zarrita/storage";
-import { create_codec_pipeline } from "./codecs.js";
 import { create_sharded_chunk_getter } from "./codecs/sharding.js";
+import { create_codec_pipeline } from "./codecs.js";
 import type {
 	ArrayMetadata,
 	Attributes,
@@ -11,17 +11,15 @@ import type {
 	Scalar,
 	TypedArrayConstructor,
 } from "./metadata.js";
-import {
-	type DataTypeQuery,
-	type NarrowDataType,
-	is_dtype,
-	is_sharding_codec,
-} from "./util.js";
 import {
 	create_chunk_key_encoder,
+	type DataTypeQuery,
 	ensure_correct_scalar,
 	get_ctr,
 	get_strides,
+	is_dtype,
+	is_sharding_codec,
+	type NarrowDataType,
 } from "./util.js";
 
 export class Location<Store> {
diff --git a/packages/zarrita/src/index.ts b/packages/zarrita/src/index.ts
@@ -1,35 +1,34 @@
+// re-export all the storage interface types
+export type * from "@zarrita/storage";
+// re-export fetch store from storage
+export { default as FetchStore } from "@zarrita/storage/fetch";
+export { registry } from "./codecs.js";
+export type { Listable } from "./consolidated.js";
+export { tryWithConsolidated, withConsolidated } from "./consolidated.js";
+export { create } from "./create.js";
 export { KeyError, NodeNotFoundError } from "./errors.js";
-export {
-	BoolArray,
-	ByteStringArray,
-	UnicodeStringArray,
-} from "./typedarray.js";
 export { Array, Group, Location, root } from "./hierarchy.js";
-export { open } from "./open.js";
-export { create } from "./create.js";
-export { registry } from "./codecs.js";
-export { get, set } from "./indexing/ops.js";
-export { slice } from "./indexing/util.js";
+// internal exports for @zarrita/ndarray
+export { get as _zarrita_internal_get } from "./indexing/get.js";
 export { IndexError } from "./indexing/indexer.js";
-export { withConsolidated, tryWithConsolidated } from "./consolidated.js";
-
-export type { Listable } from "./consolidated.js";
-export type * from "./metadata.js";
+export { get, set } from "./indexing/ops.js";
+export { set as _zarrita_internal_set } from "./indexing/set.js";
 export type {
-	Slice,
+	GetOptions,
 	Indices,
 	Projection,
-	GetOptions,
 	SetOptions,
+	Slice,
 } from "./indexing/types.js";
-
-// internal exports for @zarrita/ndarray
-export { get as _zarrita_internal_get } from "./indexing/get.js";
-export { set as _zarrita_internal_set } from "./indexing/set.js";
+export {
+	slice,
+	slice_indices as _zarrita_internal_slice_indices,
+} from "./indexing/util.js";
+export type * from "./metadata.js";
+export { open } from "./open.js";
+export {
+	BoolArray,
+	ByteStringArray,
+	UnicodeStringArray,
+} from "./typedarray.js";
 export { get_strides as _zarrita_internal_get_strides } from "./util.js";
-export { slice_indices as _zarrita_internal_slice_indices } from "./indexing/util.js";
-
-// re-export fetch store from storage
-export { default as FetchStore } from "@zarrita/storage/fetch";
-// re-export all the storage interface types
-export type * from "@zarrita/storage";
diff --git a/packages/zarrita/src/indexing/index.ts b/packages/zarrita/src/indexing/index.ts
@@ -1,5 +1,5 @@
-export { get, set } from "./ops.js";
 export { get as get_with_setter } from "./get.js";
+export { get, set } from "./ops.js";
 export { set as set_with_setter } from "./set.js";
-export { slice, slice_indices as _slice_indices } from "./util.js";
 export type * from "./types.js";
+export { slice, slice_indices as _slice_indices } from "./util.js";
diff --git a/packages/zarrita/src/util.ts b/packages/zarrita/src/util.ts
@@ -1,9 +1,3 @@
-import {
-	BoolArray,
-	ByteStringArray,
-	UnicodeStringArray,
-} from "./typedarray.js";
-
 import type {
 	ArrayMetadata,
 	ArrayMetadataV2,
@@ -17,6 +11,11 @@ import type {
 	StringDataType,
 	TypedArrayConstructor,
 } from "./metadata.js";
+import {
+	BoolArray,
+	ByteStringArray,
+	UnicodeStringArray,
+} from "./typedarray.js";
 
 export function json_encode_object(o: Record<string, unknown>): Uint8Array {
 	const str = JSON.stringify(o, null, 2);
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
