Improved typescript-eslint setup

GMOD · Feb 21, 2024 · 24e2e16 · 24e2e16
1 parent 18f3e43
commit 24e2e16
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Showing 31 changed files with 954 additions and 848 deletions.
diff --git a/.eslintrc.js b/.eslintrc.js
@@ -0,0 +1,82 @@
+/** @type {import("eslint").Linter.Config} */
+module.exports = {
+  parser: '@typescript-eslint/parser',
+  plugins: ['prettier', '@typescript-eslint'],
+  extends: [
+    'plugin:@typescript-eslint/recommended',
+    'plugin:@typescript-eslint/recommended-type-checked',
+    'plugin:@typescript-eslint/stylistic-type-checked',
+    'plugin:prettier/recommended',
+    'plugin:unicorn/recommended',
+  ],
+  parser: '@typescript-eslint/parser',
+  parserOptions: {
+    tsconfigRootDir: __dirname,
+    project: './tsconfig.lint.json',
+  },
+  rules: {
+    '@typescript-eslint/no-unused-vars': [
+      'warn',
+      { argsIgnorePattern: '^_', ignoreRestSiblings: true },
+    ],
+    'no-underscore-dangle': 0,
+    curly: 'error',
+    '@typescript-eslint/no-explicit-any': 0,
+    '@typescript-eslint/explicit-module-boundary-types': 0,
+    '@typescript-eslint/ban-ts-comment': 0,
+    semi: ['error', 'never'],
+    'unicorn/no-new-array': 'off',
+    'unicorn/no-empty-file': 'off',
+    'unicorn/prefer-type-error': 'off',
+    'unicorn/prefer-modern-math-apis': 'off',
+    'unicorn/prefer-node-protocol': 'off',
+    'unicorn/no-unreadable-array-destructuring': 'off',
+    'unicorn/no-abusive-eslint-disable': 'off',
+    'unicorn/no-array-callback-reference': 'off',
+    'unicorn/number-literal-case': 'off',
+    'unicorn/prefer-add-event-listener': 'off',
+    'unicorn/prefer-top-level-await': 'off',
+    'unicorn/consistent-function-scoping': 'off',
+    'unicorn/no-await-expression-member': 'off',
+    'unicorn/no-lonely-if': 'off',
+    'unicorn/consistent-destructuring': 'off',
+    'unicorn/prefer-module': 'off',
+    'unicorn/prefer-optional-catch-binding': 'off',
+    'unicorn/no-useless-undefined': 'off',
+    'unicorn/no-null': 'off',
+    'unicorn/no-nested-ternary': 'off',
+    'unicorn/filename-case': 'off',
+    'unicorn/catch-error-name': 'off',
+    'unicorn/prevent-abbreviations': 'off',
+    'unicorn/prefer-code-point': 'off',
+    'unicorn/numeric-separators-style': 'off',
+    'unicorn/no-array-for-each': 'off',
+    'unicorn/prefer-spread': 'off',
+    'unicorn/explicit-length-check': 'off',
+    'unicorn/prefer-regexp-test': 'off',
+    'unicorn/relative-url-style': 'off',
+    'unicorn/prefer-math-trunc': 'off',
+    'unicorn/prefer-query-selector': 'off',
+    'unicorn/no-negated-condition': 'off',
+    'unicorn/switch-case-braces': 'off',
+    'unicorn/prefer-switch': 'off',
+    'unicorn/better-regex': 'off',
+    'unicorn/no-for-loop': 'off',
+    'unicorn/escape-case': 'off',
+    'unicorn/prefer-number-properties': 'off',
+    'unicorn/no-process-exit': 'off',
+    'unicorn/prefer-at': 'off',
+    'unicorn/prefer-string-replace-all': 'off',
+    'unicorn/no-array-reduce': 'off',
+
+    '@typescript-eslint/no-base-to-string': 'off',
+    '@typescript-eslint/no-unsafe-member-access': 'off',
+    '@typescript-eslint/no-unsafe-argument': 'off',
+    '@typescript-eslint/no-unsafe-assignment': 'off',
+    '@typescript-eslint/no-unsafe-call': 'off',
+    '@typescript-eslint/no-unsafe-return': 'off',
+    '@typescript-eslint/prefer-nullish-coalescing': 'off',
+    '@typescript-eslint/require-await': 'off',
+    '@typescript-eslint/restrict-template-expressions': 'off',
+  },
+}
diff --git a/package.json b/package.json
@@ -57,27 +57,28 @@
     "@babel/plugin-transform-modules-commonjs": "^7.18.2",
     "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.1.0",
-    "@types/jest": "^29.2.4",
+    "@types/jest": "^29.5.12",
     "@types/long": "^4.0.2",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^6.9.1",
-    "@typescript-eslint/parser": "^6.9.1",
+    "@typescript-eslint/eslint-plugin": "^7.0.2",
+    "@typescript-eslint/parser": "^7.0.2",
     "buffer": "^6.0.3",
-    "documentation": "^14.0.1",
+    "documentation": "^14.0.3",
     "eslint": "^8.30.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-import": "^2.25.4",
-    "eslint-plugin-prettier": "^5.0.1",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^51.0.1",
     "glob": "^10.3.1",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
-    "prettier": "^3.0.3",
+    "prettier": "^3.2.5",
     "rimraf": "^5.0.1",
-    "ts-jest": "^29.0.3",
+    "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
     "url": "^0.11.0",
-    "webpack": "^5.89.0",
+    "webpack": "^5.90.3",
     "webpack-cli": "^5.0.1"
   },
   "publishConfig": {

diff --git a/src/craiIndex.ts b/src/craiIndex.ts
@@ -8,7 +8,7 @@ import { Filehandle } from './cramFile/filehandle'
 
 const BAI_MAGIC = 21578050 // BAI\1
 
-export type Slice = {
+export interface Slice {
   start: number
   span: number
   containerStart: number
@@ -19,10 +19,6 @@ export type Slice = {
 type ParsedIndex = Record<string, Slice[]>
 
 function addRecordToIndex(index: ParsedIndex, record: number[]) {
-  if (record.some(el => el === undefined)) {
-    throw new CramMalformedError('invalid .crai index file')
-  }
-
   const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record
 
   if (!index[seqId]) {
@@ -61,7 +57,7 @@ export default class CraiIndex {
     this.filehandle = open(args.url, args.path, args.filehandle)
     this._parseCache = new AbortablePromiseCache<unknown, ParsedIndex>({
       cache: new QuickLRU({ maxSize: 1 }),
-      fill: (data, signal) => this.parseIndex(),
+      fill: (_data, _signal) => this.parseIndex(),
     })
   }
 
@@ -90,8 +86,7 @@ export default class CraiIndex {
         // because some .crai files can be pretty large.
         let currentRecord: number[] = []
         let currentString = ''
-        for (let i = 0; i < uncompressedBuffer.length; i += 1) {
-          const charCode = uncompressedBuffer[i]
+        for (const charCode of uncompressedBuffer) {
           if (
             (charCode >= 48 && charCode <= 57) /* 0-9 */ ||
             (!currentString && charCode === 45) /* leading - */
@@ -175,10 +170,10 @@ export default class CraiIndex {
       } // entry is behind query
       return 0 // entry overlaps query
     }
-    const bins = []
-    for (let i = 0; i < seqEntries.length; i += 1) {
-      if (compare(seqEntries[i]) === 0) {
-        bins.push(seqEntries[i])
+    const bins = [] as Slice[]
+    for (const entry of seqEntries) {
+      if (compare(entry) === 0) {
+        bins.push(entry)
       }
     }
     return bins

diff --git a/src/cramFile/codecs/_base.ts b/src/cramFile/codecs/_base.ts
@@ -2,19 +2,19 @@ import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
 import { DataType } from './dataSeriesTypes'
 
-export type DataTypeMapping = {
+export interface DataTypeMapping {
   byte: number
   int: number
   long: number
   byteArray: Uint8Array
 }
 
-export type Cursor = {
+export interface Cursor {
   bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7
   bytePosition: number
 }
 
-export type Cursors = {
+export interface Cursors {
   lastAlignmentStart: number
   coreBlock: Cursor
   externalBlocks: {

diff --git a/src/cramFile/codecs/external.ts b/src/cramFile/codecs/external.ts
@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError, CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { parseItf8 } from '../util'

diff --git a/src/cramFile/codecs/huffman.ts b/src/cramFile/codecs/huffman.ts
@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { getBits } from './getBits'
@@ -12,15 +13,18 @@ function numberOfSetBits(ii: number) {
   return (((i + (i >> 4)) & 0x0f0f0f0f) * 0x01010101) >> 24
 }
 
-type Code = { bitLength: number; value: number; bitCode: number }
+interface Code {
+  bitLength: number
+  value: number
+  bitCode: number
+}
 
 export default class HuffmanIntCodec extends CramCodec<
   'byte' | 'int',
   HuffmanEncoding['parameters']
 > {
   private codes: Record<number, Code> = {}
   private codeBook: Record<number, number[]> = {}
-  private sortedByValue: Code[] = []
   private sortedCodes: Code[] = []
   private sortedValuesByBitCode: number[] = []
   private sortedBitCodes: number[] = []
@@ -50,7 +54,7 @@ export default class HuffmanIntCodec extends CramCodec<
 
   buildCodeBook() {
     // parse the parameters together into a `codes` data structure
-    let codes: Array<{ symbol: number; bitLength: number }> = new Array(
+    let codes = new Array<{ symbol: number; bitLength: number }>(
       this.parameters.numCodes,
     )
     for (let i = 0; i < this.parameters.numCodes; i += 1) {
@@ -105,11 +109,6 @@ export default class HuffmanIntCodec extends CramCodec<
       (a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode,
     )
 
-    // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
-    this.sortedByValue = Object.values(this.codes).sort(
-      (a, b) => a.value - b.value,
-    )
-
     this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value)
     this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode)
     this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength)

diff --git a/src/cramFile/container/compressionScheme.ts b/src/cramFile/container/compressionScheme.ts
@@ -165,7 +165,7 @@ export default class CramContainerCompressionScheme {
   toJSON() {
     const data: any = {}
     Object.keys(this).forEach(k => {
-      if (/Cache$/.test(k)) {
+      if (k.endsWith('Cache')) {
         return
       }
       data[k] = (this as any)[k]

diff --git a/src/cramFile/encoding.ts b/src/cramFile/encoding.ts
@@ -1,18 +1,18 @@
-export type NullEncoding = {
+export interface NullEncoding {
   codecId: 0
   parametersBytes: number
   parameters: Record<string, never>
 }
 
-export type ExternalCramEncoding = {
+export interface ExternalCramEncoding {
   codecId: 1
   parametersBytes: number
   parameters: {
     blockContentId: number
   }
 }
 
-export type GolombEncoding = {
+export interface GolombEncoding {
   codecId: 2
   parametersBytes: number
   parameters: {
@@ -21,7 +21,7 @@ export type GolombEncoding = {
   }
 }
 
-export type HuffmanEncoding = {
+export interface HuffmanEncoding {
   codecId: 3
   parametersBytes: number
   parameters: {
@@ -32,7 +32,7 @@ export type HuffmanEncoding = {
   }
 }
 
-export type ByteArrayLengthEncoding = {
+export interface ByteArrayLengthEncoding {
   codecId: 4
   parametersBytes: number
   parameters: {
@@ -41,7 +41,7 @@ export type ByteArrayLengthEncoding = {
   }
 }
 
-export type ByteArrayStopCramEncoding = {
+export interface ByteArrayStopCramEncoding {
   codecId: 5
   parametersBytes: number
   parameters: {
@@ -50,7 +50,7 @@ export type ByteArrayStopCramEncoding = {
   }
 }
 
-export type BetaEncoding = {
+export interface BetaEncoding {
   codecId: 6
   parametersBytes: number
   parameters: {
@@ -59,7 +59,7 @@ export type BetaEncoding = {
   }
 }
 
-export type SubexpEncoding = {
+export interface SubexpEncoding {
   codecId: 7
   parametersBytes: number
   parameters: {
@@ -68,7 +68,7 @@ export type SubexpEncoding = {
   }
 }
 
-export type GolombRiceEncoding = {
+export interface GolombRiceEncoding {
   codecId: 8
   parametersBytes: number
   parameters: {
@@ -77,7 +77,7 @@ export type GolombRiceEncoding = {
   }
 }
 
-export type GammaEncoding = {
+export interface GammaEncoding {
   codecId: 9
   parametersBytes: number
   parameters: {

diff --git a/src/cramFile/file.ts b/src/cramFile/file.ts
@@ -51,7 +51,7 @@ function getEndianness() {
 //   | { path: string; url?: undefined; filehandle?: undefined }
 //   | { filehandle: Filehandle; url?: undefined; path?: undefined }
 
-export type CramFileSource = {
+export interface CramFileSource {
   filehandle?: Filehandle
   url?: string
   path?: string

diff --git a/src/cramFile/filehandle.ts b/src/cramFile/filehandle.ts
@@ -1,3 +1 @@
-import { GenericFilehandle } from 'generic-filehandle'
-
-export { GenericFilehandle as Filehandle }
+export { GenericFilehandle as Filehandle } from 'generic-filehandle'
diff --git a/src/cramFile/index.ts b/src/cramFile/index.ts
@@ -1,4 +1,3 @@
-import CramFile from './file'
 export { default as CramRecord } from './record'
 
-export default CramFile
+export { default } from './file'