Update to latest eslint

.github/workflows/pull_request.yml

@@ -22,9 +22,7 @@ jobs:
         run: yarn build
         working-directory: packages/apollo-shared
       - name: Lint codebase
-        run:
-          yarn eslint --report-unused-disable-directives --max-warnings 0 --ext
-          .js,.ts,.jsx,.tsx .
+        run: yarn eslint --max-warnings 0
       - name: Run Jest tests
         run: yarn test
       - name: Get latest JBrowse

.github/workflows/push.yml

@@ -46,7 +46,7 @@ jobs:
         run: yarn build
         working-directory: packages/apollo-shared
       - name: Lint codebase
-        run: yarn eslint --ext .js,.ts,.jsx,.tsx .
+        run: yarn eslint
   docker:
     if: ${{ github.ref == 'refs/heads/main' }}
     uses: ./.github/workflows/docker.yml

.husky/pre-commit.js

@@ -3,7 +3,7 @@
  * JS/TS files ignored since ESLint provides formatting feedback for those
  */
 
-// eslint-disable-next-line @typescript-eslint/no-var-requires, no-undef
+// eslint-disable-next-line @typescript-eslint/no-require-imports
 const spawn = require('cross-spawn')
 
 function main() {

eslint.config.mjs

@@ -0,0 +1,127 @@
+import js from '@eslint/js'
+import pluginCypress from 'eslint-plugin-cypress/flat'
+import pluginImport from 'eslint-plugin-import'
+import pluginJSXA11y from 'eslint-plugin-jsx-a11y'
+import pluginReact from 'eslint-plugin-react'
+import pluginReactHooks from 'eslint-plugin-react-hooks'
+import pluginTSDoc from 'eslint-plugin-tsdoc'
+import pluginUnicorn from 'eslint-plugin-unicorn'
+import globals from 'globals'
+import tseslint from 'typescript-eslint'
+
+/** @type {import('eslint').Linter.Config[]} */
+export default [
+  {
+    ignores: [
+      '.pnp.*',
+      '.yarn/',
+      '**/bin/',
+      '**/build/',
+      '**/coverage/',
+      '**/dist/',
+      'packages/website/.docusaurus/',
+      'packages/jbrowse-plugin-apollo/.jbrowse/',
+    ],
+  },
+  js.configs.recommended,
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+  pluginUnicorn.configs['flat/recommended'],
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+  pluginImport.flatConfigs.typescript,
+  ...tseslint.configs.strictTypeChecked,
+  ...tseslint.configs.stylisticTypeChecked,
+  pluginReact.configs.flat.recommended,
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+  pluginJSXA11y.flatConfigs.recommended,
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+  pluginCypress.configs.recommended,
+  {
+    languageOptions: {
+      globals: { ...globals.browser, ...globals.node },
+      parserOptions: {
+        projectService: {
+          allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.js'],
+        },
+        defaultProject: 'tsconfig.json',
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+        tsconfigRootDir: import.meta.dirname,
+      },
+    },
+    settings: { react: { version: 'detect' } },
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+    plugins: { tsdoc: pluginTSDoc, import: pluginImport },
+    rules: {
+      // eslint built-in rules (override recommended)
+      curly: 'warn',
+      'new-cap': [
+        'error',
+        {
+          newIsCap: true,
+          newIsCapExceptions: [],
+          capIsNew: false,
+          capIsNewExceptions: [
+            'Immutable.Map',
+            'Immutable.Set',
+            'Immutable.List',
+          ],
+        },
+      ],
+      'no-console': ['warn', { allow: ['error', 'warn', 'debug'] }],
+      'no-else-return': ['error', { allowElseIf: false }],
+      'no-extra-semi': 'off',
+      'object-shorthand': 'warn',
+      'prefer-destructuring': 'warn',
+      'prefer-template': 'warn',
+      radix: 'error',
+      // @typescript-eslint/eslint-plugin rules (override recommended)
+      '@typescript-eslint/no-extraneous-class': [
+        'error',
+        { allowWithDecorator: true },
+      ],
+      '@typescript-eslint/no-unused-vars': [
+        'warn',
+        { argsIgnorePattern: '^_', ignoreRestSiblings: true },
+      ],
+      '@typescript-eslint/restrict-template-expressions': [
+        'warn',
+        { allowNumber: true },
+      ],
+      '@typescript-eslint/return-await': 'error',
+      // eslint-plugin-import rules
+      'import/export': 'error',
+      'import/no-duplicates': 'warn',
+      'import/no-extraneous-dependencies': 'error',
+      'import/no-named-as-default': 'warn',
+      // eslint-plugin-tsdoc rules
+      'tsdoc/syntax': 'warn',
+      // eslint-plugin-unicorn rules (override recommended)
+      'unicorn/filename-case': 'off', // Doesn't match our file naming, maybe can be configured later
+      'unicorn/no-empty-file': 'off', // False positives
+      'unicorn/no-null': 'off', // A lot of null in React and other libraries
+      'unicorn/prefer-module': 'off', // Cypress and apollo-collaboration-server need this
+      'unicorn/prevent-abbreviations': 'off', // Doesn't guess a lot of abbreviations correctly
+    },
+  },
+  {
+    name: 'eslint-plugin-react-hooks/recommended',
+    files: [
+      'packages/jbrowse-plugin-apollo/src/**/*.{jsx,tsx}',
+      'packages/website/src/**/*.{jsx,tsx}',
+    ],
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+    plugins: { 'react-hooks': pluginReactHooks },
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
+    rules: { ...pluginReactHooks.configs.recommended.rules },
+  },
+  // Don't enforce tsdoc syntax in JS files
+  {
+    files: ['*.{c,m,}js', '**/*.{c,m,}js'],
+    rules: {
+      'tsdoc/syntax': 'off',
+    },
+  },
+  {
+    files: ['packages/apollo-cli/src/**/*.ts'],
+    rules: { '@typescript-eslint/no-deprecated': 'off' },
+  },
+]

package.json

@@ -6,7 +6,7 @@
     "packages/*"
   ],
   "scripts": {
-    "lint": "cross-env NODE_OPTIONS='--max-old-space-size=4096' yarn eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx .",
+    "lint": "cross-env NODE_OPTIONS='--max-old-space-size=4096' yarn eslint --max-warnings 0",
     "build:shared": "yarn workspace @apollo-annotation/shared run build",
     "release": "tsx scripts/makeGitTag.ts",
     "start:shared": "yarn workspace @apollo-annotation/shared run start",
@@ -17,30 +17,26 @@
     "postinstall": "husky"
   },
   "devDependencies": {
+    "@eslint/js": "^9.14.0",
     "@types/cross-spawn": "^6.0.6",
     "@types/node": "^18.14.2",
     "@types/semver": "^7",
     "@types/yargs": "^17.0.32",
-    "@typescript-eslint/eslint-plugin": "^7.16.0",
-    "@typescript-eslint/parser": "^7.16.0",
+    "@typescript-eslint/parser": "^8.14.0",
     "@yarnpkg/types": "^4.0.0",
     "cross-env": "^7.0.3",
     "cross-spawn": "^7.0.3",
-    "eslint": "^8.57.0",
-    "eslint-import-resolver-typescript": "^3.5.5",
-    "eslint-plugin-cypress": "^2.13.3",
-    "eslint-plugin-import": "^2.27.5",
-    "eslint-plugin-jest": "^27.2.3",
-    "eslint-plugin-jsx-a11y": "^6.7.1",
-    "eslint-plugin-react": "^7.32.2",
-    "eslint-plugin-react-hooks": "^4.6.0",
-    "eslint-plugin-sort-destructure-keys": "^1.5.0",
-    "eslint-plugin-tsdoc": "^0.2.17",
-    "eslint-plugin-unicorn": "^48.0.0",
+    "eslint": "9.14.0",
+    "eslint-import-resolver-typescript": "^3.6.3",
+    "eslint-plugin-cypress": "^4.1.0",
+    "eslint-plugin-import": "^2.31.0",
+    "eslint-plugin-jsx-a11y": "^6.10.2",
+    "eslint-plugin-react": "^7.37.2",
+    "eslint-plugin-react-hooks": "5.1.0-rc-4beb1fd8-20241118",
+    "eslint-plugin-tsdoc": "^0.3.0",
+    "eslint-plugin-unicorn": "^50.0.0",
+    "globals": "^15.12.0",
     "husky": "^9.0.11",
-    "import-sort-parser-typescript": "^6.0.0",
-    "import-sort-style-module": "^6.0.0",
-    "jest": "^29.6.2",
     "lint-staged": "^15.2.2",
     "npm-run-all": "^4.1.5",
     "prettier": "^3.3.2",
@@ -50,6 +46,7 @@
     "tslib": "^2.3.1",
     "tsx": "^4.6.2",
     "typescript": "^5.5.3",
+    "typescript-eslint": "^8.14.0",
     "yargs": "^17.7.2"
   },
   "packageManager": "yarn@4.3.1"

packages/apollo-cli/src/commands/assembly/add-from-fasta.ts

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import * as fs from 'node:fs'
-import * as path from 'node:path'
+import path from 'node:path'
 import { Args, Flags } from '@oclif/core'
 import { ObjectId } from 'bson'
 

packages/apollo-cli/src/commands/assembly/add-from-gff.ts

@@ -1,5 +1,5 @@
 import * as fs from 'node:fs'
-import * as path from 'node:path'
+import path from 'node:path'
 
 import { Args, Flags } from '@oclif/core'
 import { ObjectId } from 'bson'