Upgrade to ESLint 10

.yarnrc.yml

@@ -36,4 +36,4 @@ packageExtensions:
     peerDependencies:
       mongoose: "*"
 
-yarnPath: .yarn/releases/yarn-4.14.1.cjs
+yarnPath: .yarn/releases/yarn-4.16.0.cjs

eslint.config.mjs

@@ -2,9 +2,9 @@ import pluginCypress from 'eslint-plugin-cypress/flat'
 import tseslint from 'typescript-eslint'
 
 import js from '@eslint/js'
+import pluginReact from '@eslint-react/eslint-plugin'
 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'
@@ -30,16 +30,11 @@ export default [
   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,
-  pluginCypress.configs.recommended,
   {
     languageOptions: {
       globals: { ...globals.browser, ...globals.node },
       parserOptions: { projectService: true },
     },
-    settings: { react: { version: 'detect' } },
     // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
     plugins: { tsdoc: pluginTSDoc, import: pluginImport },
     rules: {
@@ -109,14 +104,38 @@ export default [
     },
   },
   {
-    name: 'eslint-plugin-react-hooks/recommended',
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+    ...pluginReactHooks.configs.flat.recommended,
     files: [
       'packages/jbrowse-plugin-apollo/src/**/*.{jsx,tsx}',
       'packages/website/src/**/*.{jsx,tsx}',
     ],
-    plugins: { 'react-hooks': pluginReactHooks },
-    // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
-    rules: { ...pluginReactHooks.configs.recommended.rules },
+  },
+  {
+    ...pluginReact.configs['disable-conflict-eslint-plugin-react-hooks'],
+    files: [
+      'packages/jbrowse-plugin-apollo/src/**/*.{jsx,tsx}',
+      'packages/website/src/**/*.{jsx,tsx}',
+    ],
+  },
+  {
+    ...pluginReact.configs['recommended-typescript'],
+    files: [
+      'packages/jbrowse-plugin-apollo/src/**/*.{jsx,tsx}',
+      'packages/website/src/**/*.{jsx,tsx}',
+    ],
+  },
+  {
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+    ...pluginJSXA11y.flatConfigs.recommended,
+    files: [
+      'packages/jbrowse-plugin-apollo/src/**/*.{jsx,tsx}',
+      'packages/website/src/**/*.{jsx,tsx}',
+    ],
+  },
+  {
+    ...pluginCypress.configs.recommended,
+    files: ['packages/jbrowse-plugin-apollo/cypress/**/*'],
   },
   // Don't enforce tsdoc syntax in JS files
   {

package.json

@@ -18,7 +18,8 @@
     "postinstall": "husky"
   },
   "devDependencies": {
-    "@eslint/js": "^9.21.0",
+    "@eslint-react/eslint-plugin": "^5.8.17",
+    "@eslint/js": "^10.0.1",
     "@types/cross-spawn": "^6.0.6",
     "@types/node": "^24.10.9",
     "@types/semver": "^7",
@@ -27,14 +28,13 @@
     "@yarnpkg/types": "^4.0.0",
     "cross-env": "^7.0.3",
     "cross-spawn": "^7.0.3",
-    "eslint": "9.21.0",
+    "eslint": "10.4.1",
     "eslint-import-resolver-typescript": "^4.4.4",
     "eslint-plugin-cypress": "^5.2.0",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-jsx-a11y": "^6.10.2",
-    "eslint-plugin-react": "^7.37.4",
     "eslint-plugin-react-hooks": "^7.0.0",
-    "eslint-plugin-tsdoc": "^0.4.0",
+    "eslint-plugin-tsdoc": "^0.5.2",
     "eslint-plugin-unicorn": "^57.0.0",
     "globals": "^15.12.0",
     "husky": "^9.0.11",
@@ -47,8 +47,8 @@
     "tslib": "^2.3.1",
     "tsx": "^4.6.2",
     "typescript": "^5.5.3",
-    "typescript-eslint": "^8.25.0",
+    "typescript-eslint": "^8.61.0",
     "yargs": "^17.7.2"
   },
-  "packageManager": "yarn@4.14.1"
+  "packageManager": "yarn@4.16.0"
 }

packages/apollo-cli/src/baseCommand.ts

@@ -35,9 +35,7 @@ export abstract class BaseCommand<T extends typeof Command> extends Command {
   }
 
   private getConfig(configFile: string | undefined): ApolloConf {
-    if (configFile === undefined) {
-      configFile = path.join(this.config.configDir, 'config.yml')
-    }
+    configFile ??= path.join(this.config.configDir, 'config.yml')
     checkConfigfileExists(configFile)
     const config: ApolloConf = new ApolloConf(configFile)
     return config

packages/apollo-cli/src/commands/assembly/check.ts

@@ -159,8 +159,7 @@ these checks use `apollo feature check`.'
       return
     }
 
-    let inputCheckIds: string[] = []
-    inputCheckIds = await convertCheckNameToId(
+    const inputCheckIds = await convertCheckNameToId(
       access.address,
       access.accessToken,
       flags.check,

packages/apollo-cli/src/commands/assembly/sequence.ts

@@ -98,8 +98,7 @@ export default class ApolloCmd extends BaseCommand<typeof ApolloCmd> {
       ;[assembly] = await idReader([flags.assembly])
     }
 
-    let refseqIds: string[] = []
-    refseqIds = await getRefseqId(
+    const refseqIds = await getRefseqId(
       access.address,
       access.accessToken,
       flags.refseq,

packages/apollo-cli/src/commands/config.ts

@@ -73,10 +73,7 @@ export default class ApolloConfig extends BaseCommand<typeof ApolloConfig> {
     if (args.key === undefined) {
       await this.interactiveSetup(config, flags.profile)
     } else {
-      let profileName = flags.profile
-      if (profileName === undefined) {
-        profileName = process.env.APOLLO_PROFILE ?? 'default'
-      }
+      let profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default'
       if (flags.profile !== undefined) {
         profileName = flags.profile
       }
@@ -99,9 +96,7 @@ export default class ApolloConfig extends BaseCommand<typeof ApolloConfig> {
     config: ApolloConf,
     profileName: string | undefined,
   ) {
-    if (profileName === undefined) {
-      profileName = await this.askProfileName(config.getProfileNames())
-    }
+    profileName ??= await this.askProfileName(config.getProfileNames())
 
     let setMe = true
     while (setMe) {
@@ -114,8 +109,7 @@ export default class ApolloConfig extends BaseCommand<typeof ApolloConfig> {
     const address: string = config.get(
       `${profileName}.${KEYS[KEYS.address]}`,
     ) as string
-    let accessType = ''
-    accessType = await this.selectAccessType(address)
+    const accessType = await this.selectAccessType(address)
 
     config.setAccessType(profileName, accessType)
     if (accessType === 'root') {

packages/apollo-cli/src/commands/feature/copy.ts

@@ -75,8 +75,7 @@ the database or by name and assembly or by identifier.'
     }
     const feature: AnnotationFeatureSnapshot =
       (await res.json()) as AnnotationFeatureSnapshot
-    let refseqIds: string[] = []
-    refseqIds = await getRefseqId(
+    const refseqIds = await getRefseqId(
       access.address,
       access.accessToken,
       flags.refseq,

packages/apollo-cli/src/commands/feature/edit-attribute.ts

@@ -88,9 +88,7 @@ terms to non-existing terms'
     const featureJson = JSON.parse(
       await response.text(),
     ) as AnnotationFeatureSnapshot
-    if (featureJson.attributes === undefined) {
-      featureJson.attributes = {}
-    }
+    featureJson.attributes ??= {}
 
     const oldAttributes: Record<string, string[]> = {}
     for (const [key, val] of Object.entries(featureJson.attributes)) {

packages/apollo-cli/src/commands/file/download.ts

@@ -54,10 +54,7 @@ export default class Download extends BaseCommand<typeof Download> {
       access.accessToken,
       `files/${fileId}`,
     )
-    let { output } = flags
-    if (output === undefined) {
-      output = fileRec['basename' as keyof typeof fileRec] as string
-    }
+    const { output = fileRec['basename' as keyof typeof fileRec] } = flags
     const fileWriteStream = createWriteStream(output)
     await res.body?.pipeTo(
       Writable.toWeb(output === '-' ? process.stdout : fileWriteStream),

packages/apollo-cli/src/commands/login.ts

@@ -73,15 +73,10 @@ need to execute this command again unless the token has expired. To setup a new
   public async run(): Promise<void> {
     const { flags } = await this.parse(Login)
 
-    let configFile = flags['config-file']
-    if (configFile === undefined) {
-      configFile = path.join(this.config.configDir, 'config.yml')
-    }
+    const configFile =
+      flags['config-file'] ?? path.join(this.config.configDir, 'config.yml')
 
-    let profileName = flags.profile
-    if (profileName === undefined) {
-      profileName = process.env.APOLLO_PROFILE ?? 'default'
-    }
+    const profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default'
     basicCheckConfig(configFile, profileName)
     const config: ApolloConf = new ApolloConf(configFile)
     const accessType: string = config.get(`${profileName}.accessType`) as string

packages/apollo-cli/src/commands/logout.ts

@@ -23,15 +23,10 @@ export default class Logout extends BaseCommand<typeof Logout> {
   public async run(): Promise<void> {
     const { flags } = await this.parse(Logout)
 
-    let profileName = flags.profile
-    if (profileName === undefined) {
-      profileName = process.env.APOLLO_PROFILE ?? 'default'
-    }
+    const profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default'
 
-    let configFile = flags['config-file']
-    if (configFile === undefined) {
-      configFile = path.join(this.config.configDir, 'config.yml')
-    }
+    const configFile =
+      flags['config-file'] ?? path.join(this.config.configDir, 'config.yml')
     basicCheckConfig(configFile, profileName)
     const config: ApolloConf = new ApolloConf(configFile)
     config.delete(`${profileName}.${KEYS.accessToken}`)

packages/apollo-cli/src/commands/status.ts

@@ -15,15 +15,10 @@ Note that this command does not check the validity of the access token.'
   public async run(): Promise<void> {
     const { flags } = await this.parse(Status)
 
-    let profileName = flags.profile
-    if (profileName === undefined) {
-      profileName = process.env.APOLLO_PROFILE ?? 'default'
-    }
+    const profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default'
 
-    let configFile = flags['config-file']
-    if (configFile === undefined) {
-      configFile = path.join(this.config.configDir, 'config.yml')
-    }
+    const configFile =
+      flags['config-file'] ?? path.join(this.config.configDir, 'config.yml')
     basicCheckConfig(configFile, profileName)
 
     const config: ApolloConf = new ApolloConf(configFile)