Use @mui/x-charts-vendor for d3 upgrade (#4508)

GMOD · Aug 1, 2024 · 22b48ac · 22b48ac
1 parent 1183382
commit 22b48ac
Show file tree

Hide file tree

Showing 128 changed files with 1,128 additions and 1,020 deletions.
diff --git a/.eslintrc.js b/.eslintrc.js
@@ -45,7 +45,11 @@ module.exports = {
     '@typescript-eslint/no-empty-function': 'off',
     '@typescript-eslint/no-unused-vars': [
       'warn',
-      { argsIgnorePattern: '^_', ignoreRestSiblings: true },
+      {
+        argsIgnorePattern: '^_',
+        ignoreRestSiblings: true,
+        caughtErrors: 'none',
+      },
     ],
     '@typescript-eslint/no-floating-promises': 'error',
     '@typescript-eslint/restrict-template-expressions': 'off',
@@ -55,6 +59,8 @@ module.exports = {
     '@typescript-eslint/unbound-method': 'off',
     '@typescript-eslint/no-unused-expressions': 'off',
     '@typescript-eslint/no-var-requires': 'off',
+    '@typescript-eslint/no-require-imports': 'off',
+
     '@typescript-eslint/no-unsafe-member-access': 'off',
     '@typescript-eslint/no-unsafe-argument': 'off',
     '@typescript-eslint/no-unsafe-assignment': 'off',

diff --git a/.ignore b/.ignore
@@ -10,7 +10,6 @@ test_data/yeast_synteny/
 test_data/hg38_aliases.txt
 test_data/honeybee/config.json
 test_data/honeybee/amel_hav3.1.chrom.sizes
-plugins/wiggle/src/util.ts
 plugins/protein/src/ProteinReferenceSequenceRenderer/aminoAcids.js
 plugins/spreadsheet-view/src/SpreadsheetView/test_data/starfusion_example.fusion_predictions.tsv
 products/jbrowse-aws-lambda-functions/

diff --git a/package.json b/package.json
@@ -85,8 +85,8 @@
     "@types/set-value": "^4.0.1",
     "@types/string-template": "^1.0.2",
     "@types/tmp": "^0.2.1",
-    "@typescript-eslint/eslint-plugin": "^7.0.1",
-    "@typescript-eslint/parser": "^7.0.1",
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
     "babel-loader": "^9.1.0",
     "body-parser": "^1.20.2",
     "browserslist": "^4.18.1",
@@ -101,7 +101,7 @@
     "dependency-graph": "^1.0.0",
     "dotenv": "^16.3.1",
     "dotenv-expand": "^11.0.3",
-    "electron": "31.2.1",
+    "electron": "31.3.1",
     "electron-builder": "^24.9.0",
     "electron-mock-ipc": "^0.3.8",
     "eslint": "^8.0.0",
@@ -111,7 +111,7 @@
     "eslint-plugin-react-hooks": "^4.3.0",
     "eslint-plugin-react-refresh": "^0.4.3",
     "eslint-plugin-tsdoc": "^0.3.0",
-    "eslint-plugin-unicorn": "^54.0.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "express": "^4.18.2",
     "express-basic-auth": "^1.2.1",
     "file-loader": "^6.2.0",
@@ -138,7 +138,7 @@
     "react-dom": "^18.0.0",
     "react-refresh": "^0.14.0",
     "requestidlecallback-polyfill": "^1.0.2",
-    "rimraf": "^5.0.0",
+    "rimraf": "^6.0.1",
     "rxjs": "^7.0.0",
     "semver": "^7.3.4",
     "slugify": "^1.6.5",

diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/BasicValue.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/BasicValue.tsx
@@ -18,7 +18,7 @@ const useStyles = makeStyles()(theme => ({
 
 export default function BasicValue({ value }: { value: unknown }) {
   const { classes } = useStyles()
-  const isLink = `${value}`.match(/^https?:\/\//)
+  const isLink = /^https?:\/\//.exec(`${value}`)
   return (
     <div className={classes.fieldValue}>
       {React.isValidElement(value) ? (

diff --git a/packages/core/PluginManager.ts b/packages/core/PluginManager.ts
@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-function-type */
 import {
   isModelType,
   isType,

diff --git a/packages/core/assemblyManager/assemblyConfigSchema.ts b/packages/core/assemblyManager/assemblyConfigSchema.ts
@@ -52,7 +52,6 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
         {
           preProcessSnapshot: snap => {
             // allow refNameAliases to be unspecified
-            // @ts-expect-error
             if (!snap.adapter) {
               return { adapter: { type: 'RefNameAliasAdapter' } }
             }
@@ -73,7 +72,6 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
         {
           preProcessSnapshot: snap => {
             // allow cytoBand to be unspecified
-            // @ts-expect-error
             if (!snap.adapter) {
               return { adapter: { type: 'CytobandAdapter' } }
             }

diff --git a/packages/core/assemblyManager/assemblyManager.ts b/packages/core/assemblyManager/assemblyManager.ts
@@ -111,6 +111,7 @@ function assemblyManagerFactory(conf: IAnyType, pm: PluginManager) {
             !!assembly?.error,
         )
         if (assembly.error) {
+          // eslint-disable-next-line @typescript-eslint/only-throw-error
           throw assembly.error
         }
         return assembly

diff --git a/packages/core/configuration/configurationSchema.ts b/packages/core/configuration/configurationSchema.ts
@@ -56,7 +56,9 @@ export interface ConfigurationSchemaOptions<
   actions?: (self: unknown) => any
   views?: (self: unknown) => any
   extend?: (self: unknown) => any
-  preProcessSnapshot?: (snapshot: {}) => {}
+  preProcessSnapshot?: (
+    snapshot: Record<string, unknown>,
+  ) => Record<string, unknown>
 }
 
 function preprocessConfigurationSchemaArguments(

diff --git a/packages/core/pluggableElementTypes/RpcMethodType.ts b/packages/core/pluggableElementTypes/RpcMethodType.ts
@@ -27,7 +27,10 @@ export default abstract class RpcMethodType extends PluggableElementBase {
     super({})
   }
 
-  async serializeArguments(args: {}, rpcDriverClassName: string): Promise<{}> {
+  async serializeArguments(
+    args: Record<string, unknown>,
+    rpcDriverClassName: string,
+  ): Promise<Record<string, unknown>> {
     const blobMap = getBlobMap()
     await this.augmentLocationObjects(args, rpcDriverClassName)
     return { ...args, blobMap }

diff --git a/packages/core/pluggableElementTypes/models/BaseDisplayModel.tsx b/packages/core/pluggableElementTypes/models/BaseDisplayModel.tsx
@@ -40,14 +40,14 @@ function stateModelFactory() {
        */
       get RenderingComponent(): React.FC<{
         model: typeof self
-        onHorizontalScroll?: Function
+        onHorizontalScroll?: () => void
         blockState?: Record<string, any>
       }> {
         const { pluginManager } = getEnv(self)
-        const displayType = pluginManager.getDisplayType(self.type)
-        return displayType.ReactComponent as React.FC<{
+        return pluginManager.getDisplayType(self.type)
+          .ReactComponent as React.FC<{
           model: typeof self
-          onHorizontalScroll?: Function
+          onHorizontalScroll?: () => void
           blockState?: Record<string, any>
         }>
       },

diff --git a/packages/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType.ts b/packages/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType.ts
@@ -16,18 +16,18 @@ import { dedupe, getSerializedSvg } from '../../util'
 import { firstValueFrom } from 'rxjs'
 
 export interface RenderArgs extends ServerSideRenderArgs {
-  displayModel: {}
+  displayModel: Record<string, unknown>
   blockKey: string
 }
 
 export interface RenderArgsSerialized extends ServerSideRenderArgsSerialized {
-  displayModel: {}
+  displayModel: Record<string, unknown>
   blockKey: string
 }
 
 export interface RenderArgsDeserialized
   extends ServerSideRenderArgsDeserialized {
-  displayModel: {}
+  displayModel: Record<string, unknown>
   blockKey: string
 }
 

diff --git a/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx b/packages/core/pluggableElementTypes/renderers/RpcRenderedSvgGroup.tsx
@@ -45,7 +45,9 @@ const NewHydrate = observer(function RpcRenderedSvgGroup(props: Props) {
         )
     })
     return () => {
-      clearTimeout(renderTimeout)
+      if (renderTimeout !== undefined) {
+        clearTimeout(renderTimeout)
+      }
       const root = rootRef.current
       rootRef.current = undefined
 

diff --git a/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx b/packages/core/pluggableElementTypes/renderers/ServerSideRenderedContent.tsx
@@ -51,7 +51,9 @@ const NewHydrate = observer(function ServerSideRenderedContent({
         )
     })
     return () => {
-      clearTimeout(renderTimeout)
+      if (renderTimeout !== undefined) {
+        clearTimeout(renderTimeout)
+      }
       const root = rootRef.current
       rootRef.current = undefined
 

diff --git a/packages/core/rpc/MainThreadRpcDriver.ts b/packages/core/rpc/MainThreadRpcDriver.ts
@@ -6,7 +6,7 @@ class DummyHandle {
 
   async call(
     _functionName: string,
-    _filteredArgs?: {},
+    _filteredArgs?: Record<string, unknown>,
     _options = {},
   ): Promise<unknown> {
     return undefined
@@ -28,7 +28,12 @@ export default class MainThreadRpcDriver extends BaseRpcDriver {
     this.makeWorker = async (): Promise<DummyHandle> => new DummyHandle()
   }
 
-  async call(pm: PluginManager, sessionId: string, funcName: string, args: {}) {
+  async call(
+    pm: PluginManager,
+    sessionId: string,
+    funcName: string,
+    args: Record<string, unknown>,
+  ) {
     if (!sessionId) {
       throw new TypeError('sessionId is required')
     }

diff --git a/packages/core/rpc/RpcManager.ts b/packages/core/rpc/RpcManager.ts
@@ -15,6 +15,7 @@ interface BackendConfigurations {
     'config'
   >
 }
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
 const DriverClasses = {
   WebWorkerRpcDriver,
   MainThreadRpcDriver,
@@ -86,7 +87,12 @@ export default class RpcManager {
     return this.getDriver(backendName)
   }
 
-  async call(sessionId: string, functionName: string, args: {}, opts = {}) {
+  async call(
+    sessionId: string,
+    functionName: string,
+    args: Record<string, unknown>,
+    opts = {},
+  ) {
     if (!sessionId) {
       throw new Error('sessionId is required')
     }

diff --git a/packages/core/rpc/methods/CoreFreeResources.ts b/packages/core/rpc/methods/CoreFreeResources.ts
@@ -10,7 +10,7 @@ import { freeAdapterResources } from '../../data_adapters/dataAdapterCache'
 export default class CoreFreeResources extends RpcMethodType {
   name = 'CoreFreeResources'
 
-  async execute(specification: {}) {
+  async execute(specification: Record<string, unknown>) {
     let deleteCount = 0
 
     deleteCount += freeAdapterResources(specification)
@@ -25,7 +25,7 @@ export default class CoreFreeResources extends RpcMethodType {
 
     return deleteCount
   }
-  async serializeArguments(args: {}, _rpcDriver: string): Promise<{}> {
+  async serializeArguments(args: Record<string, unknown>, _rpcDriver: string) {
     return args
   }
 }
diff --git a/packages/core/rpc/methods/CoreGetFeatureDensityStats.ts b/packages/core/rpc/methods/CoreGetFeatureDensityStats.ts
@@ -27,7 +27,7 @@ export default class CoreGetFeatureDensityStats extends RpcMethodType {
 
   async execute(
     args: {
-      adapterConfig: {}
+      adapterConfig: Record<string, unknown>
       regions: Region[]
       signal?: RemoteAbortSignal
       headers?: Record<string, string>

diff --git a/packages/core/rpc/methods/CoreGetFeatures.ts b/packages/core/rpc/methods/CoreGetFeatures.ts
@@ -42,7 +42,7 @@ export default class CoreGetFeatures extends RpcMethodType {
     args: {
       sessionId: string
       regions: Region[]
-      adapterConfig: {}
+      adapterConfig: Record<string, unknown>
       signal?: RemoteAbortSignal
       // eslint-disable-next-line @typescript-eslint/no-explicit-any
       opts?: any

diff --git a/packages/core/rpc/methods/CoreGetFileInfo.ts b/packages/core/rpc/methods/CoreGetFileInfo.ts
@@ -11,7 +11,7 @@ export default class CoreGetFileInfo extends RpcMethodType {
     args: {
       sessionId: string
       signal: RemoteAbortSignal
-      adapterConfig: {}
+      adapterConfig: Record<string, unknown>
     },
     rpcDriver: string,
   ) {

diff --git a/packages/core/rpc/methods/CoreGetMetadata.ts b/packages/core/rpc/methods/CoreGetMetadata.ts
@@ -11,7 +11,7 @@ export default class CoreGetMetadata extends RpcMethodType {
     args: {
       sessionId: string
       signal: RemoteAbortSignal
-      adapterConfig: {}
+      adapterConfig: Record<string, unknown>
     },
     rpcDriver: string,
   ) {

diff --git a/packages/core/rpc/methods/CoreGetRefNames.ts b/packages/core/rpc/methods/CoreGetRefNames.ts
@@ -11,7 +11,7 @@ export default class CoreGetRefNames extends RpcMethodType {
     args: {
       sessionId: string
       signal: RemoteAbortSignal
-      adapterConfig: {}
+      adapterConfig: Record<string, unknown>
     },
     rpcDriver: string,
   ) {

diff --git a/packages/core/rpc/methods/util.ts b/packages/core/rpc/methods/util.ts
@@ -6,14 +6,14 @@ import {
 import { Region } from '../../util'
 
 export interface RenderArgs extends ServerSideRenderArgs {
-  adapterConfig: {}
+  adapterConfig: Record<string, unknown>
   rendererType: string
 }
 
 export interface RenderArgsSerialized extends ServerSideRenderArgsSerialized {
   assemblyName: string
   regions: Region[]
-  adapterConfig: {}
+  adapterConfig: Record<string, unknown>
   rendererType: string
 }
 

diff --git a/packages/core/ui/CascadingMenu.tsx b/packages/core/ui/CascadingMenu.tsx
@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-function-type */
 import React, { useContext, useMemo } from 'react'
 import {
   Divider,

diff --git a/packages/core/ui/ErrorMessage.tsx b/packages/core/ui/ErrorMessage.tsx
@@ -23,16 +23,16 @@ function parseError(str: string) {
     // mobx-state-tree
 
     // case 1. element has a path
-    const match = trim.match(
-      /.*at path "(.*)" snapshot `(.*)` is not assignable/m,
+    const match = /.*at path "(.*)" snapshot `(.*)` is not assignable/m.exec(
+      trim,
     )
     if (match) {
       str = `Failed to load element at ${match[1]}...Failed element had snapshot`
       snapshotError = match[2]
     }
 
     // case 2. element has no path
-    const match2 = trim.match(/.*snapshot `(.*)` is not assignable/)
+    const match2 = /.*snapshot `(.*)` is not assignable/.exec(trim)
     if (match2) {
       str = `Failed to load element...Failed element had snapshot`
       snapshotError = match2[1]

diff --git a/packages/core/ui/FactoryResetDialog.tsx b/packages/core/ui/FactoryResetDialog.tsx
@@ -14,7 +14,7 @@ export default function FactoryResetDialog({
 }: {
   onClose: () => void
   open: boolean
-  onFactoryReset: Function
+  onFactoryReset: () => void
 }) {
   function handleDialogClose(action?: string) {
     if (action === 'reset') {