Update Biome to v2 (#9244)

This PR updates `biome` to version 2.x. I followed the [upgrade
guide](https://biomejs.dev/guides/upgrade-to-biome-v2/) and then
manually solved all new errors caused by new default rules. The
`biome.json` config file was auto-updated by the `biome migrate` command
as instructed by the migration guide.

Notes:
- Each fix to a rule is one self-contained commit, which might be useful
for code review.
- I disabled the linting rule
[`no-static-element-interactions`](https://biomejs.dev/linter/rules/no-static-element-interactions/
). Otherwise, every `<div onClick=...>` or `<a onClick=...>` is flagged.
Suppresses 64 errors.
- Configured linting rule
`[useExhaustiveDependencies](https://biomejs.dev/linter/rules/use-exhaustive-dependencies/)`
as warning. Otherwise, a lot of `useEffect` would be marked as errors.

### Steps to test:
- CI linting, testing should be enough

### TODOs:
- Consider removing the following rules in a follow up PR
-
[`lint/complexity/noUselessFragments`](https://biomejs.dev/linter/rules/no-useless-fragments/#_top)

### Issues:
- Contributes to #9243

------
(Please delete unneeded items, merge only when none are left open)
- [ ] Added changelog entry (create a `$PR_NUMBER.md` file in
`unreleased_changes` or use `./tools/create-changelog-entry.py`)
- [ ] Added migration guide entry if applicable (edit the same file as
for the changelog)
- [ ] Updated [documentation](../blob/master/docs) if applicable
- [ ] Adapted [wk-libs python
client](https://github.com/scalableminds/webknossos-libs/tree/master/webknossos/webknossos/client)
if relevant API parts change
- [ ] Removed dev-only changes like prints and application.conf edits
- [ ] Considered [common edge
cases](../blob/master/.github/common_edge_cases.md)
- [ ] Needs datastore update after deployment

Author: hotzenklotz

biome.json biome.jsoncbiome.json renamed to biome.jsonc

@@ -1,32 +1,49 @@
 {
   "$schema": "./node_modules/@biomejs/biome/configuration_schema.json",
-  "organizeImports": {
-    "enabled": true,
-    "ignore": [
-      "frontend/javascripts/test/*",
-      "frontend/javascripts/viewer/model/helpers/shader_editor.ts",
-      "**/__snapshots__/**"
+  "files": {
+    "includes": [
+      "**",
+      "!**/libs/stl_exporter.ts",
+      "!**/libs/DRACOLoader.ts",
+      "!**/libs/DRACOWorker.worker.js",
+      "!**/libs/BufferGeometryUtils.ts",
+      "!**/libs/parse_stl_buffer.ts",
+      "!**/libs/trackball_controls.ts",
+      "!**/libs/fps_meter.ts",
+      "!**/*.d.ts",
+      "!**/*.json",
+      "!**/*.jsonc",
+      "!**/*.ts.snap",
+      "!**/__snapshots__",
+      "!**/frontend/javascripts/test/snapshots"
     ]
   },
+  "assist": {
+    "actions": {
+      "source": {
+        "organizeImports": "on"
+      }
+    }
+  },
   "linter": {
     "enabled": true,
-    "ignore": [
-      "libs/keyboard.ts",
-      "libs/stl_exporter.ts",
-      "libs/DRACOLoader.ts",
-      "libs/DRACOWorker.worker.js",
-      "libs/BufferGeometryUtils.ts",
-      "libs/fps_meter.ts",
-      "libs/parse_stl_buffer.ts",
-      "libs/trackball_controls.ts",
-      "*.d.ts",
-      "frontend/javascripts/test/snapshots/*",
-      "**/__snapshots__/**"
+    "includes": [
+      "!**/libs/keyboard.ts",
+      "!**/libs/stl_exporter.ts",
+      "!**/libs/DRACOLoader.ts",
+      "!**/libs/DRACOWorker.worker.js",
+      "!**/libs/BufferGeometryUtils.ts",
+      "!**/libs/fps_meter.ts",
+      "!**/libs/parse_stl_buffer.ts",
+      "!**/libs/trackball_controls.ts",
+      "!**/*.d.ts",
+      "!**/*.json",
+      "!**/frontend/javascripts/test/snapshots/**/*",
+      "**"
     ],
     "rules": {
       "recommended": true,
       "style": {
-        "useShorthandArrayType": "off",
         "useBlockStatements": "off",
         "noNegationElse": "off",
         "noImplicitBoolean": "off",
@@ -41,13 +58,26 @@
         "useDefaultParameterLast": "off",
         "useAsConstAssertion": "off",
         "noNonNullAssertion": "off",
-        "noNamespaceImport": "error"
+        "useConsistentArrayType": {
+          "level": "off",
+          "options": {
+            "syntax": "shorthand"
+          }
+        },
+        "noRestrictedImports": {
+          "level": "error",
+          "options": {
+            "paths": {
+              "lodash": "Import <method> from 'lodash/<method>' instead."
+            }
+          }
+        }
       },
       "complexity": {
-        "useSimplifiedLogicExpression": "off",
+        "useSimplifiedLogicExpression": "off", // TODO: consider removing
         "noForEach": "off",
         "noBannedTypes": "error",
-        "noUselessFragments": "off",
+        "noUselessFragments": "off", // TODO: consider removing
         "useLiteralKeys": "off",
         "useArrowFunction": "off",
         "noStaticOnlyClass": "off",
@@ -60,61 +90,48 @@
         "useKeyWithClickEvents": "off",
         "useIframeTitle": "off",
         "noAriaHiddenOnFocusable": "off",
-        "noLabelWithoutControl": "off"
+        "noLabelWithoutControl": "off",
+        "noStaticElementInteractions": "off"
       },
       "performance": {
-        "noDelete": "off"
+        "noDelete": "off",
+        "noNamespaceImport": "error"
       },
       "correctness": {
         "noUnusedVariables": "error",
         "noUnusedImports": "error",
         "noRenderReturnValue": "off",
-        "useHookAtTopLevel": "error"
+        "useHookAtTopLevel": "error",
+        "useExhaustiveDependencies": "warn" // TODO: consider turning this into an error
       },
       "suspicious": {
         "noExplicitAny": "off",
         "noAsyncPromiseExecutor": "off",
         "noShadowRestrictedNames": "off",
         "noImplicitAnyLet": "off",
         "noConfusingVoidType": "off",
-        "noGlobalIsNan": "off",
+        "noGlobalIsNan": "off", // TODO: consider turning this into an error
         "noArrayIndexKey": "off",
         "noConstEnum": "off",
         "noRedeclare": "off",
         "noFallthroughSwitchClause": "off",
         "noAssignInExpressions": "off"
       },
-      "nursery": {
-        "noRestrictedImports": {
-          "level": "error",
-          "options": {
-            "paths": {
-              "lodash": "Import <method> from 'lodash/<method>' instead."
-            }
-          }
-        }
-      }
+      "nursery": {}
     }
   },
   "formatter": {
     "enabled": true,
     "indentStyle": "space",
     "lineWidth": 100,
-    "ignore": [
-      "libs/keyboard.ts",
-      "libs/stl_exporter.ts",
-      "libs/DRACOLoader.ts",
-      "libs/DRACOWorker.worker.js",
-      "libs/BufferGeometryUtils.ts",
-      "libs/parse_stl_buffer.ts",
-      "libs/trackball_controls.ts",
-      "*.d.ts",
-      "**/__snapshots__/**"
+    "includes": [
+     
     ]
   },
+
   "overrides": [
     {
-      "include": [
+      "includes": [
         "**/package.json"
       ],
       "formatter": {

frontend/javascripts/admin/account/account_security_view.tsx

@@ -8,8 +8,10 @@ import { useState } from "react";
 import { useNavigate } from "react-router-dom";
 import { logoutUserAction } from "viewer/model/actions/user_actions";
 import { SettingsTitle } from "./helpers/settings_title";
+
 const FormItem = Form.Item;
 const { Password } = Input;
+
 import { useDispatch } from "react-redux";
 import PasskeysView from "../auth/passkeys_view";
 import { SettingsCard, type SettingsCardProps } from "./helpers/settings_card";

frontend/javascripts/admin/api/jobs.ts

@@ -3,10 +3,10 @@ import { location } from "libs/window";
 import camelCase from "lodash-es/camelCase";
 import mapKeys from "lodash-es/mapKeys";
 import type {
-  APIAnnotationType,
-  APIJob,
   AdditionalCoordinate,
   AiModel,
+  APIAnnotationType,
+  APIJob,
   RenderAnimationOptions,
 } from "types/api_types";
 import type { UnitLong, Vector3, Vector6 } from "viewer/constants";

frontend/javascripts/admin/auth/authentication_modal.tsx

@@ -8,6 +8,7 @@ import type { ComponentType } from "react";
 import React, { useState } from "react";
 import LoginForm from "./login_form";
 import RegistrationFormGeneric from "./registration_form_generic";
+
 type Props = {
   onLoggedIn: (userJustRegistered: boolean) => unknown;
   onCancel: () => void;

frontend/javascripts/admin/auth/change_email_view.tsx

@@ -3,10 +3,9 @@ import { logoutUserEverywhere, updateUser } from "admin/rest_api";
 import { Alert, Button, Form, Input, Space } from "antd";
 import { useWkSelector } from "libs/react_hooks";
 import Toast from "libs/toast";
-import { logoutUserAction } from "viewer/model/actions/user_actions";
-
 import { useDispatch } from "react-redux";
 import { useNavigate } from "react-router-dom";
+import { logoutUserAction } from "viewer/model/actions/user_actions";
 import { handleResendVerificationEmail } from "./verify_email_view";
 
 const FormItem = Form.Item;

frontend/javascripts/admin/auth/passkeys_view.tsx

@@ -1,9 +1,9 @@
 import { DeleteOutlined } from "@ant-design/icons";
 import {
-  type WebAuthnKeyDescriptor,
   doWebAuthnRegistration,
   listWebAuthnKeys,
   removeWebAuthnKey,
+  type WebAuthnKeyDescriptor,
 } from "admin/api/webauthn";
 import { Button, Input, Modal, Table } from "antd";
 import Toast from "libs/toast";

frontend/javascripts/admin/auth/start_reset_password_view.tsx

@@ -4,6 +4,7 @@ import Request from "libs/request";
 import Toast from "libs/toast";
 import messages from "messages";
 import { Link, useNavigate } from "react-router-dom";
+
 const FormItem = Form.Item;
 
 function StartResetPasswordView() {

frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx

@@ -11,9 +11,9 @@ import type { Vector3 } from "viewer/constants";
 import { parseNml } from "viewer/model/helpers/nml_helpers";
 import {
   type FileList,
+  tryToFetchDatasetsByNameOrId,
   type WizardComponentProps,
   type WizardContext,
-  tryToFetchDatasetsByNameOrId,
 } from "./common";
 
 const EXPECTED_VALUE_COUNT_PER_CSV_LINE = 8;
@@ -136,8 +136,12 @@ async function parseBigWarpFile(fileList: FileList): Promise<Partial<WizardConte
     const [_pointName, enabled, x1, y1, z1, x2, y2, z2] = fields;
 
     if (enabled) {
-      const source = [x1, y1, z1].map((el) => Number.parseInt(el.replaceAll('"', ""))) as Vector3;
-      const target = [x2, y2, z2].map((el) => Number.parseInt(el.replaceAll('"', ""))) as Vector3;
+      const source = [x1, y1, z1].map((el) =>
+        Number.parseInt(el.replaceAll('"', ""), 10),
+      ) as Vector3;
+      const target = [x2, y2, z2].map((el) =>
+        Number.parseInt(el.replaceAll('"', ""), 10),
+      ) as Vector3;
       sourcePoints.push(source);
       targetPoints.push(target);
     }
@@ -158,8 +162,12 @@ async function parseNmlFiles(fileList: FileList): Promise<Partial<WizardContext>
     throw new SoftError("Expected exactly two NML files.");
   }
 
-  const nmlString1 = await readFileAsText(fileList[0]?.originFileObj!);
-  const nmlString2 = await readFileAsText(fileList[1]?.originFileObj!);
+  if (fileList[0]?.originFileObj == null || fileList[1]?.originFileObj == null) {
+    throw new SoftError("Expected exactly two NML files.");
+  }
+
+  const nmlString1 = await readFileAsText(fileList[0]?.originFileObj);
+  const nmlString2 = await readFileAsText(fileList[1]?.originFileObj);
 
   if (nmlString1 === "" || nmlString2 === "") {
     throw new SoftError("NML files should not be empty.");

frontend/javascripts/admin/dataset/composition_wizard/03_select_datasets.tsx

@@ -5,7 +5,7 @@ import DatasetSelectionComponent, {
 } from "dashboard/dataset/dataset_selection_component";
 import { useEffectOnlyOnce } from "libs/react_hooks";
 import { useState } from "react";
-import { type WizardComponentProps, tryToFetchDatasetsByNameOrId } from "./common";
+import { tryToFetchDatasetsByNameOrId, type WizardComponentProps } from "./common";
 
 export default function SelectDatasets({ wizardContext, setWizardContext }: WizardComponentProps) {
   const [datasetValues, setDatasetValues] = useState<DatasetSelectionValue[]>([]);

frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx

@@ -22,8 +22,7 @@ import FolderSelection from "dashboard/folders/folder_selection";
 import ErrorHandling from "libs/error_handling";
 import { estimateAffineMatrix4x4 } from "libs/estimate_affine";
 import { formatNumber } from "libs/format_utils";
-import { useEffectOnlyOnce } from "libs/react_hooks";
-import { useWkSelector } from "libs/react_hooks";
+import { useEffectOnlyOnce, useWkSelector } from "libs/react_hooks";
 import Toast from "libs/toast";
 import { isUserAdminOrDatasetManager } from "libs/utils";
 import uniqBy from "lodash-es/uniqBy";