@jbrowse/core 2.17.0 → 3.0.0

package/ui/ReturnToImportFormDialog.js

@@ -3,21 +3,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
+const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const Dialog_1 = __importDefault(require("./Dialog"));
 const ReturnToImportFormDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
-    return (react_1.default.createElement(Dialog_1.default, { maxWidth: "xl", open: true, onClose: handleClose, title: "Reference sequence" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.Typography, null, "Are you sure you want to return to the import form? This will lose your current view")),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: () => {
-                    model.clearView();
-                    handleClose();
-                }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            react_1.default.createElement(material_1.Button, { onClick: () => {
-                    handleClose();
-                }, color: "secondary", variant: "contained" }, "Cancel"))));
+    return ((0, jsx_runtime_1.jsxs)(Dialog_1.default, { maxWidth: "xl", open: true, onClose: handleClose, title: "Reference sequence", children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Are you sure you want to return to the import form? This will lose your current view" }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                            model.clearView();
+                            handleClose();
+                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                            handleClose();
+                        }, color: "secondary", variant: "contained", children: "Cancel" })] })] }));
 });
 exports.default = ReturnToImportFormDialog;

package/ui/SanitizedHTML.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
 export default function SanitizedHTML({ html: pre, className, }: {
     className?: string;
-    html: string;
-}): React.JSX.Element;
+    html: unknown;
+}): import("react/jsx-runtime").JSX.Element;

package/ui/SanitizedHTML.js

@@ -4,15 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SanitizedHTML;
-const react_1 = __importDefault(require("react"));
-const escape_html_1 = __importDefault(require("escape-html"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const dompurify_1 = __importDefault(require("dompurify"));
+const escape_html_1 = __importDefault(require("escape-html"));
 const util_1 = require("../util");
-// source https://github.com/sindresorhus/html-tags/blob/master/html-tags.json
-// with some random uncommon ones removed. note: we just use this to run the content
-// through dompurify without escaping if we see an htmlTag from this list
-// otherwise we escape angle brackets and things prematurely because it might be
-// something like <TRA> in VCF. Ref #657
 const htmlTags = [
     'a',
     'b',
@@ -47,38 +42,23 @@ const htmlTags = [
     'ul',
 ];
 let added = false;
-// adapted from is-html
-// https://github.com/sindresorhus/is-html/blob/master/index.js
 const full = new RegExp(htmlTags.map(tag => `<${tag}\\b[^>]*>`).join('|'), 'i');
 function isHTML(str) {
     return full.test(str);
 }
-// note this is mocked during testing, see
-// packages/__mocks__/@jbrowse/core/ui/SanitizedHTML something about dompurify
-// behavior causes errors during tests, was seen in
-// products/jbrowse-web/src/tests/Connection.test.tsx test (can delete mock to
-// see)
-//
 function SanitizedHTML({ html: pre, className, }) {
-    // try to add links to the text first
-    const html = (0, util_1.linkify)(pre);
+    const html = (0, util_1.linkify)(`${pre}`);
     const value = isHTML(html) ? html : (0, escape_html_1.default)(html);
     if (!added) {
         added = true;
-        // see https://github.com/cure53/DOMPurify/issues/317
-        // only have to add this once, and can't do it globally because dompurify
-        // not yet initialized at global scope
         dompurify_1.default.addHook('afterSanitizeAttributes', node => {
-            // @ts-expect-error
             if (node.tagName === 'A') {
-                // @ts-expect-error
                 node.setAttribute('rel', 'noopener noreferrer');
-                // @ts-expect-error
                 node.setAttribute('target', '_blank');
             }
         });
     }
-    return (react_1.default.createElement("span", { className: className, dangerouslySetInnerHTML: {
+    return ((0, jsx_runtime_1.jsx)("span", { className: className, dangerouslySetInnerHTML: {
             __html: dompurify_1.default.sanitize(value),
         } }));
 }

package/ui/Snackbar.d.ts

@@ -1,11 +1,10 @@
-import React from 'react';
-import { AbstractSessionModel } from '../util';
-import { SnackbarMessage } from './SnackbarModel';
+import type { AbstractSessionModel } from '../util';
+import type { SnackbarMessage } from './SnackbarModel';
 interface SnackbarSession extends AbstractSessionModel {
     snackbarMessages: SnackbarMessage[];
     popSnackbarMessage: () => void;
 }
 declare const Snackbar: ({ session }: {
     session: SnackbarSession;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default Snackbar;

package/ui/Snackbar.js

@@ -1,29 +1,49 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const mobx_react_1 = require("mobx-react");
-// icons
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const SnackbarContents = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SnackbarContents'))));
 const Snackbar = (0, mobx_react_1.observer)(function ({ session }) {
     const { snackbarMessages } = session;
     const latestMessage = snackbarMessages.at(-1);
-    const handleClose = (_event, reason) => {
-        if (reason !== 'clickaway') {
-            session.popSnackbarMessage();
-        }
-    };
-    return latestMessage ? (react_1.default.createElement(material_1.Snackbar, { open: true, onClose: handleClose, anchorOrigin: { vertical: 'bottom', horizontal: 'center' } },
-        react_1.default.createElement(material_1.Alert, { onClose: handleClose, action: latestMessage.action ? (react_1.default.createElement(react_1.default.Fragment, null,
-                react_1.default.createElement(material_1.Button, { color: "inherit", onClick: e => {
-                        var _a;
-                        (_a = latestMessage.action) === null || _a === void 0 ? void 0 : _a.onClick();
-                        handleClose(e);
-                    } }, latestMessage.action.name),
-                react_1.default.createElement(material_1.IconButton, { color: "inherit", onClick: handleClose },
-                    react_1.default.createElement(Close_1.default, null)))) : null, severity: latestMessage.level || 'warning' }, latestMessage.message))) : null;
+    return latestMessage ? ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(SnackbarContents, { onClose: (_event, reason) => {
+                if (reason !== 'clickaway') {
+                    session.popSnackbarMessage();
+                }
+            }, contents: latestMessage }) })) : null;
 });
 exports.default = Snackbar;

package/ui/SnackbarContents.d.ts

@@ -0,0 +1,5 @@
+import type { SnackbarMessage } from './SnackbarModel';
+export default function SnackbarContents({ onClose, contents, }: {
+    onClose: (_event: unknown, reason?: string) => void;
+    contents: SnackbarMessage;
+}): import("react/jsx-runtime").JSX.Element;

package/ui/SnackbarContents.js

@@ -0,0 +1,16 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SnackbarContents;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const material_1 = require("@mui/material");
+function SnackbarContents({ onClose, contents, }) {
+    return ((0, jsx_runtime_1.jsx)(material_1.Snackbar, { open: true, onClose: onClose, anchorOrigin: { vertical: 'bottom', horizontal: 'center' }, children: (0, jsx_runtime_1.jsx)(material_1.Alert, { onClose: onClose, action: contents.action ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { color: "inherit", onClick: e => {
+                            var _a;
+                            (_a = contents.action) === null || _a === void 0 ? void 0 : _a.onClick();
+                            onClose(e);
+                        }, children: contents.action.name }), (0, jsx_runtime_1.jsx)(material_1.IconButton, { color: "inherit", onClick: onClose, children: (0, jsx_runtime_1.jsx)(Close_1.default, {}) })] })) : null, severity: contents.level || 'warning', children: contents.message }) }));
+}

package/ui/SnackbarModel.d.ts

@@ -1,42 +1,17 @@
-import { NotificationLevel, SnackAction } from '../util/types';
+import type { NotificationLevel, SnackAction } from '../util/types';
 export interface SnackbarMessage {
     message: string;
     level?: NotificationLevel;
     action?: SnackAction;
 }
-/**
- * #stateModel SnackbarModel
- * #category session
- */
 export default function SnackbarModel(): import("mobx-state-tree").IModelType<{}, {
-    /**
-     * #volatile
-     */
     snackbarMessages: import("mobx").IObservableArray<SnackbarMessage>;
 } & {
-    /**
-     * #getter
-     */
     readonly snackbarMessageSet: Map<string, SnackbarMessage>;
 } & {
-    /**
-     * #action
-     */
     notify(message: string, level?: NotificationLevel, action?: SnackAction): void;
-    /**
-     * #action
-     */
     notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
-    /**
-     * #action
-     */
     pushSnackbarMessage(message: string, level?: NotificationLevel, action?: SnackAction): void;
-    /**
-     * #action
-     */
     popSnackbarMessage(): SnackbarMessage | undefined;
-    /**
-     * #action
-     */
     removeSnackbarMessage(message: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/ui/SnackbarModel.js

@@ -15,50 +15,46 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SnackbarModel;
-const react_1 = __importStar(require("react"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
-// icons
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const Report_1 = __importDefault(require("@mui/icons-material/Report"));
-// lazies
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const ErrorMessageStackTraceDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ErrorMessageStackTraceDialog'))));
-/**
- * #stateModel SnackbarModel
- * #category session
- */
 function SnackbarModel() {
     return mobx_state_tree_1.types
         .model({})
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         snackbarMessages: mobx_1.observable.array(),
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get snackbarMessageSet() {
             return new Map(self.snackbarMessages.map(s => [s.message, s]));
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         notify(message, level, action) {
             this.pushSnackbarMessage(message, level, action);
             if (level === 'info' || level === 'success') {
@@ -67,14 +63,10 @@ function SnackbarModel() {
                 }, 5000);
             }
         },
-        /**
-         * #action
-         */
         notifyError(errorMessage, error, extra) {
             this.notify(errorMessage, 'error', {
-                name: react_1.default.createElement(Report_1.default, null),
+                name: (0, jsx_runtime_1.jsx)(Report_1.default, {}),
                 onClick: () => {
-                    // @ts-expect-error
                     self.queueDialog((onClose) => [
                         ErrorMessageStackTraceDialog,
                         {
@@ -86,23 +78,14 @@ function SnackbarModel() {
                 },
             });
         },
-        /**
-         * #action
-         */
         pushSnackbarMessage(message, level, action) {
             if (action || !self.snackbarMessageSet.has(message)) {
                 self.snackbarMessages.push({ message, level, action });
             }
         },
-        /**
-         * #action
-         */
         popSnackbarMessage() {
             return self.snackbarMessages.pop();
         },
-        /**
-         * #action
-         */
         removeSnackbarMessage(message) {
             const element = self.snackbarMessageSet.get(message);
             if (element !== undefined) {

package/ui/colors.d.ts

@@ -7,4 +7,4 @@ declare const ggplot2Colors6: string[];
 declare const ggplot2Colors5: string[];
 declare const ggplot2Colors4: string[];
 declare const ggplot2Colors3: string[];
-export { set1, set2, tableau10, dark2, category10, ggplot2Colors6, ggplot2Colors5, ggplot2Colors4, ggplot2Colors3, };
+export { category10, dark2, ggplot2Colors3, ggplot2Colors4, ggplot2Colors5, ggplot2Colors6, set1, set2, tableau10, };

package/ui/colors.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ggplot2Colors3 = exports.ggplot2Colors4 = exports.ggplot2Colors5 = exports.ggplot2Colors6 = exports.category10 = exports.dark2 = exports.tableau10 = exports.set2 = exports.set1 = void 0;
+exports.tableau10 = exports.set2 = exports.set1 = exports.ggplot2Colors6 = exports.ggplot2Colors5 = exports.ggplot2Colors4 = exports.ggplot2Colors3 = exports.dark2 = exports.category10 = void 0;
 const category10 = [
     '#1f77b4',
     '#ff7f0e',
@@ -26,8 +26,8 @@ const dark2 = [
 ];
 exports.dark2 = dark2;
 const set1 = [
-    '#e41a1c',
     '#377eb8',
+    '#e41a1c',
     '#4daf4a',
     '#984ea3',
     '#ff7f00',

package/ui/index.d.ts

@@ -5,13 +5,11 @@ export { default as CascadingMenu } from './CascadingMenu';
 export { default as Dialog } from './Dialog';
 export { default as EditableTypography } from './EditableTypography';
 export { default as ErrorMessage } from './ErrorMessage';
-export { default as FactoryResetDialog } from './FactoryResetDialog';
 export { default as FatalErrorDialog } from './FatalErrorDialog';
 export { default as FileSelector } from './FileSelector';
 export { default as LoadingEllipses } from './LoadingEllipses';
 export { default as Menu } from './Menu';
 export { default as PrerenderedCanvas } from './PrerenderedCanvas';
-export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog';
 export { default as ResizeHandle } from './ResizeHandle';
 export { default as SanitizedHTML } from './SanitizedHTML';
 export * from './Menu';

package/ui/index.js

@@ -17,7 +17,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SanitizedHTML = exports.ResizeHandle = exports.ReturnToImportFormDialog = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.FactoryResetDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.Logomark = exports.LogoFull = void 0;
+exports.SanitizedHTML = exports.ResizeHandle = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.Logomark = exports.LogoFull = void 0;
 __exportStar(require("./theme"), exports);
 var Logo_1 = require("./Logo");
 Object.defineProperty(exports, "LogoFull", { enumerable: true, get: function () { return Logo_1.LogoFull; } });
@@ -32,8 +32,6 @@ var EditableTypography_1 = require("./EditableTypography");
 Object.defineProperty(exports, "EditableTypography", { enumerable: true, get: function () { return __importDefault(EditableTypography_1).default; } });
 var ErrorMessage_1 = require("./ErrorMessage");
 Object.defineProperty(exports, "ErrorMessage", { enumerable: true, get: function () { return __importDefault(ErrorMessage_1).default; } });
-var FactoryResetDialog_1 = require("./FactoryResetDialog");
-Object.defineProperty(exports, "FactoryResetDialog", { enumerable: true, get: function () { return __importDefault(FactoryResetDialog_1).default; } });
 var FatalErrorDialog_1 = require("./FatalErrorDialog");
 Object.defineProperty(exports, "FatalErrorDialog", { enumerable: true, get: function () { return __importDefault(FatalErrorDialog_1).default; } });
 var FileSelector_1 = require("./FileSelector");
@@ -44,8 +42,6 @@ var Menu_1 = require("./Menu");
 Object.defineProperty(exports, "Menu", { enumerable: true, get: function () { return __importDefault(Menu_1).default; } });
 var PrerenderedCanvas_1 = require("./PrerenderedCanvas");
 Object.defineProperty(exports, "PrerenderedCanvas", { enumerable: true, get: function () { return __importDefault(PrerenderedCanvas_1).default; } });
-var ReturnToImportFormDialog_1 = require("./ReturnToImportFormDialog");
-Object.defineProperty(exports, "ReturnToImportFormDialog", { enumerable: true, get: function () { return __importDefault(ReturnToImportFormDialog_1).default; } });
 var ResizeHandle_1 = require("./ResizeHandle");
 Object.defineProperty(exports, "ResizeHandle", { enumerable: true, get: function () { return __importDefault(ResizeHandle_1).default; } });
 var SanitizedHTML_1 = require("./SanitizedHTML");

package/ui/react-colorful.js

@@ -1,7 +1,4 @@
 "use strict";
-/* eslint-disable */
-// vendored (e.g. copied into our source tree) because the tooling picks up "import" statements that confuse jest, could confuse other consumers of our modules
-// copy of react-colorful/dist/index.esmodule.js
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -18,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.setNonce = exports.RgbaStringColorPicker = exports.RgbaColorPicker = exports.RgbStringColorPicker = exports.RgbColorPicker = exports.HsvaStringColorPicker = exports.HsvaColorPicker = exports.HsvStringColorPicker = exports.HsvColorPicker = exports.HslaStringColorPicker = exports.HslaColorPicker = exports.HslStringColorPicker = exports.HslColorPicker = exports.HexColorPicker = exports.HexColorInput = void 0;
 const react_1 = __importStar(require("react"));

package/ui/theme.d.ts

@@ -1,4 +1,4 @@
-import { ThemeOptions } from '@mui/material/styles';
+import type { ThemeOptions } from '@mui/material/styles';
 declare module '@mui/material/styles/createPalette' {
     interface Palette {
         tertiary: Palette['primary'];

package/ui/theme.js

@@ -59,8 +59,6 @@ function stockTheme() {
         components: {
             MuiLink: {
                 styleOverrides: {
-                    // the default link color uses theme.palette.primary.main which is
-                    // very bad with dark mode+midnight primary
                     root: ({ theme }) => ({
                         color: theme.palette.tertiary.main,
                     }),
@@ -165,18 +163,18 @@ function createJBrowseBaseTheme(theme) {
         },
         spacing: 4,
         components: {
+            MuiTooltip: {
+                styleOverrides: {
+                    tooltip: {
+                        fontSize: 12,
+                    },
+                },
+            },
             MuiButton: {
                 defaultProps: {
                     size: 'small',
                 },
                 styleOverrides: {
-                    // the default button, especially when not using variant=contained,
-                    // uses theme.palette.primary.main for text which is very bad with
-                    // dark mode+midnight primary
-                    //
-                    // keeps text secondary for darkmode, uses
-                    // a text-like coloring to ensure contrast
-                    // xref https://stackoverflow.com/a/72546130/2129219
                     root: ({ theme }) => theme.palette.mode === 'dark'
                         ? {
                             color: theme.palette.text.primary,
@@ -252,7 +250,6 @@ function createJBrowseBaseTheme(theme) {
                 },
                 styleOverrides: {
                     secondary: {
-                        // @ts-expect-error
                         backgroundColor: (_b = (_a = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _a === void 0 ? void 0 : _a.quaternary) === null || _b === void 0 ? void 0 : _b.main,
                     },
                 },
@@ -285,8 +282,6 @@ function createJBrowseBaseTheme(theme) {
             },
             MuiLink: {
                 styleOverrides: {
-                    // the default link color uses theme.palette.primary.main which is
-                    // very bad with dark mode+midnight primary
                     root: ({ theme }) => ({
                         color: theme.palette.text.secondary,
                     }),
@@ -294,13 +289,6 @@ function createJBrowseBaseTheme(theme) {
             },
             MuiCheckbox: {
                 styleOverrides: {
-                    // the default checkbox-when-checked color uses
-                    // theme.palette.primary.main which is very bad with dark
-                    // mode+midnight primary
-                    //
-                    // keeps the forest-green checkbox by default but for darkmode, uses
-                    // a text-like coloring to ensure contrast xref
-                    // https://stackoverflow.com/a/72546130/2129219
                     root: ({ theme }) => theme.palette.mode === 'dark'
                         ? {
                             color: theme.palette.text.secondary,
@@ -313,13 +301,6 @@ function createJBrowseBaseTheme(theme) {
             },
             MuiRadio: {
                 styleOverrides: {
-                    // the default checkbox-when-checked color uses
-                    // theme.palette.primary.main which is very bad with dark
-                    // mode+midnight primary
-                    //
-                    // keeps the forest-green checkbox by default but for darkmode, uses
-                    // a text-like coloring to ensure contrast
-                    // xref https://stackoverflow.com/a/72546130/2129219
                     root: ({ theme }) => theme.palette.mode === 'dark'
                         ? {
                             color: theme.palette.text.secondary,
@@ -332,14 +313,6 @@ function createJBrowseBaseTheme(theme) {
             },
             MuiFormLabel: {
                 styleOverrides: {
-                    // the default checkbox-when-checked color uses
-                    // theme.palette.primary.main which is very bad with dark
-                    // mode+midnight primary
-                    //
-                    // keeps the forest-green checkbox by default but for darkmode, uses
-                    // a text-like coloring to ensure contrast
-                    // xref https://stackoverflow.com/a/72546130/2129219
-                    //
                     root: ({ theme }) => theme.palette.mode === 'dark'
                         ? {
                             color: theme.palette.text.secondary,
@@ -353,11 +326,9 @@ function createJBrowseBaseTheme(theme) {
             MuiAccordionSummary: {
                 styleOverrides: {
                     root: {
-                        // @ts-expect-error
                         backgroundColor: (_d = (_c = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _c === void 0 ? void 0 : _c.tertiary) === null || _d === void 0 ? void 0 : _d.main,
                     },
                     content: {
-                        // @ts-expect-error
                         color: (_f = (_e = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _e === void 0 ? void 0 : _e.tertiary) === null || _f === void 0 ? void 0 : _f.contrastText,
                     },
                 },
@@ -378,9 +349,6 @@ function createJBrowseTheme(configTheme = {}, themes = exports.defaultThemes, th
         })
         : addMissingColors(themes[themeName])));
 }
-// MUI by default allows strings like '#f00' for primary and secondary and
-// augments them to have light and dark variants but not for anything else, so
-// we augment them here
 function augmentThemeColors(theme = {}) {
     var _a;
     for (const entry of ['tertiary', 'quaternary', 'highlight']) {
@@ -396,7 +364,6 @@ function augmentThemeColors(theme = {}) {
     }
     return theme;
 }
-// adds missing colors to users theme
 function addMissingColors(theme = {}) {
     var _a, _b, _c;
     return augmentThemeColors((0, deepmerge_1.default)(theme, {

package/util/Base1DUtils.d.ts

@@ -1,4 +1,4 @@
-import { ViewSnap } from './index';
+import type { ViewSnap } from './index';
 export interface BpOffset {
     refName?: string;
     index: number;