@jbrowse/core 2.18.0 → 3.0.0

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { Feat } from '../../util';
 import type { SequenceFeatureDetailsModel } from '../model';
 declare const ProteinSequence: ({ cds, sequence, codonTable, model, }: {
@@ -6,5 +5,5 @@ declare const ProteinSequence: ({ cds, sequence, codonTable, model, }: {
     sequence: string;
     codonTable: Record<string, string>;
     model: SequenceFeatureDetailsModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ProteinSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js

@@ -3,7 +3,7 @@ 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 jsx_runtime_1 = require("react/jsx-runtime");
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("../../util");
 const util_2 = require("../util");
@@ -20,6 +20,6 @@ const ProteinSequence = (0, mobx_react_1.observer)(function ({ cds, sequence, co
         charactersPerRow,
         showCoordinates,
     });
-    return (react_1.default.createElement(SequenceDisplay_1.default, { model: model, color: util_2.proteinColor, chunks: segments, start: 0 }));
+    return ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: util_2.proteinColor, chunks: segments, start: 0 }));
 });
 exports.default = ProteinSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { SequenceFeatureDetailsModel } from '../model';
 declare const SequenceDisplay: ({ chunks, start, color, strand, coordStart, model, }: {
     chunks: string[];
@@ -7,5 +6,5 @@ declare const SequenceDisplay: ({ chunks, start, color, strand, coordStart, mode
     strand?: number;
     color?: string;
     model: SequenceFeatureDetailsModel;
-}) => React.JSX.Element[];
+}) => import("react/jsx-runtime").JSX.Element[];
 export default SequenceDisplay;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js

@@ -1,9 +1,7 @@
 "use strict";
-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 jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const mobx_react_1 = require("mobx-react");
 const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, color, strand = 1, coordStart = start, model, }) {
     const { charactersPerRow, showCoordinates } = model;
@@ -21,10 +19,7 @@ const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, co
             : showCoordinates
                 ? ' \n'
                 : '';
-        return (react_1.default.createElement(react_1.default.Fragment, { key: `${chunk}-${idx}` },
-            showCoordinates ? prefix : null,
-            react_1.default.createElement("span", { style: { background: color } }, chunk),
-            postfix));
+        return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [showCoordinates ? prefix : null, (0, jsx_runtime_1.jsx)("span", { style: { background: color }, children: chunk }), postfix] }, `${chunk}-${idx}`));
     });
 });
 exports.default = SequenceDisplay;

package/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts

@@ -0,0 +1,8 @@
+import type { SequenceFeatureDetailsModel } from './model';
+import type { SimpleFeatureSerialized } from '../../util';
+import type { SeqState } from '../util';
+export interface SequencePanelProps {
+    sequence: SeqState;
+    feature: SimpleFeatureSerialized;
+    model: SequenceFeatureDetailsModel;
+}

package/BaseFeatureWidget/SequenceFeatureDetails/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/CorePlugin.js

@@ -15,13 +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;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/PluginManager.d.ts

@@ -207,10 +207,11 @@ export default class PluginManager {
         react: typeof import("react");
         'react/jsx-runtime': typeof import("react/jsx-runtime");
         'react-dom': typeof import("react-dom");
+        'react-dom/client': typeof import("react-dom/client");
         'mobx-react': typeof import("mobx-react");
         '@mui/x-data-grid': {
             useGridApiContext: typeof import("@mui/x-data-grid").useGridApiContext;
-            useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/internals").GridApiCommunity>() => React.MutableRefObject<Api>;
+            useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/internals").GridApiCommunity>() => import("@mui/x-internals/types").RefObject<Api>;
             useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps;
         };
         '@mui/material/utils': typeof import("@mui/material/utils");

package/PluginManager.js

@@ -213,9 +213,11 @@ class PluginManager {
                 throw new Error(`cannot add a ${groupName} with no name`);
             }
             if (typeRecord.has(newElement.name)) {
-                throw new Error(`${groupName} ${newElement.name} already registered, cannot register it again`);
+                console.warn(`${groupName} ${newElement.name} already registered, cannot register it again`);
+            }
+            else {
+                typeRecord.add(newElement.name, this.evaluateExtensionPoint('Core-extendPluggableElement', newElement));
             }
-            typeRecord.add(newElement.name, this.evaluateExtensionPoint('Core-extendPluggableElement', newElement));
         });
         return this;
     }

package/ReExports/list.js

@@ -6,6 +6,7 @@ exports.default = [
     'react',
     'react/jsx-runtime',
     'react-dom',
+    'react-dom/client',
     'mobx-react',
     '@mui/x-data-grid',
     '@mui/material/utils',
@@ -57,6 +58,7 @@ exports.default = [
     '@material-ui/core/FormHelperText',
     '@material-ui/core/FormGroup',
     '@material-ui/core/Grid',
+    '@material-ui/core/Grid2',
     '@material-ui/core/Grow',
     '@material-ui/core/Icon',
     '@material-ui/core/IconButton',
@@ -166,6 +168,7 @@ exports.default = [
     '@mui/material/FormHelperText',
     '@mui/material/FormGroup',
     '@mui/material/Grid',
+    '@mui/material/Grid2',
     '@mui/material/Grow',
     '@mui/material/Icon',
     '@mui/material/IconButton',

package/ReExports/modules.d.ts

@@ -1,5 +1,5 @@
 import type { LazyExoticComponent } from 'react';
-import React from 'react';
+import * as React from 'react';
 import { useTheme } from '@mui/material';
 import * as MUIStyles from '@mui/material/styles';
 import * as MUIUtils from '@mui/material/utils';
@@ -9,6 +9,7 @@ import * as mxreact from 'mobx-react';
 import * as mst from 'mobx-state-tree';
 import * as ReactJSXRuntime from 'react/jsx-runtime';
 import * as ReactDom from 'react-dom';
+import * as ReactDomClient from 'react-dom/client';
 import Plugin from '../Plugin';
 import * as Configuration from '../configuration';
 import * as BaseAdapterExports from '../data_adapters/BaseAdapter';
@@ -126,10 +127,11 @@ declare const libs: {
     react: typeof React;
     'react/jsx-runtime': typeof ReactJSXRuntime;
     'react-dom': typeof ReactDom;
+    'react-dom/client': typeof ReactDomClient;
     'mobx-react': typeof mxreact;
     '@mui/x-data-grid': {
         useGridApiContext: typeof useGridApiContext;
-        useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/internals").GridApiCommunity>() => React.MutableRefObject<Api>;
+        useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/internals").GridApiCommunity>() => import("@mui/x-internals/types").RefObject<Api>;
         useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps;
     };
     '@mui/material/utils': typeof MUIUtils;

package/ReExports/modules.js

@@ -15,18 +15,30 @@ 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 });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const React = __importStar(require("react"));
+const react_1 = require("react");
 const material_1 = require("@mui/material");
 const MUIStyles = __importStar(require("@mui/material/styles"));
 const MUIUtils = __importStar(require("@mui/material/utils"));
@@ -36,6 +48,7 @@ const mxreact = __importStar(require("mobx-react"));
 const mst = __importStar(require("mobx-state-tree"));
 const ReactJSXRuntime = __importStar(require("react/jsx-runtime"));
 const ReactDom = __importStar(require("react-dom"));
+const ReactDomClient = __importStar(require("react-dom/client"));
 const mui_1 = require("tss-react/mui");
 const Plugin_1 = __importDefault(require("../Plugin"));
 const Configuration = __importStar(require("../configuration"));
@@ -106,6 +119,7 @@ const Entries = {
     FormHelperText: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/FormHelperText')))),
     FormGroup: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/FormGroup')))),
     Grid: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Grid')))),
+    Grid2: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Grid2')))),
     Grow: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Grow')))),
     Icon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Icon')))),
     IconButton: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/IconButton')))),
@@ -175,8 +189,7 @@ const Entries = {
     Typography: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Typography')))),
 };
 const LazyMUICore = Object.fromEntries(Object.entries(Entries).map(([key, ReactComponent]) => {
-    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-        react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
+    const Component = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(ReactComponent, { ...props, ref: ref }) })));
     Component.displayName = key;
     return [key, Component];
 }));
@@ -343,26 +356,23 @@ const DataGridEntries = {
     }))),
 };
 const LazyDataGridComponents = Object.fromEntries(Object.entries(DataGridEntries).map(([key, ReactComponent]) => {
-    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-        react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
+    const Component = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(ReactComponent, { ...props, ref: ref }) })));
     Component.displayName = key;
     return [key, Component];
 }));
-const LazyAttributes = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-    react_1.default.createElement(Attributes, { ...props, ref: ref }))));
+const LazyAttributes = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(Attributes, { ...props, ref: ref }) })));
 LazyAttributes.displayName = 'Attributes';
-const LazyFeatureDetails = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-    react_1.default.createElement(FeatureDetails, { ...props, ref: ref }))));
+const LazyFeatureDetails = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(FeatureDetails, { ...props, ref: ref }) })));
 LazyFeatureDetails.displayName = 'FeatureDetails';
-const LazyBaseCard = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-    react_1.default.createElement(BaseCard, { ...props, ref: ref }))));
+const LazyBaseCard = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(BaseCard, { ...props, ref: ref }) })));
 LazyBaseCard.displayName = 'BaseCard';
 const libs = {
     mobx,
     'mobx-state-tree': mst,
-    react: react_1.default,
+    react: React,
     'react/jsx-runtime': ReactJSXRuntime,
     'react-dom': ReactDom,
+    'react-dom/client': ReactDomClient,
     'mobx-react': mxreact,
     '@mui/x-data-grid': {
         useGridApiContext: x_data_grid_1.useGridApiContext,

package/TextSearch/BaseResults.d.ts

@@ -30,7 +30,7 @@ export default class BaseResult {
     constructor(args: BaseResultArgs);
     getLabel(): string;
     getDisplayString(): string;
-    getRenderingComponent(): React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    getRenderingComponent(): React.ReactElement<unknown, string | React.JSXElementConstructor<any>> | undefined;
     getTrackId(): string | undefined;
     getScore(): number;
     updateScore(newScore: number): number;

package/assemblyManager/assembly.js

@@ -7,8 +7,8 @@ exports.default = assemblyFactory;
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("../configuration");
-const dataAdapterCache_1 = require("../data_adapters/dataAdapterCache");
-const util_1 = require("../util");
+const util_1 = require("../data_adapters/util");
+const util_2 = require("../util");
 const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
 const refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*');
 const refNameColors = [
@@ -41,7 +41,7 @@ const refNameColors = [
 ];
 async function loadRefNameMap(assembly, adapterConfig, options, stopToken) {
     const { sessionId } = options;
-    await (0, util_1.when)(() => !!(assembly.regions && assembly.refNameAliases), {
+    await (0, util_2.when)(() => !!(assembly.regions && assembly.refNameAliases), {
         name: 'when assembly ready',
     });
     const refNames = (await assembly.rpcManager.call(sessionId || 'assemblyRpc', 'CoreGetRefNames', {
@@ -259,7 +259,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
             if (!options.sessionId) {
                 throw new Error('sessionId is required');
             }
-            return adapterLoads.get((0, dataAdapterCache_1.adapterConfigCacheKey)(adapterConf), {
+            return adapterLoads.get((0, util_1.adapterConfigCacheKey)(adapterConf), {
                 adapterConf,
                 self,
                 options: rest,

package/configuration/configurationSlot.d.ts

@@ -17,7 +17,7 @@ export default function ConfigSlot(slotName: string, { description, model, type,
     readonly isCallback: boolean;
 } & {
     readonly expr: any;
-    readonly valueJSON: string | any[] | Record<string, any> | undefined;
+    readonly valueJSON: any[] | Record<string, any> | string | undefined;
 } & {
     set(newVal: any): void;
     reset(): void;

package/data_adapters/CytobandAdapter/CytobandAdapter.js

@@ -9,10 +9,7 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
         if (conf.uri === '' || conf.uri === '/path/to/cytoband.txt.gz') {
             return [];
         }
-        const pm = this.pluginManager;
-        const buf = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(conf, pm), opts);
-        const decoder = new TextDecoder('utf8', { fatal: true });
-        const text = decoder.decode(buf);
+        const text = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(conf, this.pluginManager), opts);
         return text
             .split(/\n|\r\n|\r/)
             .filter(f => !!f.trim())

package/data_adapters/CytobandAdapter/index.js

@@ -15,13 +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;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -33,6 +43,9 @@ function CytobandAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
         name: 'CytobandAdapter',
         configSchema: configSchema_1.default,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CytobandAdapter'))).then(f => f.default),
     }));
 }

package/data_adapters/dataAdapterCache.d.ts

@@ -3,7 +3,6 @@ import type { AnyConfigurationSchemaType } from '../configuration';
 import type { AnyDataAdapter } from './BaseAdapter';
 import type { SnapshotIn } from 'mobx-state-tree';
 type ConfigSnap = SnapshotIn<AnyConfigurationSchemaType>;
-export declare function adapterConfigCacheKey(conf?: Record<string, unknown>): string;
 interface AdapterCacheEntry {
     dataAdapter: AnyDataAdapter;
     sessionIds: Set<string>;

package/data_adapters/dataAdapterCache.js

@@ -1,19 +1,12 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.adapterConfigCacheKey = adapterConfigCacheKey;
 exports.getAdapter = getAdapter;
 exports.freeAdapterResources = freeAdapterResources;
 exports.clearAdapterCache = clearAdapterCache;
-const idMaker_1 = __importDefault(require("../util/idMaker"));
-function adapterConfigCacheKey(conf = {}) {
-    return `${(0, idMaker_1.default)(conf)}`;
-}
+const util_1 = require("./util");
 let adapterCache = {};
 async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
-    const cacheKey = adapterConfigCacheKey(adapterConfigSnapshot);
+    const cacheKey = (0, util_1.adapterConfigCacheKey)(adapterConfigSnapshot);
     if (!adapterCache[cacheKey]) {
         const adapterType = adapterConfigSnapshot === null || adapterConfigSnapshot === void 0 ? void 0 : adapterConfigSnapshot.type;
         if (!adapterType) {

package/data_adapters/util.d.ts

@@ -0,0 +1 @@
+export declare function adapterConfigCacheKey(conf?: Record<string, unknown>): string;

package/data_adapters/util.js

@@ -0,0 +1,10 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.adapterConfigCacheKey = adapterConfigCacheKey;
+const idMaker_1 = __importDefault(require("../util/idMaker"));
+function adapterConfigCacheKey(conf = {}) {
+    return `${(0, idMaker_1.default)(conf)}`;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -30,11 +30,10 @@
     "build": "tsc -b tsconfig.build.json && cp package.json README.md ../../LICENSE dist/"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@floating-ui/react": "^0.27.0",
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/http-range-fetcher": "^3.0.4",
+    "@gmod/bgzf-filehandle": "^2.0.1",
+    "@gmod/http-range-fetcher": "^4.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
     "canvas-sequencer": "^3.1.0",
@@ -46,16 +45,15 @@
     "dompurify": "^3.2.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle": "^3.0.0",
-    "is-object": "^1.0.1",
+    "generic-filehandle2": "^1.0.0",
     "jexl": "^2.3.0",
     "librpc-web-mod": "^1.1.5",
     "load-script": "^2.0.0",
     "material-ui-popup-state": "^5.0.0",
     "rbush": "^3.0.1",
+    "react-draggable": "^4.4.5",
     "serialize-error": "^8.0.0",
-    "source-map-js": "^1.0.2",
-    "svg-path-generator": "^1.1.0"
+    "source-map-js": "^1.0.2"
   },
   "peerDependencies": {
     "@mui/material": "^6.0.0",
@@ -71,5 +69,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -5,12 +5,13 @@ exports.createBaseTrackModel = createBaseTrackModel;
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("../../configuration");
-const util_1 = require("../../util");
+const util_1 = require("../../data_adapters/util");
+const util_2 = require("../../util");
 const types_1 = require("../../util/types");
 const mst_1 = require("../../util/types/mst");
 function getCompatibleDisplays(self) {
-    const { pluginManager } = (0, util_1.getEnv)(self);
-    const view = (0, util_1.getContainingView)(self);
+    const { pluginManager } = (0, util_2.getEnv)(self);
+    const view = (0, util_2.getContainingView)(self);
     const viewType = pluginManager.getViewType(view.type);
     const compatTypes = new Set(viewType.displayTypes.map(d => d.name));
     const displays = self.configuration.displays;
@@ -27,7 +28,10 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
     })
         .views(self => ({
         get rpcSessionId() {
-            return self.configuration.trackId;
+            const adapter = (0, configuration_1.getConf)(self, 'adapter');
+            return adapter
+                ? (0, util_1.adapterConfigCacheKey)(adapter)
+                : self.configuration.trackId;
         },
         get name() {
             return (0, configuration_1.getConf)(self, 'name');
@@ -50,7 +54,7 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
             return self.displays.flatMap(d => d.viewMenuActions);
         },
         get canConfigure() {
-            const session = (0, util_1.getSession)(self);
+            const session = (0, util_2.getSession)(self);
             const { sessionTracks, adminMode } = session;
             return ((0, types_1.isSessionModelWithConfigEditing)(session) &&
                 (adminMode ||

package/pluggableElementTypes/renderers/CircularChordRendererType.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import FeatureRenderer from './FeatureRendererType';
 import { SimpleFeature } from '../../util';
 import type { SimpleFeatureSerialized } from '../../util';
@@ -21,7 +20,7 @@ export default class CircularChordRendererType extends FeatureRenderer {
     } | {
         features: Map<string, SimpleFeature>;
         blockKey: string;
-        reactElement: React.JSX.Element;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         html: string;
     };
 }

package/pluggableElementTypes/renderers/CircularChordRendererType.js

@@ -3,7 +3,7 @@ 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 jsx_runtime_1 = require("react/jsx-runtime");
 const FeatureRendererType_1 = __importDefault(require("./FeatureRendererType"));
 const RpcRenderedSvgGroup_1 = __importDefault(require("./RpcRenderedSvgGroup"));
 const util_1 = require("../../util");
@@ -28,7 +28,7 @@ class CircularChordRendererType extends FeatureRendererType_1.default {
             ...res,
             features: deserializedFeatures,
             blockKey: 'circularChord',
-            reactElement: (react_1.default.createElement(RpcRenderedSvgGroup_1.default, { ...args, ...res, features: deserializedFeatures, RenderingComponent: this.ReactComponent })),
+            reactElement: ((0, jsx_runtime_1.jsx)(RpcRenderedSvgGroup_1.default, { ...args, ...res, features: deserializedFeatures, RenderingComponent: this.ReactComponent })),
         };
     }
 }

package/pluggableElementTypes/renderers/RendererType.d.ts

@@ -1,11 +1,11 @@
-import type { ReactElement } from 'react';
+import type React from 'react';
 import PluggableElementBase from '../PluggableElementBase';
 import type PluginManager from '../../PluginManager';
 import type { AnyConfigurationSchemaType } from '../../configuration';
 import type { AnyReactComponentType } from '../../util';
 export type RenderProps = Record<string, unknown>;
 export interface RenderResults {
-    reactElement?: ReactElement;
+    reactElement?: React.ReactElement;
     html?: string;
 }
 export default class RendererType extends PluggableElementBase {

package/pluggableElementTypes/renderers/RendererType.js

@@ -3,7 +3,7 @@ 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 jsx_runtime_1 = require("react/jsx-runtime");
 const PluggableElementBase_1 = __importDefault(require("../PluggableElementBase"));
 class RendererType extends PluggableElementBase_1.default {
     constructor(stuff) {
@@ -15,7 +15,7 @@ class RendererType extends PluggableElementBase_1.default {
     }
     async render(props) {
         return {
-            reactElement: react_1.default.createElement(this.ReactComponent, props, null),
+            reactElement: (0, jsx_runtime_1.jsx)(this.ReactComponent, { ...props }),
         };
     }
     freeResources() {

package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AnyReactComponentType, Feature } from '../../util';
 import type { ThemeOptions } from '@mui/material';
 interface Props {
@@ -8,5 +7,5 @@ interface Props {
     displayModel?: any;
     RenderingComponent: AnyReactComponentType;
 }
-declare const RpcRenderedSvgGroup: (props: Props) => React.JSX.Element;
+declare const RpcRenderedSvgGroup: (props: Props) => import("react/jsx-runtime").JSX.Element;
 export default RpcRenderedSvgGroup;