@jbrowse/react-app2 3.7.0 → 4.0.1

package/esm/types.d.ts

@@ -1,5 +1,5 @@
 import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
-import type { SnapshotIn } from 'mobx-state-tree';
+import type { SnapshotIn } from '@jbrowse/mobx-state-tree';
 interface TextSearchAdapterConfig {
     textSearchAdapterId: string;
     [key: string]: unknown;

package/esm/util.d.ts

@@ -1,5 +1,5 @@
-import type { IAnyStateTreeNode, IAnyType } from 'mobx-state-tree';
+import type { IAnyStateTreeNode, IAnyType } from '@jbrowse/mobx-state-tree';
 export declare function b64PadSuffix(b64: string): string;
 export declare function fromUrlSafeB64(b64: string): Promise<string>;
 export declare function toUrlSafeB64(str: string): Promise<string>;
-export declare function filterSessionInPlace(node: IAnyStateTreeNode | undefined, type: IAnyType): void;
+export declare function filterSessionInPlace(node: IAnyStateTreeNode, type: IAnyType): void;

package/esm/util.js

@@ -1,4 +1,4 @@
-import { getChildType, getPropertyMembers, isArrayType, isMapType, isModelType, isReferenceType, isValidReference, } from 'mobx-state-tree';
+import { getChildType, getPropertyMembers, isArrayType, isMapType, isModelType, isReferenceType, isValidReference, } from '@jbrowse/mobx-state-tree';
 export function b64PadSuffix(b64) {
     let num = 0;
     const mo = b64.length % 4;
@@ -20,16 +20,16 @@ export function b64PadSuffix(b64) {
 export async function fromUrlSafeB64(b64) {
     const originalB64 = b64PadSuffix(b64.replaceAll('-', '+').replaceAll('_', '/'));
     const { toByteArray } = await import('base64-js');
-    const { inflate } = await import('pako');
+    const { inflate } = await import('pako-esm2');
     const bytes = toByteArray(originalB64);
-    const inflated = inflate(bytes);
+    const inflated = inflate(bytes, undefined);
     return new TextDecoder().decode(inflated);
 }
 export async function toUrlSafeB64(str) {
     const bytes = new TextEncoder().encode(str);
-    const { deflate } = await import('pako');
+    const { deflate } = await import('pako-esm2');
     const { fromByteArray } = await import('base64-js');
-    const deflated = deflate(bytes);
+    const deflated = deflate(bytes, undefined);
     const encoded = fromByteArray(deflated);
     const pos = encoded.indexOf('=');
     return pos > 0

package/esm/version.d.ts

@@ -1 +1 @@
-export const version: "3.7.0";
+export declare const version = "4.0.1";

package/esm/version.js

@@ -1 +1 @@
-export const version = '3.7.0';
+export const version = '4.0.1';

package/esm/webpack.d.ts

@@ -1,7 +1,7 @@
 import * as React from 'react';
-export { default as JBrowseApp } from './JBrowseApp';
-export { default as createModel } from './createModel';
-export { default as createViewState } from './createViewState';
-export { default as loadPlugins } from './loadPlugins';
+export { default as JBrowseApp } from './JBrowseApp/index.ts';
+export { default as createModel } from './createModel.ts';
+export { default as createViewState } from './createViewState.ts';
+export { default as loadPlugins } from './loadPlugins.ts';
 export * from 'react-dom/client';
 export { React };

package/esm/webpack.js

@@ -1,7 +1,7 @@
 import * as React from 'react';
-export { default as JBrowseApp } from './JBrowseApp';
-export { default as createModel } from './createModel';
-export { default as createViewState } from './createViewState';
-export { default as loadPlugins } from './loadPlugins';
+export { default as JBrowseApp } from "./JBrowseApp/index.js";
+export { default as createModel } from "./createModel.js";
+export { default as createViewState } from "./createViewState.js";
+export { default as loadPlugins } from "./loadPlugins.js";
 export * from 'react-dom/client';
 export { React };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/react-app2",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 app React component",
   "keywords": [
     "jbrowse",
@@ -15,82 +15,63 @@
     "directory": "products/jbrowse-react-app"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  },
   "files": [
-    "dist",
     "esm",
     "docs"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "prepublishOnly": "node output-version.js > src/version.js && git add -A src && git commit -m '[skip ci] Bump version.js'",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "build:webpack": "webpack",
-    "clean": "rimraf dist esm *.tsbuildinfo",
-    "storybook": "storybook dev --port 6006",
-    "storybook:build": "storybook build",
-    "prebuild": "yarn clean",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
-  },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
-    "@emotion/cache": "^11.7.1",
-    "@emotion/react": "^11.9.0",
-    "@emotion/styled": "^11.8.1",
-    "@jbrowse/app-core": "^3.7.0",
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-alignments": "^3.7.0",
-    "@jbrowse/plugin-arc": "^3.7.0",
-    "@jbrowse/plugin-authentication": "^3.7.0",
-    "@jbrowse/plugin-bed": "^3.7.0",
-    "@jbrowse/plugin-breakpoint-split-view": "^3.7.0",
-    "@jbrowse/plugin-circular-view": "^3.7.0",
-    "@jbrowse/plugin-comparative-adapters": "^3.7.0",
-    "@jbrowse/plugin-config": "^3.7.0",
-    "@jbrowse/plugin-data-management": "^3.7.0",
-    "@jbrowse/plugin-dotplot-view": "^3.7.0",
-    "@jbrowse/plugin-gccontent": "^3.7.0",
-    "@jbrowse/plugin-gff3": "^3.7.0",
-    "@jbrowse/plugin-grid-bookmark": "^3.7.0",
-    "@jbrowse/plugin-gtf": "^3.7.0",
-    "@jbrowse/plugin-hic": "^3.7.0",
-    "@jbrowse/plugin-legacy-jbrowse": "^3.7.0",
-    "@jbrowse/plugin-linear-comparative-view": "^3.7.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
-    "@jbrowse/plugin-lollipop": "^3.7.0",
-    "@jbrowse/plugin-menus": "^3.7.0",
-    "@jbrowse/plugin-rdf": "^3.7.0",
-    "@jbrowse/plugin-sequence": "^3.7.0",
-    "@jbrowse/plugin-spreadsheet-view": "^3.7.0",
-    "@jbrowse/plugin-sv-inspector": "^3.7.0",
-    "@jbrowse/plugin-svg": "^3.7.0",
-    "@jbrowse/plugin-trix": "^3.7.0",
-    "@jbrowse/plugin-variants": "^3.7.0",
-    "@jbrowse/plugin-wiggle": "^3.7.0",
-    "@jbrowse/product-core": "^3.7.0",
-    "@jbrowse/web-core": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "base64-js": "^1.0.0",
-    "copy-to-clipboard": "^3.3.1",
-    "crypto-js": "^4.2.0",
-    "file-saver": "^2.0.0",
-    "mobx": "^6.6.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "pako": "^1.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.4.1",
-    "use-query-params": "^2.0.0"
+    "@emotion/cache": "^11.14.0",
+    "@emotion/react": "^11.14.0",
+    "@emotion/styled": "^11.14.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "dockview-core": "^4.13.1",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "base64-js": "^1.5.1",
+    "@types/file-saver-es": "^2.0.3",
+    "file-saver-es": "^2.0.5",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "pako-esm2": "^2.0.2",
+    "@jbrowse/core": "^4.0.1",
+    "@jbrowse/plugin-alignments": "^4.0.1",
+    "@jbrowse/plugin-arc": "^4.0.1",
+    "@jbrowse/plugin-authentication": "^4.0.1",
+    "@jbrowse/plugin-bed": "^4.0.1",
+    "@jbrowse/plugin-breakpoint-split-view": "^4.0.1",
+    "@jbrowse/app-core": "^4.0.1",
+    "@jbrowse/plugin-canvas": "^4.0.1",
+    "@jbrowse/plugin-circular-view": "^4.0.1",
+    "@jbrowse/plugin-config": "^4.0.1",
+    "@jbrowse/plugin-data-management": "^4.0.1",
+    "@jbrowse/plugin-dotplot-view": "^4.0.1",
+    "@jbrowse/plugin-comparative-adapters": "^4.0.1",
+    "@jbrowse/plugin-gccontent": "^4.0.1",
+    "@jbrowse/plugin-gff3": "^4.0.1",
+    "@jbrowse/plugin-grid-bookmark": "^4.0.1",
+    "@jbrowse/plugin-gtf": "^4.0.1",
+    "@jbrowse/plugin-legacy-jbrowse": "^4.0.1",
+    "@jbrowse/plugin-hic": "^4.0.1",
+    "@jbrowse/plugin-linear-comparative-view": "^4.0.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.1",
+    "@jbrowse/plugin-menus": "^4.0.1",
+    "@jbrowse/plugin-lollipop": "^4.0.1",
+    "@jbrowse/plugin-sequence": "^4.0.1",
+    "@jbrowse/plugin-rdf": "^4.0.1",
+    "@jbrowse/plugin-spreadsheet-view": "^4.0.1",
+    "@jbrowse/plugin-sv-inspector": "^4.0.1",
+    "@jbrowse/plugin-variants": "^4.0.1",
+    "@jbrowse/plugin-trix": "^4.0.1",
+    "@jbrowse/plugin-wiggle": "^4.0.1",
+    "@jbrowse/product-core": "^4.0.1",
+    "@jbrowse/web-core": "^4.0.1"
   },
   "peerDependencies": {
     "react": ">=18.0.0"
@@ -98,5 +79,15 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:webpack": "webpack",
+    "clean": "rimraf esm *.tsbuildinfo",
+    "storybook": "storybook dev --port 6006",
+    "storybook:build": "storybook build",
+    "prebuild": "pnpm clean"
+  },
+  "types": "esm/index.d.ts"
+}

package/dist/JBrowseApp/AppReExport.d.ts

@@ -1 +0,0 @@
-export { App as default } from '@jbrowse/app-core';

package/dist/JBrowseApp/AppReExport.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var app_core_1 = require("@jbrowse/app-core");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return app_core_1.App; } });

package/dist/JBrowseApp/JBrowseApp.d.ts

@@ -1,5 +0,0 @@
-import type { ViewModel } from '../createModel';
-declare const JBrowseApp: ({ viewState }: {
-    viewState: ViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default JBrowseApp;

package/dist/JBrowseApp/JBrowseApp.js

@@ -1,55 +0,0 @@
-"use strict";
-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 jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const App = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AppReExport'))));
-const useStyles = (0, mui_1.makeStyles)()({
-    avoidParentStyle: {
-        all: 'initial',
-    },
-});
-const JBrowseApp = (0, mobx_react_1.observer)(function ({ viewState }) {
-    const { classes } = useStyles();
-    const session = viewState.session;
-    const theme = (0, ui_1.createJBrowseTheme)((0, configuration_1.getConf)(viewState.jbrowse, 'theme'));
-    return ((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: theme, children: (0, jsx_runtime_1.jsx)("div", { className: classes.avoidParentStyle, children: (0, jsx_runtime_1.jsx)(material_1.ScopedCssBaseline, { children: (0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}), children: (0, jsx_runtime_1.jsx)(App, { session: session }) }) }) }) }));
-});
-exports.default = JBrowseApp;

package/dist/JBrowseApp/index.d.ts

@@ -1 +0,0 @@
-export { default } from './JBrowseApp';

package/dist/JBrowseApp/index.js

@@ -1,8 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var JBrowseApp_1 = require("./JBrowseApp");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(JBrowseApp_1).default; } });

package/dist/components/AboutDialog.d.ts

@@ -1 +0,0 @@
-export { AboutDialog as default } from '@jbrowse/product-core';

package/dist/components/AboutDialog.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var product_core_1 = require("@jbrowse/product-core");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return product_core_1.AboutDialog; } });

package/dist/components/PreferencesDialog.d.ts

@@ -1,14 +0,0 @@
-import type { ThemeOptions } from '@mui/material';
-declare const PreferencesDialog: ({ handleClose, session, }: {
-    handleClose: () => void;
-    session: {
-        allThemes: () => Record<string, ThemeOptions & {
-            name?: string;
-        }>;
-        themeName?: string;
-        stickyViewHeaders: boolean;
-        setStickyViewHeaders(sticky: boolean): void;
-        setThemeName: (arg: string) => void;
-    };
-}) => import("react/jsx-runtime").JSX.Element;
-export default PreferencesDialog;

package/dist/components/PreferencesDialog.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
-    container: {
-        width: 800,
-    },
-}));
-const PreferencesDialog = (0, mobx_react_1.observer)(function ({ handleClose, session, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { title: "Preferences", open: true, onClose: handleClose, maxWidth: "xl", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.container, children: [(0, jsx_runtime_1.jsx)(material_1.TextField, { select: true, label: "Theme", value: session.themeName, onChange: event => {
-                            session.setThemeName(event.target.value);
-                        }, children: Object.entries(session.allThemes()).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) }), (0, jsx_runtime_1.jsx)(material_1.FormGroup, { children: (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: session.stickyViewHeaders }), onChange: (_, checked) => {
-                                session.setStickyViewHeaders(checked);
-                            }, label: "Keep view header visible" }) })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: handleClose, children: "Close" }) })] }));
-});
-exports.default = PreferencesDialog;

package/dist/corePlugins.d.ts

@@ -1,3 +0,0 @@
-import Arc from '@jbrowse/plugin-arc';
-declare const corePlugins: (typeof Arc)[];
-export default corePlugins;

package/dist/corePlugins.js

@@ -1,64 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const plugin_alignments_1 = __importDefault(require("@jbrowse/plugin-alignments"));
-const plugin_arc_1 = __importDefault(require("@jbrowse/plugin-arc"));
-const plugin_authentication_1 = __importDefault(require("@jbrowse/plugin-authentication"));
-const plugin_bed_1 = __importDefault(require("@jbrowse/plugin-bed"));
-const plugin_breakpoint_split_view_1 = __importDefault(require("@jbrowse/plugin-breakpoint-split-view"));
-const plugin_circular_view_1 = __importDefault(require("@jbrowse/plugin-circular-view"));
-const plugin_comparative_adapters_1 = __importDefault(require("@jbrowse/plugin-comparative-adapters"));
-const plugin_config_1 = __importDefault(require("@jbrowse/plugin-config"));
-const plugin_data_management_1 = __importDefault(require("@jbrowse/plugin-data-management"));
-const plugin_dotplot_view_1 = __importDefault(require("@jbrowse/plugin-dotplot-view"));
-const plugin_gccontent_1 = __importDefault(require("@jbrowse/plugin-gccontent"));
-const plugin_gff3_1 = __importDefault(require("@jbrowse/plugin-gff3"));
-const plugin_grid_bookmark_1 = __importDefault(require("@jbrowse/plugin-grid-bookmark"));
-const plugin_gtf_1 = __importDefault(require("@jbrowse/plugin-gtf"));
-const plugin_hic_1 = __importDefault(require("@jbrowse/plugin-hic"));
-const plugin_legacy_jbrowse_1 = __importDefault(require("@jbrowse/plugin-legacy-jbrowse"));
-const plugin_linear_comparative_view_1 = __importDefault(require("@jbrowse/plugin-linear-comparative-view"));
-const plugin_linear_genome_view_1 = __importDefault(require("@jbrowse/plugin-linear-genome-view"));
-const plugin_lollipop_1 = __importDefault(require("@jbrowse/plugin-lollipop"));
-const plugin_menus_1 = __importDefault(require("@jbrowse/plugin-menus"));
-const plugin_rdf_1 = __importDefault(require("@jbrowse/plugin-rdf"));
-const plugin_sequence_1 = __importDefault(require("@jbrowse/plugin-sequence"));
-const plugin_spreadsheet_view_1 = __importDefault(require("@jbrowse/plugin-spreadsheet-view"));
-const plugin_sv_inspector_1 = __importDefault(require("@jbrowse/plugin-sv-inspector"));
-const plugin_svg_1 = __importDefault(require("@jbrowse/plugin-svg"));
-const plugin_trix_1 = __importDefault(require("@jbrowse/plugin-trix"));
-const plugin_variants_1 = __importDefault(require("@jbrowse/plugin-variants"));
-const plugin_wiggle_1 = __importDefault(require("@jbrowse/plugin-wiggle"));
-const corePlugins = [
-    plugin_svg_1.default,
-    plugin_linear_genome_view_1.default,
-    plugin_alignments_1.default,
-    plugin_authentication_1.default,
-    plugin_bed_1.default,
-    plugin_circular_view_1.default,
-    plugin_config_1.default,
-    plugin_data_management_1.default,
-    plugin_dotplot_view_1.default,
-    plugin_gtf_1.default,
-    plugin_gff3_1.default,
-    plugin_legacy_jbrowse_1.default,
-    plugin_linear_comparative_view_1.default,
-    plugin_lollipop_1.default,
-    plugin_menus_1.default,
-    plugin_rdf_1.default,
-    plugin_sequence_1.default,
-    plugin_variants_1.default,
-    plugin_wiggle_1.default,
-    plugin_gccontent_1.default,
-    plugin_spreadsheet_view_1.default,
-    plugin_sv_inspector_1.default,
-    plugin_breakpoint_split_view_1.default,
-    plugin_hic_1.default,
-    plugin_trix_1.default,
-    plugin_grid_bookmark_1.default,
-    plugin_comparative_adapters_1.default,
-    plugin_arc_1.default,
-];
-exports.default = corePlugins;