@jbrowse/core 1.7.11 → 2.0.0

package/TextSearch/TextSearchManager.d.ts

@@ -28,7 +28,9 @@ export default class TextSearchManager {
      * @param args - search options/arguments include: search query
      */
     relevantAdapters(searchScope: SearchScope): any[];
-    getAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+    getAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     getTrackAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): any[];

package/assemblyManager/assembly.js

@@ -212,6 +212,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       },
 
       get rpcManager() {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return (0, _mobxStateTree.getParent)(self, 2).rpcManager;
       },
 

package/assemblyManager/assemblyManager.d.ts

@@ -65,9 +65,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    get(assemblyName: string): (import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
+    get(assemblyName: string): ({
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
@@ -191,7 +191,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     readonly assemblyNamesList: string[];
-    readonly assemblyList: (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+    readonly assemblyList: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType> & {
         name: string;
@@ -200,9 +202,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     readonly pluginManager: any;
     readonly allPossibleRefNames: string[] | undefined;
 } & {
-    waitForAssembly(assemblyName: string): Promise<(import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
+    waitForAssembly(assemblyName: string): Promise<({
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
@@ -339,9 +341,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } | undefined>;
     isValidRefName(refName: string, assemblyName?: string): boolean;
 } & {
-    removeAssembly(asm: import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
+    removeAssembly(asm: {
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {

package/assemblyManager/assemblyManager.js

@@ -61,10 +61,12 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
       },
 
       get rpcManager() {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return (0, _mobxStateTree.getParent)(self).rpcManager;
       },
 
       get pluginManager() {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         return (0, _mobxStateTree.getParent)(self).pluginManager;
       },
 

package/configuration/util.d.ts

@@ -27,6 +27,6 @@ export declare function getConf(model: unknown, slotPath?: string[] | string | u
  */
 export declare function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType: unknown): string[];
 export declare function isBareConfigurationSchemaType(thing: unknown): thing is AnyConfigurationSchemaType;
-export declare function isConfigurationSchemaType(thing: unknown): boolean;
+export declare function isConfigurationSchemaType(thing: unknown): thing is AnyConfigurationSchemaType;
 export declare function isConfigurationModel(thing: unknown): thing is AnyConfigurationModel;
 export declare function isConfigurationSlotType(thing: unknown): boolean;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.7.11",
+  "version": "2.0.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -30,7 +30,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "@material-ui/icons": "^4.0.1",
+    "@mui/icons-material": "^5.0.1",
     "abortable-promise-cache": "^1.5.0",
     "canvas-sequencer": "^3.1.0",
     "canvas2svg": "^1.0.16",
@@ -50,30 +50,29 @@
     "json-stable-stringify": "^1.0.1",
     "librpc-web-mod": "^1.1.5",
     "load-script2": "^2.0.5",
-    "material-ui-popup-state": "^1.9.3",
-    "object.fromentries": "^2.0.0",
+    "material-ui-popup-state": "^3.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
-    "react-intersection-observer": "^8.32.5",
+    "react-intersection-observer": "^9.3.0",
     "react-use-measure": "^2.1.1",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0"
   },
   "peerDependencies": {
-    "@material-ui/core": "^4.12.2",
-    "@material-ui/lab": "^4.0.0-alpha.45",
-    "@mui/x-data-grid": "^4.0.0",
-    "mobx": "^5.0.0",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "^3.14.1",
+    "@mui/material": "^5.0.0",
+    "@mui/x-data-grid": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
-    "react": "^17.0.0",
-    "react-dom": "^17.0.0",
-    "rxjs": "^6.0.0"
+    "react": ">=16.8.0",
+    "react-dom": ">=16.8.0",
+    "rxjs": "^6.0.0",
+    "tss-react": "^3.0.0"
   },
   "publishConfig": {
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }

package/pluggableElementTypes/models/BaseDisplayModel.d.ts

@@ -10,11 +10,11 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
     error: unknown;
 } & {
     readonly RenderingComponent: React.FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -29,11 +29,11 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
         blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: React.FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -21,7 +21,7 @@ export declare function createBaseTrackModel(pluginManager: PluginManager, track
     activateConfigurationUI(): void;
     showDisplay(displayId: string, initialSnapshot?: {}): void;
     hideDisplay(displayId: string): number;
-    replaceDisplay(oldDisplayId: string, newDisplayId: string, initialSnapshot?: {}): void;
+    replaceDisplay(oldId: string, newId: string, initialSnapshot?: {}): void;
 } & {
     trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -112,55 +112,54 @@ function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
       },
       showDisplay: function showDisplay(displayId) {
         var initialSnapshot = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), displayId);
-        var displayType = pluginManager.getDisplayType(configuration.type);
+        var schema = pluginManager.pluggableConfigSchemaType('display');
+        var conf = (0, _mobxStateTree.resolveIdentifier)(schema, (0, _mobxStateTree.getRoot)(self), displayId);
+        var displayType = pluginManager.getDisplayType(conf.type);
 
         if (!displayType) {
-          throw new Error("unknown display type ".concat(configuration.type));
+          throw new Error("unknown display type ".concat(conf.type));
         }
 
         var display = displayType.stateModel.create(_objectSpread(_objectSpread({}, initialSnapshot), {}, {
-          type: configuration.type,
-          configuration: configuration
+          type: conf.type,
+          configuration: conf
         }));
         self.displays.push(display);
       },
       hideDisplay: function hideDisplay(displayId) {
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), displayId); // if we have any displays with that configuration, turn them off
-
-        var shownDisplays = self.displays.filter(function (d) {
-          return d.configuration === configuration;
+        var schema = pluginManager.pluggableConfigSchemaType('display');
+        var conf = (0, _mobxStateTree.resolveIdentifier)(schema, (0, _mobxStateTree.getRoot)(self), displayId);
+        var t = self.displays.filter(function (d) {
+          return d.conf === conf;
         });
         (0, _mobx.transaction)(function () {
-          return shownDisplays.forEach(function (d) {
+          return t.forEach(function (d) {
             return self.displays.remove(d);
           });
         });
-        return shownDisplays.length;
+        return t.length;
       },
-      replaceDisplay: function replaceDisplay(oldDisplayId, newDisplayId) {
+      replaceDisplay: function replaceDisplay(oldId, newId) {
         var initialSnapshot = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
-        var displayIdx = self.displays.findIndex(function (d) {
-          return d.configuration.displayId === oldDisplayId;
+        var idx = self.displays.findIndex(function (d) {
+          return d.conf.displayId === oldId;
         });
 
-        if (displayIdx === -1) {
-          throw new Error("could not find display id ".concat(oldDisplayId, " to replace"));
+        if (idx === -1) {
+          throw new Error("could not find display id ".concat(oldId, " to replace"));
         }
 
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), newDisplayId);
-        var displayType = pluginManager.getDisplayType(configuration.type);
+        var schema = pluginManager.pluggableConfigSchemaType('display');
+        var conf = (0, _mobxStateTree.resolveIdentifier)(schema, (0, _mobxStateTree.getRoot)(self), newId);
+        var displayType = pluginManager.getDisplayType(conf.type);
 
         if (!displayType) {
-          throw new Error("unknown display type ".concat(configuration.type));
+          throw new Error("unknown display type ".concat(conf.type));
         }
 
-        self.displays.splice(displayIdx, 1, _objectSpread(_objectSpread({}, initialSnapshot), {}, {
-          type: configuration.type,
-          configuration: configuration
+        self.displays.splice(idx, 1, _objectSpread(_objectSpread({}, initialSnapshot), {}, {
+          type: conf.type,
+          configuration: conf
         }));
       }
     };

package/pluggableElementTypes/renderers/ServerSideRenderedContent.js

@@ -11,10 +11,10 @@ exports.default = ServerSideRenderedContent;
 
 var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
 
-var _styles = require("@material-ui/core/styles");
-
 var _react = _interopRequireWildcard(require("react"));
 
+var _styles = require("@mui/material/styles");
+
 var _reactDom = require("react-dom");
 
 var _ui = require("../../ui");

package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts

@@ -1,4 +1,4 @@
-import { ThemeOptions } from '@material-ui/core';
+import { DeprecatedThemeOptions } from '@mui/material';
 import { SnapshotOrInstance, SnapshotIn } from 'mobx-state-tree';
 import RendererType, { RenderProps, RenderResults } from './RendererType';
 import SerializableFilterChain, { SerializedFilterChain } from './util/serializableFilterChain';
@@ -7,7 +7,7 @@ import RpcManager from '../../rpc/RpcManager';
 interface BaseRenderArgs extends RenderProps {
     sessionId: string;
     signal?: AbortSignal;
-    theme: ThemeOptions;
+    theme: DeprecatedThemeOptions;
     exportSVG: {
         rasterizeLayers?: boolean;
     };

package/pluggableElementTypes/renderers/ServerSideRendererType.js

@@ -31,7 +31,7 @@ var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/ge
 
 var _react = _interopRequireDefault(require("react"));
 
-var _styles = require("@material-ui/core/styles");
+var _styles = require("@mui/material/styles");
 
 var _canvasSequencer = require("canvas-sequencer");
 

package/rpc/BaseRpcDriver.js

@@ -214,7 +214,7 @@ var BaseRpcDriver = /*#__PURE__*/function () {
           return thing;
         }
 
-        return (0, _util.objectFromEntries)(Object.entries(thing).filter(function (e) {
+        return Object.fromEntries(Object.entries(thing).filter(function (e) {
           return isClonable(e[1]);
         }).map(function (_ref) {
           var _ref2 = (0, _slicedToArray2.default)(_ref, 2),