@jbrowse/product-core 2.17.0 → 2.18.0

package/dist/Session/Tracks.d.ts

@@ -1,12 +1,6 @@
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
-/**
- * #stateModel TracksManagerSessionMixin
- * composed of
- * - BaseSessionModel
- * - ReferenceManagementSessionMixin
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function TracksManagerSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("mobx-state-tree").ISimpleType<string>;
@@ -593,7 +587,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal;
+                stopToken?: string;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string;
@@ -601,7 +595,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal;
+                stopToken?: string;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string;
@@ -1115,7 +1109,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal;
+                stopToken?: string;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string;
@@ -1123,7 +1117,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal;
+                stopToken?: string;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string;
@@ -1654,7 +1648,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal;
+                stopToken?: string;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string;
@@ -1662,7 +1656,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal;
+                stopToken?: string;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string;
@@ -1746,9 +1740,6 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
 } & {
     removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
 } & {
-    /**
-     * #getter
-     */
     readonly tracks: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -1761,18 +1752,9 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
-    /**
-     * #action
-     */
     addTrackConf(trackConf: AnyConfiguration): any;
-    /**
-     * #action
-     */
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for a session that has tracks */
 export type SessionWithTracksType = ReturnType<typeof TracksManagerSessionMixin>;
-/** Instance of a session that has tracks */
 export type SessionWithTracks = Instance<SessionWithTracksType>;
-/** Type guard for SessionWithTracks */
 export declare function isSessionWithTracks(thing: IAnyStateTreeNode): thing is SessionWithTracks;

package/dist/Session/Tracks.js

@@ -5,33 +5,18 @@ exports.isSessionWithTracks = isSessionWithTracks;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
 const ReferenceManagement_1 = require("./ReferenceManagement");
-/**
- * #stateModel TracksManagerSessionMixin
- * composed of
- * - BaseSessionModel
- * - ReferenceManagementSessionMixin
- */
 function TracksManagerSessionMixin(pluginManager) {
     return mobx_state_tree_1.types
         .compose('TracksManagerSessionMixin', (0, BaseSession_1.BaseSessionModel)(pluginManager), (0, ReferenceManagement_1.ReferenceManagementSessionMixin)(pluginManager))
         .views(self => ({
-        /**
-         * #getter
-         */
         get tracks() {
             return self.jbrowse.tracks;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         addTrackConf(trackConf) {
             return self.jbrowse.addTrackConf(trackConf);
         },
-        /**
-         * #action
-         */
         deleteTrackConf(trackConf) {
             const callbacksToDereferenceTrack = [];
             const dereferenceTypeCount = {};
@@ -46,7 +31,6 @@ function TracksManagerSessionMixin(pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithTracks */
 function isSessionWithTracks(thing) {
     return (0, BaseSession_1.isBaseSession)(thing) && 'tracks' in thing;
 }

package/dist/rpcWorker.d.ts

@@ -1,5 +1,5 @@
-import { LoadedPlugin } from '@jbrowse/core/PluginLoader';
-import { PluginConstructor } from '@jbrowse/core/Plugin';
+import type { PluginConstructor } from '@jbrowse/core/Plugin';
+import type { LoadedPlugin } from '@jbrowse/core/PluginLoader';
 export declare function initializeWorker(corePlugins: PluginConstructor[], opts: {
     fetchESM?: (url: string) => Promise<LoadedPlugin>;
     fetchCJS?: (url: string) => Promise<LoadedPlugin>;

package/dist/rpcWorker.js

@@ -4,13 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.initializeWorker = initializeWorker;
-const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
-const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
-const remoteAbortSignals_1 = require("@jbrowse/core/rpc/remoteAbortSignals");
 const PluginLoader_1 = __importDefault(require("@jbrowse/core/PluginLoader"));
+const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
+const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
 const serialize_error_1 = require("serialize-error");
-// waits for a message from the main thread containing our configuration, which
-// must be sent on boot
 function receiveConfiguration() {
     const configurationP = new Promise(resolve => {
         function listener(e) {
@@ -25,7 +22,6 @@ function receiveConfiguration() {
     return configurationP;
 }
 async function getPluginManager(corePlugins, opts) {
-    // Load runtime plugins
     const config = await receiveConfiguration();
     const pluginLoader = new PluginLoader_1.default(config.plugins, opts).installGlobalReExports(self);
     return new PluginManager_1.default([
@@ -41,7 +37,6 @@ function wrapForRpc(func) {
         return func({
             ...args,
             statusCallback: (message) => {
-                // @ts-expect-error
                 self.rpcServer.emit(channel, message);
             },
         }, rpcDriverClassName);
@@ -53,19 +48,10 @@ async function initializeWorker(corePlugins, opts) {
         const rpcConfig = Object.fromEntries(pluginManager
             .getRpcElements()
             .map(e => [e.name, wrapForRpc(e.execute.bind(e))]));
-        // @ts-expect-error
-        self.rpcServer = new librpc_web_mod_1.default.Server({
-            ...rpcConfig,
-            ...(0, remoteAbortSignals_1.remoteAbortRpcHandler)(),
-            ping: async () => {
-                // the ping method is required by the worker driver for checking the
-                // health of the worker
-            },
-        });
+        self.rpcServer = new librpc_web_mod_1.default.Server(rpcConfig);
         postMessage({ message: 'ready' });
     }
     catch (e) {
         postMessage({ message: 'error', error: (0, serialize_error_1.serializeError)(e) });
     }
-    /* do nothing */
 }

package/dist/ui/AboutDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function AboutDialog({ config, handleClose, }: {
     config: AnyConfigurationModel;
     handleClose: () => void;

package/dist/ui/AboutDialogContents.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const AboutDialogContents: ({ config, }: {
     config: AnyConfigurationModel;
 }) => React.JSX.Element;

package/dist/ui/AboutDialogContents.js

@@ -27,16 +27,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const clone_1 = __importDefault(require("clone"));
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
 const Attributes_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-// locals
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const FileInfoPanel_1 = __importDefault(require("./FileInfoPanel"));
 const RefNameInfoDialog_1 = __importDefault(require("./RefNameInfoDialog"));
 const useStyles = (0, mui_1.makeStyles)()({
@@ -82,7 +80,7 @@ const AboutDialogContents = (0, mobx_react_1.observer)(function ({ config, }) {
                         setShowRefNames(true);
                     } }, "Show ref names"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                        const snap = removeAttr((0, clone_1.default)(conf), 'baseUri');
+                        const snap = removeAttr(structuredClone(conf), 'baseUri');
                         (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
                         setCopied(true);
                         setTimeout(() => {

package/dist/ui/FileInfoPanel.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export default function FileInfoPanel({ config, }: {
     config: AnyConfigurationModel;
 }): React.JSX.Element;

package/dist/ui/FileInfoPanel.js

@@ -28,18 +28,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = FileInfoPanel;
 const react_1 = __importStar(require("react"));
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
 const Attributes_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 function FileInfoPanel({ config, }) {
     const [error, setError] = (0, react_1.useState)();
     const [info, setInfo] = (0, react_1.useState)();
     const session = (0, util_1.getSession)(config);
     const { rpcManager } = session;
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {

package/dist/ui/RefNameInfoDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const RefNameInfoDialog: ({ config, onClose, }: {
     config: AnyConfigurationModel;
     onClose: () => void;

package/dist/ui/RefNameInfoDialog.js

@@ -27,14 +27,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
+const material_1 = require("@mui/material");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const MAX_REF_NAMES = 10000;
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     container: {
@@ -54,7 +54,6 @@ const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose
     const [copied, setCopied] = (0, react_1.useState)(false);
     const { rpcManager } = (0, util_1.getSession)(config);
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -64,7 +63,6 @@ const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose
                         assemblyName,
                         (await rpcManager.call(config.trackId, 'CoreGetRefNames', {
                             adapterConfig,
-                            // hack for synteny adapters
                             regions: [
                                 {
                                     assemblyName,

package/esm/RootModel/BaseRootModel.d.ts

@@ -1,38 +1,17 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
-import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
-/**
- * #stateModel BaseRootModel
- * #category root
- * factory function for the Base-level root model shared by all products
- */
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import type { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }: {
     pluginManager: PluginManager;
     jbrowseModelType: IAnyType;
     sessionModelType: IAnyType;
     assemblyConfigSchema: BaseAssemblyConfigSchema;
 }): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     * `jbrowse` is a mapping of the config.json into the in-memory state
-     * tree
-     */
     jbrowse: IAnyType;
-    /**
-     * #property
-     * `session` encompasses the currently active state of the app, including
-     * views open, tracks open in those views, etc.
-     */
     session: import("mobx-state-tree").IMaybe<IAnyType>;
-    /**
-     * #property
-     */
     sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
@@ -537,7 +516,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal;
+            stopToken?: string;
             sessionId: string;
         }): Promise<{
             [x: string]: string;
@@ -545,7 +524,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal;
+            stopToken?: string;
             sessionId: string;
         }): Promise<{
             [x: string]: string;
@@ -563,28 +542,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
     textSearchManager: TextSearchManager;
     pluginManager: PluginManager;
 } & {
-    /**
-     * #action
-     */
     setError(error: unknown): void;
-    /**
-     * #action
-     */
     setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
-    /**
-     * #action
-     */
     setDefaultSession(): void;
-    /**
-     * #action
-     */
     setSessionPath(path: string): void;
-    /**
-     * #action
-     */
     renameCurrentSession(newName: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>;
 export type BaseRootModel = Instance<BaseRootModelType>;
-/** Type guard for checking if something is a JB root model */
 export declare function isRootModel(thing: unknown): thing is BaseRootModelType;

package/esm/RootModel/BaseRootModel.js

@@ -1,34 +1,13 @@
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import assemblyManagerFactory from '@jbrowse/core/assemblyManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { cast, getSnapshot, isStateTreeNode, types, } from 'mobx-state-tree';
-import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
-/**
- * #stateModel BaseRootModel
- * #category root
- * factory function for the Base-level root model shared by all products
- */
+import { cast, getSnapshot, isStateTreeNode, types } from 'mobx-state-tree';
 export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }) {
     return types
         .model('BaseRootModel', {
-        /**
-         * #property
-         * `jbrowse` is a mapping of the config.json into the in-memory state
-         * tree
-         */
         jbrowse: jbrowseModelType,
-        /**
-         * #property
-         * `session` encompasses the currently active state of the app, including
-         * views open, tracks open in those views, etc.
-         */
         session: types.maybe(sessionModelType),
-        /**
-         * #property
-         */
         sessionPath: types.optional(types.string, ''),
-        /**
-         * #property
-         */
         assemblyManager: types.optional(assemblyManagerFactory(assemblyConfigSchema, pluginManager), {}),
     })
         .volatile(self => ({
@@ -41,43 +20,28 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
         pluginManager,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setError(error) {
             self.error = error;
         },
-        /**
-         * #action
-         */
         setSession(sessionSnapshot) {
             self.session = cast(sessionSnapshot);
         },
-        /**
-         * #action
-         */
         setDefaultSession() {
             this.setSession(self.jbrowse.defaultSession);
         },
-        /**
-         * #action
-         */
         setSessionPath(path) {
             self.sessionPath = path;
         },
-        /**
-         * #action
-         */
         renameCurrentSession(newName) {
             if (self.session) {
-                const snapshot = JSON.parse(JSON.stringify(getSnapshot(self.session)));
-                snapshot.name = newName;
-                this.setSession(snapshot);
+                this.setSession({
+                    ...getSnapshot(self.session),
+                    name: newName,
+                });
             }
         },
     }));
 }
-/** Type guard for checking if something is a JB root model */
 export function isRootModel(thing) {
     return (isStateTreeNode(thing) &&
         'session' in thing &&

package/esm/RootModel/FormatAbout.d.ts

@@ -1,20 +1,10 @@
-/**
- * #config FormatAbout
- * generally exists on the config.json or root config as configuration.formatAbout
- */
 export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.formatAbout.config
-     */
     config: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatAbout.hideUris
-     */
     hideUris: {
         type: string;
         defaultValue: boolean;

package/esm/RootModel/FormatAbout.js

@@ -1,22 +1,12 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FormatAbout
- * generally exists on the config.json or root config as configuration.formatAbout
- */
 export function FormatAboutConfigSchemaFactory() {
     return ConfigurationSchema('FormatAbout', {
-        /**
-         * #slot configuration.formatAbout.config
-         */
         config: {
             type: 'frozen',
             description: 'formats configuration object in about dialog',
             defaultValue: {},
             contextVariable: ['config'],
         },
-        /**
-         * #slot configuration.formatAbout.hideUris
-         */
         hideUris: {
             type: 'boolean',
             defaultValue: false,

package/esm/RootModel/FormatDetails.d.ts

@@ -1,38 +1,21 @@
-/**
- * #config FormatDetails
- * generally exists on the tracks in the config.json or as a 'session' config as
- * configuration.formatDetails
- */
 export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.formatDetails.feature
-     */
     feature: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatDetails.subfeatures
-     */
     subfeatures: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatDetails.depth
-     */
     depth: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot configuration.formatDetails.maxDepth
-     */
     maxDepth: {
         type: string;
         defaultValue: number;

package/esm/RootModel/FormatDetails.js

@@ -1,40 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FormatDetails
- * generally exists on the tracks in the config.json or as a 'session' config as
- * configuration.formatDetails
- */
 export function FormatDetailsConfigSchemaFactory() {
     return ConfigurationSchema('FormatDetails', {
-        /**
-         * #slot configuration.formatDetails.feature
-         */
         feature: {
             type: 'frozen',
             description: 'adds extra fields to the feature details',
             defaultValue: {},
             contextVariable: ['feature'],
         },
-        /**
-         * #slot configuration.formatDetails.subfeatures
-         */
         subfeatures: {
             type: 'frozen',
             description: 'adds extra fields to the subfeatures of a feature',
             defaultValue: {},
             contextVariable: ['feature'],
         },
-        /**
-         * #slot configuration.formatDetails.depth
-         */
         depth: {
             type: 'number',
             defaultValue: 2,
             description: 'depth to iterate the formatDetails->subfeatures callback on subfeatures (used for example to only apply the callback to the first layer of subfeatures)',
         },
-        /**
-         * #slot configuration.formatDetails.maxDepth
-         */
         maxDepth: {
             type: 'number',
             defaultValue: 10000,

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -1,42 +1,23 @@
-/**
- * #config HierarchicalConfigSchema
- * generally exists on the config.json or root config as configuration.hierarchical
- */
 export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.sort.trackNames
-         */
         trackNames: {
             type: string;
             defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.sort.categories
-         */
         categories: {
             type: string;
             defaultValue: boolean;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-         */
         categoryNames: {
             type: string;
             defaultValue: never[];
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-         */
         topLevelCategories: {
             type: string;
             defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.subCategories
-         */
         subCategories: {
             type: string;
             defaultValue: boolean;