@jbrowse/product-core 5.0.0-beta.10 → 5.0.0-beta.13

package/esm/RootModel/PreferencesConfig.d.ts

@@ -24,11 +24,6 @@ export declare function PreferencesConfigSchemaFactory(): import("@jbrowse/core/
     } & {
         defaultValue: boolean;
     };
-    readonly useWorkspaces: {
-        type: "boolean";
-    } & {
-        defaultValue: boolean;
-    };
     readonly developerMode: {
         type: "boolean";
     } & {

package/esm/RootModel/PreferencesConfig.js

@@ -45,17 +45,6 @@ export function PreferencesConfigSchemaFactory() {
             type: 'boolean',
             defaultValue: true,
         },
-        /**
-         * #slot configuration.preferences.useWorkspaces
-         * when true, views open in the tabbed/tiled workspace layout rather than
-         * stacked vertically. Only the default: a session that names
-         * `useWorkspaces` itself (a shared snapshot, or a session spec carrying a
-         * `layout`) still wins, and a user's own toggle overrides it.
-         */
-        useWorkspaces: {
-            type: 'boolean',
-            defaultValue: false,
-        },
         /**
          * #slot configuration.preferences.developerMode
          * when true, the ordering-contract checks a display or plugin can break

package/esm/RootModel/createConfigModel.d.ts

@@ -69,11 +69,6 @@ declare function rootConfigurationSchema(): import("@jbrowse/core/configuration/
         } & {
             defaultValue: boolean;
         };
-        readonly useWorkspaces: {
-            type: "boolean";
-        } & {
-            defaultValue: boolean;
-        };
         readonly developerMode: {
             type: "boolean";
         } & {
@@ -191,11 +186,6 @@ export declare function createConfigModel(pluginManager: PluginManager, assembly
             } & {
                 defaultValue: boolean;
             };
-            readonly useWorkspaces: {
-                type: "boolean";
-            } & {
-                defaultValue: boolean;
-            };
             readonly developerMode: {
                 type: "boolean";
             } & {

package/esm/RootModel/index.d.ts

@@ -7,4 +7,4 @@ export { HierarchicalConfigSchemaFactory } from './HierarchicalConfig.ts';
 export { PreferencesConfigSchemaFactory } from './PreferencesConfig.ts';
 export { createConfigModel } from './createConfigModel.ts';
 export type { RootConfigurationSnapshot } from './createConfigModel.ts';
-export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './menuItems.ts';
+export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, } from './menuItems.ts';

package/esm/RootModel/index.js

@@ -7,4 +7,4 @@ export { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, } fro
 export { HierarchicalConfigSchemaFactory } from './HierarchicalConfig.js';
 export { PreferencesConfigSchemaFactory } from './PreferencesConfig.js';
 export { createConfigModel } from './createConfigModel.js';
-export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './menuItems.js';
+export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, } from './menuItems.js';

package/esm/RootModel/menuItems.d.ts

@@ -1,4 +1,3 @@
-import type { SessionWithMultipleViews } from '../Session/index.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { DialogComponentType } from '@jbrowse/core/util';
@@ -20,5 +19,4 @@ interface HistoryManager {
 }
 export declare function undoMenuItem(history: HistoryManager): MenuItem;
 export declare function redoMenuItem(history: HistoryManager): MenuItem;
-export declare function workspacesMenuItem(session: SessionWithMultipleViews | undefined): MenuItem;
 export {};

package/esm/RootModel/menuItems.js

@@ -5,14 +5,12 @@ import GetAppIcon from '@mui/icons-material/GetApp';
 import PublishIcon from '@mui/icons-material/Publish';
 import RedoIcon from '@mui/icons-material/Redo';
 import SettingsIcon from '@mui/icons-material/Settings';
-import SpaceDashboardIcon from '@mui/icons-material/SpaceDashboard';
 import StorageIcon from '@mui/icons-material/Storage';
 import UndoIcon from '@mui/icons-material/Undo';
 import { getShareableSessionSnapshot } from '../Session/index.js';
 // the renderer binds the active session into each onClick (see AppToolbar's
 // wrapMenuItems), so these handlers receive it as their argument
 const MULTI_VIEW_WARNING = 'This will add a track to the first view. Note: if you want to open a track in a specific view open the track selector for that view and use the add track (plus icon) in the bottom right';
-const WORKSPACES_HELP_TEXT = 'Workspaces allow you to organize views into tabs and tiles. There are a variety of unique features, for instance, you can drag views between tabs or split them side-by-side. Try clicking and dragging the tab header to create a new split';
 export function newSessionMenuItem(root) {
     return {
         label: 'New session',
@@ -123,19 +121,3 @@ export function redoMenuItem(history) {
         },
     };
 }
-export function workspacesMenuItem(session) {
-    return {
-        label: 'Use workspaces',
-        icon: SpaceDashboardIcon,
-        type: 'checkbox',
-        checked: session?.effectiveUseWorkspaces ?? false,
-        helpText: WORKSPACES_HELP_TEXT,
-        // opts out of the checkbox "stay open" default: this re-lays out the whole
-        // app (classic stack <-> tiled workspace), so it's a one-shot mode switch
-        // rather than a setting to flip repeatedly with the menu up
-        keepMenuOpen: false,
-        onClick: () => {
-            session?.setUseWorkspacesPreference(!session.effectiveUseWorkspaces);
-        },
-    };
-}

package/esm/Session/BaseSession.d.ts

@@ -139,10 +139,7 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     /**
      * #method
      * the admin/embedder `configuration.preferences` value for a key, ignoring
-     * any runtime override — i.e. what a reset falls back to. Exposed rather
-     * than inlined because "differs from the default" is a question the
-     * Preferences reset diff asks about settings this map doesn't hold (see
-     * `defaultUseWorkspaces`).
+     * any runtime override — i.e. what a reset falls back to
      */
     getPreferenceDefault(key: string): unknown;
     /**

package/esm/Session/BaseSession.js

@@ -172,10 +172,7 @@ export function BaseSessionModel(_pluginManager) {
         /**
          * #method
          * the admin/embedder `configuration.preferences` value for a key, ignoring
-         * any runtime override — i.e. what a reset falls back to. Exposed rather
-         * than inlined because "differs from the default" is a question the
-         * Preferences reset diff asks about settings this map doesn't hold (see
-         * `defaultUseWorkspaces`).
+         * any runtime override — i.e. what a reset falls back to
          */
         getPreferenceDefault(key) {
             const { preferences } = self.configuration;

package/esm/Session/DrawerWidgets.d.ts

@@ -86,6 +86,8 @@ export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager):
     showWidget(widget: any): void;
     /**
      * #action
+     * closes the widget, and removes it from the session when its type sets
+     * `discardOnClose`. Minimizing the drawer is not closing.
      */
     hideWidget(widget: any): void;
     /**

package/esm/Session/DrawerWidgets.js

@@ -1,6 +1,7 @@
 import { isConfigurationModel } from '@jbrowse/core/configuration';
-import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util';
-import { addDisposer, getEnv, isAlive, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
+import { localStorageGetItem, localStorageSetItem, scheduleDetachedDestroy, } from '@jbrowse/core/util';
+import { getEditableTrackConfigById } from '@jbrowse/core/util/types';
+import { addDisposer, detach, getEnv, isAlive, types, } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { isBaseSession } from './BaseSession.js';
 const minDrawerWidth = 128;
@@ -171,12 +172,19 @@ export function DrawerWidgetSessionMixin(pluginManager) {
         },
         /**
          * #action
+         * closes the widget, and removes it from the session when its type sets
+         * `discardOnClose`. Minimizing the drawer is not closing.
          */
         hideWidget(widget) {
             self.activeWidgets.delete(widget.id);
             if (self.activeWidgets.size === 0) {
                 self.poppedOut = false;
             }
+            if (self.widgets.get(widget.id) === widget &&
+                pluginManager.getWidgetType(widget.type).discardOnClose) {
+                detach(widget);
+                scheduleDetachedDestroy(widget);
+            }
         },
         /**
          * #action
@@ -213,7 +221,9 @@ export function DrawerWidgetSessionMixin(pluginManager) {
          * #action
          */
         hideAllWidgets() {
-            self.activeWidgets.clear();
+            for (const widget of [...self.activeWidgets.values()]) {
+                this.hideWidget(widget);
+            }
             self.poppedOut = false;
         },
         afterAttach() {
@@ -255,23 +265,31 @@ export function DrawerWidgetSessionMixin(pluginManager) {
          * @param configuration - can be an MST model or a frozen/plain object with trackId
          */
         editConfiguration(configuration, opts) {
-            let targetConfig;
-            if (isStateTreeNode(configuration) &&
-                isConfigurationModel(configuration)) {
-                // Already an MST model (e.g., from track.configuration), use directly
-                targetConfig = configuration;
+            const isNode = isConfigurationModel(configuration);
+            if (!isNode && !('trackId' in configuration)) {
+                throw new Error('must pass a configuration model or frozen config with trackId to editConfiguration');
             }
-            else if ('trackId' in configuration) {
-                // Frozen/plain object - create a temporary MST model for editing
-                const trackSchema = pluginManager.pluggableConfigSchemaType('track');
-                targetConfig = trackSchema.create(configuration, getEnv(self));
+            const trackId = configuration.trackId;
+            const workingCopy = typeof trackId === 'string'
+                ? getEditableTrackConfigById(self, trackId)
+                : undefined;
+            const editor = self.openWidget('ConfigurationEditorWidget', 'configEditor');
+            // A shown track edits its working copy, so the editor edits that same
+            // node, and follows it when an undo replaces it (ADR-032). A node the
+            // session does not resolve by id, such as a track a view holds
+            // inline, is edited as it stands.
+            if (typeof trackId === 'string' &&
+                workingCopy &&
+                (!isNode || workingCopy === configuration)) {
+                editor.setTrackId(trackId);
             }
             else {
-                throw new Error('must pass a configuration model or frozen config with trackId to editConfiguration');
+                editor.setTarget(isNode
+                    ? configuration
+                    : pluginManager
+                        .pluggableConfigSchemaType('track')
+                        .create(configuration, getEnv(self)));
             }
-            const editor = self.openWidget('ConfigurationEditorWidget', 'configEditor');
-            // Set target via action since it's now volatile
-            editor.setTarget(targetConfig);
             editor.setExpandedDisplayId(opts?.expandedDisplayId);
         },
     }))

package/esm/Session/MultipleViews.d.ts

@@ -19,7 +19,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
     activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "stickyViewHeaders" | "useWorkspaces" | "views"> & {
+}, "stickyViewHeaders" | "views"> & {
     /**
      * #property
      */
@@ -28,12 +28,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
      * #property
      */
     stickyViewHeaders: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    /**
-     * #property
-     * enables the tabbed/tiled workspace layout for this session. Undefined
-     * means unspecified — read `effectiveUseWorkspaces`.
-     */
-    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
 }, {
     selection: unknown;
     hovered: unknown;
@@ -1434,25 +1428,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     }, opts?: {
         expandedDisplayId?: string;
     }): void;
-} & {
-    /**
-     * #getter
-     * resolved workspaces flag (never undefined): this session's value, else
-     * the user preference over the `configuration.preferences.useWorkspaces`
-     * admin default. Every consumer reads this, not the raw property — only
-     * sessions built from a snapshot or a spec `layout` set that, so the
-     * admin default is what reaches the arrivals that bypass defaultSession.
-     */
-    readonly effectiveUseWorkspaces: boolean;
-    /**
-     * #getter
-     * what `effectiveUseWorkspaces` becomes after `resetUseWorkspaces` — the
-     * admin default, with both this session's own value and the user's
-     * override out of the way. The Preferences reset diff needs this rather
-     * than the override map, which can't see a session-scoped value (a spec
-     * `layout`, a "move view to a tab") and so reported nothing to reset.
-     */
-    readonly defaultUseWorkspaces: boolean;
 } & {
     /**
      * #action
@@ -1556,28 +1531,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     setStickyViewHeaders(sticky: boolean): void;
     /**
      * #action
-     * set the workspaces layout for this session only, leaving the user's
-     * personal default untouched. For session-scoped intent — a spec
-     * carrying a `layout`, or an ad-hoc "move view to a tab/split" — where
-     * rewriting the visitor's global preference would be a surprise. The
-     * user-facing default toggle is `setUseWorkspacesPreference`.
+     * Does nothing: the workspace is always on. Kept because published
+     * protein3d and msaview bundles call it after placing a view.
      */
-    setUseWorkspaces(useWorkspaces: boolean): void;
-    /**
-     * #action
-     * the user-facing workspaces toggle: applies to this session and
-     * becomes their default for sessions that don't specify one. Persisted
-     * only here, on an explicit toggle — an autorun mirroring the resolved
-     * value would bake the admin default into every visitor's localStorage
-     * on first load, so a later admin change could never reach them.
-     */
-    setUseWorkspacesPreference(useWorkspaces: boolean): void;
-    /**
-     * #action
-     * drop both this session's explicit value and the user's override so
-     * workspaces falls back to the admin default
-     */
-    resetUseWorkspaces(): void;
+    setUseWorkspaces(_useWorkspaces?: boolean): void;
     afterAttach(): void;
 } & {
     /**
@@ -1603,7 +1560,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
     activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "stickyViewHeaders" | "useWorkspaces" | "views"> & {
+}, "stickyViewHeaders" | "views"> & {
     /**
      * #property
      */
@@ -1612,12 +1569,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
      * #property
      */
     stickyViewHeaders: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    /**
-     * #property
-     * enables the tabbed/tiled workspace layout for this session. Undefined
-     * means unspecified — read `effectiveUseWorkspaces`.
-     */
-    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
 }>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
     drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
     drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;

package/esm/Session/MultipleViews.js

@@ -81,36 +81,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
          * #property
          */
         stickyViewHeaders: types.optional(types.boolean, () => localStorageGetBoolean('stickyViewHeaders', true)),
-        /**
-         * #property
-         * enables the tabbed/tiled workspace layout for this session. Undefined
-         * means unspecified — read `effectiveUseWorkspaces`.
-         */
-        useWorkspaces: types.stripDefault(types.maybe(types.boolean), undefined),
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         * resolved workspaces flag (never undefined): this session's value, else
-         * the user preference over the `configuration.preferences.useWorkspaces`
-         * admin default. Every consumer reads this, not the raw property — only
-         * sessions built from a snapshot or a spec `layout` set that, so the
-         * admin default is what reaches the arrivals that bypass defaultSession.
-         */
-        get effectiveUseWorkspaces() {
-            return (self.useWorkspaces ?? self.getPreference('useWorkspaces') === true);
-        },
-        /**
-         * #getter
-         * what `effectiveUseWorkspaces` becomes after `resetUseWorkspaces` — the
-         * admin default, with both this session's own value and the user's
-         * override out of the way. The Preferences reset diff needs this rather
-         * than the override map, which can't see a session-scoped value (a spec
-         * `layout`, a "move view to a tab") and so reported nothing to reset.
-         */
-        get defaultUseWorkspaces() {
-            return self.getPreferenceDefault('useWorkspaces') === true;
-        },
     }))
         .actions(self => {
         // `scopeIds` narrows the move to a subset of the stack: in a tabbed
@@ -162,11 +132,11 @@ export function MultipleViewsSessionMixin(pluginManager) {
                 viewIdsWithin(view).includes(focusedViewId)) {
                 self.setFocusedViewId(undefined);
             }
-            // Every widget, not the active ones: a widget the user closed keeps
-            // its references and its autoruns. One that pointed into the view is
-            // now empty, so hide it rather than leave the panel showing what it no
-            // longer has.
-            for (const [, widget] of self.widgets) {
+            // Every widget, not the active ones: a closed widget that stays in the
+            // session keeps its references and its autoruns. One that pointed into
+            // the view is now empty, so close it rather than leave the panel
+            // showing what it no longer has.
+            for (const widget of [...self.widgets.values()]) {
                 if (dropRefsInto(widget, view)) {
                     self.hideWidget(widget);
                 }
@@ -345,36 +315,10 @@ export function MultipleViewsSessionMixin(pluginManager) {
             },
             /**
              * #action
-             * set the workspaces layout for this session only, leaving the user's
-             * personal default untouched. For session-scoped intent — a spec
-             * carrying a `layout`, or an ad-hoc "move view to a tab/split" — where
-             * rewriting the visitor's global preference would be a surprise. The
-             * user-facing default toggle is `setUseWorkspacesPreference`.
+             * Does nothing: the workspace is always on. Kept because published
+             * protein3d and msaview bundles call it after placing a view.
              */
-            setUseWorkspaces(useWorkspaces) {
-                self.useWorkspaces = useWorkspaces;
-            },
-            /**
-             * #action
-             * the user-facing workspaces toggle: applies to this session and
-             * becomes their default for sessions that don't specify one. Persisted
-             * only here, on an explicit toggle — an autorun mirroring the resolved
-             * value would bake the admin default into every visitor's localStorage
-             * on first load, so a later admin change could never reach them.
-             */
-            setUseWorkspacesPreference(useWorkspaces) {
-                self.useWorkspaces = useWorkspaces;
-                self.setPreferenceOverride('useWorkspaces', useWorkspaces);
-            },
-            /**
-             * #action
-             * drop both this session's explicit value and the user's override so
-             * workspaces falls back to the admin default
-             */
-            resetUseWorkspaces() {
-                self.useWorkspaces = undefined;
-                self.clearPreferenceOverride('useWorkspaces');
-            },
+            setUseWorkspaces(_useWorkspaces) { },
             afterAttach() {
                 addDisposer(self, autorun(function stickyViewHeadersAutorun() {
                     localStorageSetBoolean('stickyViewHeaders', self.stickyViewHeaders);
@@ -407,8 +351,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
         // stickyViewHeaders is a personal per-browser UI preference, not shared
         // view state: destructure it out so it never lands in the snapshot. It
         // stays localStorage-backed, so each browser keeps its own value.
-        // useWorkspaces stays: it changes layout intent (and pairs with the
-        // `layout` tree the snapshot carries), which is meaningful to share.
         const { stickyViewHeaders, ...rest } = snap;
         return rest;
     });

package/esm/Session/Preferences.js

@@ -35,8 +35,10 @@ export function PreferencesSessionMixin(pluginManager) {
         .actions(self => ({
         afterAttach() {
             // the restore path bypasses `setPreferenceOverride`, so it freezes here
-            // too
-            self.preferencesOverrides.replace(freezeDeep(loadStoredPreferences()));
+            // too; a key the config no longer declares is a retired preference
+            const { preferences } = self.configuration;
+            const stored = Object.entries(loadStoredPreferences()).filter(([key]) => !preferences || key in preferences);
+            self.preferencesOverrides.replace(freezeDeep(Object.fromEntries(stored)));
             // Applied once, here, rather than reactively: the same setting has to
             // hold in the RPC workers (which format tooltip strings from jexl
             // `mouseover` slots) and they only learn it at boot, so a live

package/esm/Session/SessionTracks.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfiguration, AnyConfigurationModel, AnyTrackConfig, TrackConfigEntry } from '@jbrowse/core/configuration';
 import type { IAnyStateTreeNode, IAnyType, Instance } from '@jbrowse/mobx-state-tree';
 export interface PlainTrackConfig {
     trackId: string;
@@ -1423,14 +1423,14 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     dereferenceTrack(trackId: string, referring: import("./ReferenceManagement.ts").ReferringNode[]): void;
 } & {
-    readonly trackBasesById: Map<string, AnyConfigurationModel>;
-    withTrackEdits(base: AnyConfigurationModel): AnyConfigurationModel;
-    readonly tracks: AnyConfigurationModel[];
+    readonly trackBasesById: Map<string, TrackConfigEntry>;
+    withTrackEdits(base: TrackConfigEntry): TrackConfigEntry;
+    readonly tracks: TrackConfigEntry[];
 } & {
     afterAttach(): void;
 } & {
-    getTrackById(id: string): AnyConfigurationModel | undefined;
-    getTracksById(): Record<string, AnyConfigurationModel>;
+    getTrackById(id: string): AnyTrackConfig | undefined;
+    getTracksById(): Record<string, AnyTrackConfig>;
 } & {
     addSessionTrackConf(trackConf: AnyConfiguration): any;
     publishTrackConf(trackConf: AnyConfiguration): any;
@@ -1439,7 +1439,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         trackId: string;
         [key: string]: unknown;
     }): void;
-    deleteTrackConf(trackConf: AnyConfigurationModel): any;
+    deleteTrackConf(trackConf: AnyTrackConfig): any;
 } & {
     /**
      * Per-track private working copies, keyed by trackId. A plain
@@ -1468,21 +1468,21 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
      * config.json entry. Rebuilt when either list changes, never on an
      * edit.
      */
-    readonly trackBasesById: Map<string, AnyConfigurationModel>;
+    readonly trackBasesById: Map<string, TrackConfigEntry>;
     /**
      * #method
      * `base` with its delta (trackConfigDeltas) merged over it, or `base`
      * itself by identity when it has none, which keeps the hydration cache
      * warm.
      */
-    withTrackEdits(base: AnyConfigurationModel): AnyConfigurationModel;
+    withTrackEdits(base: TrackConfigEntry): TrackConfigEntry;
     /**
      * #getter
      * Session tracks first, then the config tracks, each with its edits.
      * An edit copies the list of bases and lays each delta at its track's
      * position, so past that copy it costs the count of edited tracks.
      */
-    readonly tracks: AnyConfigurationModel[];
+    readonly tracks: TrackConfigEntry[];
     /**
      * #method
      * The entry `trackId` edits over, hydrated: the one the session added
@@ -1490,7 +1490,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
      * arranged" and "reset" compare its live config against. Per-id
      * reactive, like `getTrackById`.
      */
-    baseTrackConfig(trackId: string): PlainTrackConfig | undefined;
+    baseTrackConfig(trackId: string): TrackConfigEntry | undefined;
     /**
      * #method
      * The config node `trackId` resolves to: a live node as it stands,
@@ -1553,7 +1553,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
      * Returns the entry, which is the track's base: edit the track through
      * `updateTrackConfiguration` or a display's `setConf`, not the entry.
      */
-    addSessionTrackConf(trackConf: AnyConfiguration): AnyConfigurationModel | undefined;
+    addSessionTrackConf(trackConf: AnyConfiguration): AnyTrackConfig | undefined;
     /**
      * #action
      * Publish a track config to the shared catalog if this user can, and
@@ -1599,7 +1599,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
      * for why it survives and why it now means the session; nothing in tree
      * may call it.
      */
-    addTrackConf(trackConf: AnyConfiguration): AnyConfigurationModel | undefined;
+    addTrackConf(trackConf: AnyConfiguration): AnyTrackConfig | undefined;
     /**
      * #action
      * Persist an edited track config as a delta (trackConfigDeltas) against
@@ -1633,7 +1633,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     /**
      * #action
      */
-    deleteTrackConf(trackConf: AnyConfigurationModel): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>)[] | undefined;
+    deleteTrackConf(trackConf: AnyTrackConfig): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>)[] | undefined;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 /** Session mixin MST type for a session that has `sessionTracks` */
 export type SessionWithSessionTracksType = ReturnType<typeof SessionTracksManagerSessionMixin>;

package/esm/Session/SessionTracks.js

@@ -1,14 +1,12 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { diffTrackConfig, flattenTrackConfigDelta, mergeTrackConfig, } from '@jbrowse/core/util';
-import { expandLooseTrackConfig } from '@jbrowse/core/util/tracks';
+import { expandLooseTrackConfig, getConfAssemblyNamesOrNone, } from '@jbrowse/core/util/tracks';
 import { applySnapshot, getSnapshot, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { compareStructural, computed } from 'mobx';
 import { TracksManagerSessionMixin } from './Tracks.js';
 import { hydratedTrackForm } from './hydratedForms.js';
 import { assertNotReaddedDifferently } from './readdedTrackConf.js';
 import { assertTrackConfOutlivesItsAssemblies } from './temporaryAssemblyTracks.js';
-// jbrowse.tracks holds frozen plain objects in every product; single site for
-// the cast from its loose frozen type.
 function baseTracks(self) {
     return self.jbrowse.tracks;
 }
@@ -38,8 +36,7 @@ function assembliesNotInTheCatalog(self, trackConf) {
         readConfObject(a, 'name'),
         ...(readConfObject(a, 'aliases') ?? []),
     ]));
-    const names = readConfObject(trackConf, 'assemblyNames');
-    return names?.filter(name => !catalog.has(name)) ?? [];
+    return getConfAssemblyNamesOrNone(trackConf).filter(name => !catalog.has(name));
 }
 function withoutDelta(deltas, trackId) {
     const { [trackId]: _dropped, ...rest } = deltas;
@@ -177,9 +174,7 @@ export function SessionTracksManagerSessionMixin(pluginManager) {
         const deltaFor = perIdComputed(trackId => self.trackConfigDeltas[trackId]);
         const baseFor = perIdComputed(trackId => {
             const base = self.trackBasesById.get(trackId);
-            return base
-                ? toPlainConfig(base)
-                : undefined;
+            return base ? toPlainConfig(base) : undefined;
         });
         const editableBySchema = new Map();
         return {
@@ -199,8 +194,7 @@ export function SessionTracksManagerSessionMixin(pluginManager) {
              * warm.
              */
             withTrackEdits(base) {
-                const plain = base;
-                return withDelta(plain, deltaFor(plain.trackId));
+                return withDelta(base, deltaFor(base.trackId));
             },
             /**
              * #getter

package/esm/Session/Themes.d.ts

@@ -18,6 +18,7 @@ export declare function ThemeManagerSessionMixin(_pluginManager: PluginManager):
     sessionThemeMode: ThemeModeSelection;
     systemThemeOverride: PaletteMode | undefined;
     systemPrefersDark: boolean;
+    darkReaderDark: boolean;
 } & {
     /**
      * #method
@@ -39,8 +40,14 @@ export declare function ThemeManagerSessionMixin(_pluginManager: PluginManager):
     readonly themeMode: ThemeModeSelection;
     /**
      * #getter
-     * Light or dark, with `system` resolved against the OS preference or
-     * the toolbar's hold on the other mode.
+     * Light or dark as the reader chose it, `system` resolved against the
+     * OS or the toolbar's hold. What a file leaves the session in, since
+     * Dark Reader never touches the file.
+     */
+    readonly selectedThemeMode: PaletteMode;
+    /**
+     * #getter
+     * `selectedThemeMode`, but dark while Dark Reader darkens the page.
      */
     readonly effectiveThemeMode: PaletteMode;
     /**
@@ -115,6 +122,10 @@ export declare function ThemeManagerSessionMixin(_pluginManager: PluginManager):
      * which would otherwise resurface on the next palette change.
      */
     setThemeName(name: string): void;
+    /**
+     * #action
+     */
+    noteDarkReader(): void;
     /**
      * #action
      */