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

package/esm/Session/Themes.js

@@ -3,7 +3,7 @@ import { resolvePalette, resolveThemeSelection } from '@jbrowse/core/ui/palette'
 import { resolveStyleTheme } from '@jbrowse/core/ui/styleTheme';
 import { createJBrowseThemeFromArgs, defaultThemes, } from '@jbrowse/core/ui/theme';
 import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util';
-import { onColorSchemeChange, prefersDarkColorScheme, } from '@jbrowse/core/util/systemColorScheme';
+import { darkReaderIsDark, onColorSchemeChange, onDarkReaderChange, prefersDarkColorScheme, } from '@jbrowse/core/util/systemColorScheme';
 import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { asSession } from '../siblingCast.js';
@@ -70,6 +70,7 @@ export function ThemeManagerSessionMixin(_pluginManager) {
         .volatile(() => ({
         ...storedSelection(),
         systemPrefersDark: prefersDarkColorScheme(),
+        darkReaderDark: darkReaderIsDark(),
     }))
         .views(s => {
         const self = asSession(s);
@@ -101,15 +102,23 @@ export function ThemeManagerSessionMixin(_pluginManager) {
             },
             /**
              * #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.
              */
-            get effectiveThemeMode() {
+            get selectedThemeMode() {
                 return this.themeMode === 'system'
                     ? (self.systemThemeOverride ??
                         (self.systemPrefersDark ? 'dark' : 'light'))
                     : this.themeMode;
             },
+            /**
+             * #getter
+             * `selectedThemeMode`, but dark while Dark Reader darkens the page.
+             */
+            get effectiveThemeMode() {
+                return self.darkReaderDark ? 'dark' : this.selectedThemeMode;
+            },
             /**
              * #getter
              * Whether what is drawn right now is dark. Read off the resolved
@@ -195,7 +204,7 @@ export function ThemeManagerSessionMixin(_pluginManager) {
                 const selection = resolveThemeSelection(name ?? this.themeName, undefined, all);
                 const themeName = resolveThemeName(all, selection.themeName);
                 const theme = all[themeName];
-                const mode = theme?.palette?.mode ?? selection.mode ?? this.effectiveThemeMode;
+                const mode = theme?.palette?.mode ?? selection.mode ?? this.selectedThemeMode;
                 if (themeName !== 'default') {
                     return { ...theme, palette: { ...theme?.palette, mode } };
                 }
@@ -231,6 +240,12 @@ export function ThemeManagerSessionMixin(_pluginManager) {
                 self.systemThemeOverride = undefined;
             }
         },
+        /**
+         * #action
+         */
+        noteDarkReader() {
+            self.darkReaderDark = darkReaderIsDark();
+        },
         /**
          * #action
          */
@@ -273,6 +288,9 @@ export function ThemeManagerSessionMixin(_pluginManager) {
             addDisposer(self, onColorSchemeChange(() => {
                 self.setSystemPrefersDark(prefersDarkColorScheme());
             }));
+            addDisposer(self, onDarkReaderChange(() => {
+                self.noteDarkReader();
+            }));
             addDisposer(self, autorun(function themeNameAutorun() {
                 // persist the raw selection, not the coerced themeName, so a
                 // theme registered later isn't clobbered with 'default'

package/esm/Session/TrackMenu.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel, AnyTrackConfig } from '@jbrowse/core/configuration';
 import type { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { DialogComponentType } from '@jbrowse/core/util';
@@ -11,7 +11,7 @@ interface TrackActionSession<C> {
         expandedDisplayId?: string;
     }) => void;
     publishTrackConf: (conf: C) => unknown;
-    deleteTrackConf: (conf: AnyConfigurationModel) => void;
+    deleteTrackConf: (conf: AnyTrackConfig) => void;
     resetTrackConfiguration?: (trackId: string) => void;
     /**
      * Declared here, though only the copy guard below reads it, so a session that
@@ -41,7 +41,7 @@ export declare function trackActionItems<C extends {
     trackId: string;
 }>({ session, config, view, canEdit, isSessionOverride, makeCopy, }: {
     session: TrackActionSession<C>;
-    config: BaseTrackConfig;
+    config: AnyTrackConfig;
     view?: TrackActionView;
     canEdit: boolean;
     isSessionOverride?: boolean;
@@ -75,7 +75,7 @@ export declare function TrackMenuItemsSessionMixin(pluginManager: PluginManager)
      * #method
      * flattened menu items for use in hierarchical track selector
      */
-    getTrackListMenuItems(config: BaseTrackConfig, view?: TrackActionView): MenuItem[];
+    getTrackListMenuItems(config: AnyTrackConfig, view?: TrackActionView): MenuItem[];
     /**
      * #method
      * track menu with About + "Track actions" submenu for the in-view label

package/esm/Session/TrackMenuSessionMixin.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel, AnyTrackConfig } from '@jbrowse/core/configuration';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { TrackActionView } from '@jbrowse/core/util/types';
 /**
@@ -16,7 +16,7 @@ export declare function TrackMenuSessionMixin(pluginManager: PluginManager): imp
      * #method
      * flattened menu items for use in hierarchical track selector
      */
-    getTrackListMenuItems(config: AnyConfigurationModel, view?: TrackActionView): MenuItem[];
+    getTrackListMenuItems(config: AnyTrackConfig, view?: TrackActionView): MenuItem[];
     /**
      * #method
      */

package/esm/Session/Tracks.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfiguration, AnyTrackConfig, TrackConfigEntry } from '@jbrowse/core/configuration';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
 /**
  * #stateModel TracksManagerSessionMixin
@@ -376,8 +376,8 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
-            readonly confByName: Map<string, AnyConfigurationModel>;
-            readonly assemblyList: AnyConfigurationModel[];
+            readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1031,8 +1031,8 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
-            readonly confByName: Map<string, AnyConfigurationModel>;
-            readonly assemblyList: AnyConfigurationModel[];
+            readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1393,17 +1393,17 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
      * Each track's base by trackId: the entry its edits diff against. Here
      * the config.json entry, which an edit writes directly.
      */
-    readonly trackBasesById: Map<string, AnyConfigurationModel>;
+    readonly trackBasesById: Map<string, TrackConfigEntry>;
     /**
      * #method
      * A track's base as the session resolves it, its edits applied. Here the
      * base itself.
      */
-    withTrackEdits(base: AnyConfigurationModel): AnyConfigurationModel;
+    withTrackEdits(base: TrackConfigEntry): TrackConfigEntry;
     /**
      * #getter
      */
-    readonly tracks: AnyConfigurationModel[];
+    readonly tracks: TrackConfigEntry[];
 } & {
     afterAttach(): void;
 } & {
@@ -1415,7 +1415,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
      * subscribes only to its own id, so one track's settings edit doesn't
      * re-render the others.
      */
-    getTrackById(id: string): AnyConfigurationModel | undefined;
+    getTrackById(id: string): AnyTrackConfig | undefined;
     /**
      * #method
      * Every track config the session can resolve, keyed by trackId.
@@ -1426,7 +1426,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
      *
      * @deprecated
      */
-    getTracksById(): Record<string, AnyConfigurationModel>;
+    getTracksById(): Record<string, AnyTrackConfig>;
 } & {
     /**
      * #action
@@ -1487,7 +1487,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     /**
      * #action
      */
-    deleteTrackConf(trackConf: AnyConfigurationModel): any;
+    deleteTrackConf(trackConf: AnyTrackConfig): any;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 /** Session mixin MST type for a session that has tracks */
 export type SessionWithTracksType = ReturnType<typeof TracksManagerSessionMixin>;

package/esm/Session/Tracks.js

@@ -218,8 +218,8 @@ export function TracksManagerSessionMixin(pluginManager) {
             updateTrackConfiguration(trackConf) {
                 // an opened connection track lives in connectionTrackConfigs, not
                 // jbrowse.tracks; persist its edit there (jbrowse.updateTrackConf would
-                // no-op, since the track isn't in the config). Desktop uses this base
-                // mixin, so without this branch a connection-track edit is lost on
+                // no-op, since the track isn't in the config). SessionTracks defers a
+                // connection track's edit here, so without this branch it is lost on
                 // reload.
                 if (isSessionWithConnections(self) &&
                     trackConf.trackId in self.connectionTrackConfigs) {

package/esm/Session/copyTrackSnapshot.d.ts

@@ -1,4 +1,4 @@
-import type { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+import type { AnyTrackConfig } from '@jbrowse/core/configuration';
 type TrackCopySnapshot = {
     trackId: string;
     name?: string;
@@ -15,7 +15,7 @@ type TrackCopySnapshot = {
  * `${trackId}-${type}` form baseTrackConfig auto-injects — keeping them unique
  * (displayId is a types.identifier, so a collision would crash MST).
  */
-export declare function copyTrackSnapshot(config: BaseTrackConfig, opts: {
+export declare function copyTrackSnapshot(config: AnyTrackConfig, opts: {
     clearCategory: boolean;
 }): TrackCopySnapshot;
 export {};

package/esm/Session/index.d.ts

@@ -18,7 +18,7 @@ export { SessionTracksManagerSessionMixin } from './SessionTracks.ts';
 export type { EditableTrackConfig, PlainTrackConfig, SessionWithSessionTracks, SessionWithSessionTracksType, } from './SessionTracks.ts';
 export { hydratedForms } from './hydratedForms.ts';
 export type { HydratedForms } from './hydratedForms.ts';
-export { bakeSessionCascades, getShareableSessionSnapshot, } from './shareableSnapshot.ts';
+export { getShareableSessionSnapshot } from './shareableSnapshot.ts';
 export { TrackMenuItemsSessionMixin, aboutTrackMenuItem, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './TrackMenu.ts';
 export { copyTrackSnapshot } from './copyTrackSnapshot.ts';
 export { pluginExtraTrackItems } from './pluginExtraTrackItems.ts';

package/esm/Session/index.js

@@ -8,7 +8,7 @@ export { PreferencesSessionMixin } from './Preferences.js';
 export { BaseSessionModel, isBaseSession, isSession } from './BaseSession.js';
 export { SessionTracksManagerSessionMixin } from './SessionTracks.js';
 export { hydratedForms } from './hydratedForms.js';
-export { bakeSessionCascades, getShareableSessionSnapshot, } from './shareableSnapshot.js';
+export { getShareableSessionSnapshot } from './shareableSnapshot.js';
 export { TrackMenuItemsSessionMixin, aboutTrackMenuItem, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './TrackMenu.js';
 export { copyTrackSnapshot } from './copyTrackSnapshot.js';
 export { pluginExtraTrackItems } from './pluginExtraTrackItems.js';

package/esm/Session/pluginExtraTrackItems.d.ts

@@ -1,6 +1,6 @@
 import type { SessionWithDialog } from './TrackMenu.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyTrackConfig } from '@jbrowse/core/configuration';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { TrackActionView } from '@jbrowse/core/util/types';
 /**
@@ -8,4 +8,4 @@ import type { TrackActionView } from '@jbrowse/core/util/types';
  * both the hierarchical selector and the in-view label menu so plugins reach
  * every track menu consistently
  */
-export declare function pluginExtraTrackItems(pluginManager: PluginManager, session: SessionWithDialog, config: AnyConfigurationModel, view?: TrackActionView): MenuItem[];
+export declare function pluginExtraTrackItems(pluginManager: PluginManager, session: SessionWithDialog, config: AnyTrackConfig, view?: TrackActionView): MenuItem[];

package/esm/Session/shareableSnapshot.d.ts

@@ -1,23 +1,7 @@
 import type { AbstractSessionModel } from '@jbrowse/core/util';
 /**
- * The session snapshot to hand to anyone else — a share link, an exported
- * `session.json`, a desktop→web export. Snapshotting and baking are one call so
- * the pair can't be split: a bare `getSnapshot(session)` is never a correct
- * outgoing snapshot (see `bakeSessionCascades`), and three of the four
- * boundaries were spelling the two steps out identically.
- *
- * The fourth (desktop `ExportToWebDialog`) bakes a *transformed* snapshot from
- * `planWebExport`, so it calls `bakeSessionCascades` directly.
+ * The session snapshot to hand to anyone else: a share link, an exported
+ * `session.json`. The one place an outgoing snapshot is taken, so anything the
+ * live session resolves against state that stays behind has a place to go.
  */
 export declare function getShareableSessionSnapshot(session: AbstractSessionModel): Record<string, unknown>;
-/**
- * Everything an outgoing snapshot has to resolve because the live session
- * resolves it at read time against state that is staying behind — currently the
- * workspaces intent alone.
- *
- * It keeps its own entry point rather than being inlined into the one caller
- * because the failure of a boundary that performs half of them is invisible at
- * that boundary: the export succeeds, and what is missing only shows up on
- * someone else's screen.
- */
-export declare function bakeSessionCascades(session: AbstractSessionModel, snapshot: Record<string, unknown>): Record<string, unknown>;

package/esm/Session/shareableSnapshot.js

@@ -1,66 +1,9 @@
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 /**
- * The session snapshot to hand to anyone else — a share link, an exported
- * `session.json`, a desktop→web export. Snapshotting and baking are one call so
- * the pair can't be split: a bare `getSnapshot(session)` is never a correct
- * outgoing snapshot (see `bakeSessionCascades`), and three of the four
- * boundaries were spelling the two steps out identically.
- *
- * The fourth (desktop `ExportToWebDialog`) bakes a *transformed* snapshot from
- * `planWebExport`, so it calls `bakeSessionCascades` directly.
+ * The session snapshot to hand to anyone else: a share link, an exported
+ * `session.json`. The one place an outgoing snapshot is taken, so anything the
+ * live session resolves against state that stays behind has a place to go.
  */
 export function getShareableSessionSnapshot(session) {
-    return bakeSessionCascades(session, getSnapshot(session));
-}
-/**
- * Everything an outgoing snapshot has to resolve because the live session
- * resolves it at read time against state that is staying behind — currently the
- * workspaces intent alone.
- *
- * It keeps its own entry point rather than being inlined into the one caller
- * because the failure of a boundary that performs half of them is invisible at
- * that boundary: the export succeeds, and what is missing only shows up on
- * someone else's screen.
- */
-export function bakeSessionCascades(session, snapshot) {
-    const snap = structuredClone(snapshot);
-    bakeWorkspacesIntent(session, snap);
-    return snap;
-}
-/**
- * The workspaces cascade: session property -> user preference -> admin
- * `configuration.preferences.useWorkspaces`, of which only the first is in the
- * snapshot.
- *
- * So a sender whose workspace is on because *their admin turned it on* exports
- * a fully arranged `layout` with no statement that it is a workspace at all,
- * and a recipient resolving their own cascade to false renders the classic
- * stack: the arrangement arrives intact and invisible, with nothing to say it
- * was dropped.
- *
- * Only the on case is baked. At `false` there is no arrangement to carry, so
- * stamping it would be a sender with nothing to say overriding a recipient who
- * prefers workspaces.
- *
- * The paths that build a layout through an explicit user intent already set the
- * property themselves (`setUseWorkspacesPreference`, ViewMenu's move-view-out,
- * a spec `layout`), which is exactly what hides this: every arrangement made by
- * a *drag* — split a cell, drag a tab into it, open a new tab — goes through
- * `WorkspaceLayoutMixin` alone, which owns the tree and knows nothing about the
- * preference.
- *
- * `effectiveUseWorkspaces` is read behind an `in` guard because
- * `AbstractSessionModel` cannot name it (it lives on MultipleViewsSessionMixin,
- * one layer up), so renaming that getter silently stops the bake rather than
- * failing to compile — the hazard app-core/src/WorkspaceLayout/CLAUDE.md describes for
- * `setPendingMove`. jbrowse-web's `sessionModel/exportLayout.test.ts` is the
- * canary, since the bake needs a real session to have a cascade at all.
- */
-function bakeWorkspacesIntent(session, snap) {
-    if (snap.useWorkspaces === undefined &&
-        'effectiveUseWorkspaces' in session &&
-        session.effectiveUseWorkspaces ===
-            true) {
-        snap.useWorkspaces = true;
-    }
+    return structuredClone(getSnapshot(session));
 }

package/esm/controllerTracks.js

@@ -1,10 +1,10 @@
 import { getEnv } from '@jbrowse/core/util';
 import { withPageBaseUri } from '@jbrowse/core/util/addRelativeUris';
-import { guessTrackConf } from '@jbrowse/core/util/tracks';
+import { guessTrackConf, isLooseTrackConfig } from '@jbrowse/core/util/tracks';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { resolveLocalFileUris } from './localFiles.js';
 export function isLooseTrack(track) {
-    return typeof track === 'string' || (!('adapter' in track) && 'uri' in track);
+    return typeof track === 'string' || isLooseTrackConfig(track);
 }
 /**
  * Stamp the view's assembly onto a full-config track that omits

package/esm/index.d.ts

@@ -1,9 +1,9 @@
 export type { AssertExtends, AssertNotAny } from './assertExtends.ts';
 export { asRoot, asSession } from './siblingCast.ts';
 export { scheduleDetachedDestroy } from '@jbrowse/core/util';
-export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './RootModel/index.ts';
+export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, } from './RootModel/index.ts';
 export type { BaseRootModel, BaseRootModelType, RootConfigurationSnapshot, RootModelWithInternetAccounts, RootModelWithInternetAccountsType, } from './RootModel/index.ts';
-export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, hydratedForms, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, storedThemeArgs, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';
+export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, hydratedForms, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, storedThemeArgs, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';
 export type { AssertSessionModel, BaseSession, BaseSessionType, ConnectionTrackConfigEntry, EditableTrackConfig, HydratedForms, PlainTrackConfig, ReferringNode, SessionWithConnections, SessionWithConnectionsType, SessionWithDrawerWidgets, SessionWithDrawerWidgetsType, SessionWithMultipleViews, SessionWithMultipleViewsType, SessionWithReferenceManagement, SessionWithReferenceManagementType, SessionWithSessionTracks, SessionWithSessionTracksType, SessionWithThemes, SessionWithThemesType, SessionWithTracks, SessionWithTracksType, ThemeModeSelection, } from './Session/index.ts';
 export { AboutDialog, AppReadyMarker, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.ts';
 export type { AboutPanelProps, PreferencesDialogSession, PreferencesPanelDescriptor, } from './ui/index.ts';

package/esm/index.js

@@ -1,7 +1,7 @@
 export { asRoot, asSession } from './siblingCast.js';
 export { scheduleDetachedDestroy } from '@jbrowse/core/util';
-export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './RootModel/index.js';
-export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, hydratedForms, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, storedThemeArgs, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
+export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, } from './RootModel/index.js';
+export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, hydratedForms, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, storedThemeArgs, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
 export { AboutDialog, AppReadyMarker, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.js';
 export { initializeWorker } from './rpcWorker.js';
 export { toPluginLoadRecord } from './pluginInput.js';

package/esm/sessionUrl.d.ts

@@ -12,10 +12,6 @@ export interface SessionSnapshot {
  * hash fragment. Deflated then base64url-encoded, so it survives a URL intact
  * and stays far smaller than raw JSON.
  *
- * Not a plain `getSnapshot`: a workspace arrangement turned on by the sender's
- * preference is not in the snapshot, so a raw one renders as a classic stack
- * for whoever opens the link. `getShareableSessionSnapshot` stamps it first.
- *
  * The session travels but the config does not — the receiving app supplies its
  * own assembly/tracks. Put the result somewhere the server never sees (the hash
  * fragment) if it may be long: a query string can exceed the request-line limit

package/esm/sessionUrl.js

@@ -5,10 +5,6 @@ import { getShareableSessionSnapshot } from './Session/shareableSnapshot.js';
  * hash fragment. Deflated then base64url-encoded, so it survives a URL intact
  * and stays far smaller than raw JSON.
  *
- * Not a plain `getSnapshot`: a workspace arrangement turned on by the sender's
- * preference is not in the snapshot, so a raw one renders as a classic stack
- * for whoever opens the link. `getShareableSessionSnapshot` stamps it first.
- *
  * The session travels but the config does not — the receiving app supplies its
  * own assembly/tracks. Put the result somewhere the server never sees (the hash
  * fragment) if it may be long: a query string can exceed the request-line limit

package/esm/sessionUtils.js

@@ -312,7 +312,7 @@ function nonPortableUserTracks(report, droppable) {
 // place, keeping the base trackId, and persists the whole config). So a track the
 // hub itself changed since then also lands in `editDeltas`, pinning the recipient
 // to the values the sender is looking at. That is the export's stated intent —
-// reproduce the sender's screen, the same reason `bakeSessionCascades` exists —
+// reproduce the sender's screen —
 // but the delta channel it travels in means "user override" on the far side, and
 // a delta masks later admin changes to that track. Telling the two apart needs
 // the base as it was at session creation, which nothing persists.

package/esm/ui/AboutDialogContents.js

@@ -1,8 +1,7 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
-import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
+import Attributes, { hasAttributeRows, withoutLocations, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-import { readConfObject } from '@jbrowse/core/configuration';
 import PluggableComponents from '@jbrowse/core/ui/PluggableComponents';
 import { getEnv } from '@jbrowse/core/util';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
@@ -12,6 +11,7 @@ import DescriptionPanel from './DescriptionPanel.js';
 import FileInfoPanel from './FileInfoPanel.js';
 import HeaderButtons from './HeaderButtons.js';
 import RefNameInfoDialog from './RefNameInfoDialog.js';
+import { omitTrackDescription } from './descriptionHtml.js';
 import { getAboutDialogConfig } from './util.js';
 const useStyles = makeStyles()({
     content: {
@@ -23,8 +23,9 @@ const AboutDialogContents = observer(function AboutDialogContents({ config, sess
     const { classes } = useStyles();
     const [showRefNames, setShowRefNames] = useState(false);
     const { pluginManager } = getEnv(session);
-    const { config: shown, hideUris } = getAboutDialogConfig({ config, session });
-    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: readConfObject(config), hideUris: hideUris, setShowRefNames: setShowRefNames }), _jsx(Attributes, { attributes: shown, omit: [...hideFields, 'metadata'], hideUris: hideUris })] }), shown.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: shown.metadata, hideUris: hideUris }) })) : null, _jsx(DescriptionPanel, { config: config, session: session }), _jsx(AssemblyInfoPanel, { config: config, session: session, hideUris: hideUris }), _jsx(PluggableComponents, { pluginManager: pluginManager, 
+    const { conf, config: shown, advanced, hideUris, } = getAboutDialogConfig({ config, session });
+    const advancedShown = hideUris ? withoutLocations(advanced) : advanced;
+    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: conf, hideUris: hideUris, setShowRefNames: setShowRefNames }), _jsx(Attributes, { attributes: shown, omit: [...hideFields, 'metadata'], hideUris: hideUris })] }), hasAttributeRows(advancedShown, hideFields) ? (_jsx(BaseCard, { title: "Advanced", defaultExpanded: false, children: _jsx(Attributes, { attributes: advancedShown, omit: hideFields }) })) : null, shown.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: omitTrackDescription(shown.metadata), hideUris: hideUris }) })) : null, _jsx(DescriptionPanel, { config: config, session: session }), _jsx(AssemblyInfoPanel, { config: config, session: session, hideUris: hideUris }), _jsx(PluggableComponents, { pluginManager: pluginManager, 
                 /** #extensionPoint Core-extraAboutPanel | sync | Add extra panels to a track's About dialog */
                 name: "Core-extraAboutPanel", props: { session, config } }), hideUris ? null : _jsx(FileInfoPanel, { config: config, session: session }), showRefNames ? (_jsx(RefNameInfoDialog, { session: session, config: config, onClose: () => {
                     setShowRefNames(false);

package/esm/ui/DescriptionPanel.js

@@ -1,4 +1,4 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorBanner, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
@@ -7,19 +7,56 @@ import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { useFetch } from '@jbrowse/core/util/useFetch';
 import { Link, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import { getDescriptionHtmlUrl, rebaseDescriptionHtml, } from './descriptionHtml.js';
+import { getTrackDescription, rebaseDescriptionHtml, } from './descriptionHtml.js';
 const useStyles = makeStyles()(theme => ({
     provenance: {
         marginBottom: theme.spacing(1),
     },
+    prose: {
+        display: 'block',
+        '& h1, & h2': {
+            fontSize: theme.typography.pxToRem(16),
+            fontWeight: theme.typography.fontWeightBold,
+            margin: theme.spacing(2, 0, 0.5),
+        },
+        '& h3, & h4': {
+            fontSize: theme.typography.pxToRem(14),
+            fontWeight: theme.typography.fontWeightBold,
+            margin: theme.spacing(1.5, 0, 0.5),
+        },
+        '& > :first-child': {
+            marginTop: 0,
+        },
+        '& p': {
+            margin: theme.spacing(0, 0, 1),
+        },
+        '& table': {
+            borderCollapse: 'collapse',
+            margin: theme.spacing(1, 0),
+        },
+        '& th, & td': {
+            padding: theme.spacing(0.25, 1),
+            border: `1px solid ${theme.palette.divider}`,
+        },
+        '& img': {
+            maxWidth: '100%',
+        },
+    },
 }));
-const DescriptionCard = observer(function DescriptionCard({ url, }) {
+function Prose({ html }) {
+    const { classes } = useStyles();
+    return _jsx(SanitizedHTML, { html: html, className: classes.prose });
+}
+function DescriptionCard({ url, children, }) {
     const { classes } = useStyles();
+    return (_jsxs(BaseCard, { title: "Description", children: [_jsxs(Typography, { variant: "caption", color: "textSecondary", component: "div", className: classes.provenance, children: ["The track's description, written for the UCSC Genome Browser \u2014 some display options it describes differ in JBrowse.", url ? (_jsxs(_Fragment, { children: [' ', _jsx(Link, { href: url, target: "_blank", rel: "noopener noreferrer", children: "View original" })] })) : null] }), children] }));
+}
+const FetchedDescription = observer(function FetchedDescription({ url, }) {
     const { data: html, error, isLoading, } = useFetch(['trackDescriptionHtml', url], async (_name, url) => rebaseDescriptionHtml(await openLocation({ uri: url, locationType: 'UriLocation' }).readFile('utf8'), url));
-    return (_jsxs(BaseCard, { title: "Description", children: [_jsxs(Typography, { variant: "caption", color: "textSecondary", component: "div", className: classes.provenance, children: ["From the track hub, written for the UCSC Genome Browser \u2014 some display options it describes differ in JBrowse.", ' ', _jsx(Link, { href: url, target: "_blank", rel: "noopener noreferrer", children: "View original" })] }), error ? (_jsx(ErrorBanner, { error: error })) : isLoading || html === undefined ? (_jsx(LoadingEllipses, { message: "Loading description" })) : (_jsx(SanitizedHTML, { html: html }))] }));
+    return (_jsx(DescriptionCard, { url: url, children: error ? (_jsx(ErrorBanner, { error: error })) : isLoading || html === undefined ? (_jsx(LoadingEllipses, { message: "Loading description" })) : (_jsx(Prose, { html: html })) }));
 });
 const DescriptionPanel = observer(function DescriptionPanel({ config, }) {
-    const url = getDescriptionHtmlUrl(readConfObject(config, 'metadata'));
-    return url ? _jsx(DescriptionCard, { url: url }) : null;
+    const description = getTrackDescription(readConfObject(config, 'metadata'));
+    return !description ? null : 'url' in description ? (_jsx(FetchedDescription, { url: description.url })) : (_jsx(DescriptionCard, { children: _jsx(Prose, { html: description.html }) }));
 });
 export default DescriptionPanel;

package/esm/ui/GeneralPreferencesTab.d.ts

@@ -7,6 +7,7 @@ export interface GeneralPreferencesSession {
     setThemeName: (arg: string) => void;
     themeMode: ThemeModeSelection;
     setThemeMode: (arg: ThemeModeSelection) => void;
+    darkReaderDark?: boolean;
     animationMode: AnimationMode;
     numberGrouping: boolean;
     setPreferenceOverride: (key: string, value: unknown) => void;

package/esm/ui/GeneralPreferencesTab.js

@@ -23,7 +23,9 @@ const GeneralPreferencesTab = observer(function GeneralPreferencesTab({ session,
     const { classes } = useStyles();
     return (_jsxs(_Fragment, { children: [_jsx(TextField, { select: true, variant: "outlined", className: classes.field, label: "Theme", value: session.themeName, onChange: event => {
                     session.setThemeName(event.target.value);
-                }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) }), _jsx(TextField, { select: true, variant: "outlined", className: classes.field, label: "Light/dark", value: session.themeMode, onChange: event => {
+                }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) }), _jsx(TextField, { select: true, variant: "outlined", className: classes.field, label: "Light/dark", value: session.themeMode, helperText: session.darkReaderDark
+                    ? 'Dark while Dark Reader darkens this page'
+                    : undefined, onChange: event => {
                     session.setThemeMode(event.target.value);
                 }, children: THEME_MODES.map(opt => (_jsx(MenuItem, { value: opt.value, children: opt.label }, opt.value))) }), _jsx(TextField, { select: true, variant: "outlined", className: classes.field, label: "Animations", value: session.animationMode, onChange: event => {
                     session.setPreferenceOverride('animationMode', event.target.value);

package/esm/ui/ViewPreferencesTab.d.ts

@@ -3,8 +3,6 @@ export interface ViewPreferencesSession {
     setScrollZoom: (flag: boolean) => void;
     stickyViewHeaders: boolean;
     setStickyViewHeaders: (sticky: boolean) => void;
-    effectiveUseWorkspaces: boolean;
-    setUseWorkspacesPreference: (useWorkspaces: boolean) => void;
 }
 declare const ViewPreferencesTab: ({ session, }: {
     session: ViewPreferencesSession;

package/esm/ui/ViewPreferencesTab.js

@@ -8,8 +8,6 @@ const ViewPreferencesTab = observer(function ViewPreferencesTab({ session, }) {
                     session.setScrollZoom(checked);
                 } }), _jsx(PreferenceCheckbox, { checked: session.stickyViewHeaders, label: "Keep view header visible", help: "The view header stays at the top of the page while its tracks scroll under it.", onChange: checked => {
                     session.setStickyViewHeaders(checked);
-                } }), _jsx(PreferenceCheckbox, { checked: session.effectiveUseWorkspaces, label: "Use workspaces", help: "Views open as tabs and tiles instead of stacking down the page.", onChange: checked => {
-                    session.setUseWorkspacesPreference(checked);
                 } })] }));
 });
 export default ViewPreferencesTab;