@jbrowse/product-core 5.0.0-beta.4 → 5.0.0-beta.7

package/esm/RootModel/menuItems.js

@@ -39,9 +39,9 @@ export function exportSessionMenuItem() {
             const { saveAs } = await import('@jbrowse/core/util/FileSaver');
             saveAs(new Blob([
                 JSON.stringify({
-                    // an exported file is read by someone who doesn't have this
-                    // browser's promoted display-type defaults, so flatten the
-                    // cascade into it (same rule as ShareDialog)
+                    // an exported file is read by someone whose own preferences
+                    // differ, so stamp what the live session resolves at read
+                    // time (same rule as ShareDialog)
                     session: getShareableSessionSnapshot(session),
                 }, null, 2),
             ], { type: 'text/plain;charset=utf-8' }), 'session.json');

package/esm/Session/BaseSession.d.ts

@@ -75,23 +75,15 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
      *
      * An `observable.map` (not a plain object reassigned wholesale) so each
      * preference is its own tracked key: writing one (`setScrollZoom`) can't
-     * invalidate a reader of another (`getDisplayTypeDefault` in a track's
-     * `rpcProps`). A single spread-replaced object made every setter wake
-     * every reader, so toggling scroll-to-zoom re-fetched every track. For the
-     * same reason each promoted per-display-type default is a flat composite
-     * key (see `displayTypeDefaultKey`), not a single nested `displayTypeDefaults`
-     * object — promoting one default can't wake readers of a different one.
+     * invalidate a reader of another. A single spread-replaced object made
+     * every setter wake every reader, so toggling scroll-to-zoom re-fetched
+     * every track.
      *
-     * `deep: false` is load-bearing, not a micro-optimization. The default
-     * enhancer wraps an object/array value in a MobX Proxy on `set`, and a
-     * promoted default is handed straight back out by `getConf` — so an
-     * object-valued promotable slot (alignments `colorBy`) put a Proxy into
-     * `rpcProps()`, and V8's structured-clone serializer rejects a Proxy:
-     * `worker.postMessage` threw `DataCloneError` on the next fetch of any
-     * track following that default (electron IPC and `structuredClone` in the
-     * share bake likewise). The map still notifies per key on `set`, so shallow
-     * values lose no reactivity — and nothing can mutate a preference in place,
-     * because `setPreferenceOverride` freezes what it stores.
+     * `deep: false` keeps an object-valued preference a plain object rather
+     * than a MobX Proxy, which V8's structured-clone serializer rejects. The
+     * map still notifies per key on `set`, so shallow values lose no
+     * reactivity — and nothing can mutate a preference in place, because
+     * `setPreferenceOverride` freezes what it stores.
      */
     preferencesOverrides: import("mobx").ObservableMap<string, unknown>;
 } & {
@@ -150,35 +142,12 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
      * The override map is empty unless the product loads it (web/desktop).
      */
     getPreference(key: string): unknown;
-    /**
-     * #method
-     * resolved value of a per-display-type slot default the user promoted
-     * (see `setDisplayTypeDefault`); undefined when nothing was promoted.
-     */
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    /**
-     * #method
-     * every per-display-type default the user has promoted, as
-     * `{ displayType, slot, value }` — the inventory the Preferences dialog
-     * lists and clears one at a time (`setDisplayTypeDefault(…, undefined)`).
-     *
-     * Parsed here rather than by the dialog, because the composite-key
-     * layout is this file's and nothing outside it should depend on it.
-     */
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     /**
      * #method
      * every scalar preference override that currently differs from its
      * config/admin default, as `{ path, from, to }` rows whose path is the
      * override's own key. A scalar pref (animationMode, scrollZoom) whose
      * override equals the default is omitted, since reverting it is a no-op.
-     * Promoted display-type defaults share the map but are not here: they
-     * are `getDisplayTypeDefaults`, and the Preferences dialog lists them
-     * through one builder on both of its surfaces.
      */
     getPreferenceChanges(): TrackConfigChange[];
 } & {
@@ -244,10 +213,9 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     setPreferenceOverride(key: string, value: unknown): void;
     /**
      * #action
-     * clear every runtime preference override at once — scrollZoom,
-     * animationMode, and every promoted per-display-type default (see
-     * `setDisplayTypeDefault`) — so each falls back to its config/admin
-     * default. Backs the Preferences dialog "Reset to defaults" button.
+     * clear every runtime preference override at once, so each falls back to
+     * its config/admin default. Backs the Preferences dialog "Reset to
+     * defaults" button.
      */
     clearPreferenceOverrides(): void;
     /**
@@ -262,14 +230,6 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
      * set the global scroll-to-zoom preference (see the `scrollZoom` getter)
      */
     setScrollZoom(flag: boolean): void;
-    /**
-     * #action
-     * promote (or, with `value` undefined, clear) a per-display-type slot
-     * default. Just a preference override under one flat composite key (see
-     * `displayTypeDefaultKey`), so it persists and independently tracks like
-     * any other pref, and clearing deletes only that key.
-     */
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     /**
      * #action
      */

package/esm/Session/BaseSession.js

@@ -10,35 +10,6 @@ import { applyDeveloperMode } from './developerMode.js';
 function isAnimationMode(val) {
     return val === 'system' || val === 'enabled' || val === 'disabled';
 }
-// Promoted per-display-type slot defaults live flat in `preferencesOverrides`
-// under one composite key each (`displayTypeDefault\0<type>\0<slot>`), not under
-// a single nested `displayTypeDefaults` object. Flat keys make each promoted
-// default its own tracked observable-map entry — promoting one can't invalidate
-// a reader of another (every promotable display's `rpcProps` reads one via
-// `getDisplayTypeDefault`) — and collapse the get/set/diff logic to one lookup.
-// The `\0` delimiter can't appear in a display type or slot name.
-// The literal is a **persisted localStorage key prefix**, so treat it as data
-// rather than as an identifier a rename should sweep — a blanket
-// `displayTypeDefault` → `pin` pass did sweep it, and orphans every promoted
-// default already in a browser's storage. Nothing released stores these yet, so
-// the reason it keeps this spelling is naming, not compatibility: the key names
-// *what is stored* (a display-type default, reached through
-// `get/setDisplayTypeDefault`), while `Pin` names the menu control the write
-// is offered from.
-const DISPLAY_TYPE_DEFAULT_PREFIX = 'displayTypeDefault\0';
-// Module-private on purpose: the composite-key spelling is a storage detail of
-// this file's get/set/diff methods, and nothing outside it should be able to
-// depend on the layout.
-function displayTypeDefaultKey(displayType, slot) {
-    return `${DISPLAY_TYPE_DEFAULT_PREFIX}${displayType}\0${slot}`;
-}
-function parseDisplayTypeDefaultKey(key) {
-    const rest = key.startsWith(DISPLAY_TYPE_DEFAULT_PREFIX)
-        ? key.slice(DISPLAY_TYPE_DEFAULT_PREFIX.length)
-        : '';
-    const [displayType, slot] = rest.split('\0');
-    return displayType && slot ? { displayType, slot } : undefined;
-}
 /**
  * #stateModel BaseSessionModel
  *
@@ -113,23 +84,15 @@ export function BaseSessionModel(_pluginManager) {
          *
          * An `observable.map` (not a plain object reassigned wholesale) so each
          * preference is its own tracked key: writing one (`setScrollZoom`) can't
-         * invalidate a reader of another (`getDisplayTypeDefault` in a track's
-         * `rpcProps`). A single spread-replaced object made every setter wake
-         * every reader, so toggling scroll-to-zoom re-fetched every track. For the
-         * same reason each promoted per-display-type default is a flat composite
-         * key (see `displayTypeDefaultKey`), not a single nested `displayTypeDefaults`
-         * object — promoting one default can't wake readers of a different one.
+         * invalidate a reader of another. A single spread-replaced object made
+         * every setter wake every reader, so toggling scroll-to-zoom re-fetched
+         * every track.
          *
-         * `deep: false` is load-bearing, not a micro-optimization. The default
-         * enhancer wraps an object/array value in a MobX Proxy on `set`, and a
-         * promoted default is handed straight back out by `getConf` — so an
-         * object-valued promotable slot (alignments `colorBy`) put a Proxy into
-         * `rpcProps()`, and V8's structured-clone serializer rejects a Proxy:
-         * `worker.postMessage` threw `DataCloneError` on the next fetch of any
-         * track following that default (electron IPC and `structuredClone` in the
-         * share bake likewise). The map still notifies per key on `set`, so shallow
-         * values lose no reactivity — and nothing can mutate a preference in place,
-         * because `setPreferenceOverride` freezes what it stores.
+         * `deep: false` keeps an object-valued preference a plain object rather
+         * than a MobX Proxy, which V8's structured-clone serializer rejects. The
+         * map still notifies per key on `set`, so shallow values lose no
+         * reactivity — and nothing can mutate a preference in place, because
+         * `setPreferenceOverride` freezes what it stores.
          */
         preferencesOverrides: observable.map(undefined, {
             deep: false,
@@ -219,55 +182,23 @@ export function BaseSessionModel(_pluginManager) {
                 ? this.getPreferenceDefault(key)
                 : override;
         },
-        /**
-         * #method
-         * resolved value of a per-display-type slot default the user promoted
-         * (see `setDisplayTypeDefault`); undefined when nothing was promoted.
-         */
-        getDisplayTypeDefault(displayType, slot) {
-            return self.preferencesOverrides.get(displayTypeDefaultKey(displayType, slot));
-        },
-        /**
-         * #method
-         * every per-display-type default the user has promoted, as
-         * `{ displayType, slot, value }` — the inventory the Preferences dialog
-         * lists and clears one at a time (`setDisplayTypeDefault(…, undefined)`).
-         *
-         * Parsed here rather than by the dialog, because the composite-key
-         * layout is this file's and nothing outside it should depend on it.
-         */
-        getDisplayTypeDefaults() {
-            const found = [];
-            for (const [key, value] of self.preferencesOverrides.entries()) {
-                const parsed = parseDisplayTypeDefaultKey(key);
-                if (parsed) {
-                    found.push({ ...parsed, value });
-                }
-            }
-            return found;
-        },
         /**
          * #method
          * every scalar preference override that currently differs from its
          * config/admin default, as `{ path, from, to }` rows whose path is the
          * override's own key. A scalar pref (animationMode, scrollZoom) whose
          * override equals the default is omitted, since reverting it is a no-op.
-         * Promoted display-type defaults share the map but are not here: they
-         * are `getDisplayTypeDefaults`, and the Preferences dialog lists them
-         * through one builder on both of its surfaces.
          */
         getPreferenceChanges() {
             const changes = [];
             for (const [key, value] of self.preferencesOverrides.entries()) {
-                if (!key.startsWith(DISPLAY_TYPE_DEFAULT_PREFIX)) {
-                    const dflt = this.getPreferenceDefault(key);
-                    if (value !== dflt) {
-                        changes.push({
-                            path: [key],
-                            from: dflt,
-                            to: value,
-                        });
-                    }
+                const dflt = this.getPreferenceDefault(key);
+                if (value !== dflt) {
+                    changes.push({
+                        path: [key],
+                        from: dflt,
+                        to: value,
+                    });
                 }
             }
             return changes;
@@ -364,19 +295,18 @@ export function BaseSessionModel(_pluginManager) {
                 self.preferencesOverrides.delete(key);
             }
             else {
-                // frozen because `deep: false` hands an object-valued preference (a
-                // promoted `colorBy`) straight back out by reference to every display
-                // following it, so the "nothing mutates a preference in place" this
-                // store relies on is enforced rather than assumed
+                // frozen because `deep: false` hands an object-valued preference
+                // straight back out by reference, so the "nothing mutates a
+                // preference in place" this store relies on is enforced rather than
+                // assumed
                 self.preferencesOverrides.set(key, freezeDeep(value));
             }
         },
         /**
          * #action
-         * clear every runtime preference override at once — scrollZoom,
-         * animationMode, and every promoted per-display-type default (see
-         * `setDisplayTypeDefault`) — so each falls back to its config/admin
-         * default. Backs the Preferences dialog "Reset to defaults" button.
+         * clear every runtime preference override at once, so each falls back to
+         * its config/admin default. Backs the Preferences dialog "Reset to
+         * defaults" button.
          */
         clearPreferenceOverrides() {
             self.preferencesOverrides.clear();
@@ -397,16 +327,6 @@ export function BaseSessionModel(_pluginManager) {
         setScrollZoom(flag) {
             this.setPreferenceOverride('scrollZoom', flag);
         },
-        /**
-         * #action
-         * promote (or, with `value` undefined, clear) a per-display-type slot
-         * default. Just a preference override under one flat composite key (see
-         * `displayTypeDefaultKey`), so it persists and independently tracks like
-         * any other pref, and clearing deletes only that key.
-         */
-        setDisplayTypeDefault(displayType, slot, value) {
-            this.setPreferenceOverride(displayTypeDefaultKey(displayType, slot), value);
-        },
         /**
          * #action
          */

package/esm/Session/MultipleViews.d.ts

@@ -1639,12 +1639,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
 } & {
     getPreferenceDefault(key: string): unknown;
     getPreference(key: string): unknown;
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
     readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1661,7 +1655,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
     setScrollZoom(flag: boolean): void;
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
     setFocusedViewId(viewId: string | undefined): void;
     removeActiveDialog(): void;

package/esm/Session/Preferences.d.ts

@@ -1620,12 +1620,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
 } & {
     getPreferenceDefault(key: string): unknown;
     getPreference(key: string): unknown;
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
     readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1642,7 +1636,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
     setScrollZoom(flag: boolean): void;
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
     setFocusedViewId(viewId: string | undefined): void;
     removeActiveDialog(): void;

package/esm/Session/Preferences.js

@@ -5,6 +5,11 @@ import { autorun } from 'mobx';
 import { BaseSessionModel } from './BaseSession.js';
 import { applyDeveloperMode } from './developerMode.js';
 const PREFS_KEY = 'jbrowsePreferences';
+// v5.0.0-beta.4 shipped session-wide display-type defaults, which persisted here
+// under composite keys of this shape. They resolve to nothing now, and left in
+// place they would show up as unnamed rows in the Preferences reset diff, so a
+// beta user's stored ones are dropped on load.
+const RETIRED_DISPLAY_TYPE_DEFAULT_PREFIX = 'displayTypeDefault\0';
 function loadStoredPreferences() {
     const stored = localStorageGetItem(PREFS_KEY);
     let result = {};
@@ -12,7 +17,7 @@ function loadStoredPreferences() {
         try {
             const parsed = JSON.parse(stored);
             if (typeof parsed === 'object' && parsed !== null) {
-                result = parsed;
+                result = Object.fromEntries(Object.entries(parsed).filter(([key]) => !key.startsWith(RETIRED_DISPLAY_TYPE_DEFAULT_PREFIX)));
             }
         }
         catch {
@@ -35,8 +40,7 @@ export function PreferencesSessionMixin(pluginManager) {
         .actions(self => ({
         afterAttach() {
             // the restore path bypasses `setPreferenceOverride`, so it freezes here
-            // too — a promoted default read back from localStorage is shared by
-            // reference exactly like a freshly set one
+            // too
             self.preferencesOverrides.replace(freezeDeep(loadStoredPreferences()));
             // Applied once, here, rather than reactively: the same setting has to
             // hold in the RPC workers (which format tooltip strings from jexl

package/esm/Session/SessionTracks.d.ts

@@ -1649,12 +1649,6 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     getPreferenceDefault(key: string): unknown;
     getPreference(key: string): unknown;
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
     readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1671,7 +1665,6 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
     setScrollZoom(flag: boolean): void;
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
     setFocusedViewId(viewId: string | undefined): void;
     removeActiveDialog(): void;

package/esm/Session/SessionTracks.js

@@ -486,8 +486,8 @@ export function SessionTracksManagerSessionMixin(pluginManager) {
                         // base sets diffs to nothing exactly as netting back to the base
                         // does — and reverting the working copy then undid the edit ~400ms
                         // after the user watched it land. The reachable case is a size
-                        // row's reset, whose whole job is to unset a slot, over a
-                        // promotable slot an admin `config.json` declares.
+                        // row's reset, whose whole job is to unset a slot an admin
+                        // `config.json` declares.
                         //
                         // The removal still doesn't survive a reload, which is the
                         // tombstone-free delta's documented limitation; what it no longer

package/esm/Session/Tracks.d.ts

@@ -1617,12 +1617,6 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
 } & {
     getPreferenceDefault(key: string): unknown;
     getPreference(key: string): unknown;
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
     readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1639,7 +1633,6 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
     setScrollZoom(flag: boolean): void;
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
     setFocusedViewId(viewId: string | undefined): void;
     removeActiveDialog(): void;

package/esm/Session/index.d.ts

@@ -15,7 +15,7 @@ export { BaseSessionModel, isBaseSession, isSession } from './BaseSession.ts';
 export type { BaseSession, BaseSessionType } from './BaseSession.ts';
 export { SessionTracksManagerSessionMixin } from './SessionTracks.ts';
 export type { EditableTrackConfig, PlainTrackConfig, SessionWithSessionTracks, SessionWithSessionTracksType, } from './SessionTracks.ts';
-export { bakePromotedDefaultsIntoSnapshot, bakeSessionCascades, getShareableSessionSnapshot, } from './shareableSnapshot.ts';
+export { bakeSessionCascades, getShareableSessionSnapshot, } from './shareableSnapshot.ts';
 export { TrackMenuItemsSessionMixin, aboutTrackMenuItem, copyTrackSnapshot, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './TrackMenu.ts';
 export { TrackMenuSessionMixin } from './TrackMenuSessionMixin.ts';
 export { finalizeSession } from './finalizeSession.ts';

package/esm/Session/index.js

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

package/esm/Session/shareableSnapshot.d.ts

@@ -12,66 +12,12 @@ import type { AbstractSessionModel } from '@jbrowse/core/util';
 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.
+ * resolves it at read time against state that is staying behind — currently the
+ * workspaces intent alone.
  *
- * Two such cascades, and they have nothing to do with each other — promoted
- * display-type defaults are per-track rendering, workspaces intent is the
- * session's layout mode. What they share is only this: both live partly in the
- * sender's own browser, so a raw `getSnapshot` records neither, and the
- * recipient silently resolves their own.
- *
- * They get one entry point rather than a call each 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.
- * Adding a third cascade should mean editing this function, not auditing four
- * call sites.
+ * 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>;
-/**
- * `getComputedStyle` for the promotable-default cascade.
- *
- * A track that "follows" a session-wide promoted display-type default holds no
- * value of its own — its rendered value is resolved at read time from the
- * promoted display-type defaults in `preferencesOverrides`, which are personal,
- * localStorage-backed, and deliberately never serialized into a shared session.
- * So a raw `getSnapshot(session)` records a track as at-default even when the
- * sender is looking at a promoted value, and the recipient (who lacks the sender's
- * preferences) sees something different. This flattens the live cascade into a
- * self-contained snapshot:
- *
- * Every slot an open display *inherits* from a promoted default (i.e.
- * `getDisplayTypeDefaultChanges` — non-customized, differs from base) is baked
- * into that track's config layer: its own config for a user-added or connection
- * track, else a `trackConfigDeltas` entry against the admin base (see
- * `ownTrackConfig`). So the concrete value travels with the document, and
- * because it lands in the track's config the recipient reads it as *customized*
- * — a customized value is the top of the cascade, so their own promoted defaults
- * never get consulted for it.
- *
- * **What this deliberately does not cover**, and the reason there is no flag
- * here: a slot the sender was viewing at its *base* value. Nothing is baked for
- * it (the value equals base, and `stripDefault` drops it from the snapshot
- * regardless), so a recipient who has promoted something else resolves it from
- * their own cascade and sees their value. There is no value that can express "I
- * deliberately saw the default" — at-base and unset are byte-identical once
- * stripped. That case used to be covered by stamping a per-display
- * `ignorePromotedDefaults` on every open display, which cost a second
- * shape-aware walk that had to stay in step with `openPromotableDisplays` by
- * hand, and permanently detached received tracks from the recipient's own pins
- * until they clicked "use this default" on each one. A promoted default is
- * personal and local — the same as the theme a session is viewed in, which this
- * function has never baked either.
- *
- * The live session is untouched; a modified deep copy of `snapshot` is returned.
- * Tracks the sender never opened carry no display state to resolve, so they're
- * left to pick up the recipient's defaults when opened — matching "export the
- * actual state of the (open) tracks".
- *
- * Reach is `openPromotableDisplays` — literally the same walk the cascade's own
- * "apply to open tracks" uses, so the two can't drift. It recurses into a
- * composite view's `views` array (breakpoint-split, the linear-comparative /
- * synteny family), which holds child views rather than tracks of its own —
- * `LGVSyntenyDisplay` is only reachable that way, and before the recursion a
- * shared session containing one rendered differently for the recipient.
- */
-export declare function bakePromotedDefaultsIntoSnapshot(session: AbstractSessionModel, snapshot: Record<string, unknown>): Record<string, unknown>;

package/esm/Session/shareableSnapshot.js

@@ -1,7 +1,4 @@
-import { getConf, getDisplayTypeDefaultChanges, } from '@jbrowse/core/configuration';
-import { getContainingTrack, mergeTrackConfig, openPromotableDisplays, } from '@jbrowse/core/util';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
-import { asArray, isRecord } from '../snapshotUtils.js';
 /**
  * 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
@@ -17,22 +14,16 @@ export function getShareableSessionSnapshot(session) {
 }
 /**
  * Everything an outgoing snapshot has to resolve because the live session
- * resolves it at read time against state that is staying behind.
+ * resolves it at read time against state that is staying behind — currently the
+ * workspaces intent alone.
  *
- * Two such cascades, and they have nothing to do with each other — promoted
- * display-type defaults are per-track rendering, workspaces intent is the
- * session's layout mode. What they share is only this: both live partly in the
- * sender's own browser, so a raw `getSnapshot` records neither, and the
- * recipient silently resolves their own.
- *
- * They get one entry point rather than a call each 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.
- * Adding a third cascade should mean editing this function, not auditing four
- * call sites.
+ * 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 = bakePromotedDefaultsIntoSnapshot(session, snapshot);
+    const snap = structuredClone(snapshot);
     bakeWorkspacesIntent(session, snap);
     return snap;
 }
@@ -49,8 +40,7 @@ export function bakeSessionCascades(session, snapshot) {
  *
  * 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 same line the promoted-default bake draws at a slot
- * the sender was viewing at its base value.
+ * prefers workspaces.
  *
  * The paths that build a layout through an explicit user intent already set the
  * property themselves (`setUseWorkspacesPreference`, ViewMenu's move-view-out,
@@ -74,123 +64,3 @@ function bakeWorkspacesIntent(session, snap) {
         snap.useWorkspaces = true;
     }
 }
-/**
- * `getComputedStyle` for the promotable-default cascade.
- *
- * A track that "follows" a session-wide promoted display-type default holds no
- * value of its own — its rendered value is resolved at read time from the
- * promoted display-type defaults in `preferencesOverrides`, which are personal,
- * localStorage-backed, and deliberately never serialized into a shared session.
- * So a raw `getSnapshot(session)` records a track as at-default even when the
- * sender is looking at a promoted value, and the recipient (who lacks the sender's
- * preferences) sees something different. This flattens the live cascade into a
- * self-contained snapshot:
- *
- * Every slot an open display *inherits* from a promoted default (i.e.
- * `getDisplayTypeDefaultChanges` — non-customized, differs from base) is baked
- * into that track's config layer: its own config for a user-added or connection
- * track, else a `trackConfigDeltas` entry against the admin base (see
- * `ownTrackConfig`). So the concrete value travels with the document, and
- * because it lands in the track's config the recipient reads it as *customized*
- * — a customized value is the top of the cascade, so their own promoted defaults
- * never get consulted for it.
- *
- * **What this deliberately does not cover**, and the reason there is no flag
- * here: a slot the sender was viewing at its *base* value. Nothing is baked for
- * it (the value equals base, and `stripDefault` drops it from the snapshot
- * regardless), so a recipient who has promoted something else resolves it from
- * their own cascade and sees their value. There is no value that can express "I
- * deliberately saw the default" — at-base and unset are byte-identical once
- * stripped. That case used to be covered by stamping a per-display
- * `ignorePromotedDefaults` on every open display, which cost a second
- * shape-aware walk that had to stay in step with `openPromotableDisplays` by
- * hand, and permanently detached received tracks from the recipient's own pins
- * until they clicked "use this default" on each one. A promoted default is
- * personal and local — the same as the theme a session is viewed in, which this
- * function has never baked either.
- *
- * The live session is untouched; a modified deep copy of `snapshot` is returned.
- * Tracks the sender never opened carry no display state to resolve, so they're
- * left to pick up the recipient's defaults when opened — matching "export the
- * actual state of the (open) tracks".
- *
- * Reach is `openPromotableDisplays` — literally the same walk the cascade's own
- * "apply to open tracks" uses, so the two can't drift. It recurses into a
- * composite view's `views` array (breakpoint-split, the linear-comparative /
- * synteny family), which holds child views rather than tracks of its own —
- * `LGVSyntenyDisplay` is only reachable that way, and before the recursion a
- * shared session containing one rendered differently for the recipient.
- */
-export function bakePromotedDefaultsIntoSnapshot(session, snapshot) {
-    const snap = structuredClone(snapshot);
-    // `openPromotableDisplays` is the one walk that decides reach — shared with
-    // the cascade's own "apply to open tracks", so the set this bakes and the set
-    // that acts on a promoted default can't drift
-    for (const display of openPromotableDisplays(session)) {
-        const changes = getDisplayTypeDefaultChanges(display);
-        if (changes.length > 0) {
-            bakeValues(snap, {
-                trackId: getConf(getContainingTrack(display), 'trackId'),
-                displayId: getConf(display, 'displayId'),
-                displayType: display.type,
-                values: Object.fromEntries(changes.map(c => [c.path[0], c.to])),
-            });
-        }
-    }
-    return snap;
-}
-// The track's own full config in the snapshot, when it has one: a user-added
-// track's `sessionTracks` entry, or an opened connection track's persisted
-// `connectionTrackConfigs` config. Everything else is an admin-base track,
-// which carries only a delta.
-//
-// The connection case is not optional. `trackConfigDeltas` is merged over
-// `jbrowse.tracks` alone, so a delta written for a connection track resolves
-// nowhere — the recipient would render the base value, which is the exact
-// failure the bake exists to prevent. `updateTrackConfiguration` splits on the
-// same line.
-function ownTrackConfig(snap, trackId) {
-    const sessionTrack = asArray(snap.sessionTracks).find(t => isRecord(t) && t.trackId === trackId);
-    const connectionEntry = isRecord(snap.connectionTrackConfigs)
-        ? snap.connectionTrackConfigs[trackId]
-        : undefined;
-    return isRecord(sessionTrack)
-        ? sessionTrack
-        : isRecord(connectionEntry) && isRecord(connectionEntry.config)
-            ? connectionEntry.config
-            : undefined;
-}
-// Bake one display's inherited values into the config layer: into the matching
-// display of the track's own config when it has one, else merged as a
-// `trackConfigDeltas` entry against the admin base.
-function bakeValues(snap, bake) {
-    const partialDisplay = {
-        type: bake.displayType,
-        displayId: bake.displayId,
-        ...bake.values,
-    };
-    const ownConfig = ownTrackConfig(snap, bake.trackId);
-    if (ownConfig) {
-        const displays = asArray(ownConfig.displays);
-        const target = displays.find(d => isRecord(d) && d.displayId === bake.displayId);
-        if (isRecord(target)) {
-            Object.assign(target, bake.values);
-        }
-        else {
-            ownConfig.displays = [...displays, partialDisplay];
-        }
-    }
-    else {
-        const deltas = isRecord(snap.trackConfigDeltas)
-            ? { ...snap.trackConfigDeltas }
-            : {};
-        const existing = isRecord(deltas[bake.trackId])
-            ? deltas[bake.trackId]
-            : { trackId: bake.trackId };
-        deltas[bake.trackId] = mergeTrackConfig(existing, {
-            trackId: bake.trackId,
-            displays: [partialDisplay],
-        });
-        snap.trackConfigDeltas = deltas;
-    }
-}

package/esm/index.d.ts

@@ -3,7 +3,7 @@ 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 type { BaseRootModel, BaseRootModelType, RootConfigurationSnapshot, RootModelWithInternetAccounts, RootModelWithInternetAccountsType, } from './RootModel/index.ts';
-export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakePromotedDefaultsIntoSnapshot, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';
+export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';
 export type { AssertSessionModel, BaseSession, BaseSessionType, ConnectionTrackConfigEntry, EditableTrackConfig, PlainTrackConfig, ReferringNode, SessionWithConnections, SessionWithConnectionsType, SessionWithDrawerWidgets, SessionWithDrawerWidgetsType, SessionWithMultipleViews, SessionWithMultipleViewsType, SessionWithReferenceManagement, SessionWithReferenceManagementType, SessionWithSessionTracks, SessionWithSessionTracksType, SessionWithThemes, SessionWithThemesType, SessionWithTracks, SessionWithTracksType, } from './Session/index.ts';
 export { AboutDialog, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.ts';
 export type { 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, bakePromotedDefaultsIntoSnapshot, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
+export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
 export { AboutDialog, 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/observeSession.d.ts

@@ -43,10 +43,9 @@ export interface SessionObservers {
  * uncompressed twin of `encodeSession`, for hosts that move JSON rather than
  * URLs — a notebook kernel, an R session, a "save this layout" button.
  *
- * Not a plain `getSnapshot`, and for the same reason `encodeSession` isn't:
- * display settings a user is *inheriting* from a promoted display-type default
- * live in their own browser, never in the session, so a raw snapshot replays
- * differently for whoever opens it.
+ * Not a plain `getSnapshot`, and for the same reason `encodeSession` isn't: a
+ * workspace arrangement turned on by the sender's preference is not in the
+ * snapshot, so a raw one replays as a classic stack for whoever opens it.
  */
 export declare function getSessionSnapshot(session: ObservedSession): SessionSnapshot;
 /**

package/esm/observeSession.js

@@ -7,10 +7,9 @@ import { getShareableSessionSnapshot } from './Session/shareableSnapshot.js';
  * uncompressed twin of `encodeSession`, for hosts that move JSON rather than
  * URLs — a notebook kernel, an R session, a "save this layout" button.
  *
- * Not a plain `getSnapshot`, and for the same reason `encodeSession` isn't:
- * display settings a user is *inheriting* from a promoted display-type default
- * live in their own browser, never in the session, so a raw snapshot replays
- * differently for whoever opens it.
+ * Not a plain `getSnapshot`, and for the same reason `encodeSession` isn't: a
+ * workspace arrangement turned on by the sender's preference is not in the
+ * snapshot, so a raw one replays as a classic stack for whoever opens it.
  */
 export function getSessionSnapshot(session) {
     // `name` is restated rather than the whole thing cast: the bake returns an

package/esm/sessionMigrations/index.js

@@ -136,9 +136,9 @@ function isObject(v) {
 // The standalone `methylation` colorBy scheme was removed; it is now the
 // `modifications` scheme with `fillUnmarked` set. It is NOT rewritten here: the
 // alignments model normalizes it at read time (`normalizeColorBy`, applied in
-// its `colorBy` getter), which covers every persistence path — instance slot,
-// session-wide promoted default, and config-file display default — so session
-// migration deliberately leaves a `methylation` colorBy untouched.
+// its `colorBy` getter), which covers every persistence path — instance slot and
+// config-file display default alike — so session migration deliberately leaves a
+// `methylation` colorBy untouched.
 function migrateDisplayType(display, trackConfigId, collected) {
     const entry = displayTypeMap[display.type];
     if (!entry) {

package/esm/sessionUrl.d.ts

@@ -12,10 +12,9 @@ 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`: display settings a user is *inheriting* from a
- * promoted display-type default live in their own browser, never in the
- * session, so a raw snapshot renders differently for whoever opens the link.
- * `getShareableSessionSnapshot` flattens that cascade into the snapshot first.
+ * 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

package/esm/sessionUrl.js

@@ -5,10 +5,9 @@ import { getShareableSessionSnapshot } from './Session/index.js';
  * hash fragment. Deflated then base64url-encoded, so it survives a URL intact
  * and stays far smaller than raw JSON.
  *
- * Not a plain `getSnapshot`: display settings a user is *inheriting* from a
- * promoted display-type default live in their own browser, never in the
- * session, so a raw snapshot renders differently for whoever opens the link.
- * `getShareableSessionSnapshot` flattens that cascade into the snapshot first.
+ * 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

package/esm/ui/AboutDialogContents.js

@@ -2,11 +2,11 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-import { getTrackConfigWithPromotables, hydrateTrackConfig, } from '@jbrowse/core/configuration';
+import { hydrateTrackConfig } 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';
-import { isStateTreeNode } from '@jbrowse/mobx-state-tree';
+import { getSnapshot, isStateTreeNode } from '@jbrowse/mobx-state-tree';
 import { observer } from 'mobx-react';
 import AssemblyInfoPanel from './AssemblyInfoPanel.js';
 import DescriptionPanel from './DescriptionPanel.js';
@@ -24,33 +24,25 @@ const AboutDialogContents = observer(function AboutDialogContents({ config, sess
     const { classes } = useStyles();
     const [showRefNames, setShowRefNames] = useState(false);
     const { pluginManager } = getEnv(session);
-    // "Copy config" output leaves the cascade for good (a user pastes it into a
-    // config.json), so promotable slots are resolved rather than left stripped —
-    // otherwise the copied config renders differently from the track it came from.
-    // `fromDisplayTypeDefaults` names what that folded in, so materializing a
-    // session-wide preference into a track config isn't silent.
-    //
     // The two menus that open this dialog hand over different things: the in-view
     // track label passes `track.configuration`, a live node, while the
     // hierarchical selector passes a `session.tracks` entry, which is a
-    // `types.frozen` plain object until something references the track. Resolving
-    // only the first meant the same track copied a different config depending on
-    // which menu you came from — and the selector is the one you can reach
-    // without opening the track at all. Hydrating converges them; it returns
-    // undefined for a config no plugin can build, and that falls back to copying
-    // it as authored.
+    // `types.frozen` plain object until something references the track. Hydrating
+    // converges them, so "Copy config" gives the same JSON whichever menu you came
+    // from; it returns undefined for a config no plugin can build, and that falls
+    // back to copying it as authored.
     const live = isStateTreeNode(config)
         ? config
         : hydrateTrackConfig(pluginManager, config);
-    const { config: conf, fromDisplayTypeDefaults } = live
-        ? getTrackConfigWithPromotables(session, live)
-        : { config, fromDisplayTypeDefaults: [] };
+    const conf = live
+        ? getSnapshot(live)
+        : config;
     const { config: shown, hideUris } = getAboutDialogConfig({
         config,
         session,
         pluginManager,
     });
-    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: conf, hideUris: hideUris, fromDisplayTypeDefaults: fromDisplayTypeDefaults, 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, 
+    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 })] }), 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, 
                 /** #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/HeaderButtons.d.ts

@@ -1,12 +1,7 @@
 interface HeaderButtonsProps {
     conf: Record<string, unknown>;
     hideUris?: boolean;
-    /**
-     * `<displayType>.<slot>` for each value the copied config inherited from a
-     * session-wide display-type default rather than from the config itself
-     */
-    fromDisplayTypeDefaults?: string[];
     setShowRefNames: (show: boolean) => void;
 }
-declare function HeaderButtons({ conf, hideUris, fromDisplayTypeDefaults, setShowRefNames, }: HeaderButtonsProps): import("react").JSX.Element;
+declare function HeaderButtons({ conf, hideUris, setShowRefNames, }: HeaderButtonsProps): import("react").JSX.Element;
 export default HeaderButtons;

package/esm/ui/HeaderButtons.js

@@ -1,9 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { CopyToClipboardButton } from '@jbrowse/core/ui';
-import { pluralize } from '@jbrowse/core/util';
 import { stripBaseUris } from '@jbrowse/core/util/addRelativeUris';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { Button, Tooltip, Typography } from '@mui/material';
+import { Button } from '@mui/material';
 const useStyles = makeStyles()(theme => ({
     button: {
         float: 'right',
@@ -15,17 +14,11 @@ const useStyles = makeStyles()(theme => ({
         gap: theme.spacing(1),
         justifyContent: 'flex-end',
     },
-    note: {
-        clear: 'both',
-        display: 'block',
-        textAlign: 'right',
-    },
 }));
-function HeaderButtons({ conf, hideUris, fromDisplayTypeDefaults = [], setShowRefNames, }) {
+function HeaderButtons({ conf, hideUris, setShowRefNames, }) {
     const { classes } = useStyles();
-    const n = fromDisplayTypeDefaults.length;
-    return (_jsxs("span", { className: classes.button, children: [_jsxs("span", { className: classes.buttons, children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            setShowRefNames(true);
-                        }, children: "Show ref names" }), hideUris ? null : (_jsx(CopyToClipboardButton, { variant: "contained", value: () => JSON.stringify(stripBaseUris(structuredClone(conf)), null, 2), children: "Copy config" }))] }), hideUris || !n ? null : (_jsx(Tooltip, { title: fromDisplayTypeDefaults.join(', '), children: _jsxs(Typography, { variant: "caption", color: "textSecondary", className: classes.note, children: ["includes ", n, " ", pluralize(n, 'setting'), " from your session-wide defaults"] }) }))] }));
+    return (_jsx("span", { className: classes.button, children: _jsxs("span", { className: classes.buttons, children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                        setShowRefNames(true);
+                    }, children: "Show ref names" }), hideUris ? null : (_jsx(CopyToClipboardButton, { variant: "contained", value: () => JSON.stringify(stripBaseUris(structuredClone(conf)), null, 2), children: "Copy config" }))] }) }));
 }
 export default HeaderButtons;

package/esm/ui/PreferencesDialog.d.ts

@@ -1,10 +1,9 @@
-import type { DisplayDefaultsSession } from './DisplayDefaultsSection.tsx';
 import type { GeneralPreferencesSession } from './GeneralPreferencesTab.tsx';
 import type { ViewPreferencesSession } from './ViewPreferencesTab.tsx';
 import type { ResettablePreferencesSession } from './preferencesReset.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type React from 'react';
-export interface PreferencesDialogSession extends GeneralPreferencesSession, ViewPreferencesSession, DisplayDefaultsSession, ResettablePreferencesSession {
+export interface PreferencesDialogSession extends GeneralPreferencesSession, ViewPreferencesSession, ResettablePreferencesSession {
 }
 /**
  * Descriptor returned from the `Core-preferencesDialogPanels` extension point.

package/esm/ui/PreferencesDialog.js

@@ -4,7 +4,6 @@ import { Dialog } from '@jbrowse/core/ui';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Button, DialogActions, DialogContent, Tab, Tabs } from '@mui/material';
 import { observer } from 'mobx-react';
-import DisplayDefaultsSection from './DisplayDefaultsSection.js';
 import GeneralPreferencesTab from './GeneralPreferencesTab.js';
 import PreferencesResetDialog from './PreferencesResetDialog.js';
 import ViewPreferencesTab from './ViewPreferencesTab.js';
@@ -22,7 +21,6 @@ const PreferencesDialog = observer(function PreferencesDialog({ handleClose, ses
     const pluginPanels = pluginManager.evaluateExtensionPoint(
     /** #extensionPoint Core-preferencesDialogPanels | sync | Add tabs to the preferences dialog */
     'Core-preferencesDialogPanels', [], { session });
-    const displayDefaultCount = session.getDisplayTypeDefaults().length;
     const tabs = [
         {
             value: 'general',
@@ -34,13 +32,6 @@ const PreferencesDialog = observer(function PreferencesDialog({ handleClose, ses
             label: 'Views',
             content: _jsx(ViewPreferencesTab, { session: session }),
         },
-        {
-            value: 'displayDefaults',
-            label: displayDefaultCount
-                ? `Display defaults (${displayDefaultCount})`
-                : 'Display defaults',
-            content: (_jsx(DisplayDefaultsSection, { session: session, pluginManager: pluginManager })),
-        },
         ...pluginPanels.map(({ name, Component }) => ({
             value: `plugin:${name}`,
             label: name,
@@ -53,7 +44,7 @@ const PreferencesDialog = observer(function PreferencesDialog({ handleClose, ses
                             setResetDialogOpen(true);
                         }, children: "Reset to defaults\u2026" }), _jsx(Button, { variant: "contained", onClick: () => {
                             handleClose();
-                        }, children: "Close" })] }), resetDialogOpen ? (_jsx(PreferencesResetDialog, { changes: collectPreferenceChanges(session, pluginManager), onReset: () => {
+                        }, children: "Close" })] }), resetDialogOpen ? (_jsx(PreferencesResetDialog, { changes: collectPreferenceChanges(session), onReset: () => {
                     resetAllPreferences(session);
                 }, onResetRow: change => {
                     resetPreferenceChange(session, change);

package/esm/ui/preferencesReset.d.ts

@@ -1,7 +1,5 @@
-import type { DisplayDefaultsSession } from './displayDefaultChanges.ts';
-import type PluginManager from '@jbrowse/core/PluginManager';
 import type { TrackConfigChange } from '@jbrowse/core/util';
-export interface ResettablePreferencesSession extends DisplayDefaultsSession {
+export interface ResettablePreferencesSession {
     themeName?: string;
     setThemeName: (arg: string) => void;
     stickyViewHeaders: boolean;
@@ -13,6 +11,6 @@ export interface ResettablePreferencesSession extends DisplayDefaultsSession {
     clearPreferenceOverride: (key: string) => void;
     getPreferenceChanges: () => TrackConfigChange[];
 }
-export declare function collectPreferenceChanges(session: ResettablePreferencesSession, pluginManager: PluginManager): TrackConfigChange[];
+export declare function collectPreferenceChanges(session: ResettablePreferencesSession): TrackConfigChange[];
 export declare function resetAllPreferences(session: ResettablePreferencesSession): void;
 export declare function resetPreferenceChange(session: ResettablePreferencesSession, change: TrackConfigChange): void;

package/esm/ui/preferencesReset.js

@@ -1,4 +1,3 @@
-import { displayDefaultChanges, resetDisplayDefault, } from './displayDefaultChanges.js';
 const NON_MAP_PREFERENCES = [
     {
         head: 'theme',
@@ -34,15 +33,12 @@ const NON_MAP_PREFERENCES = [
 ];
 const NON_MAP_HEADS = new Set(NON_MAP_PREFERENCES.map(p => p.head));
 // Everything "Reset to defaults" reverts, as rows: the scalar overrides in the
-// preference map, the promoted display-type defaults (same map, listed through
-// the builder the Display defaults section uses so both surfaces read alike),
-// and the preferences held outside the map.
-export function collectPreferenceChanges(session, pluginManager) {
+// preference map, and the preferences held outside it.
+export function collectPreferenceChanges(session) {
     return [
         ...session
             .getPreferenceChanges()
             .filter(c => !NON_MAP_HEADS.has(c.path[0])),
-        ...displayDefaultChanges(session, pluginManager),
         ...NON_MAP_PREFERENCES.map(p => p.change(session)).filter(c => c !== undefined),
     ];
 }
@@ -58,7 +54,7 @@ export function resetPreferenceChange(session, change) {
     if (pref) {
         pref.reset(session);
     }
-    else if (!resetDisplayDefault(session, change) && head) {
+    else if (head) {
         session.clearPreferenceOverride(head);
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "5.0.0-beta.4",
+  "version": "5.0.0-beta.7",
   "type": "module",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
@@ -30,8 +30,8 @@
     "@mui/material": "^9.4.0",
     "mobx": "^7.0.3",
     "mobx-react": "^10.0.2",
-    "@jbrowse/render-core": "^5.0.0-beta.4",
-    "@jbrowse/core": "^5.0.0-beta.4"
+    "@jbrowse/core": "^5.0.0-beta.7",
+    "@jbrowse/render-core": "^5.0.0-beta.7"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/ui/DisplayDefaultsSection.d.ts

@@ -1,23 +0,0 @@
-import type { DisplayDefaultsSession } from './displayDefaultChanges.ts';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export type { DisplayDefaultsSession } from './displayDefaultChanges.ts';
-/**
- * The inventory of session-wide display-type defaults: every value the user has
- * pinned from a track menu, what it overrides, and a button to clear one.
- *
- * The pin is easy to set and, until this, hard to find again. A pinned default
- * shows on the track-selector badge of any **open** track it moves — but one
- * affecting nothing currently open, and one that no longer resolves at all (a
- * stale value the cascade refuses, or a display type whose plugin is gone)
- * appear nowhere. The only place that listed them was the "Reset preferences to
- * defaults" confirmation, which is a destructive dialog to have to open in
- * order to read something.
- *
- * The empty state is deliberate rather than rendering nothing: it is the one
- * place the app says the capability exists to someone who has never used it.
- */
-declare const DisplayDefaultsSection: ({ session, pluginManager, }: {
-    session: DisplayDefaultsSession;
-    pluginManager: PluginManager;
-}) => import("react").JSX.Element;
-export default DisplayDefaultsSection;

package/esm/ui/DisplayDefaultsSection.js

@@ -1,27 +0,0 @@
-import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { SettingsChangesTable } from '@jbrowse/core/ui';
-import { Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-import { displayDefaultChanges, resetDisplayDefault, } from './displayDefaultChanges.js';
-/**
- * The inventory of session-wide display-type defaults: every value the user has
- * pinned from a track menu, what it overrides, and a button to clear one.
- *
- * The pin is easy to set and, until this, hard to find again. A pinned default
- * shows on the track-selector badge of any **open** track it moves — but one
- * affecting nothing currently open, and one that no longer resolves at all (a
- * stale value the cascade refuses, or a display type whose plugin is gone)
- * appear nowhere. The only place that listed them was the "Reset preferences to
- * defaults" confirmation, which is a destructive dialog to have to open in
- * order to read something.
- *
- * The empty state is deliberate rather than rendering nothing: it is the one
- * place the app says the capability exists to someone who has never used it.
- */
-const DisplayDefaultsSection = observer(function DisplayDefaultsSection({ session, pluginManager, }) {
-    const changes = displayDefaultChanges(session, pluginManager);
-    return changes.length ? (_jsxs(_Fragment, { children: [_jsx(Typography, { children: "These apply to every track of a display type that hasn't set its own value. Clear one to put those tracks back on the setting's default." }), _jsx(SettingsChangesTable, { changes: changes, onResetRow: change => {
-                    resetDisplayDefault(session, change);
-                } })] })) : (_jsx(Typography, { children: "None set. The pin beside a setting in a track menu applies that value to every open track of the same display type, and then offers to keep it as the default for the ones you open later." }));
-});
-export default DisplayDefaultsSection;

package/esm/ui/displayDefaultChanges.d.ts

@@ -1,31 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { TrackConfigChange } from '@jbrowse/core/util';
-export interface DisplayDefaultsSession {
-    getDisplayTypeDefaults: () => {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
-    setDisplayTypeDefault: (displayType: string, slot: string, value: unknown) => void;
-}
-/**
- * Every promoted display-type default as a settings row: what it overrides
- * (the slot's `promotedBase`), the value, and a label naming the display type
- * the way the user knows it. One builder for the two surfaces that list them,
- * the Display defaults section and the "Reset to defaults" confirmation, which
- * used to render the same default two ways.
- *
- * **The slot keeps its schema name**, while the display type gets its authored
- * one. A slot has no menu label to borrow — which row a setting is offered on is
- * a menu fact and declaring the slot promotable is a schema fact, and nothing
- * joins them (that split is why `promotableSlotsWithoutPin` has to walk a built
- * menu at all). A raw slot name is also what the config editor labels its fields
- * with, so the two surfaces agree.
- */
-export declare function displayDefaultChanges(session: DisplayDefaultsSession, pluginManager: PluginManager): TrackConfigChange[];
-/**
- * Clear the promoted default a row built by {@link displayDefaultChanges}
- * stands for. Returns false for any other row, so a table mixing both kinds
- * can hand every reset here first.
- */
-export declare function resetDisplayDefault(session: DisplayDefaultsSession, change: TrackConfigChange): boolean;

package/esm/ui/displayDefaultChanges.js

@@ -1,66 +0,0 @@
-import { getConfigurationSchemaDefinition, isSlotDefinitionEntry, } from '@jbrowse/core/configuration';
-// Head of the path a promoted default's row carries, so `resetDisplayDefault`
-// can tell it from a scalar preference row in the same table. Module-private:
-// the one producer and the one consumer of the shape are both here, which is
-// what lets the session know nothing about how the Preferences dialog
-// addresses a row.
-const DISPLAY_DEFAULT_PATH_HEAD = 'displayTypeDefaults';
-// The registered display types, by name.
-//
-// **Built rather than reached through `getDisplayType`, which THROWS** on a name
-// no plugin registers — an optional chain over it guards nothing. A default left
-// behind by a plugin that has since been uninstalled is exactly a row this
-// section has to render, so reaching for that getter would crash the whole
-// Preferences dialog for the one user whose pins most need clearing.
-function displayTypesByName(pluginManager) {
-    return new Map(pluginManager.getDisplayElements().map(d => [d.name, d]));
-}
-// What a track sitting at the bottom of the cascade shows for this slot — the
-// value clearing the pin would restore. Read off the display type's schema
-// rather than off the session, which holds only what was promoted. Undefined
-// for a display type that is gone, whose row then reads "(default)" like any
-// other unknown.
-function promotedBaseOf(configSchema, slot) {
-    const def = configSchema
-        ? getConfigurationSchemaDefinition(configSchema)?.[slot]
-        : undefined;
-    return isSlotDefinitionEntry(def) ? def.promotedBase : undefined;
-}
-/**
- * Every promoted display-type default as a settings row: what it overrides
- * (the slot's `promotedBase`), the value, and a label naming the display type
- * the way the user knows it. One builder for the two surfaces that list them,
- * the Display defaults section and the "Reset to defaults" confirmation, which
- * used to render the same default two ways.
- *
- * **The slot keeps its schema name**, while the display type gets its authored
- * one. A slot has no menu label to borrow — which row a setting is offered on is
- * a menu fact and declaring the slot promotable is a schema fact, and nothing
- * joins them (that split is why `promotableSlotsWithoutPin` has to walk a built
- * menu at all). A raw slot name is also what the config editor labels its fields
- * with, so the two surfaces agree.
- */
-export function displayDefaultChanges(session, pluginManager) {
-    const byName = displayTypesByName(pluginManager);
-    return session
-        .getDisplayTypeDefaults()
-        .map(({ displayType, slot, value }) => ({
-        path: [DISPLAY_DEFAULT_PATH_HEAD, displayType, slot],
-        label: `${byName.get(displayType)?.displayName ?? displayType} › ${slot}`,
-        from: promotedBaseOf(byName.get(displayType)?.configSchema, slot),
-        to: value,
-    }));
-}
-/**
- * Clear the promoted default a row built by {@link displayDefaultChanges}
- * stands for. Returns false for any other row, so a table mixing both kinds
- * can hand every reset here first.
- */
-export function resetDisplayDefault(session, change) {
-    const [head, displayType, slot] = change.path;
-    const isDisplayDefault = head === DISPLAY_DEFAULT_PATH_HEAD && !!displayType && !!slot;
-    if (isDisplayDefault) {
-        session.setDisplayTypeDefault(displayType, slot, undefined);
-    }
-    return isDisplayDefault;
-}