@jbrowse/core 5.0.0-beta.2 → 5.0.0-beta.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.2",
+  "version": "5.0.0-beta.3",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -46,6 +46,7 @@
     "./data_adapters/BaseAdapter/getAdapterId": "./esm/data_adapters/BaseAdapter/getAdapterId.js",
     "./data_adapters/BaseAdapter/stats": "./esm/data_adapters/BaseAdapter/stats.js",
     "./data_adapters/BaseAdapter/types": "./esm/data_adapters/BaseAdapter/types.js",
+    "./data_adapters/adapterSessionRefcount": "./esm/data_adapters/adapterSessionRefcount.js",
     "./data_adapters/dataAdapterCache": "./esm/data_adapters/dataAdapterCache.js",
     "./data_adapters/getFeatureAdapter": "./esm/data_adapters/getFeatureAdapter.js",
     "./data_adapters/getSequenceSubAdapter": "./esm/data_adapters/getSequenceSubAdapter.js",
@@ -145,6 +146,7 @@
     "./util/SvgCanvas": "./esm/util/SvgCanvas.js",
     "./util/TimeTraveller": "./esm/util/TimeTraveller.js",
     "./util/aborting": "./esm/util/aborting.js",
+    "./util/adapterConfigKey": "./esm/util/adapterConfigKey.js",
     "./util/adapterMetadata": "./esm/util/adapterMetadata.js",
     "./util/addRelativeUris": "./esm/util/addRelativeUris.js",
     "./util/analytics": "./esm/util/analytics.js",
@@ -185,6 +187,7 @@
     "./util/installClearHoverOnSurfaceMove": "./esm/util/installClearHoverOnSurfaceMove.js",
     "./util/installFetch": "./esm/util/installFetch.js",
     "./util/installInitAutorun": "./esm/util/installInitAutorun.js",
+    "./util/installPrerequisiteFetch": "./esm/util/installPrerequisiteFetch.js",
     "./util/io": "./esm/util/io/index.js",
     "./util/io/RemoteFileWithRangeCache": "./esm/util/io/RemoteFileWithRangeCache.js",
     "./util/isDataCurrent": "./esm/util/isDataCurrent.js",
@@ -200,10 +203,12 @@
     "./util/librpc": "./esm/util/librpc.js",
     "./util/localStorage": "./esm/util/localStorage.js",
     "./util/makeAssembly": "./esm/util/makeAssembly.js",
+    "./util/mst-reflection": "./esm/util/mst-reflection.js",
     "./util/mstUtils": "./esm/util/mstUtils.js",
     "./util/nanoid": "./esm/util/nanoid.js",
     "./util/numericUtils": "./esm/util/numericUtils.js",
     "./util/offscreenCanvasPonyfill": "./esm/util/offscreenCanvasPonyfill.js",
+    "./util/openViews": "./esm/util/openViews.js",
     "./util/paintLayer": "./esm/util/paintLayer.js",
     "./util/parseLineByLine": "./esm/util/parseLineByLine.js",
     "./util/progress": "./esm/util/progress.js",
@@ -259,10 +264,10 @@
     "@mui/icons-material": "^9.4.0",
     "@mui/material": "^9.4.0",
     "@mui/system": "^9.4.0",
-    "@mui/x-data-grid": "^9.12.0",
+    "@mui/x-data-grid": "^9.13.0",
     "canvas-sequencer-ts": "^3.1.3",
     "compare-versions": "^6.1.1",
-    "dompurify": "^3.4.14",
+    "dompurify": "^3.4.15",
     "generic-filehandle2": "^2.4.0",
     "idb": "^8.0.3",
     "mobx": "^7.0.3",
@@ -270,8 +275,8 @@
     "pako-esm2": "^2.0.2",
     "rxjs": "^7.8.2",
     "source-map-js": "^1.2.1",
-    "@jbrowse/add-track-core": "^5.0.0-beta.2",
-    "@jbrowse/render-core": "^5.0.0-beta.2"
+    "@jbrowse/add-track-core": "^5.0.0-beta.3",
+    "@jbrowse/render-core": "^5.0.0-beta.3"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/ui/promotableMenuItems.d.ts

@@ -1,19 +0,0 @@
-import type { Pin } from '../configuration/promotablePin.ts';
-import type { CheckboxMenuItem, RadioMenuItem } from './MenuTypes.ts';
-import type { RadioOption, SettingRowOptions } from './toggleMenuItems.ts';
-/** #menuBuilder promotableToggleItem | `checkboxItem` plus an apply-to-open-tracks pin */
-export declare function promotableToggleItem({ label, checked, onToggle, pin, ...opts }: {
-    label: string;
-    checked: boolean;
-    onToggle: () => void;
-    pin: Pin;
-} & SettingRowOptions): CheckboxMenuItem;
-/** #menuBuilder promotableRadioItem | `radioItem` plus an apply-to-open-tracks pin */
-export declare function promotableRadioItem({ label, checked, onClick, pin, ...opts }: {
-    label: string;
-    checked: boolean;
-    onClick: () => void;
-    pin?: Pin;
-} & SettingRowOptions): RadioMenuItem;
-/** #menuBuilder promotableRadioItems | `radioItems` plus a pin per option, from a factory over the value */
-export declare function promotableRadioItems<T extends string>(options: readonly RadioOption<T>[], current: T | undefined, setMode: (m: T) => void, pin: (value: T) => Pin): RadioMenuItem[];

package/esm/ui/promotableMenuItems.js

@@ -1,91 +0,0 @@
-import { checkboxItem, radioItem, radioItems } from './toggleMenuItems.js';
-// Every builder here describes the trailing pin (`pin`) rather than
-// rendering it. That is what keeps this module — and therefore every state
-// model and menu file that calls it — free of React and of MUI's
-// ToggleButton/Tooltip. `menuItemAdornment.tsx` turns the description into
-// `PinAdornment` at the point the menu is drawn. See
-// reference/EAGER_BUNDLE.md; `menuItems.purity.test.ts` holds it.
-//
-// Each is the plain builder in `toggleMenuItems.ts` plus a pin, and each is
-// written that way — `checkboxItem` / `radioItems` build the row — so the
-// promotable and plain forms of a row can differ only by the pin.
-// A promotable setting as one native checkbox menu row: the value toggles the
-// track (inheriting native hover/sizing/keyboard), and a trailing pin applies
-// this value to every open track of the display type, offering the display-type
-// default as its snackbar's one action. Always shown so the capability is
-// discoverable.
-//
-// **The row itself is `checkboxItem`'s**, so the two builders can only ever
-// differ by the pin. They used to be two literals, and had already drifted: this
-// one accepted `helpText` and `keepMenuOpen` while silently dropping `disabled`
-// and `disabledHelpText`, so a promotable row could not be greyed out the way
-// its plain sibling could. Sharing the body is also what makes a future
-// change to what a checkbox row *is* reach both — the failure `checkboxItem`'s
-// own comment records is a menu regressing by omission.
-//
-// `keepMenuOpen` is left unset by default, so `CascadingMenu` keeps the row open
-// by its checkbox type: these rows only write a setting, users flip several in
-// one visit, and the menu is an observer so the ticks and pins move live. A row
-// whose click opens a dialog instead (colorBy's "Tag...") passes false.
-/** #menuBuilder promotableToggleItem | `checkboxItem` plus an apply-to-open-tracks pin */
-export function promotableToggleItem({ label, checked, onToggle, pin, ...opts }) {
-    return {
-        ...checkboxItem(label, checked, onToggle, opts),
-        pin: { control: pin, label },
-    };
-}
-// ONE radio row of a promotable-value group — the escape hatch, for a group the
-// plural builder below can't express. **Reach for `promotableRadioItems` first**:
-// every option in a group has to get a pin, and hand-naming the rows is what
-// leaves one without.
-//
-// The rows that genuinely need this: `pin` is optional here, for a row with no
-// single value to promote yet (the colorBy "Tag..." row before a tag is picked)
-// or a display whose slot isn't promotable at all (the shared colorBy menu on
-// gwas/variants); and the alignments size presets, whose group is gated row by
-// row (`needsContent`) and mixes in a non-promotable "Custom..." peer.
-//
-// **The row itself is `radioItem`'s**, for the reason `promotableToggleItem`'s
-// is `checkboxItem`'s: it was a second literal, and it had drifted the same way
-// its checkbox sibling had — naming `helpText`/`keepMenuOpen` by hand and so
-// silently dropping `disabled` and `disabledHelpText`, which the
-// alignments size presets have to bolt back on afterwards (`needsContent`).
-/** #menuBuilder promotableRadioItem | `radioItem` plus an apply-to-open-tracks pin */
-export function promotableRadioItem({ label, checked, onClick, pin, ...opts }) {
-    return {
-        ...radioItem(label, checked, onClick, opts),
-        ...(pin && {
-            pin: { control: pin, label },
-        }),
-    };
-}
-// A whole promotable radio group: `radioItems` plus one pin per option. The
-// plural form of the builder above, and the one to reach for on a group whose
-// options differ only in their value — which is all five of them today
-// (`heightMode`, `displayMode`, `showLabels`, `subfeatureLabels`,
-// `sashimiArcsMode`; the two label groups reach it through canvas's
-// `inlineRadioGroup`).
-//
-// **Every option in a group gets a pin, the `promotedBase` value included** —
-// once a non-base value is promoted, pinning the base back is the only per-value
-// way to undo it from its own row, and a radio group with one row silently
-// missing its trailing control reads as a bug. Building the group here is what
-// makes that structural instead of a rule to remember: `sashimiArcsMode`'s base
-// looked unpinnable precisely because each row had been named by hand. Prefer
-// this over `.map(promotableRadioItem)` whenever the pin is a function of the
-// option's value.
-//
-// `pin` is a factory rather than an array so it can't be a row short. Pass
-// `value => makePin(self, slot, value)`, or a model member of that shape where
-// the menu module is handed a duck-typed model (alignments).
-//
-// The rows are `radioItems`' own, so the promotable and plain groups can't drift
-// on anything but the pin. `radioItems` maps `options` in order, which is what
-// lets each row be paired back to the option that built it.
-/** #menuBuilder promotableRadioItems | `radioItems` plus a pin per option, from a factory over the value */
-export function promotableRadioItems(options, current, setMode, pin) {
-    return radioItems(options, current, setMode).map((item, i) => {
-        const { value, label } = options[i];
-        return { ...item, pin: { control: pin(value), label } };
-    });
-}