archaeopteryx 3.23.0 → 3.25.0

package/README.md

@@ -25,7 +25,7 @@ config key live and shows the exact config JSON to copy into your own
 `launch()` call.
 
 * [Auspice / Nextstrain JSON (Time | Div, Clock plot)](https://cmzmasek.github.io/archaeopteryx-js/demo.html?tree=auspice)
-* [Swine H1 HA1 + alignment (Nexus)](https://cmzmasek.github.io/archaeopteryx-js/demo.html?tree=swh1)
+* [Swine H1 HA1 + alignment (Nexus; Clock plot from the years in the names)](https://cmzmasek.github.io/archaeopteryx-js/demo.html?tree=swh1)
 * [BEAST annotations (Nexus)](https://cmzmasek.github.io/archaeopteryx-js/demo.html?tree=beast)
 * [Flavivirus mature peptides (10 trees)](https://cmzmasek.github.io/archaeopteryx-js/demo.html?tree=flavivirus)
 * [SARS-CoV-2 time tree (calendar)](https://cmzmasek.github.io/archaeopteryx-js/demo.html?tree=sarscov2)
@@ -64,23 +64,32 @@ Archaeopteryx.js has the following dependencies:
  * d3.js (version 7): https://www.npmjs.com/package/d3
  * sax.js (1.6.1): https://www.npmjs.com/package/sax/v/1.6.1
  
-For **raster PNG export** (optional — the PNG entry appears in the Download
-menu only when `window.Canvg` is present):
- * canvg (4.x): https://www.npmjs.com/package/canvg — publishes ES modules
-   only (no classic-script global build), so bridge it yourself:
-   ```html
-   <script type="module">
-       import {Canvg} from 'http://path/to/canvg.js'; // a self-contained build; see below
-       window.Canvg = Canvg;
-   </script>
-   ```
-   A module script is deferred regardless of where it sits in the page, and
-   PNG export only runs later from a Download click, so this can go anywhere
-   before the click — it does not need to precede archaeopteryx.js's own
-   `<script>` tag. `docs/lib/canvg.js` in this repository is one such
-   self-contained build (npm's `canvg@4.0.3` bundled into one file, e.g. via
-   `esm.sh/canvg@4?bundle`, with its one unnecessary Node-environment shim
-   import removed — see the file's own header comment).
+For **raster PNG export** (optional — the PNG entry, the Copy PNG button and
+the PNG-scale row appear only when `window.Canvg` is present):
+ * canvg (4.x): https://www.npmjs.com/package/canvg. **Load it before
+   `launch()` is called:** the Download menu looks for it at click time, but
+   the Copy PNG button and the PNG-scale row are built with the control
+   panel at launch, so a page that provides it later gets a PNG entry and
+   nothing else. canvg publishes ES modules only (no classic-script global
+   build); this repository ships two ready-made files:
+   * `docs/lib/canvg.global.js` — a classic-script build for a plain
+     `<script src="canvg.global.js"></script>`, or for one more file in a
+     site's concatenated bundle; it defines `window.Canvg` itself. This is
+     what the demo pages use. (Generated from `canvg.js` by
+     `test/make_canvg_global.js`; a unit test keeps the two in step.)
+   * `docs/lib/canvg.js` — the self-contained ES module build (npm's
+     `canvg@4.0.3` bundled into one file via `esm.sh/canvg@4?bundle`, with
+     its one unnecessary Node-environment shim import removed — see the
+     file's own header), for a page that prefers a module bridge of its own:
+     ```html
+     <script type="module">
+         import {Canvg} from 'http://path/to/canvg.js';
+         window.Canvg = Canvg;
+     </script>
+     ```
+     A module script runs after the document is parsed, so a page that calls
+     `launch()` from an inline script during parsing must use the classic
+     build instead.
 
 For **vector PDF export** (optional — the PDF entry appears in the Download
 menu only when both are loaded before archaeopteryx.js):
@@ -933,11 +942,28 @@ ancestors' points, each at its own date and divergence; the panel opens
 without them, since the line is the tips' and a deep root would crowd them
 into a corner.
 
-The button is offered on a tree that has **Time | Div** and whose line can
-be drawn: three tips or more, not all on one date. A tree sampled at one
-moment has no slope to estimate. (A tree whose branch lengths are divergence
-and whose tips alone are dated — the tree a root-to-tip plot is run on
-*before* dating — has no plot yet.)
+The button is offered on two kinds of tree, whenever the line can be drawn
+(three tips or more, not all on one date; a tree sampled at one moment has
+no slope to estimate):
+
+- a tree that has **Time | Div**: every node is dated and has a divergence,
+  so the ancestors can be shown too;
+- a tree whose **branch lengths are its divergence and whose tips alone are
+  dated** — the tree a root-to-tip plot is run on *before* dating, TempEst's
+  case. A tip's divergence is the sum of the branch lengths from the root;
+  the plot has tips only (**Internal nodes** is not offered, since no
+  ancestor is dated); **Root date, in the tree** says `none`, since the tree
+  states no root date, and **Rate** is in the tree's own branch length unit,
+  where it states one. A tip's date is what the file states for it (a
+  phyloXML `<date>`, a `num_date` annotation) or, failing that, the date in
+  its **name**, as TempEst reads it: the rightmost date the label carries
+  (`A/swine/Iowa/A02524571/2020|1A.3.3.3` is 2020; a year alone is taken as
+  mid-year, 2020.5; a day/month-ambiguous `03/04/2020` is read day first),
+  and the panel's note says how many names it read and how many were
+  ambiguous. An ancestor is never dated by its name. Every tip must be
+  dated, by the file or by its name, and every branch must have a length: a
+  tree with a gap is not offered the plot, rather than plotted with tips
+  missing.
 
 # forester.js
 forester.js is a general suite for dealing with phylogenetic trees.
@@ -1039,8 +1065,8 @@ Both entry points take **exactly** the arguments shown — a call with the old
 trailing arguments (the separate settings bag, `nodeVisualizations`,
 `nodeLabels`, `specialVisualizations`, or the positional Newick parse
 options) **throws** with a message saying where each one went: everything now
-lives in the **one config object** (`nodeLabels` and
-`internalNumericLabels` are config keys). `config` itself is optional — `archaeopteryx.launch('#phylogram1',
+lives in the **one config object** (`internalNumericLabels` is a config key;
+`nodeLabels` is retired, see the deprecated keys below). `config` itself is optional — `archaeopteryx.launch('#phylogram1',
 tree)` works.
 
 `container` is a **CSS selector or the DOM element itself** (frameworks hand
@@ -1534,14 +1560,13 @@ copy-pastable JSON.
 | `onViewChange` | `null` | `function (state, encoded)`, called once per settled redraw when the view changed: `state` as `getViewState()` returns it, `encoded` its hash-ready string. The demo pages write it into the URL. |
 | `searchBinitialValue` | `null` | Prefill search box B. |
 | `enableVisualizations` | `true` | Offer the Color / Shape visualizations (which fields they cover is decided from the tree). |
-| `initialVisualization` | `null` | The visualization to open with, by its Color-menu name (e.g. `'Host'`; case-insensitive). A name the tree cannot honour logs a console warning and falls back to the automatic choice, so a site-wide value is safe on trees without that field. Default: Archaeopteryx.js picks the most informative field itself. |
+| `initialVisualization` | `null` | The visualization to open with, by its Color-menu name (e.g. `'Host'`; case-insensitive). A name the tree cannot honour logs a console warning and falls back to the automatic choice, so a site-wide value is safe on trees without that field. A name the tree *can* honour is always honoured, but when it is a field the automatic choice would not have opened with -- more than 20 values, or a value on fewer than two thirds of the tips -- a console warning says so and names the field the viewer would have chosen. Default: Archaeopteryx.js picks the most informative field itself. |
 | `visualizationsLegendXpos` | `254` | Legend position, x. |
 | `visualizationsLegendYpos` | `30` | Legend position, y. |
 | `enableDownloads` | `true` | Offer the download buttons. |
 | `pngExportScale` | `4` | The PNG resolution the Download section starts on: 2, 4 or 8 (any other value is snapped to the nearest, with a console warning). |
 | `nhExportWriteConfidences` | `true` | Write confidences into exported Newick. |
 | `internalNumericLabels` | `'auto'` | Newick / Nexus parsing: how a bare numeric internal label (`)100:0.05`) is read. `'auto'` reads them as confidence values only when *every* internal label looks like support; `'confidence'` reads every numeric label as one, whatever its value; `'label'` keeps them as names. Replaces `nhConfidenceValuesAsInternalNames` (still accepted, with a warning; its `true` maps to `'confidence'`). |
-| `nodeLabels` | `null` | Custom label-field checkboxes: `{key: {label, description, propertyRef, showButton, selected}}` — each adds a panel checkbox labelling nodes with the named property's value. (Was `launch()`'s sixth positional argument.) |
 | `enableSubtreeDeletion` | `true` | Offer node / subtree deletion in the node menu. |
 | `enableAccessToDatabases` | `true` | Offer the “Access DB” link in the node menu. |
 | `enableManualNodeSelection` | `false` | Add the Select/Deselect entries to the node menu. |
@@ -1564,7 +1589,7 @@ whatever it names.
 
 ### Accepted, with a warning
 
-Four keys are neither current nor removed: they are accepted so an existing
+Five keys are neither current nor removed: they are accepted so an existing
 embed keeps working, and warn on the console.
 
 | Key | What happens |
@@ -1573,6 +1598,7 @@ embed keeps working, and warn on the console.
 | `nhConfidenceValuesInBrackets` | Retired: ignored. It gated whether `[95]` is read as a confidence, but setting it `false` never reinterpreted the bracket — it *discarded* it, so the option's only effect was to throw support values away. A bracket that is not a number is a Newick comment and was ignored either way, and NHX / BEAST blobs go through a different path. Bracketed values are now always read as confidences. |
 | `showTimeAxis` | Translated to `showScaleAxis`, value unchanged: the switch now also draws a distance axis on a tree that is not in time. An explicit `showScaleAxis` always wins. |
 | `timeAxisGrid` | Translated to `showScaleGrid`, value unchanged. |
+| `nodeLabels` | Retired in 3.25.0: ignored, with a warning. The custom label checkboxes it declared predate the Metadata checkbox and its "Metadata fields…" chooser, which offer exactly the fields the tree carries; a fixed site-wide list put checkboxes for absent fields on every tree. `labelProperties` sets the starting fields where the automatic choice is not wanted. Removed in a later release. |
 
 ### What replaced the rest
 
@@ -1717,6 +1743,21 @@ All 118 of them, alphabetically:
 | `visualizationsLegendXposOrig` | Internal bookkeeping; set visualizationsLegendXpos. |
 | `visualizationsLegendYposOrig` | Internal bookkeeping; set visualizationsLegendYpos. |
 
+### Removed from `forester` — calling these throws `TypeError`
+
+3.0.0 also dropped twelve exports of `forester.js` that the viewer no longer
+used. They are gone, not stubbed, so a 2.x embedding that calls one fails with
+`TypeError: forester.<name> is not a function` — inside its own parse step, if
+that is where it called it.
+
+| Function | Why, and what to do instead |
+| --- | --- |
+| `collectPropertyRefs` | Nothing to call. The viewer derives the Color-by candidates (`forester.visualizationCandidates(tree)`, below) and the label-field chooser's list from the tree itself, and substitutes a readable name property (`genome_name`) for identifier-like tip names on its own. A 2.x embedding that built `nodeLabels` from this function's result should delete that block together with the `nodeLabels` key; `labelProperties` sets the starting label fields where the automatic choice is not wanted. |
+| `collapse`, `unCollapse` | The subtree-collapse feature was removed; they were its only writers. |
+| `getChildren` | Only meant something while collapse existed; read `node.children`. |
+| `findByTaxonomyCode`, `findByTaxonomyScientificName` | Superseded by the search (the panel's search fields). |
+| `calcAverageTreeHeight`, `calcMaxDepth`, `calcBranchLengthSimpleStatistics`, `removeMaxBranchLength`, `isHasNodeData`, `getOneDistinctTaxonomy` | Never used by the viewer; nothing replaces them. |
+
 ## The automatic visualization system (developer spec)
 
 This section, together with **Value grouping** below, is written to be
@@ -2599,15 +2640,25 @@ deliberate difference.)
 ### The clock plot
 
 **Model** (`forester.js`, pure). `forester.clockPlotKind(phy)` answers
-`'divergence'` or `null`: the tree has Time and Div
-(`forester.hasTimeAndDivergence`) and three tips or more, not all on one
-date. It is asked of the **tree**, never of the view. A second kind,
-`'root-to-tip'` — divergence branch lengths, dated tips, no dated ancestors —
-is described beside the function and not built. `forester.clockPlotData(phy,
-view)` returns `{kind, forward, unit, fromRates, points, root, fit}`: a point
+`'divergence'`, `'root-to-tip'` or `null`: `'divergence'` where the tree has
+Time and Div (`forester.hasTimeAndDivergence`); `'root-to-tip'` where every
+tip is dated (by the file, or by the date in its name:
+`forester.parseTipLabelDate`), no ancestor is, every branch states a length
+and no branch states a clock rate (a clock-model tree's lengths are time) — and in
+both cases three tips or more, not all on one date. It is asked of the
+**tree**, never of the view. `forester.clockPlotData(phy, view)` returns
+`{kind, forward, unit, divUnit, fromRates, points, root, fit}`: a point
 `{node, date, div, tip}` per node of the view (a tip also carries its
-`residual`), `forward` false where the dates are ages, `fromRates` true where
-the divergence is time × clock rate, and `fit` =
+`residual`; on a root-to-tip tree the tips only, their `div` the sum of the
+branch lengths from the tree's root), `forward` false where the dates are
+ages (on a root-to-tip tree: where their unit is geologic), `divUnit` the
+divergence's unit (`subs/site` on a Time | Div tree, a root-to-tip tree's
+stated branch length unit, or `null`), `fromRates` true where the divergence
+is time × clock rate, `calendar` true where the dates are calendar years
+(their unit says so, or they were read off the tips' names), `fromNames` and
+`ambiguousNames` how many tips a root-to-tip tree dates by their names and
+how many of those are day/month-ambiguous (read day first), `root.date`
+`null` on a root-to-tip tree, and `fit` =
 `forester.clockRegression(dates, divergences)` over the tips — ordinary least
 squares about the means, `{n, slope, intercept, r2}` — plus `rate` (the slope
 in the direction time runs) and `rootDate` (where the line reaches the view

package/archaeopteryx.d.ts

@@ -29,9 +29,13 @@ export interface Phylogeny extends PhylogenyNode {
 
 export type Layout = 'rectangular' | 'circular' | 'unrooted';
 
-/** One custom label-field entry (the config's nodeLabels values).
+/** @deprecated Retired in 3.25.0 with `nodeLabels`: accepted with a console
+ * warning, no effect; removed in a later release. The Metadata checkbox and
+ * its "Metadata fields…" chooser offer the tree's own fields.
  *
- * Two modes:
+ * One custom label-field entry (the config's nodeLabels values).
+ *
+ * Two modes (3.0.0 to 3.24.0):
  *  - a PANEL CHECKBOX needs label, description AND propertyRef set, plus
  *    showButton: true -- omit showButton (or any of the three) and no
  *    checkbox appears;
@@ -85,6 +89,10 @@ export interface ArchaeopteryxConfig {
     nhConfidenceValuesAsInternalNames?: boolean;
     nhConfidenceValuesInBrackets?: boolean;
     nhExportWriteConfidences?: boolean;
+    /** @deprecated Retired in 3.25.0: accepted with a console warning, no
+     * effect; removed in a later release. The Metadata checkbox and its
+     * "Metadata fields…" chooser offer the tree's own fields; labelProperties
+     * sets the starting fields. */
     nodeLabels?: Record<string, NodeLabelSpec> | null;
     /** Called once per settled redraw when the view changed: the state as
      * getViewState() returns it, and its hash-ready string. */
@@ -176,8 +184,8 @@ export interface ViewState {
     shapeBy?: string;
     /** The panel's checked boxes: name, taxonomy, sequence, confidence,
      * madValues, branchLength, external, internal, nodeEvents, branchEvents,
-     * supportDots, shortNames, autoHide, visualizations, visualStyles, and
-     * custom:<key> for a nodeLabels checkbox. */
+     * supportDots, shortNames, autoHide, visualizations, visualStyles. (A
+     * custom:<key> flag from a 3.24.0 hash is read and ignored.) */
     show?: string[];
     font?: number;
     node?: number;

package/archaeopteryx.js

@@ -20,7 +20,7 @@
  *
  */
 
-// v 3.23.0
+// v 3.25.0
 // 2026-09-17
 //
 // Archaeopteryx.js is a software tool for the visualization and
@@ -103,7 +103,7 @@ function (root, d3, forester, phyloXml) {
     // IIFE's own function name -- a plain object says what it is.)
     let archaeopteryx = {};
 
-    const VERSION = '3.23.0';
+    const VERSION = '3.25.0';
     const WEBSITE = 'https://cmzmasek.github.io/archaeopteryx-js/';
     const DESKTOP_WEBSITE = 'https://cmzmasek.github.io/archaeopteryx/';
     const SOURCE_WEBSITE = 'https://github.com/cmzmasek/archaeopteryx-js';
@@ -539,7 +539,6 @@ function (root, d3, forester, phyloXml) {
     let _container = null;            // the resolved container ELEMENT (never a selector string)
     let _intervalId = 0;
     let _maxLabelLength = 0;
-    let _nodeLabels = null;
     let _state = null;      // live display state: what the control panel writes to
     let _root = null;
     let _root_const = null;
@@ -606,6 +605,7 @@ function (root, d3, forester, phyloXml) {
     const DOMAIN_SCALE_HEADROOM = 0.9;    // drawn length over reserved length
     const DOMAIN_BOX_MIN_H = 6;
     const DOMAIN_BOX_MAX_H = 16;
+    const LEGEND_MAX_ROWS = 20;           // value rows a legend lists before "n more"; the rest fold
     const DOMAIN_BACKBONE_COLOR = 'rgb(100,100,100)';   // the same in both themes and in exports
     const DOMAIN_SHADOW_COLOR = 'rgb(8,18,21)';
     const DOMAIN_SHADOWS = [[0.4, 0.7, 40], [0.9, 1.5, 28], [1.6, 2.5, 17]];   // dx, dy, alpha of 255, in drawing order
@@ -1948,7 +1948,32 @@ function (root, d3, forester, phyloXml) {
             // an explicit request is honoured even for a wide field (21+
             // values) the automatic path would only offer, never impose;
             // autoColorId too, so it survives subtree views like the
-            // automatic pick does
+            // automatic pick does.
+            //
+            // Honoured, but not in silence. A request for a field the
+            // automatic choice would not open with -- wide, or sparse (on
+            // fewer than 2/3 of the tips; it opens only when nothing denser
+            // exists) -- says so in the console and names the field the
+            // viewer would have chosen. BV-BRC's virus trees carried a
+            // site-wide 'Host' from the influenza days: family trees opened
+            // coloured by 39 to 168 hosts while Genus (4 to 15 values) sat
+            // in the file, and nothing anywhere said the viewer had been
+            // overruled (Christian, 2026-10-08: a console warning when a
+            // sub-optimal visualization is forced is needed). A request for
+            // a clean field that merely ranks below the automatic pick is a
+            // site's taste and warns nothing; nor does a sparse field that
+            // is the automatic pick itself.
+            let auto = forester.openingVisualization(_vis.candidates);
+            if ((requested.wide || requested.sparse) && !(auto && auto.id === requested.id)) {
+                let why = requested.wide
+                    ? requested.values.length + ' distinct values on this tree, more than the '
+                        + LEGEND_MAX_ROWS + ' the legend lists'
+                    : 'a value on ' + requested.coverage + ' of the tree\'s ' + requested.total + ' tips';
+                console.warn(WARNING + ': initialVisualization "' + _settings.initialVisualization
+                    + '" names a field with ' + why + '; left to itself the viewer would '
+                    + (auto ? 'open with "' + auto.label + '" (' + auto.values.length + ' values)'
+                        : 'open uncoloured'));
+            }
             _vis.autoColorId = requested.id;
             _vis.colorId = requested.id;
             _state.showVisualizations = true;
@@ -2144,6 +2169,7 @@ function (root, d3, forester, phyloXml) {
         }
         dialog.addEventListener('close', close);
 
+        let placed = false;   // set by place() once the picker has been put somewhere
         render(false);
         dialog.show();
         place();
@@ -2151,40 +2177,67 @@ function (root, d3, forester, phyloXml) {
         // Beside the legend it edits, never on top of it -- a picker that hides
         // the swatch it is changing defeats the live preview.
         //
-        // Re-measured rather than remembered, for two reasons: every redraw
-        // DESTROYS and rebuilds the legend group, so a held reference goes
-        // stale and measures zero; and the card grows when the [reset colors]
-        // chip appears on the first pick, which would leave a
-        // positioned-once picker sitting over the counts. It only MOVES when
-        // it would otherwise overlap, so the dialog does not chase the legend
-        // around while the user drags.
+        // Placed OUTRIGHT the first time, viewport-fixed. A non-modal <dialog>
+        // appended to the body sits at its static position, the end of the
+        // document: on the demo page that is the top of the window (the
+        // container is out of flow), on a page that flows, such as BV-BRC's,
+        // it is below everything on it. Until 2026-10-08 the picker moved
+        // only when that spot overlapped the card, so on BV-BRC it opened
+        // under the site's own bars, off the bottom of the window
+        // (Christian's screenshot). Fixed positioning also keeps a scrolling
+        // page from carrying it away.
+        //
+        // Re-measured rather than remembered afterwards, for two reasons:
+        // every redraw DESTROYS and rebuilds the legend group, so a held
+        // reference goes stale and measures zero; and the card grows when the
+        // [reset colors] chip appears on the first pick, which would leave a
+        // positioned-once picker sitting over the counts. Once placed it only
+        // MOVES when it would otherwise overlap, so the dialog does not chase
+        // the legend around while the user drags.
         function place() {
             let el = anchorClass ? document.querySelector('g.' + anchorClass) : null;
             let box = el ? el.getBoundingClientRect() : null;
-            if (!box || !box.width) {
-                return;
+            if (box && !box.width) {
+                box = null;
             }
-            let now = dialog.getBoundingClientRect();
-            let overlaps = now.width > 0
-                && !(now.left >= box.right || now.right <= box.left
-                    || now.top >= box.bottom || now.bottom <= box.top);
-            if (now.width > 0 && !overlaps) {
-                return;
+            if (placed) {
+                if (!box) {
+                    return;
+                }
+                let now = dialog.getBoundingClientRect();
+                let overlaps = now.width > 0
+                    && !(now.left >= box.right || now.right <= box.left
+                        || now.top >= box.bottom || now.bottom <= box.top);
+                if (!overlaps) {
+                    return;
+                }
             }
             let w = dialog.offsetWidth;
             let h = dialog.offsetHeight;
-            // to the right of the card, or to its left when that would leave
-            // the viewport
-            let left = box.right + 10;
-            if (left + w > window.innerWidth - 6) {
-                left = box.left - w - 10;
+            let left;
+            let top;
+            if (box) {
+                // to the right of the card, or to its left when that would
+                // leave the viewport
+                left = box.right + 10;
+                if (left + w > window.innerWidth - 6) {
+                    left = box.left - w - 10;
+                }
+                top = box.top;
+            } else {
+                // no card to sit beside (the view has no swatch for the value):
+                // the tree area's top left corner, inside the window
+                let area = _container ? _container.getBoundingClientRect() : null;
+                left = area ? area.left + 14 : 10;
+                top = area ? Math.max(area.top, 0) + 14 : 10;
             }
             setStyles(dialog, {
                 'position': 'fixed',
                 'margin': '0',
                 'left': Math.max(6, Math.min(window.innerWidth - w - 6, left)) + 'px',
-                'top': Math.max(6, Math.min(window.innerHeight - h - 6, box.top)) + 'px'
+                'top': Math.max(6, Math.min(window.innerHeight - h - 6, top)) + 'px'
             });
+            placed = true;
         }
         setTimeout(function () {
             document.addEventListener('pointerdown', onOutside, true);
@@ -2521,7 +2574,6 @@ function (root, d3, forester, phyloXml) {
         // is then just its "no value" row
         const isRange = kind === 'color' && colorModeOf(vis) === 'range' && vis.values.length > 0;
 
-        const LEGEND_MAX_ROWS = 20;
         let rows = [];
         let hidden = 0;
         if (!isRange) {
@@ -4725,25 +4777,6 @@ function (root, d3, forester, phyloXml) {
             l = append(l, labelPropertiesOf(phynode));
         }
 
-        if (_nodeLabels && phynode.properties) {
-            const props_length = phynode.properties.length;
-            if (props_length > 0) {
-                for (const value of Object.values(_nodeLabels)) {
-                    if (value.selected === true && value.propertyRef) {
-                        let prop_text = '';
-                        for (let pm = 0; pm < props_length; ++pm) {
-                            if (phynode.properties[pm].ref === value.propertyRef && phynode.properties[pm].datatype === 'xsd:string' && forester.isNodeScopedProperty(phynode.properties[pm])) {
-                                if (prop_text.length > 0) {
-                                    prop_text += ', '
-                                }
-                                prop_text += phynode.properties[pm].value;
-                            }
-                        }
-                        l = append(l, prop_text);
-                    }
-                }
-            }
-        }
 
 
         if (_state.showDistributions && phynode.distributions && phynode.distributions.length > 0) {
@@ -5522,6 +5555,21 @@ function (root, d3, forester, phyloXml) {
                 return v;
             },
             note: 'the grid follows the scale axis, time or distance'
+        },
+        // Retired in 3.25.0 (Christian, 2026-10-08: "go with the deprecation").
+        // The custom label checkboxes it declared -- a site's fixed list of
+        // property refs, one panel checkbox each, labelling nodes with the
+        // property's value -- predate the Metadata checkbox and its
+        // "Metadata fields…" chooser, which offer exactly the fields the tree
+        // carries and replace identifier-like tip names with a name property
+        // on their own. On BV-BRC the list, written for influenza, put eight
+        // checkboxes on every virus tree, six of them for fields the tree
+        // did not have. The checkbox code went with the key (the label
+        // text, the panel rows, the view state's custom:<key> flags, which
+        // an old hash may still carry and the reader now ignores). Accepted
+        // with this warning for one release cycle, then REMOVED_CONFIG.
+        nodeLabels: {
+            note: 'the Metadata checkbox and its "Metadata fields…" chooser offer the tree\'s own fields; labelProperties sets the starting fields'
         }
     };
 
@@ -5721,7 +5769,6 @@ function (root, d3, forester, phyloXml) {
         'internalNumericLabels',
         'ladderizeTree',
         'nhExportWriteConfidences',
-        'nodeLabels',
         'onViewChange',
         'panelDensity',
         'pngExportScale',
@@ -6321,19 +6368,6 @@ function (root, d3, forester, phyloXml) {
         } else if (typeof _settings.onViewChange !== 'function') {
             throw new Error(ERROR + '"onViewChange" must be a function (state, encoded) or null');
         }
-        if (_settings.nodeLabels === undefined) {
-            _settings.nodeLabels = null;
-        } else if (_settings.nodeLabels !== null && typeof _settings.nodeLabels !== 'object') {
-            throw new Error('nodeLabels must be an object (see the README) or null');
-        }
-        if (_settings.nodeLabels) {
-            // a DEEP copy: the viewer writes runtime state into these specs
-            // (the checkbox element id, the live checked state), and the
-            // caller's config object must stay declarative -- an embedder
-            // reusing one nodeLabels constant across launches must not
-            // inherit the previous session's checkbox state
-            _settings.nodeLabels = JSON.parse(JSON.stringify(_settings.nodeLabels));
-        }
         if (_settings.pngExportScale === undefined) {
             _settings.pngExportScale = 4;
         } else if (typeof _settings.pngExportScale !== 'number'
@@ -6593,7 +6627,7 @@ function (root, d3, forester, phyloXml) {
                 + ' trailing arguments were removed. The separate settings bag merged into the one'
                 + ' config object; "nodeVisualizations" and "specialVisualizations" are gone for good'
                 + ' (visualizations are derived automatically from the tree itself); "nodeLabels"'
-                + ' moved into the config as its "nodeLabels" key.');
+                + ' is retired (the Metadata checkbox offers the tree\'s own fields).');
         }
         if (phylo === undefined || phylo === null) {
             throw new Error(ERROR + 'input tree is undefined or null');
@@ -6684,9 +6718,8 @@ function (root, d3, forester, phyloXml) {
             .on('zoom', zoom);
         _basicTreeProperties = forester.collectBasicTreeProperties(_treeData);
 
-        // Every launch starts from a clean slate: _vis is rebuilt below and
-        // _nodeLabels reassigned, never inherited from a previous launch in
-        // the same page.
+        // Every launch starts from a clean slate: _vis is rebuilt below, never
+        // inherited from a previous launch in the same page.
         _radialRotation = 0;
         _radialLabelsHorizontal = false;
         _msaColOffset = 0;
@@ -6704,7 +6737,6 @@ function (root, d3, forester, phyloXml) {
         // candidate ranking over 13k tips before the card could even paint.
         checkLayoutValue(cfg.state ? cfg.state.layout : undefined);
         initializeSettings(cfg.settings);
-        _nodeLabels = _settings.nodeLabels || null;
 
         // whatever a previous launch left in this container (or in the
         // container before it) goes now, so the old tree does not sit under
@@ -9896,20 +9928,6 @@ function (root, d3, forester, phyloXml) {
         return found;
     }
 
-    // The config's custom label checkboxes (nodeLabels) that are offered
-    function customLabelEntries() {
-        let out = [];
-        if (_nodeLabels) {
-            Object.keys(_nodeLabels).forEach(function (key) {
-                let v = _nodeLabels[key];
-                if (v && v.label && v.showButton === true && v.propertyRef && v.description) {
-                    out.push({key: key, entry: v});
-                }
-            });
-        }
-        return out;
-    }
-
     function searchStateOf(idx) {
         let spec = currentSearchSpec(idx);
         let value = (spec.value === null || spec.value === undefined) ? '' : String(spec.value);
@@ -9957,11 +9975,6 @@ function (root, d3, forester, phyloXml) {
         }).map(function (f) {
             return f[0];
         });
-        customLabelEntries().forEach(function (c) {
-            if (c.entry.selected === true) {
-                s.show.push('custom:' + c.key);
-            }
-        });
         s.font = _state.externalNodeFontSize;
         s.node = _state.nodeSizeDefault;
         s.branch = _state.branchWidthDefault;
@@ -10107,9 +10120,6 @@ function (root, d3, forester, phyloXml) {
             VIEW_SHOW_FLAGS.forEach(function (f) {
                 _state[f[2]] = on.has(f[0]);
             });
-            customLabelEntries().forEach(function (c) {
-                c.entry.selected = on.has('custom:' + c.key);
-            });
         }
         if (isFinite(s.font)) {
             setFontSizes(Number(s.font));
@@ -10259,11 +10269,6 @@ function (root, d3, forester, phyloXml) {
         VIEW_SHOW_FLAGS.forEach(function (f) {
             setCheckboxValue(f[1], _state[f[2]] === true);
         });
-        customLabelEntries().forEach(function (c) {
-            if (c.entry.cb_id) {
-                setCheckboxValue(c.entry.cb_id, c.entry.selected === true);
-            }
-        });
         setCheckboxValue(MSA_CB, _state.showMsa === true);
         setCheckboxValue(MSA_LOGO_CB, _state.showMsaLogo === true);
         setCheckboxValue(HEATMAP_CB, _state.showHeatmap === true);
@@ -11171,10 +11176,12 @@ function (root, d3, forester, phyloXml) {
             row.appendChild(input);
             row.appendChild(span);
             options.appendChild(row);
-            return input;
+            return row;
         };
         check('Regression line', 'line', 'to show/hide the least-squares line through the tips');
-        check('Internal nodes', 'internal', 'to show/hide the internal nodes: their dates were inferred,'
+        // on a root-to-tip tree no ancestor is dated: nothing to show, so the
+        // choice is not offered (layClockPlot hides it by the data's kind)
+        let internalRow = check('Internal nodes', 'internal', 'to show/hide the internal nodes: their dates were inferred,'
             + ' and they take no part in the line');
         let deselect = document.createElement('button');
         deselect.type = 'button';
@@ -11197,7 +11204,7 @@ function (root, d3, forester, phyloXml) {
         body.appendChild(note);
 
         _clockPlot = {dialog: shell.dialog, svg: svg, axes: axes, internal: internal, line: line, tips: tips,
-            ring: ring, box: box, stats: stats, note: note, deselect: deselect,
+            ring: ring, box: box, stats: stats, note: note, deselect: deselect, internalRow: internalRow,
             data: null, marks: [], seen: null, hover: null, lays: 0, x: null, y: null};
         // the shell's close control, and anything else that closes the dialog
         let closed = function () {
@@ -11408,7 +11415,9 @@ function (root, d3, forester, phyloXml) {
     }
 
     function layClockPlot(cp, data) {
-        let calendar = data.forward && !!_timeInfo && _timeInfo.type === 'calendar';
+        let calendar = data.calendar;
+        let rootToTip = data.kind === 'root-to-tip';
+        cp.internalRow.style.display = rootToTip ? 'none' : '';
         let shown = data.points.filter(function (p) {
             return p.tip || _clockPlotOptions.internal;
         });
@@ -11464,7 +11473,7 @@ function (root, d3, forester, phyloXml) {
         seg('aptx-clock-frame', left, top, left, bottom);
         let unit = data.unit && !calendar ? ' (' + data.unit + ')' : '';
         text('aptx-clock-title', (data.forward ? 'Date' : 'Age') + unit, (left + right) / 2, CLOCK_PLOT_H - 6, 'middle');
-        let yt = text('aptx-clock-title', 'Divergence (subs/site)', 0, 0, 'middle');
+        let yt = text('aptx-clock-title', 'Divergence' + (data.divUnit ? ' (' + data.divUnit + ')' : ''), 0, 0, 'middle');
         yt.setAttribute('transform', 'translate(12,' + ((top + bottom) / 2) + ') rotate(-90)');
 
         // --- the points: ancestors under the line, tips over it
@@ -11506,12 +11515,13 @@ function (root, d3, forester, phyloXml) {
         let tipCount = data.points.reduce(function (n, p) {
             return n + (p.tip ? 1 : 0);
         }, 0);
-        let per = ' subs/site per ' + (calendar ? 'year' : (data.unit || 'unit of time'));
+        let per = (data.divUnit ? ' ' + data.divUnit : '') + ' per ' + (calendar ? 'year' : (data.unit || 'unit of time'));
         if (fit) {
             treePropRow(cp.stats, 'Rate', clockNumber(fit.rate) + per);
             treePropRow(cp.stats, 'Root date, by the line', fit.rootDate === null
                 ? 'none: divergence does not rise with time' : clockDate(fit.rootDate, calendar));
-            treePropRow(cp.stats, 'Root date, in the tree', clockDate(data.root.date, calendar));
+            treePropRow(cp.stats, 'Root date, in the tree', data.root.date === null
+                ? 'none: only the tips are dated' : clockDate(data.root.date, calendar));
             treePropRow(cp.stats, 'R²', fit.r2 === null ? 'none: every tip has one divergence' : clockNumber(fit.r2));
         } else {
             treePropRow(cp.stats, 'Line', 'none: it takes three tips, not all on one date');
@@ -11520,6 +11530,15 @@ function (root, d3, forester, phyloXml) {
         cp.note.textContent = (data.fromRates
             ? 'Divergence here is each branch’s time × its clock rate: the points show the model’s rates, not a measurement of their own. '
             : '')
+            + (rootToTip
+                ? 'Divergence here is each tip’s distance from the root along the branch lengths the file states; only the tips are dated. '
+                : '')
+            + (data.fromNames > 0
+                ? (data.fromNames === 1 ? 'One tip is dated by its name' : countNumber(data.fromNames) + ' tips are dated by their names')
+                    + ' (a year alone is taken as mid-year'
+                    + (data.ambiguousNames > 0 ? '; ' + countNumber(data.ambiguousNames) + ' with day and month ambiguous, read day first' : '')
+                    + '). '
+                : '')
             + 'The line is fitted to the tips only. Tips share ancestry, so R² describes the fit and is no test.'
             + ' Click a point to select its node; drag to select the tips in a box.';
         // what was laid down, for the browser harness: read here, where it is
@@ -15366,22 +15385,6 @@ function (root, d3, forester, phyloXml) {
     }
 
 
-    function customCbClicked(cb_id) {
-        if (_nodeLabels) {
-            const cb_value = getCheckboxValue(cb_id);
-            for (const value of Object.values(_nodeLabels)) {
-                if (value.label && value.showButton === true && value.propertyRef && value.description) {
-                    if (value.cb_id === cb_id) {
-                        value.selected = cb_value;
-                    }
-                }
-            }
-            search0();
-            search1();
-            update();
-        }
-    }
-
     function taxonomyCbClicked() {
         _state.showTaxonomy = getCheckboxValue(TAXONOMY_CB);
         if (_state.showTaxonomy) {
@@ -18225,9 +18228,12 @@ function (root, d3, forester, phyloXml) {
         // live. Injecting twice is a no-op.
         injectPanelStyles();
 
+        // REMOVED (2026-10-07): the 2.x class "node_mouseover_tooltip" beside
+        // "aptx-tip". A host's old stylesheet outranked .aptx-tip through it
+        // (div.X beats .Y) and restyled the popup; see CHANGELOG, Unreleased.
         if (!_node_mouseover_div) {
             _node_mouseover_div = d3.select("body").append("div")
-                .attr("class", "node_mouseover_tooltip aptx-tip")
+                .attr("class", "aptx-tip")
                 .style("opacity", 1e-6);
         }
 
@@ -18414,20 +18420,6 @@ function (root, d3, forester, phyloXml) {
 
         on(SHORTEN_NODE_NAME_CB, 'click', shortenCbClicked);
 
-        if (_nodeLabels) {
-            for (const [key, value] of Object.entries(_nodeLabels)) {
-                if (value.label && value.showButton === true && value.propertyRef && value.description) {
-                    const cb_id = makeIdForCustomCheckboxButton(key);
-                    on(cb_id, 'click', function () {
-                        customCbClicked(cb_id);
-                    });
-                    if (value.selected === true) {
-                        setCheckboxValue(cb_id, true);
-                    }
-                }
-            }
-        }
-
         on(LABEL_COLOR_SELECT_MENU, 'change', function () {
             let v = this.value;
             if (v && v !== DEFAULT && _vis && _vis.byId[v]) {
@@ -18868,10 +18860,6 @@ function (root, d3, forester, phyloXml) {
             return '<label class="aptx-seg" title="' + tooltip + '"><input type="radio" name="' + radioGroup + '" id="' + id + '">' + content + '</label>';
         }
 
-        function makeIdForCustomCheckboxButton(key) {
-            return key + '__cb';
-        }
-
         function makeDisplayControl() {
             let labels = [];
             let nodes = [];
@@ -18893,17 +18881,6 @@ function (root, d3, forester, phyloXml) {
                 labels.push(makeCheckboxItem('Metadata', PROPERTIES_CB, 'to show/hide the nodes\' metadata (phyloXML'
                     + ' properties: species, host, …) in their labels; Metadata fields… chooses which, and in what order'));
             }
-            if (_nodeLabels) {
-                for (const [key, value] of Object.entries(_nodeLabels)) {
-                    if (value.label && value.propertyRef && value.description) {
-                        const cb_id = makeIdForCustomCheckboxButton(key);
-                        if (value.showButton === true) {
-                            labels.push(makeCheckboxItem(value.label, cb_id, value.description));
-                        }
-                        value.cb_id = cb_id;
-                    }
-                }
-            }
             if (_basicTreeProperties.confidences) {
                 labels.push(makeCheckboxItem('Confidence', CONFIDENCE_VALUES_CB, 'to show/hide confidence values'));
             }

package/forester.js

@@ -20,7 +20,7 @@
  *
  */
 
-// v 3.23.0
+// v 3.25.0
 // 2026-09-17
 //
 // forester.js is a general suite for dealing with phylogenetic trees.
@@ -7254,18 +7254,28 @@
     // a panel linked to the tree, named "Clock plot"; JS only until the
     // design is final.
     //
-    // THE RULE, designed for two kinds of tree, the first of them built:
+    // THE RULE, designed for two kinds of tree (both built; the second on
+    // Christian's word, 2026-10-03):
     //
     // 1. 'divergence' -- a tree with Time and Div (hasTimeAndDivergence): each
     //    node states a date and a divergence from the root, recorded on it or
     //    summed from each branch's time x its clock rate. Every node is a
     //    point; which of the two layouts is on screen does not matter.
-    // 2. 'root-to-tip' (NOT BUILT) -- a tree whose branch lengths are
-    //    divergence and whose tips are dated, with no dates on its ancestors
-    //    (it is not a time tree): a tip's divergence is the sum of the stated
-    //    lengths from the root. Tips only. This is the tree a clock plot is
-    //    wanted for most -- is there a signal worth dating? -- and the one
-    //    whose answer depends on its root.
+    // 2. 'root-to-tip' -- a tree whose branch lengths are its divergence and
+    //    whose tips are dated, with no date on any ancestor (it is not a time
+    //    tree): a tip's divergence is the sum of the stated lengths from the
+    //    root. Tips only. This is the tree a clock plot is wanted for most --
+    //    is there a signal worth dating? -- and the one whose answer depends
+    //    on its root. TempEst's plot. A tip is dated by what the file STATES
+    //    for it (a phyloXML <date>, a num_date annotation), or else by the
+    //    date its NAME carries, read by the label-date parser both programs
+    //    anchor BEAST heights with (Christian, 2026-10-03: names count, as
+    //    TempEst reads them; a year alone is mid-year). An ancestor is never
+    //    dated by its name. Every tip must be dated and every branch must
+    //    state a length: a tip with either missing has no point, and a plot
+    //    that drops tips silently answers a different question than it was
+    //    asked. A clock-model tree (a rate on every branch) is never this
+    //    kind: its lengths are time.
     //
     // In both, the plot is offered when its LINE can be drawn: three tips or
     // more, and not all of them on one date. A tree sampled at one moment has
@@ -7277,19 +7287,76 @@
     // an observation; an ancestor's was inferred, usually with a clock, and
     // counting it would have the estimate confirm itself. The line is not
     // forced through the root, so the date it reaches the root's divergence
-    // at can be held against the date the tree states for the root.
+    // at can be held against the date the tree states for the root -- where
+    // the tree states one; a root-to-tip tree does not, and there the line's
+    // date is the only estimate.
     const CLOCK_PLOT_MIN_TIPS = 3;
 
+    // A tip's date on a root-to-tip tree: the one the file states, else the
+    // one its name carries (forester.parseTipLabelDate: the rightmost date in
+    // the label; a year alone is mid-year; an ambiguous numeric date is read
+    // day first). {value, fromName, ambiguous}, or null for no date at all.
+    function rootToTipDate(n) {
+        let d = auspiceNodeDate(n);
+        if (d !== null) {
+            return {value: d, fromName: false, ambiguous: false};
+        }
+        let m = (typeof n.name === 'string' && n.name.length > 0) ? forester.parseTipLabelDate(n.name) : null;
+        return m ? {value: m.decimalYear, fromName: true, ambiguous: m.ambiguous === true} : null;
+    }
+
+    // Kind 2 of THE RULE, before the tips are counted: dated tips (by the
+    // file or by their names), undated ancestors (by the file; a name dates
+    // no ancestor), a length on every branch, no clock rates.
+    function isRootToTipTree(root) {
+        if (!root || root._divergenceFromRates === true || !everyLengthWasStated(root)) {
+            return false;
+        }
+        let ok = true;
+        forester.preOrderTraversalAll(root, function (n) {
+            if (!ok) {
+                return;
+            }
+            ok = (n.children && n.children.length > 0) ? auspiceNodeDate(n) === null : rootToTipDate(n) !== null;
+        });
+        return ok;
+    }
+
+    // Each node's distance from the root along the stated branch lengths:
+    // a root-to-tip tree's divergence.
+    function rootToTipDistances(root) {
+        let dist = new Map();
+        (function walk(n, d) {
+            dist.set(n, d);
+            let children = n.children;
+            if (children) {
+                for (let i = 0; i < children.length; ++i) {
+                    let len = children[i].branch_length;
+                    walk(children[i], d + ((typeof len === 'number' && isFinite(len)) ? len : 0));
+                }
+            }
+        }(root, 0));
+        return dist;
+    }
+
     /**
      * Which clock plot the tree has, or null for none (see THE RULE above).
      *
      * @param phy the tree
-     * @returns {string|null} 'divergence', or null
+     * @returns {string|null} 'divergence', 'root-to-tip', or null
      */
     forester.clockPlotKind = function (phy) {
-        if (!phy || !forester.hasTimeAndDivergence(phy)) {
+        if (!phy) {
             return null;
         }
+        let kind = forester.hasTimeAndDivergence(phy) ? 'divergence'
+            : (isRootToTipTree(forester.getTreeRoot(phy)) ? 'root-to-tip' : null);
+        if (kind === null) {
+            return null;
+        }
+        let dateOf = kind === 'root-to-tip' ? function (n) {
+            return rootToTipDate(n).value;    // every tip has one: the kind says so
+        } : auspiceNodeDate;
         let tips = 0;
         let first = null;
         let differ = false;
@@ -7298,14 +7365,14 @@
                 return;
             }
             ++tips;
-            let d = auspiceNodeDate(n);
+            let d = dateOf(n);
             if (first === null) {
                 first = d;
             } else if (d !== first) {
                 differ = true;
             }
         });
-        return (tips >= CLOCK_PLOT_MIN_TIPS && differ) ? 'divergence' : null;
+        return (tips >= CLOCK_PLOT_MIN_TIPS && differ) ? kind : null;
     };
 
     /**
@@ -7363,14 +7430,25 @@
      * @param view the tree or clade to plot (the tree, a node, or the
      *        viewer's subtree root); the whole tree where none is given
      * @returns {object|null} null where the tree has no clock plot; else
-     *   kind      'divergence'
+     *   kind      'divergence' or 'root-to-tip'
      *   forward   whether the dates increase toward the tips (calendar
      *             dates); false for ages
      *   unit      the dates' unit as the tree states it, or null
+     *   divUnit   the divergence's unit: 'subs/site' for a tree with Time
+     *             and Div, a root-to-tip tree's stated branch length unit,
+     *             or null
      *   fromRates whether the divergence is time x clock rate
+     *   calendar  whether the dates are calendar years: their unit says so,
+     *             or they were read off the tips' names
+     *   fromNames how many tips are dated by their names (a root-to-tip
+     *             tree; 0 otherwise)
+     *   ambiguousNames how many of those names carry a day/month-ambiguous
+     *             numeric date, read day first
      *   points    [{node, date, div, tip}] in preorder; the tips'
-     *             `residual` is their divergence less the line's
-     *   root      {node, date, div}: the top of the view
+     *             `residual` is their divergence less the line's. On a
+     *             root-to-tip tree the tips only: no ancestor has a date
+     *   root      {node, date, div}: the top of the view; `date` null on a
+     *             root-to-tip tree
      *   fit       forester.clockRegression over the tips, with
      *             rate      the slope in the direction time runs: divergence
      *                       per unit of time (negative where the tips'
@@ -7391,24 +7469,49 @@
         if (view) {
             top = (!view.parent && view.children && view.children.length === 1) ? view.children[0] : view;
         }
+        // a root-to-tip tree's divergence is the path from the TREE's root,
+        // in the view of a clade too: the clade's top then has one as well
+        let rootToTip = kind === 'root-to-tip';
+        let dist = rootToTip ? rootToTipDistances(treeRoot) : null;
+        let divOf = rootToTip ? function (n) {
+            return dist.get(n);
+        } : auspiceNodeDiv;
         let points = [];
         let xs = [];
         let ys = [];
+        let fromNames = 0;
+        let ambiguousNames = 0;
         forester.preOrderTraversalAll(top, function (n) {
+            let tip = !(n.children && n.children.length > 0);
             let date = auspiceNodeDate(n);
-            let div = auspiceNodeDiv(n);
+            if (rootToTip && tip && date === null) {
+                let named = rootToTipDate(n);    // every tip has one: the kind says so
+                date = named ? named.value : null;
+                if (named && named.fromName) {
+                    ++fromNames;
+                    if (named.ambiguous) {
+                        ++ambiguousNames;
+                    }
+                }
+            }
+            let div = divOf(n);
             if (date === null || div === null) {
-                return;    // not on a tree with Time and Div; a guard, not a rule
+                return;    // an undated ancestor (root-to-tip), or a guard, not a rule
             }
-            let tip = !(n.children && n.children.length > 0);
             points.push({node: n, date: date, div: div, tip: tip});
             if (tip) {
                 xs.push(date);
                 ys.push(div);
             }
         });
-        let forward = timeIncreasesTowardTips(treeRoot);
-        let root = {node: top, date: auspiceNodeDate(top), div: auspiceNodeDiv(top)};
+        let info = forester.timeAxisInfo(treeRoot);
+        // a root-to-tip tree has no dated pair to read the direction off:
+        // its dates are calendar dates unless their unit says ages
+        let forward = rootToTip ? info.type !== 'geologic' : timeIncreasesTowardTips(treeRoot);
+        // calendar years: the dates' unit says so, or they were read off the
+        // tips' names, which carry no other kind of date
+        let calendar = forward && (info.type === 'calendar' || (rootToTip && info.type === null && fromNames > 0));
+        let root = {node: top, date: auspiceNodeDate(top), div: divOf(top)};
         let fit = forester.clockRegression(xs, ys);
         if (fit) {
             fit.rate = forward ? fit.slope : -fit.slope;
@@ -7420,11 +7523,17 @@
                 }
             }
         }
+        let lengthUnit = (phy !== treeRoot && typeof phy.branch_length_unit === 'string'
+            && phy.branch_length_unit.trim().length > 0) ? phy.branch_length_unit.trim() : null;
         return {
             kind: kind,
             forward: forward,
             unit: dateUnitOf(treeRoot),
-            fromRates: treeRoot._divergenceFromRates === true && !recordsDivergence(treeRoot),
+            divUnit: rootToTip ? lengthUnit : DIVERGENCE_LENGTH_UNIT,
+            fromRates: !rootToTip && treeRoot._divergenceFromRates === true && !recordsDivergence(treeRoot),
+            calendar: calendar,
+            fromNames: fromNames,
+            ambiguousNames: ambiguousNames,
             points: points,
             root: root,
             fit: fit

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "archaeopteryx",
-  "version": "3.23.0",
+  "version": "3.25.0",
   "description": "Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.",
   "main": "archaeopteryx.js",
   "types": "archaeopteryx.d.ts",
@@ -20,7 +20,7 @@
     "LICENSE"
   ],
   "scripts": {
-    "test": "node test/forester_test.js && node test/search_test.js && node test/visualization_test.js && node test/domain_test.js && node test/gene_test.js && node test/clock_test.js && node test/metadata_test.js && node test/heatmap_test.js && node test/clustering_test.js",
+    "test": "node test/forester_test.js && node test/search_test.js && node test/visualization_test.js && node test/domain_test.js && node test/gene_test.js && node test/clock_test.js && node test/metadata_test.js && node test/heatmap_test.js && node test/clustering_test.js && node test/canvg_global_test.js",
     "lint": "eslint .",
     "lint:fix": "eslint . --fix",
     "format": "prettier --write .",