archaeopteryx 3.24.0 → 3.25.0

package/README.md

@@ -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):
@@ -1056,8 +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
@@ -1551,14 +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. |
@@ -1581,7 +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 |
@@ -1590,6 +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
 
@@ -1734,6 +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

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 3.24.0
+// 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 = '3.24.0';
+    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);
@@ -15380,22 +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) {
@@ -18431,20 +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]) {
@@ -18885,10 +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 = [];
@@ -18910,17 +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 3.24.0
+// v 3.25.0
 // 2026-09-17
 //
 // forester.js is a general suite for dealing with phylogenetic trees.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "archaeopteryx",
-  "version": "3.24.0",
+  "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 .",