@graphty/graph-io 0.3.24 → 0.3.26

package/dist/chunks/{importer-D_e7e7LX.js → importer-Bcl1d4xH.js}

@@ -1,8 +1,7 @@
 import { INVALID_INDEX, GraphFormatError } from "@graphty/graph-format";
-import { af as MIXED_DIRECTION_CODE, D as DIRECTION_FORCED_CODE, a as DIRECTION_REFUSED_CODE, S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, I as ID_MERGED_CODE, R as ROLE_TAKEN_CODE, C as COLUMN_RENAMED_CODE, A as AMBIGUOUS_GRAPH_NAME_CODE, G as GRAPH_NOT_FOUND_CODE, M as MULTIPLE_GRAPHS_CODE, au as STRAY_TEXT_CODE, Y as UNKNOWN_ELEMENT_CODE, k as UNKNOWN_ATTR_TYPE_CODE, am as EQUATION_AS_TEXT_CODE, h as PARENT_CYCLE_CODE, U as UNKNOWN_PARENT_CODE, i as DUPLICATE_ATTRIBUTE_CODE, j as DANGLING_REFERENCE_CODE, P as PRECISION_CODE, W as WIDENED_CODE, B as BAD_VALUE_CODE, c as DUPLICATE_EDGE_ID_CODE, d as DUPLICATE_NODE_CODE, e as MISSING_ENDPOINT_CODE, f as MISSING_ID_CODE, N as NO_GRAPH_CODE, q as UNKNOWN_ENCODING_CODE, E as ENCODING_FALLBACK_CODE, r as INVALID_ENCODING_CODE, s as INVALID_UTF8_CODE, u as EMPTY_INPUT_CODE, aw as XML_SYNTAX_CODE, a3 as STORAGE_CLASS_CODE, a7 as WEIGHT_KEY_CLASH_CODE, a6 as ROLE_ASSUMED_CODE, a5 as COLUMN_RENAMED_LOSS_CODE, b as ID_TEXT_TYPE_CODE, aa as MUTUAL_EXPANDED_CODE, ab as PARENTS_DROPPED_CODE, ac as ROLE_DROPPED_CODE, ad as TEMPORAL_TEXT_DROPPED_CODE, ae as TEMPORAL_DROPPED_CODE, a0 as XML_ILLEGAL_CHAR_CODE, Q as uniqueColumnName, L as declareResolved, _ as DictHeuristic, K as IdCoercer, J as DirectionResolver, y as throwIfAborted, F as reportSinkOptions, z as reportUnusedOptions, H as chooseGraph, v as resolveImportOptions, w as ImportReportBuilder, x as textChunks } from "./report-B1z4WT9e.js";
-import { l as localName, a as escapeXmlText, g as isWhitespace, e as escapeXmlAttribute, t as tokenizeXml, f as xmlDeclaredEncoding, X as XmlSyntaxError } from "./escape-B-tkk_Cl.js";
-import { p as parseWeightText } from "./weights-Dzba96G3.js";
-import { p as parseTextCell, i as inferTextDtype } from "./text-Dr0Ifpag.js";
+import { M as MIXED_DIRECTION_CODE, D as DIRECTION_FORCED_CODE, d as DIRECTION_REFUSED_CODE, S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, I as ID_MERGED_CODE, R as ROLE_TAKEN_CODE, C as COLUMN_RENAMED_CODE, ae as AMBIGUOUS_GRAPH_NAME_CODE, af as GRAPH_NOT_FOUND_CODE, l as MULTIPLE_GRAPHS_CODE, f as STRAY_TEXT_CODE, g as UNKNOWN_ELEMENT_CODE, U as UNKNOWN_ATTR_TYPE_CODE, b7 as EQUATION_AS_TEXT_CODE, ai as PARENT_CYCLE_CODE, q as UNKNOWN_PARENT_CODE, o as DUPLICATE_ATTRIBUTE_CODE, i as DANGLING_REFERENCE_CODE, P as PRECISION_CODE, aj as WIDENED_CODE, a3 as BAD_VALUE_CODE, m as DUPLICATE_EDGE_ID_CODE, n as DUPLICATE_NODE_CODE, s as MISSING_ENDPOINT_CODE, t as MISSING_ID_CODE, N as NO_GRAPH_CODE, v as ENCODING_CONFLICT_CODE, w as UNKNOWN_ENCODING_CODE, x as ENCODING_FALLBACK_CODE, y as INVALID_ENCODING_CODE, z as INVALID_UTF8_CODE, E as EMPTY_INPUT_CODE, X as XML_SYNTAX_CODE, F as ELEMENT_ISSUE, G as INPUT_ISSUE, bk as STORAGE_CLASS_CODE, bq as WEIGHT_KEY_CLASH_CODE, au as ROLE_ASSUMED_CODE, b0 as COLUMN_RENAMED_LOSS_CODE, J as ID_TEXT_TYPE_CODE, bd as MUTUAL_EXPANDED_CODE, Q as PARENTS_DROPPED_CODE, K as ROLE_DROPPED_CODE, bm as TEMPORAL_TEXT_DROPPED_CODE, bl as TEMPORAL_DROPPED_CODE, ax as XML_ILLEGAL_CHAR_CODE, a0 as uniqueColumnName, a1 as declareResolved, ac as DictHeuristic, ar as IdCoercer, aq as DirectionResolver, b as plural, $ as agree, am as throwIfAborted, aL as parseWeightText, ao as reportSinkOptions, an as reportUnusedOptions, a7 as chooseGraph, ap as graphChosen, al as resolveImportOptions, a8 as ImportReportBuilder, a4 as textChunks, c1 as elementCount } from "./export-BTI4yQgy.js";
+import { l as localName, a as escapeXmlText, j as isWhitespace, e as escapeXmlAttribute, t as tokenizeXml, f as xmlDeclaredEncoding, X as XmlSyntaxError } from "./escape-D0g6NNUy.js";
+import { p as parseTextCell, i as inferTextDtype } from "./text-DmcUs5_Q.js";
 const FORMAT = "xgmml";
 const EXTENSIONS = Object.freeze([".xgmml", ".xml"]);
 const MIME_TYPES = Object.freeze(["application/xgmml", "text/xgmml", "text/xgmml+xml"]);
@@ -25,26 +24,41 @@ const INTERACTION_COLUMN = "interaction";
 const XGMML_ORIGIN_NAMESPACE = "xgmml";
 const CYTOSCAPE_ORIGIN_NAMESPACE = "cytoscape";
 const XGMML_ISSUE = Object.freeze({
-  /** Fatal: the input is not well-formed XML. */
+  ...INPUT_ISSUE,
+  ...ELEMENT_ISSUE,
+  /** The input is not well-formed XML. The import stops. */
   XML_SYNTAX: XML_SYNTAX_CODE,
-  /** Fatal: the input is empty or whitespace only. */
+  /** The input is empty or whitespace only. The import stops. */
   EMPTY_INPUT: EMPTY_INPUT_CODE,
-  /** Fatal: the input holds invalid UTF-8. */
+  /** The input is not valid UTF-8. The import stops. */
   INVALID_UTF8: INVALID_UTF8_CODE,
-  /** Fatal: bytes invalid in the encoding a BOM, a declaration or the option chose. */
+  /**
+   * Some bytes are not valid in the encoding that was chosen (by a byte order mark, the file's declaration or the
+   * `encoding` option). The import stops.
+   */
   INVALID_ENCODING: INVALID_ENCODING_CODE,
   /** Undeclared non-UTF-8 bytes were read as windows-1252. */
   ENCODING_FALLBACK: ENCODING_FALLBACK_CODE,
   /** A declared encoding the platform cannot decode was ignored. */
   UNKNOWN_ENCODING: UNKNOWN_ENCODING_CODE,
-  /** Fatal: the root element is not `<graph>` (an XHTML page embedding one, a GraphML file). */
+  /** A declared encoding the byte order mark contradicts (the mark wins). */
+  ENCODING_CONFLICT: ENCODING_CONFLICT_CODE,
+  /**
+   * The root element is not `<graph>` (it may be an XHTML page with a graph inside, or a GraphML file). The import
+   * stops.
+   */
   NO_GRAPH: NO_GRAPH_CODE,
-  /** Fatal: a session view document (`cy:view="1"`): view SUIDs and no topology. */
+  /**
+   * The file is a Cytoscape session view (`cy:view="1"`), which holds only view settings and no nodes or edges. The
+   * import stops.
+   */
   VIEW_DOCUMENT: "E_XGMML_VIEW_DOCUMENT",
   /** A node with neither an id nor a label; it is skipped with its subtree. */
   MISSING_ID: MISSING_ID_CODE,
   /** A node without an id; its label is used as the id. */
   ID_FROM_LABEL: "W_XGMML_ID_FROM_LABEL",
+  /** A node or edge with both an id and an `xlink:href`; it is read as the reference. */
+  ID_AND_HREF: "W_XGMML_ID_AND_HREF",
   /** An edge without a source or a target that no label alias resolves. */
   MISSING_ENDPOINT: MISSING_ENDPOINT_CODE,
   /** An edge endpoint that names no node (addMissingNodes false); the edge is skipped. */
@@ -55,7 +69,10 @@ const XGMML_ISSUE = Object.freeze({
   DUPLICATE_NODE: DUPLICATE_NODE_CODE,
   /** An edge id used twice; the second edge is skipped. */
   DUPLICATE_EDGE_ID: DUPLICATE_EDGE_ID_CODE,
-  /** A meta-edge the 2.x writer repeats inside a group; the copy is dropped. */
+  /**
+   * Cytoscape 2.x writes each edge of a group a second time, inside the group. The repeats are dropped, so every edge
+   * is read once; nothing is lost.
+   */
   GROUP_DUPLICATE_EDGE: "W_XGMML_GROUP_DUPLICATE_EDGE",
   /** A `directed` or `cy:directed` value other than 0 / 1. */
   BAD_DIRECTED: "W_XGMML_BAD_DIRECTED",
@@ -71,19 +88,28 @@ const XGMML_ISSUE = Object.freeze({
   SURROGATE_PAIRED: "W_XGMML_SURROGATE_PAIRED",
   /** An empty list whose element type nothing states; a list of strings is assumed. */
   EMPTY_LIST_TYPE: "W_XGMML_EMPTY_LIST_TYPE",
-  /** A record list, a list of lists, a 2.x map or foreign XML in an att, kept as json. */
+  /**
+   * An attribute holds a structure a single column cannot (a list of records, a list of lists, a Cytoscape 2.x map
+   * or XML from another tool). Its value is kept as a JSON value, which a save as XGMML writes back.
+   */
   RECORD_LIST: "W_XGMML_RECORD_LIST",
   /** A pointer into another file (`file.xgmml#id`); kept as text. */
   CROSS_FILE_REFERENCE: "W_XGMML_CROSS_FILE_REFERENCE",
   /** A graph nested in an edge's att; there is no model for it. */
   EDGE_NESTED_GRAPH: "W_XGMML_EDGE_NESTED_GRAPH",
-  /** Elements of a session network declared outside every registered subnetwork. */
+  /**
+   * Some nodes or edges of a Cytoscape session belong to none of its networks (Cytoscape keeps group meta-edges and
+   * the members of collapsed groups this way). They are not read; the message counts them.
+   */
   ROOT_ONLY_ELEMENTS: "W_XGMML_ROOT_ONLY_ELEMENTS",
   /** A value that does not parse as its declared type; the cell is unset. */
   BAD_VALUE: BAD_VALUE_CODE,
-  /** A column widened because its values or declared types disagree. */
+  /**
+   * An attribute's type was widened because a later value did not fit: an integer above 2^31 in an integer column,
+   * or two declared types for one attribute.
+   */
   WIDENED: WIDENED_CODE,
-  /** A long or real beyond what a double holds exactly. */
+  /** An integer beyond 2^53 was stored as the nearest 64-bit float; pass `long: "string"` to keep every digit. */
   PRECISION: PRECISION_CODE,
   /** A reference (xlink:href, nested-network pointer) that names nothing. */
   DANGLING_REFERENCE: DANGLING_REFERENCE_CODE,
@@ -101,49 +127,73 @@ const XGMML_ISSUE = Object.freeze({
   UNKNOWN_ELEMENT: UNKNOWN_ELEMENT_CODE,
   /** Character data where XGMML allows only elements, or inside an att. */
   STRAY_TEXT: STRAY_TEXT_CODE,
-  /** A session network document holds several registered networks; one was read. */
+  /**
+   * The file holds several graphs and only the first was read. It is not added when `graphIndex` or `graphName` chose the graph.
+   * `importAllGraphs()` reads every one.
+   */
   MULTIPLE_GRAPHS: MULTIPLE_GRAPHS_CODE,
-  /** graphIndex / graphName names no network (fatal). */
+  /** `graphIndex` or `graphName` matches no network in the session. The import stops. */
   GRAPH_NOT_FOUND: GRAPH_NOT_FOUND_CODE,
-  /** graphName names several networks (fatal). */
+  /** `graphName` matches several networks in the session. The import stops. */
   AMBIGUOUS_GRAPH_NAME: AMBIGUOUS_GRAPH_NAME_CODE,
-  /** A column renamed `<name>#<n>` because its name was taken. */
+  /**
+   * An attribute was renamed `<name>#<suffix>` because another attribute already has its name, for example
+   * two attributes declared with the same name.
+   */
   COLUMN_RENAMED: COLUMN_RENAMED_CODE,
-  /** A column declared without its role because the table already holds it. */
+  /**
+   * You read into a graph builder that already has an id, label or position attribute, so this file's one is kept as
+   * a plain attribute.
+   */
   ROLE_TAKEN: ROLE_TAKEN_CODE,
-  /** Two id texts merged into one number under ids "number". */
+  /** Two different id texts became the same number because `ids` is "number", so their nodes were merged. */
   ID_MERGED: ID_MERGED_CODE,
-  /** An option the format has no use for. */
+  /** You set an option this format does not use; it had no effect. The message names the option. */
   OPTION_IGNORED: OPTION_IGNORED_CODE,
-  /** A builder-policy option the sink does not honour. */
+  /**
+   * You read into your own graph builder, which was created with a different `addMissingNodes`, `duplicateEdges`,
+   * `selfLoops` or `weightDtype` than the option you passed; the builder's setting applies.
+   */
   SINK_OPTION: SINK_OPTION_CODE,
-  /** The sink refused the file's direction. */
+  /**
+   * You read into a graph builder whose direction is already set, or which already holds edges, so the file is read
+   * with the builder's direction instead of its own.
+   */
   DIRECTION_REFUSED: DIRECTION_REFUSED_CODE,
-  /** Edges forced to the policy's direction. */
+  /** Edges of the other direction were read with the direction `onMixedDirection` chose. */
   DIRECTION_FORCED: DIRECTION_FORCED_CODE,
-  /** A mixed file under onMixedDirection "error" (fatal). */
+  /**
+   * The graph has both directed and undirected edges and `onMixedDirection` is "error". An import stops; a save to a
+   * format that holds one direction per file fails with E_DIRECTED. Pass "directed" or "undirected" to read or write
+   * it anyway.
+   */
   MIXED_DIRECTION: MIXED_DIRECTION_CODE
 });
 const XGMML_LOSS = Object.freeze({
   /** A json or nested-list column written as a string att. */
   JSON_AS_STRING: "W_XGMML_JSON_AS_STRING",
-  /** A dtype written as a wider Cytoscape type (f32 as Double, u32 above i32 as Long, u8 as Integer, dict as String). */
+  /**
+   * An attribute type Cytoscape does not have is written as a wider one (a 32-bit float as Double, a large unsigned
+   * integer as Long, a byte as Integer, a dictionary as String).
+   */
   WIDENED_TYPE: "W_XGMML_WIDENED_TYPE",
-  /** A string holding a character XML 1.0 cannot carry; export() throws. */
+  /** A text value holds a character XML 1.0 forbids (most control characters); the save fails with E_COLUMN_TYPE. */
   XML_ILLEGAL_CHAR: XML_ILLEGAL_CHAR_CODE,
   /** A temporal column written as plain numbers. */
   TEMPORAL_DROPPED: TEMPORAL_DROPPED_CODE,
   /** A temporal text companion written as a plain string att. */
   TEMPORAL_TEXT_DROPPED: TEMPORAL_TEXT_DROPPED_CODE,
-  /** A role the format has no slot for, written as a plain att. */
+  /** An attribute with a role the format has no place for is written as a plain attribute; the role is lost. */
   ROLE_DROPPED: ROLE_DROPPED_CODE,
-  /** A parents column not written because the snapshot also has a parent column. */
+  /**
+   * A `parents` attribute (several parents per node) is not written because the graph also has a `parent` attribute.
+   */
   PARENTS_DROPPED: PARENTS_DROPPED_CODE,
   /** A mutual pair written as two directed edges. */
   MUTUAL_EXPANDED: MUTUAL_EXPANDED_CODE,
   /** Node ids whose text reads back as the other type. */
   ID_TEXT_TYPE: ID_TEXT_TYPE_CODE,
-  /** An edge id column of another dtype written as text; it reads back as strings. */
+  /** Edge ids that are not text are written as text and read back as text. */
   EDGE_ID_TEXT: "W_XGMML_EDGE_ID_TEXT",
   /** Strings holding a literal backslash-n or backslash-t read back as newline / tab (Cytoscape's escapes). */
   BACKSLASH_ESCAPE: "W_XGMML_BACKSLASH_ESCAPE",
@@ -151,13 +201,22 @@ const XGMML_LOSS = Object.freeze({
   POSITION: "W_XGMML_POSITION",
   /** Nodes whose parent chain never reaches a root are written at the top level. */
   PARENT_CYCLE: "W_XGMML_PARENT_CYCLE",
-  /** A column named like a column the importer owns reads back renamed. */
+  /**
+   * An attribute with a role (for example, the label) is written where the format keeps that role, and reads back under the
+   * name the format's importer gives it.
+   */
   COLUMN_NAME_CHANGED: COLUMN_RENAMED_LOSS_CODE,
-  /** A role-less column written into a slot reads back with the slot's role. */
+  /**
+   * An attribute without a role is written where the format keeps a role (for example, a `name` column as the label), and
+   * reads back with that role.
+   */
   ROLE_ASSUMED: ROLE_ASSUMED_CODE,
-  /** A plain `weight` edge column reads back as THE weight. */
+  /** An attribute named `weight` without the weight role reads back as the edge weight. */
   WEIGHT_KEY_CLASH: WEIGHT_KEY_CLASH_CODE,
-  /** A string / dict column that reads back as the other storage class. */
+  /**
+   * A text attribute reads back as a dictionary attribute, or the reverse, because the importer chooses by how often
+   * its values repeat. The values are the same.
+   */
   STORAGE_CLASS_CHANGED: STORAGE_CLASS_CODE,
   /** Edge labels shaped `a (i) b` read back with an `interaction` column (Cytoscape's label alias). */
   INTERACTION_FROM_LABEL: "W_XGMML_INTERACTION_FROM_LABEL"
@@ -189,13 +248,18 @@ const TRUE_TEXT = /^(1|true|yes)$/i;
 function isCyTrue(text) {
   return text !== null && text !== void 0 && TRUE_TEXT.test(text.trim());
 }
-function normaliseName(name, xlinkPrefixes) {
+function normaliseName(name, scope) {
   const colon = name.indexOf(":");
-  if (colon > 0 && xlinkPrefixes.has(name.slice(0, colon))) {
+  if (colon <= 0) {
+    return name;
+  }
+  const prefix = name.slice(0, colon);
+  if (prefix === "xlink" || scope.get(prefix) === XLINK_NAMESPACE) {
     return `xlink:${name.slice(colon + 1)}`;
   }
   return name;
 }
+const NO_SCOPE = /* @__PURE__ */ new Map();
 class XgmmlParser {
   /**
    * Create a parser.
@@ -203,7 +267,7 @@ class XgmmlParser {
    */
   constructor(report) {
     this.frames = [];
-    this.xlinkPrefixes = /* @__PURE__ */ new Set(["xlink"]);
+    this.scopes = [];
     this.rootGraph = null;
     this.nodes = [];
     this.edges = [];
@@ -213,6 +277,7 @@ class XgmmlParser {
     this.rootPrefix = null;
     this.rdf = {};
     this.rdfXml = null;
+    this.doctypeText = null;
     this.rdfElement = null;
     this.report = report;
   }
@@ -233,9 +298,17 @@ class XgmmlParser {
       cytoscape: this.cytoscape,
       xgmmlNamespace: this.xgmmlNamespace,
       rdf: this.rdf,
-      rdfXml: this.rdfXml
+      rdfXml: this.rdfXml,
+      doctype: this.doctypeText
     };
   }
+  /**
+   * The DOCTYPE declaration.
+   * @param text - the declaration as written
+   */
+  doctype(text) {
+    this.doctypeText ??= text;
+  }
   /**
    * An element starts.
    * @param rawName - the element name as written
@@ -243,6 +316,7 @@ class XgmmlParser {
    * @param line - the line
    */
   start(rawName, rawAttrs, line) {
+    this.enterScope(rawAttrs);
     const top = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];
     if (top === null) {
       this.startRoot(rawName, rawAttrs, line);
@@ -256,8 +330,8 @@ class XgmmlParser {
       this.capture(top, rawName, rawAttrs);
       return;
     }
-    const attrs = this.normalise(rawAttrs);
-    const name = localName(rawName);
+    const attrs = this.normalize(rawAttrs);
+    const name = this.isXgmmlName(rawName) ? localName(rawName) : rawName;
     switch (top.kind) {
       case "graph":
         this.startInGraph(top.graph, rawName, name, attrs, line);
@@ -294,6 +368,7 @@ class XgmmlParser {
    * @param _line - the line
    */
   end(name, _line) {
+    this.scopes.pop();
     const frame = this.frames.pop();
     const below = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];
     switch (frame?.kind) {
@@ -302,7 +377,11 @@ class XgmmlParser {
         frame.depth--;
         if (frame.depth > 0) {
           this.frames.push(frame);
-        } else if (frame.att.name === "networkMetadata") {
+          this.rdfElement = null;
+          return;
+        }
+        frame.att.xml = bindPrefixes(frame.att.xml, frame.start, frame.scope);
+        if (frame.att.name === "networkMetadata") {
           this.rdfXml = frame.att.xml;
         }
         this.rdfElement = null;
@@ -348,15 +427,40 @@ class XgmmlParser {
     );
   }
   // ------------------------------------------------------------------ structure
+  /**
+   * Open the namespace scope of an element: its parent's, plus the prefixes it declares.
+   * @param attrs - the element's attributes as written
+   */
+  enterScope(attrs) {
+    const parent = this.scopes.at(-1) ?? NO_SCOPE;
+    let scope = parent;
+    for (const [key2, value] of attrs) {
+      if (key2 === "xmlns" || key2.startsWith("xmlns:")) {
+        if (scope === parent) {
+          scope = new Map(parent);
+        }
+        scope.set(key2 === "xmlns" ? "" : key2.slice(6), value);
+      }
+    }
+    this.scopes.push(scope);
+  }
+  /**
+   * The namespace prefixes in scope at the innermost open element.
+   * @returns prefix to URI
+   */
+  get scope() {
+    return this.scopes.at(-1) ?? NO_SCOPE;
+  }
   /**
    * The XML attribute map with every XLink prefix written `xlink:`.
    * @param attrs - the attributes as written
-   * @returns the normalised map
+   * @returns the normalized map
    */
-  normalise(attrs) {
+  normalize(attrs) {
     const out = /* @__PURE__ */ new Map();
+    const { scope } = this;
     for (const [key2, value] of attrs) {
-      out.set(normaliseName(key2, this.xlinkPrefixes), value);
+      out.set(normaliseName(key2, scope), value);
     }
     return out;
   }
@@ -369,10 +473,7 @@ class XgmmlParser {
   startRoot(rawName, rawAttrs, line) {
     const local = localName(rawName);
     const prefix = rawName.includes(":") ? rawName.slice(0, rawName.indexOf(":")) : null;
-    for (const [key2, value] of rawAttrs) {
-      if (key2.startsWith("xmlns:") && value === "http://www.w3.org/1999/xlink") {
-        this.xlinkPrefixes.add(key2.slice(6));
-      }
+    for (const key2 of rawAttrs.keys()) {
       if (key2 === "xmlns:cy" || key2.startsWith("cy:")) {
         this.cytoscape = true;
       }
@@ -387,7 +488,7 @@ class XgmmlParser {
         { line }
       );
     }
-    const graph = this.newGraph(this.normalise(rawAttrs), line, null, null);
+    const graph = this.newGraph(this.normalize(rawAttrs), line, null, null);
     this.rootGraph = graph;
     this.frames.push({ kind: "graph", graph });
   }
@@ -447,7 +548,7 @@ class XgmmlParser {
         return;
       }
       case "graphics":
-        this.beginGraphics(graph, attrs);
+        this.beginGraphics(graph, attrs, line);
         return;
       default:
         this.unknownElement(rawName, line);
@@ -470,7 +571,7 @@ class XgmmlParser {
         return;
       }
       case "graphics":
-        this.beginGraphics(element, attrs);
+        this.beginGraphics(element, attrs, line);
         return;
       default:
         this.unknownElement(rawName, line);
@@ -499,19 +600,30 @@ class XgmmlParser {
       return;
     }
     att.xml ??= "";
-    const capture = { kind: "capture", att, depth: 0 };
+    const capture = {
+      kind: "capture",
+      att,
+      depth: 0,
+      start: att.xml.length,
+      scope: this.scope
+    };
     this.frames.push(capture);
     this.capture(capture, rawName, attrs);
   }
   /**
-   * Whether an element name inside an att is XGMML's own (unprefixed, or with the root's prefix,
-   * as in a document whose root is `<xgmml:graph>`) rather than foreign XML such as `rdf:RDF`.
+   * Whether an element name is XGMML's own (unprefixed, with the root's prefix as in a document
+   * whose root is `<xgmml:graph>`, or with any prefix bound to the XGMML namespace) rather than
+   * foreign XML such as `rdf:RDF` or `svg:node`.
    * @param rawName - the name as written
    * @returns true for an XGMML element name
    */
   isXgmmlName(rawName) {
     const colon = rawName.indexOf(":");
-    return colon < 0 || this.rootPrefix !== null && rawName.slice(0, colon) === this.rootPrefix;
+    if (colon < 0) {
+      return true;
+    }
+    const prefix = rawName.slice(0, colon);
+    return prefix === this.rootPrefix || this.scope.get(prefix) === XGMML_NAMESPACE;
   }
   /**
    * A `<graph>` inside an `<att>`: a subnetwork of the root, a group or nested-network pointer
@@ -583,6 +695,9 @@ class XgmmlParser {
     const labelAttr = attrs.get("label") ?? null;
     const nameAttr = attrs.get("name") ?? null;
     const label = labelAttr ?? nameAttr;
+    if (href !== null && id !== null) {
+      this.idAndHref("node", id, href, line);
+    }
     if (href === null && id === null) {
       if (label === null || label.length === 0) {
         this.report.counts.skippedNodes++;
@@ -631,9 +746,13 @@ class XgmmlParser {
    */
   beginEdge(graph, attrs, line) {
     const href = attrs.get("xlink:href") ?? null;
+    const id = attrs.get("id") ?? null;
+    if (href !== null && id !== null) {
+      this.idAndHref("edge", id, href, line);
+    }
     const edge = {
       kind: "edge",
-      id: href === null ? attrs.get("id") ?? null : null,
+      id: href === null ? id : null,
       href,
       source: attrs.get("source") ?? null,
       target: attrs.get("target") ?? null,
@@ -654,6 +773,21 @@ class XgmmlParser {
     }
     this.frames.push({ kind: "edge", edge });
   }
+  /**
+   * W_XGMML_ID_AND_HREF: an element that both declares an id and references another element.
+   * @param kind - node or edge
+   * @param id - the id
+   * @param href - the reference
+   * @param line - the line
+   */
+  idAndHref(kind, id, href, line) {
+    this.report.warning(
+      "validation-error",
+      XGMML_ISSUE.ID_AND_HREF,
+      `<${kind}> has both id "${id}" and xlink:href "${href}"; it is read as a reference to ${href} and the id is not used`,
+      { line, element: id }
+    );
+  }
   // ------------------------------------------------------------------ atts
   /**
    * An att record from its XML attributes.
@@ -707,7 +841,17 @@ class XgmmlParser {
     frame.att.xml = `${frame.att.xml ?? ""}${tag}>`;
     frame.depth++;
     if (frame.att.name === "networkMetadata") {
-      this.rdfElement = localName(rawName);
+      const field = localName(rawName);
+      this.rdfElement = field;
+      if (this.rdf[field] !== void 0) {
+        this.rdfElement = null;
+        this.report.warning(
+          "validation-error",
+          XGMML_ISSUE.DUPLICATE_ATTRIBUTE,
+          `the network metadata gives <${rawName}> twice; the first ("${this.rdf[field]}") is kept`,
+          { line: frame.att.line, element: field }
+        );
+      }
     }
   }
   /**
@@ -725,13 +869,20 @@ class XgmmlParser {
    * attribute is kept as written, merged key by key with an earlier `<graphics>`.
    * @param target - the node, edge or graph
    * @param attrs - its attributes
+   * @param line - the line
    */
-  beginGraphics(target, attrs) {
+  beginGraphics(target, attrs, line) {
     const graphics = { ...target.graphics ?? {} };
     for (const [key2, value] of attrs) {
       if ("x" in target && (key2 === "x" || key2 === "y" || key2 === "z")) {
+        if (target[key2] !== null && target[key2] !== void 0) {
+          this.duplicateGraphics(key2, line);
+        }
         target[key2] = value;
       } else if (key2 !== "xmlns" && !key2.startsWith("xmlns:")) {
+        if (key2 in graphics) {
+          this.duplicateGraphics(key2, line);
+        }
         graphics[key2] = value;
       }
     }
@@ -789,8 +940,25 @@ class XgmmlParser {
       );
       return;
     }
+    if (target.graphics !== null && att.name in target.graphics) {
+      this.duplicateGraphics(att.name, att.line);
+    }
     target.graphics = { ...target.graphics ?? {}, [att.name]: attJson(att) };
   }
+  /**
+   * W_DUPLICATE_ATTRIBUTE for a graphics property given twice on one element (once per name).
+   * @param key - the property
+   * @param line - the line
+   */
+  duplicateGraphics(key2, line) {
+    this.report.warnOnce(
+      "validation-error",
+      XGMML_ISSUE.DUPLICATE_ATTRIBUTE,
+      `the graphics property "${key2}" is given twice on one element; the later value is kept`,
+      { line, element: key2 },
+      `${XGMML_ISSUE.DUPLICATE_ATTRIBUTE}:graphics:${key2}`
+    );
+  }
 }
 function isListLike(att) {
   const names = new Set(att.children.map((c) => c.name));
@@ -816,6 +984,26 @@ function attJson(att) {
   }
   return out;
 }
+function bindPrefixes(xml, start, scope) {
+  const segment = xml.slice(start);
+  const used = /* @__PURE__ */ new Set();
+  for (const match of segment.matchAll(/<\/?([A-Za-z_][\w.-]*):|\s([A-Za-z_][\w.-]*):[\w.-]+="/g)) {
+    used.add(match[1] ?? match[2]);
+  }
+  let declarations = "";
+  for (const prefix of used) {
+    const uri = scope.get(prefix);
+    if (prefix !== "xmlns" && prefix !== "xml" && uri !== void 0 && !segment.includes(` xmlns:${prefix}="`)) {
+      declarations += ` xmlns:${prefix}="${escapeXmlAttribute(uri)}"`;
+    }
+  }
+  if (declarations.length === 0) {
+    return xml;
+  }
+  const nameEnd = xml.slice(start).search(/[\s>]/);
+  const at = start + (nameEnd < 0 ? segment.length : nameEnd);
+  return `${xml.slice(0, at)}${declarations}${xml.slice(at)}`;
+}
 function otherAttributes(attrs, read) {
   const out = [];
   for (const [key2, value] of attrs) {
@@ -881,7 +1069,8 @@ function widenScalar(a, b) {
   return "long";
 }
 const INTEGER_TEXT = /^[+-]?[0-9]+$/;
-const REAL_TEXT = /^[+-]?(NaN|Infinity|([0-9]+\.?[0-9]*|\.[0-9]+)([eE][+-]?[0-9]+)?)$/;
+const REAL_TEXT = /^[+-]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][+-]?\d+)?$/;
+const NON_FINITE_TEXT = /^[+-]?(?:NaN|Infinity)$/;
 const I32_MIN = -2147483648;
 const I32_MAX = 2147483647;
 function parseScalar(text, kind, unescape) {
@@ -912,7 +1101,7 @@ function parseScalar(text, kind, unescape) {
     }
     case "real": {
       const t = text.trim();
-      if (!REAL_TEXT.test(t)) {
+      if (!REAL_TEXT.test(t) && !NON_FINITE_TEXT.test(t)) {
         return null;
       }
       const n = Number(t);
@@ -1167,6 +1356,15 @@ class ColumnSet {
       return jsonCell(names.size > 1 ? recordOf(att) : children.map(jsonOfAtt));
     }
     let itemKind = elementKind(att.elementType);
+    if (itemKind === null && att.elementType !== null && att.elementType.trim().length > 0) {
+      this.report.warnOnce(
+        "unsupported",
+        XGMML_ISSUE.UNKNOWN_ATTR_TYPE,
+        `list element type "${att.elementType}" of "${name}" is not a Cytoscape type; the items are read by their own types`,
+        at,
+        `${XGMML_ISSUE.UNKNOWN_ATTR_TYPE}:${this.domain}:${name}:items`
+      );
+    }
     if (itemKind === null) {
       const kinds = /* @__PURE__ */ new Set();
       for (const child of children) {
@@ -1519,7 +1717,7 @@ function dialectOf(doc, report) {
   let version = 0;
   if (versionText !== null) {
     version = Number(versionText.trim());
-    if (!Number.isFinite(version) || versionText.trim().length === 0) {
+    if (!Number.isFinite(version) || version < 0 || versionText.trim().length === 0) {
       report.warning(
         "validation-error",
         XGMML_ISSUE.DOCUMENT_VERSION,
@@ -1542,6 +1740,10 @@ function dialectOf(doc, report) {
 function graphsOf(doc, dialect) {
   return dialect.session ? doc.root.subgraphs.filter((g) => isCyTrue(g.registered)) : [doc.root];
 }
+function parseCoordinate(text) {
+  const parsed = parseScalar(text, "real", false);
+  return parsed === null || !Number.isFinite(parsed.value) ? null : parsed.value;
+}
 function localRef(href) {
   return href.startsWith("#") ? href.slice(1) : null;
 }
@@ -1607,6 +1809,7 @@ class XgmmlEmitter {
     this.aliasInteractions = 0;
     this.weighted = false;
     this.directions = /* @__PURE__ */ new Map();
+    this.nameLabel = { node: false, edge: false };
     this.labelRows = null;
     this.doc = doc;
     this.dialect = dialect;
@@ -1618,10 +1821,11 @@ class XgmmlEmitter {
     this.coercer = new IdCoercer(options.ids);
     this.direction = new DirectionResolver(sink, report, options.onMixedDirection);
     const base = { unescape: settings.cytoscapeEscapes, long: options.long };
+    const label = extras.labelFromName === true ? [] : [LABEL_COLUMN];
     this.nodeColumns = new ColumnSet("node", report, {
       ...base,
       reserved: /* @__PURE__ */ new Set([
-        LABEL_COLUMN,
+        ...label,
         POSITION_COLUMN,
         Z_COLUMN,
         GRAPHICS_COLUMN,
@@ -1635,7 +1839,7 @@ class XgmmlEmitter {
     });
     this.edgeColumns = new ColumnSet("edge", report, {
       ...base,
-      reserved: /* @__PURE__ */ new Set([EDGE_ID_COLUMN, LABEL_COLUMN, GRAPHICS_COLUMN])
+      reserved: /* @__PURE__ */ new Set([EDGE_ID_COLUMN, ...label, GRAPHICS_COLUMN])
     });
     this.graphColumns = new ColumnSet("graph", report, { ...base, reserved: /* @__PURE__ */ new Set([GRAPHICS_COLUMN]) });
   }
@@ -1649,7 +1853,7 @@ class XgmmlEmitter {
       this.report.warning(
         "validation-error",
         XGMML_ISSUE.DANGLING_REFERENCE,
-        `${this.prefix()}${members.dangling} xlink:href member reference(s) name no node or edge of the document`,
+        `${this.prefix()}${members.dangling} xlink:href member reference${plural(members.dangling)} ${agree(members.dangling, "names", "name")} no node or edge of the document`,
         { line: graph?.line ?? null }
       );
     }
@@ -1775,11 +1979,28 @@ class XgmmlEmitter {
   edgeDirection(record, header) {
     let directed = this.directions.get(record);
     if (directed === void 0) {
-      directed = record.directed === null ? header : this.flag(record.directed, header, { line: record.line, element: record.id ?? record.label });
+      const fallback = this.graphDirected(record.graph, header);
+      directed = record.directed === null ? fallback : this.flag(record.directed, fallback, { line: record.line, element: record.id ?? record.label });
       this.directions.set(record, directed);
     }
     return directed;
   }
+  /**
+   * The default direction of the edges of a graph: the `directed` attribute of the graph or of
+   * the nearest graph it is nested in that has one, else the header.
+   * @param graph - the graph that holds the edge
+   * @param header - the header direction
+   * @returns whether the graph's edges are directed by default
+   */
+  graphDirected(graph, header) {
+    for (let g = graph; g !== null && g !== this.doc.root; g = g.parent) {
+      const text = g.attrs.get("directed");
+      if (text !== void 0) {
+        return this.flag(text, header, { line: g.line, element: "directed" });
+      }
+    }
+    return header;
+  }
   /**
    * The direction the sink starts with: the one every edge has when they all agree (a
    * Cytoscape file writes cy:directed on every edge and may omit the root attribute), else the
@@ -1858,6 +2079,33 @@ class XgmmlEmitter {
       this.checkAbort();
     }
   }
+  /**
+   * The sink id of a node's written id: the restored original, else the written id, coerced.
+   * @param text - the written id
+   * @returns the id
+   */
+  idOf(text) {
+    return this.coercer.text(this.extras.restoredIds?.get(text) ?? text);
+  }
+  /**
+   * Decide whether a table's label comes from its `name` atts.
+   * @param domain - node or edge
+   * @param records - the table's records
+   */
+  decideNameLabel(domain, records) {
+    this.nameLabel[domain] = this.extras.labelFromName === true && records.some((r) => r.atts.some(isNameAtt));
+  }
+  /**
+   * The label of a record: its `name` att, or its XGMML label.
+   * @param record - the node or edge
+   * @returns the label, or undefined
+   */
+  labelOf(record) {
+    if (this.nameLabel[record.kind]) {
+      return record.atts.find(isNameAtt)?.value ?? void 0;
+    }
+    return record.label ?? void 0;
+  }
   /**
    * The coerced id of a node text.
    * @param text - the id text
@@ -1865,7 +2113,7 @@ class XgmmlEmitter {
    * @returns the id
    */
   nodeId(text, line) {
-    const id = this.coercer.text(text);
+    const id = this.idOf(text);
     const merge = this.coercer.lastMerge;
     if (merge !== null) {
       this.report.warning(
@@ -1923,7 +2171,7 @@ class XgmmlEmitter {
       this.report.warning(
         "validation-error",
         XGMML_ISSUE.DANGLING_REFERENCE,
-        `${this.prefix()}${dangling} xlink:href reference(s) name no node or edge of the document`
+        `${this.prefix()}${dangling} xlink:href reference${plural(dangling)} ${agree(dangling, "names", "name")} no node or edge of the document`
       );
     }
   }
@@ -1937,11 +2185,15 @@ class XgmmlEmitter {
     const positions = new Positions(this, this.dialect.cytoscape ? this.settings.zAs : "position");
     const graphics = new JsonColumn(this, "node", GRAPHICS_COLUMN, XGMML_ORIGIN_NAMESPACE, "graphics");
     const pointers = new Pointers(this, this.groupTest());
+    this.decideNameLabel(
+      "node",
+      this.rowList.flatMap((r) => r.records)
+    );
     for (const row of this.rowList) {
       const where = { line: row.records[0].line, element: row.id };
       const seen = /* @__PURE__ */ new Set();
       for (const record of row.records) {
-        labels[row.row] ??= record.label ?? void 0;
+        labels[row.row] ??= this.labelOf(record);
         this.addElementColumns(this.nodeColumns, row.row, record, seen, where);
         positions.add(row, record);
         if (record.graphics !== null && Object.keys(record.graphics).length > 0) {
@@ -1983,7 +2235,7 @@ class XgmmlEmitter {
       names.add(key2);
     }
     for (const att of record.atts) {
-      if (this.skipAtt(record, att) || merging && att.name !== null && seen.has(att.name)) {
+      if (this.skipAtt(record, att) || this.nameLabel[record.kind] && isNameAtt(att) || merging && att.name !== null && seen.has(att.name)) {
         continue;
       }
       if (record.kind === "node" && att.name === "__isGroup" && record.nested.length > 0 && isCyTrue(att.value)) {
@@ -2008,7 +2260,19 @@ class XgmmlEmitter {
    * @returns true to skip it
    */
   skipAtt(record, att) {
-    return record.kind === "edge" && record.weight === null && att.name === this.options.weightFrom;
+    if (record.kind !== "edge" || att.name !== this.options.weightFrom) {
+      return false;
+    }
+    if (record.weight === null || att.name !== "weight" || att.children.length > 0) {
+      return record.weight === null;
+    }
+    this.report.warning(
+      "validation-error",
+      XGMML_ISSUE.DUPLICATE_ATTRIBUTE,
+      `${this.prefix()}an edge has weight="${record.weight}" and a weight att "${att.value ?? ""}"; the weight attribute is the weight and the att is not read`,
+      { line: att.line, element: record.id ?? record.label ?? "weight" }
+    );
+    return true;
   }
   /**
    * Write a label column (role label).
@@ -2021,7 +2285,7 @@ class XgmmlEmitter {
       return;
     }
     const handle = this.declare(domain, {
-      name: LABEL_COLUMN,
+      name: this.nameLabel[domain] ? "name" : LABEL_COLUMN,
       dtype: "string",
       role: "label",
       nullable: true,
@@ -2085,21 +2349,20 @@ class XgmmlEmitter {
   addEdges(records, header) {
     const ids = /* @__PURE__ */ new Set();
     const dedupe = this.dialect.cy2 && this.doc.nodes.some((n) => n.nested.length > 0) ? /* @__PURE__ */ new Set() : null;
+    let repeats = 0;
+    let firstRepeat = null;
     const labels = [];
     const edgeIds = [];
     const graphics = [];
     let row = 0;
+    this.decideNameLabel("edge", records);
     for (const record of records) {
       const where = { line: record.line, element: record.id ?? record.label };
-      const key2 = record.id ?? record.label;
+      const key2 = record.id ?? (record.label === null ? null : JSON.stringify([record.label, record.source, record.target]));
       if (dedupe !== null && key2 !== null) {
         if (dedupe.has(key2)) {
-          this.report.warnOnce(
-            "merged",
-            XGMML_ISSUE.GROUP_DUPLICATE_EDGE,
-            `${this.prefix()}the Cytoscape 2.x writer repeats the edges of a group; each repeat is dropped`,
-            where
-          );
+          repeats++;
+          firstRepeat ??= where;
           continue;
         }
         dedupe.add(key2);
@@ -2110,7 +2373,7 @@ class XgmmlEmitter {
         continue;
       }
       this.edgeIndex[row] = index;
-      labels[row] = record.label ?? void 0;
+      labels[row] = this.labelOf(record);
       edgeIds[row] = record.id ?? void 0;
       this.addElementColumns(this.edgeColumns, row, record, /* @__PURE__ */ new Set(), where);
       this.fillInteraction(record, row, where);
@@ -2119,6 +2382,14 @@ class XgmmlEmitter {
       }
       row++;
     }
+    if (repeats > 0) {
+      this.report.warning(
+        "merged",
+        XGMML_ISSUE.GROUP_DUPLICATE_EDGE,
+        `${this.prefix()}the Cytoscape 2.x writer repeats the edges of a group; ${repeats} repeat${plural(repeats)} ${agree(repeats, "was", "were")} dropped`,
+        firstRepeat ?? void 0
+      );
+    }
     this.writeEdgeIds(edgeIds);
     this.writeLabels("edge", labels, (r) => this.edgeIndex[r] ?? -1);
     const column = new JsonColumn(this, "edge", GRAPHICS_COLUMN, XGMML_ORIGIN_NAMESPACE, "graphics");
@@ -2195,7 +2466,7 @@ class XgmmlEmitter {
     if (text === null) {
       return void 0;
     }
-    const weight = parseWeightText(text);
+    const weight = parseWeightText(text, this.report);
     this.weighted ||= weight !== void 0;
     return weight;
   }
@@ -2213,21 +2484,22 @@ class XgmmlEmitter {
     if (text !== null) {
       const row = this.rows.get(text);
       if (row !== void 0 && row.index >= 0) {
-        return this.coercer.text(text);
+        return this.idOf(text);
       }
     }
     if (alias !== null) {
       const resolved = this.aliasRow(alias);
       if (resolved !== null) {
         this.aliasResolved++;
-        return this.coercer.text(resolved.id);
+        return this.idOf(resolved.id);
       }
     }
     if (text === null) {
+      const ambiguous = alias !== null && this.aliasRow(alias) === null && this.labelRows?.get(alias) === null;
       this.report.error(
         "missing-value",
         XGMML_ISSUE.MISSING_ENDPOINT,
-        `${this.prefix()}<edge> without a ${side}`,
+        ambiguous ? `${this.prefix()}<edge> without a ${side}: its label alias "${alias}" is ambiguous (several nodes have that label); the edge is skipped` : `${this.prefix()}<edge> without a ${side}`,
         where
       );
       return null;
@@ -2293,7 +2565,7 @@ class XgmmlEmitter {
     this.report.warning(
       "coercion",
       XGMML_ISSUE.LABEL_ALIAS,
-      `${this.prefix()}Cytoscape label aliases ("a (pp) b"): ${this.aliasResolved} endpoint(s) resolved, ${this.aliasInteractions} interaction(s) filled from edge labels`
+      `${this.prefix()}Cytoscape label aliases ("a (pp) b"): ${this.aliasResolved} endpoint${plural(this.aliasResolved)} resolved, ${this.aliasInteractions} interaction${plural(this.aliasInteractions)} filled from edge labels`
     );
   }
   /**
@@ -2391,6 +2663,9 @@ class XgmmlEmitter {
     });
   }
 }
+function isNameAtt(att) {
+  return att.name === "name" && (att.namespace ?? null) === null && att.value !== null && att.children.length === 0 && (att.cyType ?? "String") === "String";
+}
 function aliasesOf(label) {
   if (label === null) {
     return null;
@@ -2491,8 +2766,8 @@ class Positions {
     if (text === null) {
       return null;
     }
-    const n = Number(text.trim());
-    if (text.trim().length === 0 || !Number.isFinite(n)) {
+    const n = parseCoordinate(text);
+    if (n === null) {
       this.emitter.issues.error(
         "validation-error",
         XGMML_ISSUE.BAD_VALUE,
@@ -2595,7 +2870,7 @@ class Pointers {
       this.emitter.issues.warning(
         "validation-error",
         XGMML_ISSUE.DANGLING_REFERENCE,
-        `${prefix}${this.dangling} nested-network pointer(s) name no graph of the document`
+        `${prefix}${this.dangling} nested-network pointer${plural(this.dangling)} ${agree(this.dangling, "names", "name")} no graph of the document`
       );
     }
     const names = new JsonColumn(
@@ -2613,7 +2888,7 @@ class Pointers {
       this.emitter.issues.warning(
         "unsupported",
         XGMML_ISSUE.CROSS_FILE_REFERENCE,
-        `${prefix}${this.crossFile.size} nested-network pointer(s) point into another file; each is kept as text in ${NETWORK_POINTER_COLUMN}`
+        `${prefix}${this.crossFile.size} nested-network pointer${plural(this.crossFile.size)} ${agree(this.crossFile.size, "points", "point")} into another file; each is kept as text in ${NETWORK_POINTER_COLUMN}`
       );
       const column = new JsonColumn(
         this.emitter,
@@ -2638,6 +2913,7 @@ class Containment {
     this.emitter = emitter;
     this.parents = /* @__PURE__ */ new Map();
     this.subgraphs = /* @__PURE__ */ new Map();
+    this.groups = /* @__PURE__ */ new Set();
   }
   /**
    * Collect the memberships of every group node of the graph.
@@ -2683,7 +2959,7 @@ class Containment {
       this.emitter.issues.error(
         "missing-value",
         XGMML_ISSUE.UNKNOWN_PARENT,
-        `${this.emitter.prefix()}${unknown} group member(s) name no node of this graph`
+        `${this.emitter.prefix()}${unknown} group member${plural(unknown)} ${agree(unknown, "names", "name")} no node of this graph`
       );
     }
   }
@@ -2694,7 +2970,7 @@ class Containment {
    * @param line - the line
    */
   link(child, parent, line) {
-    if (child === parent || this.isAncestor(child, parent)) {
+    if (child === parent || this.groups.has(child) && this.isAncestor(child, parent)) {
       this.emitter.issues.error(
         "validation-error",
         XGMML_ISSUE.PARENT_CYCLE,
@@ -2708,6 +2984,7 @@ class Containment {
       list.push(parent);
     }
     this.parents.set(child, list);
+    this.groups.add(parent);
   }
   /**
    * Whether a node is an ancestor of another through the memberships so far.
@@ -2780,8 +3057,6 @@ const USED_OPTIONS = /* @__PURE__ */ new Set([
   "onProgress",
   "encoding"
 ]);
-const SNIFF_BYTES = 4096;
-const HEAD_CHARS = 2048;
 const XGMML_DOCTYPE = /<!DOCTYPE\s+graph\s[^<>]*xgmml\.dtd/i;
 function resolveSettings(options, cytoscape) {
   const zAs = options?.zAs ?? "column";
@@ -2828,10 +3103,10 @@ async function parseXgmml(input, report, common, options) {
     } : void 0
   };
   const parser = new XgmmlParser(report);
-  const seen = { head: "", content: false };
+  const seen = { content: false };
   try {
     await tokenizeXml(
-      watch(textChunks(input, report, { ...common, declaredEncoding: xmlDeclaredEncoding }), seen),
+      watch(textChunks(input, report, { ...common, declaredEncoding: xmlDeclaredEncoding, xml: true }), seen),
       parser,
       repairs
     );
@@ -2845,7 +3120,7 @@ async function parseXgmml(input, report, common, options) {
     throw err;
   }
   const doc = parser.document();
-  if (!doc.xgmmlNamespace && !XGMML_DOCTYPE.test(seen.head)) {
+  if (!doc.xgmmlNamespace && !XGMML_DOCTYPE.test(doc.doctype ?? "")) {
     report.warning(
       "validation-error",
       XGMML_ISSUE.NO_NAMESPACE,
@@ -2857,9 +3132,6 @@ async function parseXgmml(input, report, common, options) {
 }
 async function* watch(chunks, seen) {
   for await (const chunk of chunks) {
-    if (seen.head.length < HEAD_CHARS) {
-      seen.head += chunk.slice(0, HEAD_CHARS - seen.head.length);
-    }
     seen.content ||= !isWhitespace(chunk);
     yield chunk;
   }
@@ -2913,7 +3185,7 @@ function reportRootOnly(prepared) {
     prepared.report.warning(
       "unsupported",
       XGMML_ISSUE.ROOT_ONLY_ELEMENTS,
-      `${nodes} node(s) and ${edges} edge(s) belong to no registered network (group meta-edges, collapsed group members) and were not read`
+      `${elementCount(nodes, edges)} ${agree(nodes + edges, "belongs", "belong")} to none of the file's networks (group meta-edges or collapsed group members) and ${agree(nodes + edges, "was", "were")} not read`
     );
   }
 }
@@ -2924,22 +3196,22 @@ async function importXgmml(input, sink, options) {
     options,
     prepared.report
   );
-  if (prepared.graphs.length > 1) {
+  if (prepared.graphs.length > 1 && !graphChosen(options)) {
     prepared.report.warning(
       "unsupported",
       XGMML_ISSUE.MULTIPLE_GRAPHS,
-      `the session network document holds ${prepared.graphs.length} registered networks; ${prepared.graphs.length - 1} were not read (use importAll, graphIndex or graphName)`
+      `the session network document holds ${prepared.graphs.length} registered networks; only the first is read (importAllGraphs() reads every one; graphIndex or graphName chooses one)`
     );
   }
   return emitOne(prepared, prepared.graphs[index], sink);
 }
 async function importAllXgmml(input, sinkFor, options) {
-  const bytes = await reread(input);
-  const first = await prepare(bytes, null, options);
+  const first = await prepare(input, null, options);
+  const parsed = first.report.fork();
   const reports = [];
   for (let i = 0; i < first.graphs.length; i++) {
     const sink = sinkFor(i);
-    const prepared = i === 0 ? first : await prepare(bytes, null, options);
+    const prepared = i === 0 ? first : { ...first, report: parsed.fork() };
     reportSinkOptions(sink, options, prepared.report, true);
     reportUnusedOptions(options, prepared.report, USED_OPTIONS);
     reports.push(emitOne(prepared, prepared.graphs[i], sink));
@@ -2961,50 +3233,23 @@ async function listXgmmlGraphs(input, options) {
 function graphName(graph, doc) {
   return graph.label ?? (graph === doc.root ? doc.rdf.title ?? null : null) ?? graph.id ?? null;
 }
-async function reread(input) {
-  if (typeof input === "string" || input instanceof Uint8Array) {
-    return input;
-  }
-  const parts = [];
-  const iterable = typeof input.getReader === "function" ? streamIterable(input) : input;
-  for await (const chunk of iterable) {
-    parts.push(chunk);
-  }
-  if (parts.every((p) => typeof p === "string")) {
-    return parts.join("");
-  }
-  const bytes = parts.map((p) => typeof p === "string" ? new TextEncoder().encode(p) : p);
-  const out = new Uint8Array(bytes.reduce((n, b) => n + b.byteLength, 0));
-  let at = 0;
-  for (const b of bytes) {
-    out.set(b, at);
-    at += b.byteLength;
-  }
-  return out;
-}
-async function* streamIterable(stream) {
-  const reader = stream.getReader();
-  try {
-    for (; ; ) {
-      const { done, value } = await reader.read();
-      if (done) {
-        return;
-      }
-      yield value;
-    }
-  } finally {
-    reader.releaseLock();
-  }
-}
 function sniffXgmml(head) {
-  const text = new TextDecoder("utf-8", { fatal: false }).decode(head.subarray(0, SNIFF_BYTES));
+  let encoding = "utf-8";
+  if (head[0] === 255 && head[1] === 254 || head[0] === 60 && head[1] === 0 && head[2] === 63) {
+    encoding = "utf-16le";
+  } else if (head[0] === 254 && head[1] === 255 || head[0] === 0 && head[1] === 60 && head[2] === 0) {
+    encoding = "utf-16be";
+  }
+  const text = new TextDecoder(encoding, { fatal: false }).decode(head);
   if (!/^\uFEFF?\s*</.test(text)) {
     return 0;
   }
   if (XGMML_DOCTYPE.test(text)) {
     return 0.95;
   }
-  const root = /<(?!\?|!)([A-Za-z_][\w.-]*:)?([A-Za-z_][\w.-]*)[\s/>]/.exec(text.replace(/<!--[\s\S]*?-->/g, ""));
+  const root = /<(?![?!])([A-Za-z_][\w.-]*:)?([A-Za-z_][\w.-]*)[\s/>]/.exec(
+    text.replaceAll(/<!--[\s\S]*?(-->|$)/g, "")
+  );
   if (root === null || root[2] !== "graph") {
     return 0;
   }
@@ -3014,6 +3259,13 @@ function sniffXgmml(head) {
 }
 const xgmmlImporter = Object.freeze({
   format: FORMAT,
+  options: Object.freeze([
+    "cytoscapeEscapes",
+    "labelAliases",
+    "pairSurrogateReferences",
+    "repairBareAmpersands",
+    "zAs"
+  ]),
   extensions: EXTENSIONS,
   mimeTypes: MIME_TYPES,
   sniff: sniffXgmml,
@@ -3044,12 +3296,13 @@ export {
   PARENTS_COLUMN as h,
   XGMML_ORIGIN_NAMESPACE as i,
   CYTOSCAPE_ORIGIN_NAMESPACE as j,
-  isCyTrue as k,
-  XgmmlEmitter as l,
+  XgmmlEmitter as k,
+  isCyTrue as l,
   membersOf as m,
   dialectOf as n,
+  parseCoordinate as o,
   parseXgmml as p,
   resolveSettings as r,
   xgmmlImporter as x
 };
-//# sourceMappingURL=importer-D_e7e7LX.js.map
+//# sourceMappingURL=importer-Bcl1d4xH.js.map