libpetri 2.3.0 → 2.3.2

package/dist/{chunk-RNWTYK5B.js → render-UFO543NR.js}

@@ -1,3 +1,6 @@
+// src/viewer/render.ts
+import { instance as vizInstance } from "@viz-js/viz";
+
 // src/viewer/layout/preprocess.ts
 function classifyKind(id) {
   if (id.startsWith("p_")) return "place";
@@ -238,6 +241,124 @@ var ORCHESTRATOR_OPTIONS = {
   "elk.aspectRatio": "2.4",
   "elk.spacing.nodeNode": "10"
 };
+var FLAT_OPTIONS = {
+  "elk.padding": `[top=24,left=24,bottom=24,right=24]`,
+  "elk.algorithm": "layered",
+  "elk.direction": "DOWN",
+  "elk.spacing.nodeNode": "45",
+  "elk.layered.spacing.nodeNodeBetweenLayers": "60",
+  "elk.edgeRouting": "ORTHOGONAL"
+};
+var RECTPACK_CLUSTER_OPTIONS = {
+  "elk.padding": `[top=${FONT_CLUSTER + 16},left=16,bottom=16,right=16]`,
+  "elk.algorithm": "org.eclipse.elk.rectpacking",
+  "elk.aspectRatio": "1.3",
+  "elk.spacing.nodeNode": String(CLUSTER_SPACING)
+};
+var FLOW_SUB_OPTIONS = {
+  "elk.algorithm": "layered",
+  "elk.direction": "DOWN",
+  "elk.spacing.nodeNode": String(CLUSTER_SPACING),
+  "elk.layered.spacing.nodeNodeBetweenLayers": String(CLUSTER_SPACING + 6),
+  "elk.edgeRouting": "ORTHOGONAL"
+};
+var LEAF_SUB_OPTIONS = {
+  "elk.algorithm": "org.eclipse.elk.rectpacking",
+  "elk.aspectRatio": "1.4",
+  "elk.spacing.nodeNode": String(CLUSTER_SPACING)
+};
+var LEAF_BLOCK_GAP = 40;
+var SUB_PAD = 16;
+var SUB_PAD_TOP = FONT_CLUSTER + 16;
+var DEFAULT_MIN_LEAVES = 10;
+function resolveConfig(cfg) {
+  const lp = cfg?.leafPacking ?? true;
+  const lpObj = typeof lp === "object" ? lp : {};
+  return {
+    clusterLayout: cfg?.clusterLayout ?? "layered",
+    leafPacking: {
+      enabled: lp !== false,
+      minLeaves: lpObj.minLeaves ?? DEFAULT_MIN_LEAVES,
+      arcs: new Set(lpObj.arcs ?? ["reset", "read"])
+    }
+  };
+}
+function classifyLeaves(graph, cluster, arcs) {
+  const members = new Set(cluster.nodes);
+  const intraDegree = /* @__PURE__ */ new Map();
+  const intraSideEffect = /* @__PURE__ */ new Map();
+  for (const e of graph.edges) {
+    if (!members.has(e.src) || !members.has(e.dst)) continue;
+    const sideEffect = arcs.has(e.arc) ? 1 : 0;
+    for (const id of [e.src, e.dst]) {
+      intraDegree.set(id, (intraDegree.get(id) ?? 0) + 1);
+      intraSideEffect.set(id, (intraSideEffect.get(id) ?? 0) + sideEffect);
+    }
+  }
+  const flow = [];
+  const leaves = [];
+  for (const id of cluster.nodes) {
+    const node = graph.nodes.get(id);
+    if (!node) continue;
+    const deg = intraDegree.get(id) ?? 0;
+    const isLeaf = node.kind === "place" && deg >= 1 && (intraSideEffect.get(id) ?? 0) === deg;
+    (isLeaf ? leaves : flow).push(id);
+  }
+  return { flow, leaves };
+}
+async function layoutDominatedCluster(elk, graph, flow, leaves) {
+  const dimsOf = (id) => nodeDims(graph.nodes.get(id));
+  const flowSet = new Set(flow);
+  const flowEdges = [];
+  graph.edges.forEach((e, i) => {
+    if (flowSet.has(e.src) && flowSet.has(e.dst)) {
+      flowEdges.push({ id: `fe${i}`, sources: [e.src], targets: [e.dst] });
+    }
+  });
+  const flowLayout = await elk.layout({
+    id: "__flow",
+    layoutOptions: FLOW_SUB_OPTIONS,
+    children: flow.map((id) => ({ id, ...dimsOf(id) })),
+    edges: flowEdges
+  });
+  const leafLayout = await elk.layout({
+    id: "__leaves",
+    layoutOptions: LEAF_SUB_OPTIONS,
+    children: leaves.map((id) => ({ id, ...dimsOf(id) })),
+    edges: []
+  });
+  const flowW = flowLayout.width ?? 0;
+  const flowH = flowLayout.height ?? 0;
+  const leafW = leafLayout.width ?? 0;
+  const leafH = leafLayout.height ?? 0;
+  const contentW = Math.max(flowW, leafW);
+  const contentH = flowH + (leaves.length > 0 ? LEAF_BLOCK_GAP + leafH : 0);
+  const rel = /* @__PURE__ */ new Map();
+  const flowOffX = SUB_PAD + (contentW - flowW) / 2;
+  for (const ch of flowLayout.children ?? []) {
+    rel.set(ch.id, {
+      x: flowOffX + (ch.x ?? 0),
+      y: SUB_PAD_TOP + (ch.y ?? 0),
+      width: ch.width ?? 0,
+      height: ch.height ?? 0
+    });
+  }
+  const leafOffX = SUB_PAD + (contentW - leafW) / 2;
+  const leafOffY = SUB_PAD_TOP + flowH + LEAF_BLOCK_GAP;
+  for (const ch of leafLayout.children ?? []) {
+    rel.set(ch.id, {
+      x: leafOffX + (ch.x ?? 0),
+      y: leafOffY + (ch.y ?? 0),
+      width: ch.width ?? 0,
+      height: ch.height ?? 0
+    });
+  }
+  return {
+    width: contentW + 2 * SUB_PAD,
+    height: contentH + SUB_PAD_TOP + SUB_PAD,
+    rel
+  };
+}
 function partitionEdges(graph) {
   const byCluster = /* @__PURE__ */ new Map();
   const cross = [];
@@ -266,29 +387,50 @@ function partitionEdges(graph) {
   });
   return { byCluster, cross, edgeIdToKey };
 }
-async function elkLayout(graph) {
+async function elkLayout(graph, cfg) {
+  const config = resolveConfig(cfg);
   const { byCluster, cross, edgeIdToKey } = partitionEdges(graph);
+  const elk = new ELK();
+  const clusterOptions = config.clusterLayout === "rectpacking" ? RECTPACK_CLUSTER_OPTIONS : CLUSTER_OPTIONS;
+  const prebuilt = /* @__PURE__ */ new Map();
+  if (config.clusterLayout === "layered" && config.leafPacking.enabled) {
+    for (const [clusterId, cluster] of graph.clusters) {
+      const { flow, leaves } = classifyLeaves(graph, cluster, config.leafPacking.arcs);
+      if (leaves.length >= config.leafPacking.minLeaves && flow.length > 0) {
+        prebuilt.set(clusterId, await layoutDominatedCluster(elk, graph, flow, leaves));
+      }
+    }
+  }
   const elkChildren = [];
   for (const [clusterId, cluster] of graph.clusters) {
+    const pre = prebuilt.get(clusterId);
+    if (pre) {
+      elkChildren.push({ id: clusterId, width: pre.width, height: pre.height });
+      continue;
+    }
     elkChildren.push({
       id: clusterId,
-      layoutOptions: CLUSTER_OPTIONS,
+      layoutOptions: clusterOptions,
       children: cluster.nodes.map((id) => graph.nodes.get(id)).filter((n) => n !== void 0).map((n) => ({ id: n.id, ...nodeDims(n) })),
       edges: byCluster.get(clusterId) ?? []
     });
   }
+  const orchestratorOptions = graph.clusters.size === 0 ? FLAT_OPTIONS : config.clusterLayout === "rectpacking" ? RECTPACK_CLUSTER_OPTIONS : ORCHESTRATOR_OPTIONS;
   elkChildren.push({
     id: ORCHESTRATOR_CLUSTER_ID,
-    layoutOptions: ORCHESTRATOR_OPTIONS,
+    layoutOptions: orchestratorOptions,
     children: graph.orphans.map((id) => graph.nodes.get(id)).filter((n) => n !== void 0).map((n) => ({ id: n.id, ...nodeDims(n) })),
     edges: byCluster.get(ORCHESTRATOR_CLUSTER_ID) ?? []
   });
-  const elk = new ELK();
   const rootGraph = {
     id: "root",
     layoutOptions: ROOT_OPTIONS,
     children: elkChildren,
-    edges: cross
+    // Cross-cluster edges only ever fed `edgePaths` (an unused nop2
+    // affordance); `rectpacking` ignores them for placement. Drop them when
+    // any cluster is a childless prebuilt box — the edges reference member
+    // nodes ELK can no longer resolve in the hierarchy.
+    edges: prebuilt.size > 0 ? [] : cross
   };
   const layout = await elk.layout(rootGraph);
   const nodePositions = /* @__PURE__ */ new Map();
@@ -297,7 +439,8 @@ async function elkLayout(graph) {
   const walk = (node, parentX, parentY) => {
     const ax = parentX + (node.x ?? 0);
     const ay = parentY + (node.y ?? 0);
-    const isCluster = node.id !== "root" && (node.children?.length ?? 0) > 0;
+    const pre = node.id !== "root" ? prebuilt.get(node.id) : void 0;
+    const isCluster = node.id !== "root" && ((node.children?.length ?? 0) > 0 || pre !== void 0);
     if (isCluster) {
       clusterBoxes.set(node.id, {
         x: ax,
@@ -305,6 +448,16 @@ async function elkLayout(graph) {
         width: node.width ?? 0,
         height: node.height ?? 0
       });
+      if (pre) {
+        for (const [memberId, r] of pre.rel) {
+          nodePositions.set(memberId, {
+            x: ax + r.x,
+            y: ay + r.y,
+            width: r.width,
+            height: r.height
+          });
+        }
+      }
     }
     if (node.id !== "root" && !isCluster) {
       nodePositions.set(node.id, {
@@ -409,11 +562,67 @@ function writeBack(graph, layout) {
   return lines.join("\n");
 }
 
+// src/viewer/render.ts
+var vizPromise = null;
+function getViz() {
+  if (!vizPromise) vizPromise = vizInstance();
+  return vizPromise;
+}
+async function renderDotToSvg(dotSource) {
+  const viz = await getViz();
+  return viz.renderSVGElement(dotSource, { engine: "dot" });
+}
+function fnv1a(input) {
+  let h = 2166136261;
+  for (let i = 0; i < input.length; i++) {
+    h ^= input.charCodeAt(i);
+    h = Math.imul(h, 16777619);
+  }
+  return (h >>> 0).toString(16);
+}
+var PINNED_DOT_CACHE_CAP = 16;
+var pinnedDotCache = /* @__PURE__ */ new Map();
+function getCachedPinnedDot(key) {
+  const hit = pinnedDotCache.get(key);
+  if (hit !== void 0) {
+    pinnedDotCache.delete(key);
+    pinnedDotCache.set(key, hit);
+  }
+  return hit;
+}
+function setCachedPinnedDot(key, value) {
+  pinnedDotCache.set(key, value);
+  while (pinnedDotCache.size > PINNED_DOT_CACHE_CAP) {
+    const oldest = pinnedDotCache.keys().next().value;
+    if (oldest === void 0) break;
+    pinnedDotCache.delete(oldest);
+  }
+}
+function _clearElkLayoutCache() {
+  pinnedDotCache.clear();
+}
+async function renderDotToSvgWithElkLayout(dotSource, cfg) {
+  const key = fnv1a(dotSource + "\0" + JSON.stringify(cfg ?? {}));
+  let pinnedDot = getCachedPinnedDot(key);
+  if (pinnedDot === void 0) {
+    const graph = replicateShared(
+      foldOrphans(parseLibpetriDot(dotSource), 0.7),
+      { max: Infinity }
+    );
+    const layout = await elkLayout(graph, cfg);
+    pinnedDot = writeBack(graph, layout);
+    setCachedPinnedDot(key, pinnedDot);
+  }
+  const viz = await getViz();
+  return viz.renderSVGElement(pinnedDot, {
+    engine: "nop",
+    yInvert: true
+  });
+}
 export {
-  parseLibpetriDot,
-  foldOrphans,
-  replicateShared,
-  elkLayout,
-  writeBack
+  _clearElkLayoutCache,
+  getViz,
+  renderDotToSvg,
+  renderDotToSvgWithElkLayout
 };
-//# sourceMappingURL=chunk-RNWTYK5B.js.map
+//# sourceMappingURL=render-UFO543NR.js.map

package/dist/render-UFO543NR.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/viewer/render.ts","../src/viewer/layout/preprocess.ts","../src/viewer/layout/elk-place.ts"],"sourcesContent":["/**\n * DOT → SVG rendering for the canonical libpetri viewer.\n *\n * Two render paths:\n *\n *   renderDotToSvg(dot)                — plain Graphviz `dot` engine.\n *   renderDotToSvgWithElkLayout(dot)   — C0 pipeline: parse → fold →\n *                                        replicate → ELK → writeBack →\n *                                        Graphviz `neato` with `nop=1`\n *                                        (pin mode). Cached by DOT hash.\n *\n * The ELK path is the default for {@link mount}; the plain-Graphviz path\n * remains as a fallback for callers that want stock layout (or for\n * environments where elkjs isn't installed).\n *\n * @module viewer/render\n */\n\nimport { instance as vizInstance } from '@viz-js/viz';\nimport {\n  foldOrphans,\n  parseLibpetriDot,\n  replicateShared,\n} from './layout/preprocess.js';\nimport { elkLayout, writeBack } from './layout/elk-place.js';\nimport type { ElkLayoutConfig } from './layout/elk-place.js';\n\ntype Viz = Awaited<ReturnType<typeof vizInstance>>;\n\nlet vizPromise: Promise<Viz> | null = null;\n\n/** Memoize the viz.js instance so the wasm loads only once per page. */\nexport function getViz(): Promise<Viz> {\n  if (!vizPromise) vizPromise = vizInstance();\n  return vizPromise;\n}\n\n/**\n * Render a DOT source string to an SVGSVGElement using the plain `dot`\n * engine. Deterministic across runs; libpetri exporters emit byte-stable\n * DOT per spec EXP-014 so the same DOT yields the same SVG.\n */\nexport async function renderDotToSvg(dotSource: string): Promise<SVGSVGElement> {\n  const viz = await getViz();\n  return viz.renderSVGElement(dotSource, { engine: 'dot' });\n}\n\n// ---- C0 / ELK pin-mode cache ---------------------------------------------\n\n/** FNV-1a 32-bit hash. Fast enough that a SHA isn't worth the import. */\nfunction fnv1a(input: string): string {\n  let h = 0x811c9dc5;\n  for (let i = 0; i < input.length; i++) {\n    h ^= input.charCodeAt(i);\n    h = Math.imul(h, 0x01000193);\n  }\n  return (h >>> 0).toString(16);\n}\n\nconst PINNED_DOT_CACHE_CAP = 16;\nconst pinnedDotCache = new Map<string, string>();\n\nfunction getCachedPinnedDot(key: string): string | undefined {\n  const hit = pinnedDotCache.get(key);\n  if (hit !== undefined) {\n    // LRU touch: re-insert moves to most-recent position in Map ordering.\n    pinnedDotCache.delete(key);\n    pinnedDotCache.set(key, hit);\n  }\n  return hit;\n}\n\nfunction setCachedPinnedDot(key: string, value: string): void {\n  pinnedDotCache.set(key, value);\n  while (pinnedDotCache.size > PINNED_DOT_CACHE_CAP) {\n    const oldest = pinnedDotCache.keys().next().value;\n    if (oldest === undefined) break;\n    pinnedDotCache.delete(oldest);\n  }\n}\n\n/** Test helper — clears the pinned-DOT LRU cache between mounts. */\nexport function _clearElkLayoutCache(): void {\n  pinnedDotCache.clear();\n}\n\n/**\n * Run the C0 layout pipeline against a libpetri DOT source and return the\n * rendered SVG. The expensive steps (preprocess + ELK layout + DOT rewrite)\n * are cached keyed on the input DOT's hash plus the layout config, so\n * re-mounts on the same net structure and config skip everything except the\n * Graphviz pin-mode draw.\n *\n * Per-tick marking updates do NOT call this — they toggle classes on the\n * already-mounted SVG. ELK only runs when the net structure changes.\n *\n * `cfg` tunes the ELK stage — see {@link ElkLayoutConfig}.\n */\nexport async function renderDotToSvgWithElkLayout(\n  dotSource: string,\n  cfg?: ElkLayoutConfig,\n): Promise<SVGSVGElement> {\n  const key = fnv1a(dotSource + '\\0' + JSON.stringify(cfg ?? {}));\n  let pinnedDot = getCachedPinnedDot(key);\n  if (pinnedDot === undefined) {\n    const graph = replicateShared(\n      foldOrphans(parseLibpetriDot(dotSource), 0.7),\n      { max: Infinity },\n    );\n    const layout = await elkLayout(graph, cfg);\n    pinnedDot = writeBack(graph, layout);\n    setCachedPinnedDot(key, pinnedDot);\n  }\n  const viz = await getViz();\n  return viz.renderSVGElement(pinnedDot, {\n    engine: 'nop',\n    yInvert: true,\n  });\n}\n","/**\n * Graph pre-processing for the C0-replicate-default layout pipeline.\n *\n * Three pure-ish transforms operate on a {@link GraphModel} parsed from a\n * libpetri-exported DOT string:\n *\n *   parseLibpetriDot(dot)           → GraphModel\n *   foldOrphans(graph, threshold)   → GraphModel    (REASSIGN_ORPHANS)\n *   replicateShared(graph, opts)    → GraphModel    (REPLICATE_SHARED)\n *\n * The pipeline turns a flat cluster soup into a cluster-internal one by\n * (a) folding orphan nodes whose edges concentrate in one cluster into that\n * cluster, and (b) cloning shared places into every foreign cluster they\n * touch so cross-cluster spaghetti disappears. The resulting GraphModel is\n * what ELK lays out (Stage 2) and Graphviz then renders in pin-mode.\n *\n * Algorithm lineage: ported from\n * `/home/db/otto-repos/nucleus_marvin/.scratch/javadoc-layout-exp/CHECKPOINTS/run16_GOOD_v3_skip-junctions.mjs`\n * lines 14–220. The arc-type detection, replica naming\n * (`${placeId}__rep__${clusterShortName}`), and the `__replica` /\n * `replicaOf` markers are load-bearing — downstream stages key off them.\n *\n * @module viewer/layout/preprocess\n */\n\nexport type ArcType = 'normal' | 'reset' | 'inhibitor' | 'read';\nexport type NodeKind = 'place' | 'transition' | 'junction';\n\nexport interface ParsedNode {\n  readonly id: string;\n  readonly kind: NodeKind;\n  readonly attrs: Record<string, string>;\n  /** True iff this node was emitted by replicateShared. */\n  readonly replica?: boolean;\n  /** For a replica, the id of the original logical place. */\n  readonly replicaOf?: string;\n}\n\nexport interface ParsedEdge {\n  readonly src: string;\n  readonly dst: string;\n  readonly arc: ArcType;\n  /**\n   * Raw attribute body from the libpetri DOT (between the `[…]` brackets,\n   * brackets stripped). Carries style/penwidth/label that we want to\n   * round-trip verbatim so the rendered output matches `DotExporter`'s\n   * native look.\n   */\n  readonly rawAttrs: string;\n}\n\nexport interface ParsedCluster {\n  readonly id: string;          // \"cluster_productSearch\"\n  readonly shortName: string;   // \"productSearch\"\n  readonly nodes: readonly string[];\n}\n\nexport interface GraphModel {\n  readonly nodes: ReadonlyMap<string, ParsedNode>;\n  readonly clusters: ReadonlyMap<string, ParsedCluster>;\n  readonly nodeToCluster: ReadonlyMap<string, string>;\n  /** Node ids not in any cluster (rendered at the orchestrator root). */\n  readonly orphans: readonly string[];\n  readonly edges: readonly ParsedEdge[];\n}\n\nfunction classifyKind(id: string): NodeKind {\n  if (id.startsWith('p_')) return 'place';\n  if (id.startsWith('t_')) return 'transition';\n  return 'junction';\n}\n\n/**\n * Recover key=value attributes from inside a DOT `[...]` block.\n *\n * Mirrors v3 line 29. The regex is intentionally permissive about quoted\n * values containing escaped quotes; it does not validate DOT syntax.\n */\nfunction parseAttrs(body: string): Record<string, string> {\n  const attrs: Record<string, string> = {};\n  for (const m of body.matchAll(/(\\w+)=(\"(?:[^\"]|\\\\.)*\"|\\S+?)(?=[\\s,]|$)/g)) {\n    const [, key, raw] = m as unknown as [string, string, string];\n    const v = raw.startsWith('\"') && raw.endsWith('\"') ? raw.slice(1, -1) : raw;\n    attrs[key] = v;\n  }\n  return attrs;\n}\n\n/**\n * Parse a libpetri-exported DOT string into a {@link GraphModel}.\n *\n * Tolerates the current exporter shape (see\n * `java/src/main/java/org/libpetri/export/StyleConstants.java`):\n *  - inhibitor arcs use `arrowhead=\"odot\"` + color `#dc3545`\n *  - reset arcs use `label=\"reset\"` + color `#fd7e14`\n *  - read arcs use `label=\"read\"` + color `#6c757d`\n *\n * Mirrors v3 lines 24–103.\n */\nexport function parseLibpetriDot(dot: string): GraphModel {\n  const nodes = new Map<string, ParsedNode>();\n  // Greedy `.*` (no /s flag) consumes the full attrs body up to the line's\n  // trailing `];`. The v3 reference used `[^\\]]*` which silently dropped\n  // transitions whose label contained `[…]` text (e.g., `\"[0, ∞]ms\"`); we\n  // can't tolerate that here because the typed model wants every cluster\n  // member to have a Node entry.\n  for (const m of dot.matchAll(/^\\s*([pjt]_[A-Za-z0-9_]+)\\s*\\[(.*)\\];\\s*$/gm)) {\n    const [, id, body] = m as unknown as [string, string, string];\n    nodes.set(id, { id, kind: classifyKind(id), attrs: parseAttrs(body) });\n  }\n\n  const clusters = new Map<string, ParsedCluster>();\n  const nodeToCluster = new Map<string, string>();\n  for (const cm of dot.matchAll(/subgraph (cluster_\\w+)\\s*\\{([^]*?)^\\s*\\}/gm)) {\n    const [, clusterId, body] = cm as unknown as [string, string, string];\n    const memberIds = [...body.matchAll(/^\\s*([pjt]_[A-Za-z0-9_]+)\\s*\\[/gm)]\n      .map(m => (m as unknown as [string, string])[1]);\n    clusters.set(clusterId, {\n      id: clusterId,\n      shortName: clusterId.replace(/^cluster_/, ''),\n      nodes: memberIds,\n    });\n    for (const n of memberIds) nodeToCluster.set(n, clusterId);\n  }\n\n  // Catch nodes declared at root (orphans) — strip cluster bodies, then scan\n  const stripped = dot.replace(/subgraph cluster_\\w+\\s*\\{[^]*?^\\s*\\}/gm, '');\n  for (const m of stripped.matchAll(/^\\s*([pjt]_[A-Za-z0-9_]+)\\s*\\[/gm)) {\n    const id = (m as unknown as [string, string])[1];\n    if (!nodes.has(id)) {\n      // Root-declared node without full attrs (rare); seed with empty attrs.\n      nodes.set(id, { id, kind: classifyKind(id), attrs: {} });\n    }\n  }\n\n  const orphans = [...nodes.keys()].filter(n => !nodeToCluster.has(n));\n\n  const edges: ParsedEdge[] = [];\n  for (const m of dot.matchAll(/([pjt]_[A-Za-z0-9_]+)\\s*->\\s*([pjt]_[A-Za-z0-9_]+)\\s*(\\[[^\\]]*\\])?/g)) {\n    const [, src, dst, rawAttrs] = m as unknown as [string, string, string, string | undefined];\n    const attrs = rawAttrs ?? '';\n    // Cluster-anchor edges (lhead/ltail) are exporter-internal routing hints,\n    // not real arcs in the Petri net — skip per v3 line 97.\n    if (attrs.includes('lhead=') || attrs.includes('ltail=')) continue;\n    let arc: ArcType = 'normal';\n    if (attrs.includes('label=\"reset\"') || attrs.includes('#fd7e14')) arc = 'reset';\n    else if (attrs.includes('arrowhead=\"odot\"') || attrs.includes('#dc3545')) arc = 'inhibitor';\n    else if (attrs.includes('label=\"read\"')) arc = 'read';\n    // Strip the `[…]` brackets so writeBack can splice the body into a new\n    // attr list. Empty if libpetri emitted a bare `src -> dst;`.\n    const stripped = attrs.startsWith('[') && attrs.endsWith(']')\n      ? attrs.slice(1, -1)\n      : '';\n    edges.push({ src, dst, arc, rawAttrs: stripped });\n  }\n\n  return { nodes, clusters, nodeToCluster, orphans, edges };\n}\n\n/**\n * Adopt orphan nodes into the cluster their edges most prefer.\n *\n * For each orphan, tally how many of its edges touch each cluster. If the\n * dominant cluster gets at least `threshold` of the orphan's cluster-touching\n * edges, the orphan is reassigned to that cluster.\n *\n * Mirrors v3 lines 105–136. Default threshold 0.7 matches REASSIGN_ORPHANS.\n */\nexport function foldOrphans(graph: GraphModel, threshold = 0.7): GraphModel {\n  if (threshold <= 0) return graph;\n\n  const nodeToCluster = new Map(graph.nodeToCluster);\n  const clusterMembers = new Map<string, string[]>();\n  for (const [id, c] of graph.clusters) clusterMembers.set(id, [...c.nodes]);\n\n  const tally = new Map<string, Map<string, number>>();\n  const bump = (orphan: string, other: string): void => {\n    const oc = nodeToCluster.get(other);\n    if (!oc) return;\n    let t = tally.get(orphan);\n    if (!t) { t = new Map(); tally.set(orphan, t); }\n    t.set(oc, (t.get(oc) ?? 0) + 1);\n  };\n\n  for (const e of graph.edges) {\n    const sIsOrphan = !nodeToCluster.has(e.src);\n    const dIsOrphan = !nodeToCluster.has(e.dst);\n    if (sIsOrphan && !dIsOrphan) bump(e.src, e.dst);\n    if (dIsOrphan && !sIsOrphan) bump(e.dst, e.src);\n  }\n\n  for (const id of graph.orphans) {\n    const t = tally.get(id);\n    if (!t) continue;\n    let total = 0;\n    let bestCluster: string | null = null;\n    let bestCount = 0;\n    for (const [c, n] of t) {\n      total += n;\n      if (n > bestCount) { bestCount = n; bestCluster = c; }\n    }\n    if (bestCluster && total > 0 && bestCount / total >= threshold) {\n      clusterMembers.get(bestCluster)!.push(id);\n      nodeToCluster.set(id, bestCluster);\n    }\n  }\n\n  const clusters = new Map<string, ParsedCluster>();\n  for (const [id, c] of graph.clusters) {\n    clusters.set(id, { ...c, nodes: clusterMembers.get(id)! });\n  }\n  const orphans = [...graph.nodes.keys()].filter(n => !nodeToCluster.has(n));\n  return { ...graph, clusters, nodeToCluster, orphans };\n}\n\nexport interface ReplicateOptions {\n  /**\n   * Skip places that touch more than this many foreign clusters. Per the\n   * plan's \"no cap\" decision, default is `Infinity`. Set to a finite value\n   * to suppress replication of hub places that would otherwise produce many\n   * copies.\n   */\n  readonly max?: number;\n  /** If true, replicate transitions as well as places. Default false. */\n  readonly replicateTransitions?: boolean;\n}\n\nexport interface ReplicateStats {\n  readonly replicatedPlaces: number;\n  readonly totalCopies: number;\n}\n\n/**\n * For each place P, replicate it into every foreign cluster touched by its\n * edges, and redirect those cross-cluster edges to the local copy.\n *\n * Replica id convention is load-bearing: `${placeId}__rep__${shortClusterName}`.\n * Downstream stages (mount-time tagging, overlay highlight, click-all-copies)\n * key off this naming and the `replica: true` / `replicaOf` markers.\n *\n * If P has a home cluster (folded earlier), the original stays as the primary\n * copy and is also marked as a replica so the ⇄ glyph renders consistently.\n * If P is an orphan with all its edges redirected, the original is dropped.\n *\n * Mirrors v3 lines 138–221.\n */\nexport function replicateShared(\n  graph: GraphModel,\n  opts: ReplicateOptions = {},\n): GraphModel & { readonly replicateStats: ReplicateStats } {\n  const max = opts.max ?? Infinity;\n  const replicateTransitions = opts.replicateTransitions ?? false;\n\n  const nodes = new Map(graph.nodes);\n  const nodeToCluster = new Map(graph.nodeToCluster);\n  const clusterMembers = new Map<string, string[]>();\n  for (const [id, c] of graph.clusters) clusterMembers.set(id, [...c.nodes]);\n  const edges = graph.edges.map(e => ({ ...e }));\n\n  // 1. Compute foreign-cluster set per replicable node.\n  const foreignByNode = new Map<string, Set<string>>();\n  const noteForeign = (nodeId: string, otherId: string): void => {\n    if (!nodeId.startsWith('p_') && !(replicateTransitions && nodeId.startsWith('t_'))) return;\n    const home = nodeToCluster.get(nodeId);\n    const otherCluster = nodeToCluster.get(otherId);\n    if (!otherCluster) return;\n    if (otherCluster === home) return;\n    let s = foreignByNode.get(nodeId);\n    if (!s) { s = new Set(); foreignByNode.set(nodeId, s); }\n    s.add(otherCluster);\n  };\n  for (const e of edges) {\n    noteForeign(e.src, e.dst);\n    noteForeign(e.dst, e.src);\n  }\n\n  // 2. Emit replicas for nodes within the cap.\n  const replicaMap = new Map<string, Map<string, string>>();  // orig → cluster → replicaId\n  let replicatedPlaces = 0;\n  let totalCopies = 0;\n  for (const [placeId, foreigns] of foreignByNode) {\n    if (foreigns.size === 0) continue;\n    if (foreigns.size > max) continue;\n    const perCluster = new Map<string, string>();\n    const orig = nodes.get(placeId);\n    if (!orig) continue;\n    for (const clusterId of foreigns) {\n      const shortName = clusterId.replace(/^cluster_/, '');\n      const repId = `${placeId}__rep__${shortName}`;\n      perCluster.set(clusterId, repId);\n      clusterMembers.get(clusterId)!.push(repId);\n      nodeToCluster.set(repId, clusterId);\n      nodes.set(repId, {\n        id: repId,\n        kind: orig.kind,\n        attrs: { ...orig.attrs },\n        replica: true,\n        replicaOf: placeId,\n      });\n      totalCopies++;\n    }\n    replicaMap.set(placeId, perCluster);\n    replicatedPlaces++;\n    // Mark the original as a shared place so the ⇄ glyph renders uniformly.\n    nodes.set(placeId, { ...orig, replica: true, replicaOf: placeId });\n  }\n\n  // 3. Redirect cross-cluster edges to the local replica on each end.\n  for (const e of edges) {\n    const sMap = replicaMap.get(e.src);\n    const dMap = replicaMap.get(e.dst);\n    if (sMap) {\n      const dCl = nodeToCluster.get(e.dst);\n      if (dCl && sMap.has(dCl)) e.src = sMap.get(dCl)!;\n    }\n    if (dMap) {\n      const sCl = nodeToCluster.get(e.src);\n      if (sCl && dMap.has(sCl)) e.dst = dMap.get(sCl)!;\n    }\n  }\n\n  // 4. Drop orphan originals whose edges all got redirected away.\n  for (const [origId] of replicaMap) {\n    if (nodeToCluster.has(origId)) continue;  // folded — keep as primary\n    const stillHasEdge = edges.some(e => e.src === origId || e.dst === origId);\n    if (!stillHasEdge) nodes.delete(origId);\n  }\n\n  const clusters = new Map<string, ParsedCluster>();\n  for (const [id, c] of graph.clusters) {\n    clusters.set(id, { ...c, nodes: clusterMembers.get(id)! });\n  }\n  const orphans = [...nodes.keys()].filter(n => !nodeToCluster.has(n));\n\n  return {\n    nodes,\n    clusters,\n    nodeToCluster,\n    orphans,\n    edges,\n    replicateStats: { replicatedPlaces, totalCopies },\n  };\n}\n","/**\n * ELK placement + DOT pin-mode rewrite.\n *\n * Stage 2 of the C0 pipeline. Takes the {@link GraphModel} produced by\n * {@link parseLibpetriDot} → {@link foldOrphans} → {@link replicateShared},\n * runs ELKjs to compute absolute `(x, y)` per node and bounding boxes per\n * cluster, then emits a fresh DOT string with positions pinned via\n * `pos=\"x,y!\"` and `bb=\"…\"`. Downstream callers render the result through\n * `@viz-js/viz` with `engine: 'neato'` + `graphAttributes: { nop: '1' }` —\n * Graphviz uses the pinned positions verbatim and routes edges around the\n * pinned cluster boundaries.\n *\n * `elkLayout` takes (graph, cfg?); `writeBack` takes (graph, layout).\n * Neither touches the original DOT text — the model after replication has\n * nodes the original DOT doesn't, so patching the original would be\n * incorrect.\n *\n * Layout is configurable via {@link ElkLayoutConfig}: the per-subnet\n * algorithm (`clusterLayout`) and whether clusters dominated by side-effect\n * leaf places pack those leaves into a grid sub-block (`leafPacking`).\n *\n * @module viewer/layout/elk-place\n */\n\nimport ELK from 'elkjs/lib/elk.bundled.js';\nimport type {\n  ElkExtendedEdge,\n  ElkNode,\n} from 'elkjs/lib/elk-api.js';\nimport type { ArcType, GraphModel, ParsedCluster, ParsedNode } from './preprocess.js';\n\nconst ORCHESTRATOR_CLUSTER_ID = 'cluster_orchestrator';\n\n// Visual sizing — kept proportional to the v3 reference renderer so the\n// resulting bounding box is comparable to C0-GOOD_v3.svg.\nconst PLACE_RADIUS = 22;\nconst PLACE_CHARW = 7.4;\nconst PLACE_PAD_BELOW = 16;\nconst FONT_PLACE = 13;\nconst TRANSITION_MIN_W = 180;\nconst TRANSITION_H = 40;\nconst TRANSITION_CHARW = 8.5;\nconst JUNCTION_SIZE = 28;\nconst FONT_CLUSTER = 17;\nconst ROOT_SPACING = 90;\nconst CLUSTER_SPACING = 16;\n\n/**\n * Width/height in points that ELK should reserve for a node. Mirrors\n * `nodeDims` in v3 lines 66–78 — places get extra height to leave room for\n * the xlabel underneath the circle.\n */\nfunction nodeDims(node: ParsedNode): { width: number; height: number } {\n  if (node.kind === 'place') {\n    const label = (node.attrs.xlabel ?? node.attrs.label ?? node.id).replace(/\\\\n/g, ' ');\n    const labelWidth = label.length * PLACE_CHARW;\n    const circleD = PLACE_RADIUS * 2 + 4;\n    return {\n      width: Math.max(circleD, labelWidth),\n      height: circleD + PLACE_PAD_BELOW + FONT_PLACE,\n    };\n  }\n  if (node.kind === 'junction') {\n    return { width: JUNCTION_SIZE, height: JUNCTION_SIZE };\n  }\n  const label = (node.attrs.label ?? node.id).replace(/\\\\n/g, ' ');\n  return {\n    width: Math.max(TRANSITION_MIN_W, label.length * TRANSITION_CHARW),\n    height: TRANSITION_H,\n  };\n}\n\nexport interface NodePosition {\n  readonly x: number;\n  readonly y: number;\n  readonly width: number;\n  readonly height: number;\n}\n\nexport interface ClusterBox {\n  readonly x: number;\n  readonly y: number;\n  readonly width: number;\n  readonly height: number;\n}\n\nexport interface EdgePath {\n  readonly start: { x: number; y: number };\n  readonly end: { x: number; y: number };\n  readonly bends: ReadonlyArray<{ x: number; y: number }>;\n}\n\nexport interface LayoutResult {\n  readonly nodePositions: ReadonlyMap<string, NodePosition>;\n  readonly clusterBoxes: ReadonlyMap<string, ClusterBox>;\n  /** Keyed on `${src}->${dst}` — ELK-computed edge routes for `nop=2`. */\n  readonly edgePaths: ReadonlyMap<string, EdgePath>;\n  readonly totalWidth: number;\n  readonly totalHeight: number;\n}\n\nconst CLUSTER_OPTIONS: Record<string, string> = {\n  'elk.padding': `[top=${FONT_CLUSTER + 16},left=16,bottom=16,right=16]`,\n  'elk.algorithm': 'layered',\n  'elk.direction': 'DOWN',\n  'elk.spacing.nodeNode': String(CLUSTER_SPACING),\n  'elk.layered.spacing.nodeNodeBetweenLayers': String(CLUSTER_SPACING + 6),\n  'elk.edgeRouting': 'ORTHOGONAL',\n};\n\nconst ROOT_OPTIONS: Record<string, string> = {\n  'elk.algorithm': 'org.eclipse.elk.rectpacking',\n  'elk.aspectRatio': '1.4',\n  'elk.padding': '[top=24,left=24,bottom=24,right=24]',\n  'elk.spacing.nodeNode': String(ROOT_SPACING),\n};\n\nconst ORCHESTRATOR_OPTIONS: Record<string, string> = {\n  ...CLUSTER_OPTIONS,\n  'elk.aspectRatio': '2.4',\n  'elk.spacing.nodeNode': '10',\n};\n\n/**\n * Layout options for the synthetic orchestrator when it IS the whole\n * diagram — the flat \"one-net\" view (no real subnet clusters).\n *\n * `ORCHESTRATOR_OPTIONS` deliberately packs the orphan block tight\n * (`nodeNode: 10`, `aspectRatio: 2.4`) so it stays compact next to the\n * real subnet blocks the `rectpacking` root arranges. When the graph is\n * flat there are no other blocks: that compaction just bunches the whole\n * net up. Flat mode instead gets a generous layered layout — a clean\n * place→transition rank flow — with no forced aspect ratio.\n */\nconst FLAT_OPTIONS: Record<string, string> = {\n  'elk.padding': `[top=24,left=24,bottom=24,right=24]`,\n  'elk.algorithm': 'layered',\n  'elk.direction': 'DOWN',\n  'elk.spacing.nodeNode': '45',\n  'elk.layered.spacing.nodeNodeBetweenLayers': '60',\n  'elk.edgeRouting': 'ORTHOGONAL',\n};\n\n/**\n * Per-subnet ELK algorithm used when {@link ElkLayoutConfig.clusterLayout}\n * is `'rectpacking'` — packs a cluster's nodes as a 2-D grid, ignoring\n * intra-cluster edges. Maximally compact, but the place→transition flow\n * reading order is lost.\n */\nconst RECTPACK_CLUSTER_OPTIONS: Record<string, string> = {\n  'elk.padding': `[top=${FONT_CLUSTER + 16},left=16,bottom=16,right=16]`,\n  'elk.algorithm': 'org.eclipse.elk.rectpacking',\n  'elk.aspectRatio': '1.3',\n  'elk.spacing.nodeNode': String(CLUSTER_SPACING),\n};\n\n// Sub-layout options for a leaf-packed cluster: the flow part keeps the\n// layered place→transition rank flow; the leaf part is a compact grid.\nconst FLOW_SUB_OPTIONS: Record<string, string> = {\n  'elk.algorithm': 'layered',\n  'elk.direction': 'DOWN',\n  'elk.spacing.nodeNode': String(CLUSTER_SPACING),\n  'elk.layered.spacing.nodeNodeBetweenLayers': String(CLUSTER_SPACING + 6),\n  'elk.edgeRouting': 'ORTHOGONAL',\n};\nconst LEAF_SUB_OPTIONS: Record<string, string> = {\n  'elk.algorithm': 'org.eclipse.elk.rectpacking',\n  'elk.aspectRatio': '1.4',\n  'elk.spacing.nodeNode': String(CLUSTER_SPACING),\n};\n/** Gap between the layered flow and the packed leaf block, in points. */\nconst LEAF_BLOCK_GAP = 40;\n/** Padding inside a leaf-packed cluster box (left/right/bottom). */\nconst SUB_PAD = 16;\n/** Top padding inside a cluster box — room for the cluster label. */\nconst SUB_PAD_TOP = FONT_CLUSTER + 16;\n\n// ======================== Layout configuration ========================\n\n/** Per-subnet ELK algorithm. */\nexport type ClusterLayout = 'layered' | 'rectpacking';\n\n/** Tuning for side-effect-leaf packing — see {@link ElkLayoutConfig}. */\nexport interface LeafPackingOptions {\n  /**\n   * A cluster is \"dominated\" — and its side-effect leaf places get packed\n   * into a grid sub-block — when it has at least this many of them.\n   * Default 10.\n   */\n  readonly minLeaves?: number;\n  /**\n   * Arc types that mark a place as a side-effect leaf (a place whose every\n   * intra-cluster arc is one of these carries no data-flow ordering).\n   * Default `['reset', 'read']`.\n   */\n  readonly arcs?: readonly ArcType[];\n}\n\n/**\n * Layout configuration for {@link elkLayout}, surfaced to viewer callers\n * via `MountOptions`.\n */\nexport interface ElkLayoutConfig {\n  /** Per-subnet ELK algorithm. Default `'layered'`. */\n  readonly clusterLayout?: ClusterLayout;\n  /**\n   * Pack side-effect leaf places into a rectpacking sub-block, in clusters\n   * where they dominate. `true` (default) enables it with defaults; `false`\n   * disables it; an object tunes the threshold / arc types. Only takes\n   * effect when `clusterLayout` is `'layered'`.\n   */\n  readonly leafPacking?: boolean | LeafPackingOptions;\n}\n\ninterface ResolvedConfig {\n  readonly clusterLayout: ClusterLayout;\n  readonly leafPacking: {\n    readonly enabled: boolean;\n    readonly minLeaves: number;\n    readonly arcs: ReadonlySet<ArcType>;\n  };\n}\n\nconst DEFAULT_MIN_LEAVES = 10;\n\nfunction resolveConfig(cfg?: ElkLayoutConfig): ResolvedConfig {\n  const lp = cfg?.leafPacking ?? true;\n  const lpObj: LeafPackingOptions = typeof lp === 'object' ? lp : {};\n  return {\n    clusterLayout: cfg?.clusterLayout ?? 'layered',\n    leafPacking: {\n      enabled: lp !== false,\n      minLeaves: lpObj.minLeaves ?? DEFAULT_MIN_LEAVES,\n      arcs: new Set(lpObj.arcs ?? ['reset', 'read']),\n    },\n  };\n}\n\n/** A cluster pre-laid-out as [layered flow] stacked over [packed leaves]. */\ninterface PrebuiltCluster {\n  readonly width: number;\n  readonly height: number;\n  /** member node id → position relative to the cluster's top-left. */\n  readonly rel: ReadonlyMap<string, NodePosition>;\n}\n\n/**\n * Split a cluster's members into flow nodes and \"side-effect leaf places\".\n *\n * A side-effect leaf is a place whose every intra-cluster arc is a\n * side-effect arc (per `arcs` — reset/read). Such a place is not on any\n * data-flow path, so packing it as a grid cell loses no reading order.\n */\nfunction classifyLeaves(\n  graph: GraphModel,\n  cluster: ParsedCluster,\n  arcs: ReadonlySet<ArcType>,\n): { flow: string[]; leaves: string[] } {\n  const members = new Set(cluster.nodes);\n  const intraDegree = new Map<string, number>();\n  const intraSideEffect = new Map<string, number>();\n  for (const e of graph.edges) {\n    if (!members.has(e.src) || !members.has(e.dst)) continue;\n    const sideEffect = arcs.has(e.arc) ? 1 : 0;\n    for (const id of [e.src, e.dst]) {\n      intraDegree.set(id, (intraDegree.get(id) ?? 0) + 1);\n      intraSideEffect.set(id, (intraSideEffect.get(id) ?? 0) + sideEffect);\n    }\n  }\n  const flow: string[] = [];\n  const leaves: string[] = [];\n  for (const id of cluster.nodes) {\n    const node = graph.nodes.get(id);\n    if (!node) continue;\n    const deg = intraDegree.get(id) ?? 0;\n    const isLeaf =\n      node.kind === 'place' &&\n      deg >= 1 &&\n      (intraSideEffect.get(id) ?? 0) === deg;\n    (isLeaf ? leaves : flow).push(id);\n  }\n  return { flow, leaves };\n}\n\n/**\n * Lay a dominated cluster out as two stacked blocks: the flow nodes via\n * `layered` (place→transition rank flow), the side-effect leaves via\n * `rectpacking` (a compact grid). Returns the cluster's overall size and\n * every member node's position relative to the cluster's top-left.\n */\nasync function layoutDominatedCluster(\n  elk: InstanceType<typeof ELK>,\n  graph: GraphModel,\n  flow: string[],\n  leaves: string[],\n): Promise<PrebuiltCluster> {\n  const dimsOf = (id: string): { width: number; height: number } =>\n    nodeDims(graph.nodes.get(id)!);\n\n  const flowSet = new Set(flow);\n  const flowEdges: ElkExtendedEdge[] = [];\n  graph.edges.forEach((e, i) => {\n    if (flowSet.has(e.src) && flowSet.has(e.dst)) {\n      flowEdges.push({ id: `fe${i}`, sources: [e.src], targets: [e.dst] });\n    }\n  });\n\n  const flowLayout: ElkNode = await elk.layout({\n    id: '__flow',\n    layoutOptions: FLOW_SUB_OPTIONS,\n    children: flow.map(id => ({ id, ...dimsOf(id) })),\n    edges: flowEdges,\n  });\n  const leafLayout: ElkNode = await elk.layout({\n    id: '__leaves',\n    layoutOptions: LEAF_SUB_OPTIONS,\n    children: leaves.map(id => ({ id, ...dimsOf(id) })),\n    edges: [],\n  });\n\n  const flowW = flowLayout.width ?? 0;\n  const flowH = flowLayout.height ?? 0;\n  const leafW = leafLayout.width ?? 0;\n  const leafH = leafLayout.height ?? 0;\n  const contentW = Math.max(flowW, leafW);\n  const contentH = flowH + (leaves.length > 0 ? LEAF_BLOCK_GAP + leafH : 0);\n\n  const rel = new Map<string, NodePosition>();\n  const flowOffX = SUB_PAD + (contentW - flowW) / 2;\n  for (const ch of flowLayout.children ?? []) {\n    rel.set(ch.id, {\n      x: flowOffX + (ch.x ?? 0),\n      y: SUB_PAD_TOP + (ch.y ?? 0),\n      width: ch.width ?? 0,\n      height: ch.height ?? 0,\n    });\n  }\n  const leafOffX = SUB_PAD + (contentW - leafW) / 2;\n  const leafOffY = SUB_PAD_TOP + flowH + LEAF_BLOCK_GAP;\n  for (const ch of leafLayout.children ?? []) {\n    rel.set(ch.id, {\n      x: leafOffX + (ch.x ?? 0),\n      y: leafOffY + (ch.y ?? 0),\n      width: ch.width ?? 0,\n      height: ch.height ?? 0,\n    });\n  }\n\n  return {\n    width: contentW + 2 * SUB_PAD,\n    height: contentH + SUB_PAD_TOP + SUB_PAD,\n    rel,\n  };\n}\n\n/**\n * Group edges by the cluster that contains both endpoints (or 'root' if\n * the edge crosses cluster boundaries).\n *\n * Orphans count as living in `cluster_orchestrator` for routing purposes,\n * matching v3's `ownerOf` (line 223).\n */\nfunction partitionEdges(graph: GraphModel): {\n  byCluster: Map<string, ElkExtendedEdge[]>;\n  cross: ElkExtendedEdge[];\n  /** edgeId → \"src->dst\" so the layout walk can recover the original key. */\n  edgeIdToKey: Map<string, string>;\n} {\n  const byCluster = new Map<string, ElkExtendedEdge[]>();\n  const cross: ElkExtendedEdge[] = [];\n  const edgeIdToKey = new Map<string, string>();\n  const ownerOf = (id: string): string =>\n    graph.nodeToCluster.get(id) ?? ORCHESTRATOR_CLUSTER_ID;\n\n  graph.edges.forEach((e, i) => {\n    const so = ownerOf(e.src);\n    const dt = ownerOf(e.dst);\n    const id = `e${i}`;\n    edgeIdToKey.set(id, `${e.src}->${e.dst}`);\n    const elkEdge: ElkExtendedEdge = {\n      id,\n      sources: [e.src],\n      targets: [e.dst],\n    };\n    if (so === dt) {\n      let list = byCluster.get(so);\n      if (!list) { list = []; byCluster.set(so, list); }\n      list.push(elkEdge);\n    } else {\n      cross.push(elkEdge);\n    }\n  });\n  return { byCluster, cross, edgeIdToKey };\n}\n\n/**\n * Run ELK layout against the C0 graph and return absolute positions.\n *\n * Orphan nodes are wrapped in a synthetic `cluster_orchestrator` so ELK\n * lays them out as a single block alongside the real subnets, which the\n * `rectpacking` root algorithm then packs.\n *\n * With the default config a cluster dominated by side-effect leaf places\n * (≥ `leafPacking.minLeaves` of them) is pre-laid-out as a layered flow\n * stacked over a packed grid of those leaves — so a transition with many\n * reset arcs no longer strings its leaves into one wide row. See\n * {@link ElkLayoutConfig}.\n */\nexport async function elkLayout(\n  graph: GraphModel,\n  cfg?: ElkLayoutConfig,\n): Promise<LayoutResult> {\n  const config = resolveConfig(cfg);\n  const { byCluster, cross, edgeIdToKey } = partitionEdges(graph);\n  const elk = new ELK();\n  const clusterOptions =\n    config.clusterLayout === 'rectpacking' ? RECTPACK_CLUSTER_OPTIONS : CLUSTER_OPTIONS;\n\n  // Pre-lay-out clusters dominated by side-effect leaf places. Only in\n  // 'layered' mode — 'rectpacking' already packs every cluster's nodes.\n  const prebuilt = new Map<string, PrebuiltCluster>();\n  if (config.clusterLayout === 'layered' && config.leafPacking.enabled) {\n    for (const [clusterId, cluster] of graph.clusters) {\n      const { flow, leaves } = classifyLeaves(graph, cluster, config.leafPacking.arcs);\n      if (leaves.length >= config.leafPacking.minLeaves && flow.length > 0) {\n        prebuilt.set(clusterId, await layoutDominatedCluster(elk, graph, flow, leaves));\n      }\n    }\n  }\n\n  const elkChildren: ElkNode[] = [];\n  for (const [clusterId, cluster] of graph.clusters) {\n    const pre = prebuilt.get(clusterId);\n    if (pre) {\n      // Childless fixed-size box — ELK's root packer places it; the member\n      // node positions are spliced back in during the walk.\n      elkChildren.push({ id: clusterId, width: pre.width, height: pre.height });\n      continue;\n    }\n    elkChildren.push({\n      id: clusterId,\n      layoutOptions: clusterOptions,\n      children: cluster.nodes\n        .map(id => graph.nodes.get(id))\n        .filter((n): n is ParsedNode => n !== undefined)\n        .map(n => ({ id: n.id, ...nodeDims(n) })),\n      edges: byCluster.get(clusterId) ?? [],\n    });\n  }\n  // Synthetic orchestrator cluster holds the remaining orphans. When there\n  // are no real clusters the orchestrator IS the whole diagram (flat view),\n  // so it gets a generous full layered layout instead of the compact block\n  // packing tuned for sitting beside real subnets.\n  const orchestratorOptions =\n    graph.clusters.size === 0\n      ? FLAT_OPTIONS\n      : config.clusterLayout === 'rectpacking'\n        ? RECTPACK_CLUSTER_OPTIONS\n        : ORCHESTRATOR_OPTIONS;\n  elkChildren.push({\n    id: ORCHESTRATOR_CLUSTER_ID,\n    layoutOptions: orchestratorOptions,\n    children: graph.orphans\n      .map(id => graph.nodes.get(id))\n      .filter((n): n is ParsedNode => n !== undefined)\n      .map(n => ({ id: n.id, ...nodeDims(n) })),\n    edges: byCluster.get(ORCHESTRATOR_CLUSTER_ID) ?? [],\n  });\n\n  const rootGraph: ElkNode = {\n    id: 'root',\n    layoutOptions: ROOT_OPTIONS,\n    children: elkChildren,\n    // Cross-cluster edges only ever fed `edgePaths` (an unused nop2\n    // affordance); `rectpacking` ignores them for placement. Drop them when\n    // any cluster is a childless prebuilt box — the edges reference member\n    // nodes ELK can no longer resolve in the hierarchy.\n    edges: prebuilt.size > 0 ? [] : cross,\n  };\n  const layout: ElkNode = await elk.layout(rootGraph);\n\n  const nodePositions = new Map<string, NodePosition>();\n  const clusterBoxes = new Map<string, ClusterBox>();\n  const edgePaths = new Map<string, EdgePath>();\n\n  const walk = (node: ElkNode, parentX: number, parentY: number): void => {\n    const ax = parentX + (node.x ?? 0);\n    const ay = parentY + (node.y ?? 0);\n    const pre = node.id !== 'root' ? prebuilt.get(node.id) : undefined;\n    const isCluster =\n      node.id !== 'root' && ((node.children?.length ?? 0) > 0 || pre !== undefined);\n    if (isCluster) {\n      clusterBoxes.set(node.id, {\n        x: ax, y: ay,\n        width: node.width ?? 0,\n        height: node.height ?? 0,\n      });\n      // Prebuilt cluster: splice in the pre-computed member positions,\n      // offset by the cluster's ELK-assigned absolute origin.\n      if (pre) {\n        for (const [memberId, r] of pre.rel) {\n          nodePositions.set(memberId, {\n            x: ax + r.x, y: ay + r.y, width: r.width, height: r.height,\n          });\n        }\n      }\n    }\n    if (node.id !== 'root' && !isCluster) {\n      nodePositions.set(node.id, {\n        x: ax, y: ay,\n        width: node.width ?? 0,\n        height: node.height ?? 0,\n      });\n    }\n    // Edges inside this node — their section coords are in the parent's\n    // coordinate frame, so the offset to absolutize is (parentX, parentY)\n    // for root edges, or (ax, ay) for cluster-internal edges.\n    const edgeOffsetX = node.id === 'root' ? parentX : ax;\n    const edgeOffsetY = node.id === 'root' ? parentY : ay;\n    for (const edge of node.edges ?? []) {\n      const key = edge.id ? edgeIdToKey.get(edge.id) : undefined;\n      const section = edge.sections?.[0];\n      if (!key || !section) continue;\n      edgePaths.set(key, {\n        start: {\n          x: edgeOffsetX + section.startPoint.x,\n          y: edgeOffsetY + section.startPoint.y,\n        },\n        end: {\n          x: edgeOffsetX + section.endPoint.x,\n          y: edgeOffsetY + section.endPoint.y,\n        },\n        bends: (section.bendPoints ?? []).map(p => ({\n          x: edgeOffsetX + p.x,\n          y: edgeOffsetY + p.y,\n        })),\n      });\n    }\n    for (const child of node.children ?? []) walk(child, ax, ay);\n  };\n  walk(layout, 0, 0);\n\n  return {\n    nodePositions,\n    clusterBoxes,\n    edgePaths,\n    totalWidth: layout.width ?? 0,\n    totalHeight: layout.height ?? 0,\n  };\n}\n\n/**\n * Escape an attribute value for inclusion in a DOT string literal.\n *\n * Quotes are doubled (per the DOT escape convention `\\\"`).\n */\nfunction quote(value: string): string {\n  return `\"${value.replace(/\\\\/g, '\\\\\\\\').replace(/\"/g, '\\\\\"')}\"`;\n}\n\n/**\n * Render a node's attribute list — preserving the parsed attrs (including\n * libpetri's `width`/`height`, which are the *visual* shape dimensions)\n * and adding the ELK-computed `pos` so Graphviz `nop` can pin it.\n *\n * The `pos=\"x,y!\"` form (with trailing `!`) is the neato pin-mode marker.\n * Do NOT emit ELK's layout-reserved width/height to Graphviz — those are\n * the bounding boxes needed for ELK packing (which account for xlabel\n * spillover), not the visible shape sizes. libpetri's standard styles use\n * `width=0.35` for places (25pt circles); overriding with ELK's\n * ~3 inch label-padded box made Graphviz render 114pt-radius circles.\n */\nfunction nodeAttrLine(node: ParsedNode, pos: NodePosition): string {\n  const attrs: string[] = [];\n  // Center the pinned position on the node's bbox (ELK gives the top-left).\n  const cx = pos.x + pos.width / 2;\n  const cy = pos.y + pos.height / 2;\n  attrs.push(`pos=${quote(`${cx.toFixed(2)},${cy.toFixed(2)}!`)}`);\n  for (const [k, v] of Object.entries(node.attrs)) {\n    if (k === 'pos') continue;\n    attrs.push(`${k}=${quote(v)}`);\n  }\n  return `${node.id} [${attrs.join(', ')}];`;\n}\n\nfunction edgeAttrLine(src: string, dst: string, rawAttrs: string): string {\n  // Splice libpetri's original attrs verbatim so style/penwidth/label/color\n  // match `DotExporter` 1:1. We do NOT emit `pos=` for edges — under engine\n  // `nop` Graphviz routes edges itself around the pinned node positions,\n  // which gives proper boundary clipping (arrowheads land at the visual\n  // node edge) and avoids needing a custom polyline-to-spline converter.\n  // The only \"custom\" arrowhead is `arrowhead=\"odot\"` for inhibitor edges,\n  // which libpetri's exporter already writes into rawAttrs.\n  const body = rawAttrs.trim();\n  return `${src} -> ${dst}` + (body ? ` [${body}];` : ';');\n}\n\n/**\n * Emit a Graphviz DOT string with positions pinned. Render the result with\n * `@viz-js/viz` using:\n *\n * ```ts\n * viz.renderSVGElement(dot, {\n *   engine: 'nop',\n *   yInvert: true,\n * });\n * ```\n *\n * `engine: 'nop'` (a.k.a. `nop1`) honours the pinned `pos=` on every node\n * and routes edges around them. We use this rather than `nop2` because\n * `nop2` would force us to provide a spline for every edge ourselves (no\n * routing) — and Graphviz's own routing produces correctly-clipped\n * arrowheads at the visual node boundary, which our ELK polylines did not\n * (ELK uses the layout-reserved bbox, our visual circle is much smaller).\n *\n * `yInvert: true` matches ELK's Y-down convention to Graphviz's Y-up.\n */\nexport function writeBack(graph: GraphModel, layout: LayoutResult): string {\n  const lines: string[] = [];\n  lines.push('digraph LibpetriPinned {');\n  lines.push('    rankdir=TB;');\n  lines.push('    overlap=\"false\";');\n  lines.push('    compound=\"true\";');\n  lines.push('    fontname=\"Helvetica,Arial,sans-serif\";');\n  lines.push('    outputorder=\"edgesfirst\";');\n  lines.push('    node [fontname=\"Helvetica,Arial,sans-serif\", fontsize=10];');\n  lines.push('    edge [fontname=\"Helvetica,Arial,sans-serif\", fontsize=9];');\n\n  // Clusters with their pinned bounding boxes\n  for (const [clusterId, cluster] of graph.clusters) {\n    const box = layout.clusterBoxes.get(clusterId);\n    lines.push(`    subgraph ${clusterId} {`);\n    lines.push(`        label=${quote(cluster.shortName)};`);\n    lines.push(`        style=\"rounded,dashed\";`);\n    lines.push(`        bgcolor=\"#FAFAFA\";`);\n    lines.push(`        penwidth=1.5;`);\n    if (box) {\n      const x1 = box.x.toFixed(2);\n      const y1 = box.y.toFixed(2);\n      const x2 = (box.x + box.width).toFixed(2);\n      const y2 = (box.y + box.height).toFixed(2);\n      lines.push(`        bb=${quote(`${x1},${y1},${x2},${y2}`)};`);\n    }\n    for (const nodeId of cluster.nodes) {\n      const node = graph.nodes.get(nodeId);\n      const pos = layout.nodePositions.get(nodeId);\n      if (!node || !pos) continue;\n      lines.push('        ' + nodeAttrLine(node, pos));\n    }\n    lines.push('    }');\n  }\n\n  // Orphans (root-level nodes) — laid out inside the synthetic\n  // orchestrator cluster but emitted at root so they sit alongside the\n  // real subnets without their own labelled box.\n  for (const orphanId of graph.orphans) {\n    const node = graph.nodes.get(orphanId);\n    const pos = layout.nodePositions.get(orphanId);\n    if (!node || !pos) continue;\n    lines.push('    ' + nodeAttrLine(node, pos));\n  }\n\n  // Edges — emit just the source -> dest pair plus libpetri's original\n  // styling attrs. Graphviz `nop` routes the line itself and clips arrow\n  // heads to the visual node boundary.\n  for (const edge of graph.edges) {\n    lines.push('    ' + edgeAttrLine(edge.src, edge.dst, edge.rawAttrs));\n  }\n\n  lines.push('}');\n  return 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package/dist/viewer/index.d.ts

@@ -109,6 +109,89 @@ interface VisibilityState {
 /** CSS custom property names that the canonical stylesheet honours. */
 declare const VIEWER_CSS_VARIABLES: readonly ["--lpv-bg", "--lpv-header-bg", "--lpv-border", "--lpv-text", "--lpv-muted", "--lpv-cluster-bg", "--lpv-cluster-bg-collapsed", "--lpv-cluster-stroke-width", "--lpv-cluster-stroke-dash", "--lpv-cluster-fill-tint", "--lpv-dim-opacity", "--lpv-active-filter-outline", "--lpv-legend-bg", "--lpv-chip-bg", "--lpv-chip-active-bg", "--lpv-sidebar-bg", "--lpv-sidebar-border", "--lpv-sidebar-text", "--lpv-sidebar-muted", "--lpv-sidebar-chip-bg", "--lpv-sidebar-chip-hover-bg", "--lpv-sidebar-chip-off-opacity", "--lpv-shared-glyph-color", "--lpv-replica-fill", "--lpv-replica-stroke", "--lpv-highlight-stroke", "--lpv-highlight-glow", "--lpv-neighbor-stroke", "--lpv-faded-node-opacity", "--lpv-faded-edge-opacity", "--lpv-faded-cluster-opacity"];
 
+/**
+ * Graph pre-processing for the C0-replicate-default layout pipeline.
+ *
+ * Three pure-ish transforms operate on a {@link GraphModel} parsed from a
+ * libpetri-exported DOT string:
+ *
+ *   parseLibpetriDot(dot)           → GraphModel
+ *   foldOrphans(graph, threshold)   → GraphModel    (REASSIGN_ORPHANS)
+ *   replicateShared(graph, opts)    → GraphModel    (REPLICATE_SHARED)
+ *
+ * The pipeline turns a flat cluster soup into a cluster-internal one by
+ * (a) folding orphan nodes whose edges concentrate in one cluster into that
+ * cluster, and (b) cloning shared places into every foreign cluster they
+ * touch so cross-cluster spaghetti disappears. The resulting GraphModel is
+ * what ELK lays out (Stage 2) and Graphviz then renders in pin-mode.
+ *
+ * Algorithm lineage: ported from
+ * `/home/db/otto-repos/nucleus_marvin/.scratch/javadoc-layout-exp/CHECKPOINTS/run16_GOOD_v3_skip-junctions.mjs`
+ * lines 14–220. The arc-type detection, replica naming
+ * (`${placeId}__rep__${clusterShortName}`), and the `__replica` /
+ * `replicaOf` markers are load-bearing — downstream stages key off them.
+ *
+ * @module viewer/layout/preprocess
+ */
+type ArcType = 'normal' | 'reset' | 'inhibitor' | 'read';
+
+/**
+ * ELK placement + DOT pin-mode rewrite.
+ *
+ * Stage 2 of the C0 pipeline. Takes the {@link GraphModel} produced by
+ * {@link parseLibpetriDot} → {@link foldOrphans} → {@link replicateShared},
+ * runs ELKjs to compute absolute `(x, y)` per node and bounding boxes per
+ * cluster, then emits a fresh DOT string with positions pinned via
+ * `pos="x,y!"` and `bb="…"`. Downstream callers render the result through
+ * `@viz-js/viz` with `engine: 'neato'` + `graphAttributes: { nop: '1' }` —
+ * Graphviz uses the pinned positions verbatim and routes edges around the
+ * pinned cluster boundaries.
+ *
+ * `elkLayout` takes (graph, cfg?); `writeBack` takes (graph, layout).
+ * Neither touches the original DOT text — the model after replication has
+ * nodes the original DOT doesn't, so patching the original would be
+ * incorrect.
+ *
+ * Layout is configurable via {@link ElkLayoutConfig}: the per-subnet
+ * algorithm (`clusterLayout`) and whether clusters dominated by side-effect
+ * leaf places pack those leaves into a grid sub-block (`leafPacking`).
+ *
+ * @module viewer/layout/elk-place
+ */
+
+/** Per-subnet ELK algorithm. */
+type ClusterLayout = 'layered' | 'rectpacking';
+/** Tuning for side-effect-leaf packing — see {@link ElkLayoutConfig}. */
+interface LeafPackingOptions {
+    /**
+     * A cluster is "dominated" — and its side-effect leaf places get packed
+     * into a grid sub-block — when it has at least this many of them.
+     * Default 10.
+     */
+    readonly minLeaves?: number;
+    /**
+     * Arc types that mark a place as a side-effect leaf (a place whose every
+     * intra-cluster arc is one of these carries no data-flow ordering).
+     * Default `['reset', 'read']`.
+     */
+    readonly arcs?: readonly ArcType[];
+}
+/**
+ * Layout configuration for {@link elkLayout}, surfaced to viewer callers
+ * via `MountOptions`.
+ */
+interface ElkLayoutConfig {
+    /** Per-subnet ELK algorithm. Default `'layered'`. */
+    readonly clusterLayout?: ClusterLayout;
+    /**
+     * Pack side-effect leaf places into a rectpacking sub-block, in clusters
+     * where they dominate. `true` (default) enables it with defaults; `false`
+     * disables it; an object tunes the threshold / arc types. Only takes
+     * effect when `clusterLayout` is `'layered'`.
+     */
+    readonly leafPacking?: boolean | LeafPackingOptions;
+}
+
 /**
  * Canonical libpetri Petri-net diagram viewer.
  *
@@ -229,6 +312,23 @@ interface MountOptions {
      * cached on the DOT hash; re-mounts on identical DOT skip the pipeline.
      */
     readonly layout?: 'elk' | 'graphviz';
+    /**
+     * Per-subnet ELK algorithm, used within the `'elk'` pipeline. `'layered'`
+     * (default) gives each subnet a place→transition rank flow; `'rectpacking'`
+     * packs every subnet's nodes as a compact 2-D grid (maximally compact, but
+     * intra-cluster flow order is lost). Ignored when {@link layout} is
+     * `'graphviz'`.
+     */
+    readonly clusterLayout?: ClusterLayout;
+    /**
+     * Within the `'elk'` + `'layered'` pipeline, pack "side-effect leaf"
+     * places (places whose only arcs are reset/read) into a grid sub-block,
+     * in clusters where they dominate — so a transition with many reset arcs
+     * doesn't string its leaves into one wide row. `true` (default) enables
+     * it; `false` disables it; an object tunes the threshold / arc types.
+     * See {@link LeafPackingOptions}.
+     */
+    readonly leafPacking?: boolean | LeafPackingOptions;
     /**
      * Initial subnet visibility mode. Defaults to `'show'` (clustered view).
      * Pass `'hide'` to mount with the flat view from the start. The chrome
@@ -244,19 +344,8 @@ interface MountOptions {
  * and surface cluster overlay controls.
  *
  * The container's existing children are removed before the new SVG is
- * appended (the same teardown behaviour `renderDotToContainer` used to provide).
- *
- * Pass `dotSource === null` to adopt an SVG already present as a direct child
- * of `container` (pre-rendered SVG path — e.g. the Java javadoc taglet emits
- * `dot -Tsvg` at build time). In that mode the viewer never imports the
- * runtime DOT renderer, which lets the static IIFE bundle drop `@viz-js/viz`
- * entirely.
- *
- * NOTE: when shipping a pre-rendered SVG (`dotSource === null`), do NOT also
- * pass `previousHandle` — the handle's `dispose()` runs before SVG detection
- * and would orphan the host. The Java taglet mounts once per page so this is
- * a non-issue in practice.
+ * appended.
  */
-declare function mount(dotSource: string | null, container: HTMLElement, opts?: MountOptions): Promise<ViewerHandle>;
+declare function mount(dotSource: string, container: HTMLElement, opts?: MountOptions): Promise<ViewerHandle>;
 
-export { type ClusterDescriptor, DEFAULT_PANZOOM_OPTS, type MountOptions, type PanzoomInstance, type PanzoomOptions, type SubnetVisibility, VIEWER_CSS_VARIABLES, type ViewerHandle, colorForPrefix, discoverClusters, mount };
+export { type ClusterDescriptor, type ClusterLayout, DEFAULT_PANZOOM_OPTS, type ElkLayoutConfig, type LeafPackingOptions, type MountOptions, type PanzoomInstance, type PanzoomOptions, type SubnetVisibility, VIEWER_CSS_VARIABLES, type ViewerHandle, colorForPrefix, discoverClusters, mount };

package/dist/viewer/index.js

@@ -698,21 +698,16 @@ async function mount(dotSource, container, opts = {}) {
   if (previousHandle) {
     previousHandle.dispose();
   }
-  let svg;
-  const existing = container.querySelector(":scope > svg");
-  if (dotSource == null) {
-    if (!(existing instanceof SVGSVGElement)) {
-      throw new Error("mount: no DOT source and no pre-rendered SVG");
-    }
-    svg = existing;
-  } else {
-    const renderModule = await import("../render-QK57X4TP.js");
-    const useElk = (opts.layout ?? "elk") === "elk";
-    const renderedDot = subnetsMode === "hide" ? flattenClusters(dotSource) : dotSource;
-    svg = useElk ? await renderModule.renderDotToSvgWithElkLayout(renderedDot) : await renderModule.renderDotToSvg(renderedDot);
-    container.innerHTML = "";
-    container.appendChild(svg);
-  }
+  const renderModule = await import("../render-UFO543NR.js");
+  const useElk = (opts.layout ?? "elk") === "elk";
+  const renderedDot = subnetsMode === "hide" ? flattenClusters(dotSource) : dotSource;
+  const elkConfig = {
+    clusterLayout: opts.clusterLayout,
+    leafPacking: opts.leafPacking
+  };
+  const svg = useElk ? await renderModule.renderDotToSvgWithElkLayout(renderedDot, elkConfig) : await renderModule.renderDotToSvg(renderedDot);
+  container.innerHTML = "";
+  container.appendChild(svg);
   container.classList.add("libpetri-viewer");
   const panzoomInstance = attachPanzoom(svg, opts.panzoom);
   const clusters = discoverClusters(svg);
@@ -757,10 +752,6 @@ async function mount(dotSource, container, opts = {}) {
     subnetsBtn.className = "diagram-btn btn-subnets";
     subnetsBtn.title = subnetsMode === "show" ? "Hide subnet groupings" : "Show subnet groupings";
     subnetsBtn.textContent = subnetsMode === "show" ? "Flat view" : "Subnets view";
-    if (dotSource == null) {
-      subnetsBtn.disabled = true;
-      subnetsBtn.title = "Subnet toggle unavailable for pre-rendered SVG";
-    }
     subnetsBtn.addEventListener("click", () => {
       void handle.toggleSubnets();
     });
@@ -801,7 +792,6 @@ async function mount(dotSource, container, opts = {}) {
       return subnetsMode;
     },
     setSubnets(mode) {
-      if (dotSource == null) return Promise.resolve(handle);
       if (mode === subnetsMode) return Promise.resolve(handle);
       return mount(dotSource, container, {
         ...opts,