fix(visualize): show summary sources + review cleanup

- build_graph: summaries have no `sources` field — their origin is
  `full_text` (e.g. sources/nvda-10q.md). Include it so summary nodes show
  their source in the inspector instead of 'none'.
- graph.html cleanup from review: cache per-node color (drops a per-frame
  colorOf lookup), store adjacency as a Set (O(1) neighbour test, was
  O(deg) per node per frame), one degree-sort feeding both hubs and labels,
  a TAU constant for the seven full-circle arcs, and a corrected comment on
  the spring degree-softening (it intentionally only damps hub-hub edges).

Author: KylinMountain

openkb/templates/graph.html

@@ -174,6 +174,7 @@
   Work:"168,160,255", Event:"94,234,212", Entity:"148,163,184"
 };
 const colorOf = t => TYPE_COLORS[t] || "148,163,184";
+const TAU = Math.PI * 2;                  // full circle for ctx.arc
 
 /* ===================== canvas + state ===================== */
 const canvas = document.getElementById("c");
@@ -189,23 +190,19 @@
 const nodes = GRAPH.nodes.map(n => ({
   ...n, x:0, y:0, z:0, vx:0, vy:0, vz:0,
   r: 8 + Math.min(10, (n.in || 0) + (n.out || 0)),   // radius scales with degree
+  col: colorOf(n.type),                               // cached neon color → no per-frame lookup
   alpha: 1,                                            // per-node fade (legend toggle)
   sx:0, sy:0, rz:0, pp:1, hl:1, pinned:false           // projection cache + smoothed highlight + pinned (drag to pull out)
 }));
 const byId = Object.fromEntries(nodes.map(n => [n.id, n]));
 const edges = GRAPH.edges.filter(e => byId[e.source] && byId[e.target]);
-const adj = {}; nodes.forEach(n => adj[n.id] = []);
-edges.forEach(e => { adj[e.source].push(e.target); adj[e.target].push(e.source); });
-
-// the few highest-degree hubs get an idle breathing glow
-const hubIds = new Set(
-  [...nodes].sort((a,b) => ((b.in+b.out)-(a.in+a.out))).slice(0, Math.min(3, nodes.length)).map(n => n.id)
-);
-// labels shown at rest = the most-connected nodes; the rest reveal on hover/zoom
-const labelIds = new Set(
-  [...nodes].sort((a,b) => ((b.in+b.out)-(a.in+a.out)))
-            .slice(0, Math.max(6, Math.round(nodes.length*0.18))).map(n => n.id)
-);
+const adj = {}; nodes.forEach(n => adj[n.id] = new Set());
+edges.forEach(e => { adj[e.source].add(e.target); adj[e.target].add(e.source); });   // Set → O(1) neighbour test
+
+// rank nodes by degree once; top 3 hubs breathe at rest, top ~18% keep labels at rest
+const byDeg = [...nodes].sort((a,b) => (b.in+b.out)-(a.in+a.out)).map(n => n.id);
+const hubIds = new Set(byDeg.slice(0, Math.min(3, nodes.length)));
+const labelIds = new Set(byDeg.slice(0, Math.max(6, Math.round(nodes.length*0.18))));
 
 const hiddenTypes = new Set();           // legend filter
 const typeVisible = t => !hiddenTypes.has(t);
@@ -261,8 +258,9 @@
     const a = byId[e.source], b = byId[e.target];
     if(!visible(a) || !visible(b)) return;
     let dx = b.x-a.x, dy = b.y-a.y, dz = b.z-a.z, d = Math.hypot(dx,dy,dz) || 1;
-    // normalize the pull by degree: a hub with N springs shouldn't feel N× the force
-    const s = 1 / Math.min(adj[e.source].length || 1, adj[e.target].length || 1);
+    // soften by the lower-degree endpoint so dense hub↔hub edges don't dominate
+    // (a leaf↔hub edge stays full strength — that's intended)
+    const s = 1 / Math.min(adj[e.source].size || 1, adj[e.target].size || 1);
     const f = (d-118)*0.012 * s * alpha;
     a.vx += dx/d*f; a.vy += dy/d*f; a.vz += dz/d*f;
     b.vx -= dx/d*f; b.vy -= dy/d*f; b.vz -= dz/d*f;
@@ -365,15 +363,15 @@
     const fx = ax + (bx-ax)*k, fy = ay + (by-ay)*k;
     ctx.shadowColor = "rgba(45,212,191,.9)"; ctx.shadowBlur = 8;
     ctx.fillStyle = "rgba(170,255,240,.98)";
-    ctx.beginPath(); ctx.arc(fx, fy, 2.8, 0, 6.2832); ctx.fill();
+    ctx.beginPath(); ctx.arc(fx, fy, 2.8, 0, TAU); ctx.fill();
     ctx.shadowBlur = 0;
   }
   ctx.globalAlpha = 1;
 }
 
 function drawNode(n, t){
   if(n.alpha < 0.02) return;
-  const col = colorOf(n.type);
+  const col = n.col;
   const hl = n.hl;   // smoothed highlight: 1 = lit; eases down (not snaps) when another node is hovered
   const breathe = (!hover && hubIds.has(n.id)) ? (1 + 0.05*Math.sin(t*0.0024)) : 1;
   const pulse = (n.id===hover) ? (1.16 + 0.03*Math.sin(t*0.006)) : 1;
@@ -383,30 +381,30 @@
   ctx.globalAlpha = n.alpha * fog * (0.34 + 0.66*hl);            // dim non-neighbors gently, never to black
   // selected ring
   if(n.id === selected){
-    ctx.beginPath(); ctx.arc(x, y, r+6, 0, 6.2832);
+    ctx.beginPath(); ctx.arc(x, y, r+6, 0, TAU);
     ctx.strokeStyle = `rgba(${col},.85)`; ctx.lineWidth = 2; ctx.stroke();
   }
   // pinned marker (dashed ring → "pulled out and held")
   if(n.pinned){
-    ctx.beginPath(); ctx.arc(x, y, r+4, 0, 6.2832);
+    ctx.beginPath(); ctx.arc(x, y, r+4, 0, TAU);
     ctx.strokeStyle = "rgba(255,255,255,.65)"; ctx.lineWidth = 1.5;
     ctx.setLineDash([3,3]); ctx.stroke(); ctx.setLineDash([]);
   }
   // hover halo
   if(n.id === hover){
-    ctx.beginPath(); ctx.arc(x, y, r+11, 0, 6.2832);
+    ctx.beginPath(); ctx.arc(x, y, r+11, 0, TAU);
     ctx.fillStyle = `rgba(${col},.16)`; ctx.fill();
   }
   // disc + glow (glow eases with highlight so hovering doesn't flash the whole scene)
-  ctx.beginPath(); ctx.arc(x, y, r, 0, 6.2832);
+  ctx.beginPath(); ctx.arc(x, y, r, 0, TAU);
   ctx.fillStyle = `rgba(${col},${0.5 + 0.5*hl})`;
   ctx.shadowColor = `rgba(${col},.8)`;
   ctx.shadowBlur = (n.id===hover ? 17 : 11) * fog * hl;
   ctx.fill();
   ctx.shadowBlur = 0;
   // bright inner core
   if(hl > 0.35){
-    ctx.beginPath(); ctx.arc(x-r*0.28, y-r*0.28, r*0.34, 0, 6.2832);
+    ctx.beginPath(); ctx.arc(x-r*0.28, y-r*0.28, r*0.34, 0, TAU);
     ctx.fillStyle = `rgba(255,255,255,${0.5*hl})`; ctx.fill();
   }
   // label — declutter: hubs at rest; hovered node + neighbors; selection; zoomed in; near depth only
@@ -428,7 +426,7 @@
   // ease each node's highlight toward its target so hover brightens/dims smoothly (no flash)
   const focus = hover || selected;   // hovering OR an open inspector keeps that node's connections lit
   for(const n of nodes){
-    const near = !focus || n.id===focus || adj[focus].includes(n.id);
+    const near = !focus || n.id===focus || adj[focus].has(n.id);
     n.hl += ((near ? 1 : 0.22) - n.hl) * 0.12;
   }
   ctx.setTransform(DPR,0,0,DPR,0,0);

openkb/visualize.py

@@ -37,6 +37,9 @@ def build_graph(wiki_dir: Path) -> dict:
             desc = desc.strip() if isinstance(desc, str) else ""
             srcs = fm.get("sources")
             srcs = [str(s) for s in srcs] if isinstance(srcs, list) else []
+            ft = fm.get("full_text")   # summaries record their origin document here, not in `sources`
+            if isinstance(ft, str) and ft.strip():
+                srcs.insert(0, ft.strip())
             nodes[nid] = {"id": nid, "label": p.stem, "type": t,
                           "description": desc, "sources": srcs, "out": 0, "in": 0}
 

tests/test_visualize.py

@@ -14,7 +14,7 @@ def _wiki(tmp_path: Path) -> Path:
 def test_build_graph_nodes_edges_types(tmp_path):
     wiki = _wiki(tmp_path)
     (wiki / "summaries" / "paper.md").write_text(
-        '---\ntype: "Summary"\ndescription: "A paper."\n---\n\n'
+        '---\ntype: "Summary"\ndescription: "A paper."\nfull_text: "sources/paper.json"\n---\n\n'
         "Discusses [[concepts/attention]] and [[entities/anthropic]].\n", encoding="utf-8")
     (wiki / "concepts" / "attention.md").write_text(
         '---\ntype: "Concept"\ndescription: "Focus."\nsources: ["summaries/paper"]\n---\n\n'
@@ -37,6 +37,9 @@ def test_build_graph_nodes_edges_types(tmp_path):
     assert not any(e["source"] == e["target"] for e in g["edges"])
     assert by["concepts/attention"]["in"] == 1 and by["summaries/paper"]["out"] == 2
     assert g["types"] == ["Concept", "Organization", "Summary"]
+    # sources: concepts use the `sources` field; summaries fall back to `full_text` (the origin doc)
+    assert by["concepts/attention"]["sources"] == ["summaries/paper"]
+    assert by["summaries/paper"]["sources"] == ["sources/paper.json"]
 
 
 def test_build_graph_empty_wiki(tmp_path):