af666aaa3f5449f08e009f9a620905d7264f0a62
9
Commits
| Author | SHA1 | Message | Date | |
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 amosblomqvist
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af666aaa3f |
physics: bundles join their cluster; depth runs over the logical graph
Owner-approved brief (orchestrator, physics arc): two laws.
1. IMP-NODE CLUSTER ASSIGNMENT. Imp nodes were unclustered (the partition
runs over stored propositions only) — no centroid pull, outside the
painted hulls, bundles sitting on the periphery pointing outward.
Now: a derived imp node's cluster is a function of its derivation —
MAJORITY among its PREMISES' birth sessions (owner: premises, NOT the
conclusion), ties to the chain's OWN birth (its provenance's first
point — the asserting session; deterministic, coincides with the
unanimous common case). Imp nodes are always re-derived, never
birthed, so the assignment must be exactly this.
Seam chosen: core/session-clusters.ts exports impClusterKey + a
shared attachImpToCommunities that mutates a communities list's
members IN PLACE. graphSnapshot attaches AFTER the hull filter (a
2-proposition community + its bundle never resurrects a hull — the
filter counts propositions); settleGraphLayout attaches to the
unfiltered partition (settle pulls every community; hulls are a
canvas-only concern). Both cluster-membership consumers — the sim's
centroid pull and buildRegions' rasterization — read it through the
members lists that went through the one helper, so the resting
ledger and the live sim agree on where bundles belong.
2. DEPTHS OVER THE LOGICAL GRAPH. inferenceDepths ran Tarjan over the
DRAWN edges (premise→imp→conclusion), inflating every multi-premise
conclusion one hop (depth(imp)+1 instead of depth(premises)+1) and
ranking the geometry point itself. Now:
- deriveView additionally emits logicalEdges — every chain contracted
to direct premise→conclusion arrows over PROPOSITION ids only
(per-premise, deduped — a conclusion's rank is max over premises,
which a single arbitrary premise edge could not express).
- GraphSnapshot carries logicalEdges; createGraphSimulation /
incrementalLayout accept a logicalEdges option: the depth
machinery (orphan detection AND the rank pass) reads it, springs
keep the drawn edges. Absent = edges (legacy behavior).
- Imp nodes join the ORPHAN-EXEMPTION mask explicitly — never pinned
to a level, keep the full regular forces (gravity, cluster pull,
springs), settle naturally between premise and conclusion levels;
the rank map is computed over propositions only, so arg_ ids are
absent from it by construction.
Wiring: settle + canvas (CanvasData.logicalEdges → buildSim) +
replay-layout all pass the logical set.
EXTRA FIX (in-slice discovery, one line, graph-server domain):
server/graph.ts graphClusters — the practice picker's /api/graph/
clusters — partitioned snap.NODES (the canvas image, imp nodes riding
it since chains-primary), leaking arg_ ids into nodeIds: pickable ids
that silently vanish inside chainsForSelection while nodeCount lied.
Now partitions snap.propositions — same purity law as the chain
table's 767a559 fix.
Tests (+13): impClusterKey pins (unanimous; cross-session majority; tie
→ chain's own birth, not the conclusion's); attach pins (members gain
the imp id, sorted; single-premise attaches nothing — no node exists;
dangling mints nothing; home absent from the list stays unattached);
snapshot pins (imp id rides cluster members to both consumers; the hull
filter counts propositions); logical-depth pins (multi-premise
conclusion at premises'+1 NOT +2; imp absent from the rank map);
depth-force exemption pin (rows pin crisply, arg_x floats unpinned —
old behavior stamped it onto the conclusion's row); deriveView logical
arrows (per-premise, deduped, proposition ids only).
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amosblomqvist
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719f7f9934 |
rendering arc: the imp node becomes the argument's geometry, not a fake proposition
Owner-approved brief (orchestrator): the canvas stops drawing implication nodes as first-class nodes and starts drawing them as what they are — the point where co-premise lines converge. - deriveView (core/graph.ts): single-premise chains collapse to ONE direct premise->conclusion arrow — no imp node minted (a chain is always N-in/ 1-out; one premise is the degenerate case). Multi-premise chains keep the imp node + fan. Dangling guard unchanged. - physics (core/layout.ts createGraphSimulation): per-link rest length — a link touching an arg_-prefixed endpoint gets HALF the base link distance, default or user-tuned alike; everything else about imp-node physics citizenship unchanged. - canvas (components/graph-canvas.ts): imp nodes are PURE GEOMETRY — invisible (no disc, no label) and unpickable (excluded from pickAt's hit-test projection). Edges INTO an imp node: headless, shaft runs to its CENTER (toRadius 0, no head triangle). Edges OUT: shaft starts at the center (fromRadius 0), arrowhead lands on the conclusion's disc edge. Single-premise direct arrows render as today's plain arrows. - comment repairs (same commit): the two stale double-shaft claims (CanvasEdge doc + the draw-pass block) rewritten to the truth — plain single shafts; bundles are headless converging lines + one arrowed out-edge; no double-shaft glyph exists anywhere. - tests (+9): deriveView pins (single-premise collapse, multi-premise fan, shared-conclusion distinctness, dangling drop); imp-link half- distance settle pins; arrowGeometry zero-radius laws + isImpNodeId pin; graph.test.ts's snapshot invariant now counts only MULTI-premise live chains (its fixture's single-premise chains mint zero imp nodes); layout settle fixture updated for the collapse. |
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amosblomqvist
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0f93124c7e |
feat: canonical world-scale renderer — sizes become world units + baked tuning + nice-number ladders
The world-scale pivot (2026-09-17): node/label/arrowhead sizes were
calibrated as "screen px at fit zoom", a unit whose meaning depended on
the graph's own extent — a 13-node graph at kFit 3.65 rendered 5.3x
smaller nodes than a 338-node graph at kFit 0.69, with no slider values
able to reproduce the dense feel. Sizes are now canonical WORLD units
(graph-canvas.ts drops the ÷kFit division in geometry/regions/hit-test);
kFit survives only as the label-gate 1x reference. The renderer's module
doc and the SIZE SEMANTICS block in render-settings.ts carry the story.
Camera becomes pure persisted view state: {k, x, y} stored to localStorage
(lh.graph.camera.v1, 250ms debounce, flush on unmount), restored on mount
via the new initialCamera constructor arg; the hardcoded fit() runs only
on first-ever open. A pin test locks the d3 zoomIdentity composition.
Region blur becomes world units too (the last span-coupled quantity): the
old bitmap-px reach scaled with graph span, so the 2026-09-14
search-filter collapse fix is now structural (blurW = tuning.blur; the
cellRef anchor is gone). Charge default bumps to -240 (single source:
CHARGE_STRENGTH in layout.ts; CHARGE_RANGE re-anchored so -240 sits
dead-center).
The 2026-09-17 bake — the user's live-tuned defaults (nodeSize 2,
edgeWidth 1, arrowLength 2, labelSize 3, labelZoom 4 / "8x", dilation 20,
blur 20, edgeAlpha 0.2, bitmap 256) — plus the ladder pivot: every
non-physics knob moves on a hand-authored 11-stop ladder (x1.5/x1.33
series, quarter/half steps at the low end), default dead-center at slider
position 50, step 10 = one stop per detent. The sanitizer snaps ANY
incoming value to the nearest stop (ties break low), so stored files can
never hold 2.18137...977-style artifacts; pre-pivot files (sizeUnits !=
"world") reset only the four resemanticized size fields. Physics sliders
keep the fine-grained log mapping.
The label cross-fade becomes PROPORTIONAL to the gate (span = gate x
LABELS_FADE_RATIO): the old absolute 0.5-ratio span read as a 100%
relative change at the old 0.5 gate but a 12% sliver at the tuned 8x —
"lower zoom levels naturally produce a longer transitionary period".
At the 8x default the node→cluster handoff now fades across one full
ladder stop (8x -> 12x). labelZoomDisplay is absolute (ratio / 0.5) so
the tuned gate keeps reading "8x" now that 4 IS the default.
Gates: 495/495 tests, tsc/eslint/build clean.
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amosblomqvist
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652a25e382 |
Orphan discs in regions + orphan exemption from depth anchoring
Two follow-ups on the semantic-cluster wave, both user-reported: 1. Region coloring: edge-only dilation (the anti-double-counting rule from the Louvain era) left 114 of 338 cluster members completely uncolored — semantic clusters contain members that share no intra-cluster edge with anyone (90 edge-orphans + isolated micro-topics), and 20 of 45 clusters painted nothing at all. Fix: a disc (radius = dilation, same as a round cap) for exactly the members no intra-cluster edge stroke reached. Every member is painted by its edges' caps OR one disc, never both — the no-double-counting rule survives. Verified live: all 74 orphans-in-clusters sit on tinted region pixels. 2. Depth modes (ORPHAN RULE): a node with no edges has no dependency structure, so depth-0 stamping put 90 unconnected propositions on the vertical baseline / radial base ring — meaning they don't have. Orphans are now exempt from the depth force and get the regular view's unprojected forces instead (full center gravity + full cluster pull). Structured-node projections unchanged (x-only gravity in vertical, none in radial; tangential-only cluster pull in radial). Gravity in depth modes is a custom force with EXACTLY d3's forceX/forceY math (strength × alpha — the first draft forgot the alpha and shifted the settle). Verified live: radial orphans follow their topics instead of the base ring; vertical orphans spread 1006 world units (6/90 near the baseline band vs 90/90 before). |
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amosblomqvist
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f5edc7f0a5 |
Semantic topic clusters: local embeddings replace Louvain
Louvain only ever found the reasoning chains (the graph is disconnected by nature — every connected component became its own cluster) and edge-orphans could never join anything. Clusters are now RELATED TOPICS: propositions grouped by meaning. - Embedder (src/server/embeddings.ts): in-process transformers.js v4 running EmbeddingGemma-300M q8 (MTEB 68.4, ~300MB one-time download), MRL-truncated to 512d, "title: none | text:" prefix on 100% of inputs, L2-normalized so cosine = dot. Model/dim mismatch voids the ledger (full re-embed). Injected at the composition root — the agent layer never imports the server layer (architecture law). - Ledger (data/graph/embeddings.json): model + dim + vectors + the persisted cluster partition. Reclustering runs at the END of every embedding batch (post-merge hook, both front doors) — never per read (the agglomerative pass is ~1.5s at 338 nodes). - Clustering (src/core/semantic-clusters.ts): hand-rolled average-linkage agglomerative over cosine (npm HDBSCAN is an abandoned alpha). Stragglers stay singletons by default; attachStragglers is the all-in toggle. Threshold 0.60 swept on the real graph: 26 topics, 74/90 edge-orphans land in real topics, 10 stragglers. - Consumers (snapshot, settle, namer, replay) read the persisted partition — one cluster concept everywhere; core-survival label matching unchanged (20/26 topics kept labels). - Louvain retired: detectCommunities + graphology* deps deleted (graphology-louvain had leaked into the client bundle since the clusters wave); scripts/bench-graph.ts (dead FA2 bench) removed. - scripts/embed-graph.ts: backfill/cold-start (338 nodes in 150s including the one-time model download). |
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amosblomqvist
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3a1c18b9de |
Inference-depth anchoring playground: vertical + radial modes
The graph's follows/supports edges encode derivation (premise -> conclusion); the layout can now express that rank spatially, as a session-only playground toggle (nothing promoted yet): - inferenceDepths: longest chain from a base node, CYCLE-SAFE by SCC condensation (Tarjan, iterative) — the DAG property is typical, not guaranteed; cycle members share their component's depth (mutual support = equal footing). O(V+E), pure, deterministic. - DepthAnchor force: per-node target scalar — vertical mode rows (baseline at the anchor centroid, arrows up), radial mode rings (foundations center, outer boundary = edge of knowledge). The rank is computed, not simulated: pairwise up-forces can't give baselines. - Mode projections: gravity x-only in vertical / dropped in radial; cluster pull x-only in vertical / tangential-only in radial; the anchor re-blend preserves user arrangement in the FREE dimension only (x / angle) — meaning owns the constrained axis, memory owns the free one. - setPhysicsTuning reheats (alpha 1): toggling a mode re-forms the graph live and commits the new rest state; drag release is springy along the constrained axis (node returns toward its level/ring). - Sweep on the real graph: strength 0.8 = 215/216 arrows correct with organic sag; 1.5 = crisp rows. 174 base nodes, max chain depth 7, zero cycles in current data. replay-layout --depth=<mode> bakes a mode into the ledger for rest-state experiments. |
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amosblomqvist
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975a78a304 |
Cluster gravity: per-cluster centroid pull force in the engine
The 'virtual node' realized as a centroid force: two allocation-free O(n) passes per tick (membership resolved once at sim creation; Float64Array sums). Measured indistinguishable from force-off at 338 nodes (271ms vs 272ms per 400-tick settle). - createGraphSimulation: SimOptions.clusterPull + linkStrength + velocityDecay (physics controls plumbing); degree-scaled link stiffness so linkStrength=1 is exactly d3's default - settleGraphLayout split into layout-settle.ts (it computes the Louvain partition for the pull); layout.ts stays browser-barrel-pure - barrel no longer re-exports clusters.ts: graphology + louvain are fully out of the client bundle (verified against built chunks) - replay passes the per-batch partition; CLUSTER_PULL_STRENGTH=0.15 tuned by sweep: cluster spread 63->36 world units, centroid separation and total span unchanged (no blob merge, no collapse) |
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amosblomqvist
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7eceb58303 |
Engine unification: d3-force replaces forceAtlas2 everywhere
One engine owns the equilibrium: the merge settle and (next commit) the live drag both run createGraphSimulation — d3-force link springs, 1/d charge, weak centroid gravity — so a drag's rest state IS the server's rest state. The FA2-era anchor mechanism survives as a post-tick POSITION-SPACE re-blend (retention 0.85): d3's forceLink is a Hooke spring (strength*(d-L)*alpha), which overpowers any force-space anchor at long range — the re-blend is alpha-independent and always wins as the sim anneals (the 675-unit drift bug). Gravity retuned for d3's 1/d many-body falloff (bootstrap 0.2 / incremental 0.12: cluster spacing lands ~400 world units, the FA2-era density). Rim orphans seed (and anchor) at 1.7x the CONNECTED core's mean radius — a max-span-based rim fed back on itself and ran the layout away to 6000 units. Replay: 338 positions in 1.6s, old-node shift within a batch 4.8 (FA2: 23). |
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amosblomqvist
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0c14ea425d |
Option A: incremental anchored force layout, persisted server-side
The layout now EVOLVES instead of reshuffling on every extraction. A pure
core module (src/core/layout.ts) warm-starts forceAtlas2 from the positions
ledger (data/graph/positions.json, read-modify-write like sources.json,
updatedAt stamp for future live-physics conflict handling), re-blends every
previously-positioned node toward its anchor each iteration (retention 0.85
- old placements stay recognizable, strong forces still win), seeds new
nodes near their positioned neighbors, and seeds orphans on the rim outside
the core so they read as unconnected knowledge.
- Port/store: GraphStore.readPositions/writePositions; snapshot carries
positions when the ledger exists (optional - fresh graphs unchanged).
- Extraction pipeline settles synchronously after every merge (chat and
notes paths), before usage persist - the next /api/graph fetch already
reflects new nodes.
- View: the ledger IS the layout; the local one-shot FA2 pass survives
only as a fallback when no ledger exists.
- scripts/replay-layout.ts: simulates organic growth by replaying the
current 338-node graph one imported file at a time (real import order,
edges activate when both endpoints exist). Real run: 338 positions in
0.3s, 90-degree-0 orphans collecting at mean r=338 vs connected r=194.
- Also restores the cluster region fills (hull background colors) that
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