daftari 1.9.1 → 1.11.0

package/dist/themes/clustering.js

@@ -0,0 +1,439 @@
+// Clustering primitives for vault_themes.
+//
+// All functions are pure. The k-means implementation is hand-rolled (no
+// new dependency) and seeded by a caller-supplied RNG so the same vault
+// produces the same themes across runs.
+//
+// Input vectors are L2-normalised by the caller, so Euclidean distance on
+// the unit sphere is equivalent to cosine distance (1 - cos θ). We use
+// squared Euclidean inside k-means because it is monotonic with Euclidean
+// distance and avoids per-iteration sqrt work.
+//
+// Two distinct quality scores live here and must not be confused:
+//   - silhouetteScore: the internal k-picker. Mean over all points of
+//     (b - a) / max(a, b) where a is mean intra-cluster distance and b is
+//     mean nearest-other-cluster distance. Higher = better separation.
+//   - clusterCoherence: the per-theme number returned in the tool output.
+//     Mean pairwise cosine similarity inside one cluster. Higher = tighter.
+// --- Seeded RNG ------------------------------------------------------------
+// Mulberry32: a 32-bit, single-state PRNG. Cheap, deterministic, sufficient
+// for clustering's stochastic init. Returns numbers in [0, 1). Seed 0 still
+// produces a valid (constant-free) sequence because the increment 0x6D2B79F5
+// keeps the state moving.
+export function seededRng(seed) {
+    let a = seed | 0;
+    return () => {
+        a = (a + 0x6d2b79f5) | 0;
+        let t = a;
+        t = Math.imul(t ^ (t >>> 15), t | 1);
+        t ^= t + Math.imul(t ^ (t >>> 7), t | 61);
+        return ((t ^ (t >>> 14)) >>> 0) / 4294967296;
+    };
+}
+// --- Vector math -----------------------------------------------------------
+// In-place is tempting but every caller wants a fresh array; allocating
+// here avoids surprise mutations.
+export function l2Normalize(vec) {
+    let norm = 0;
+    for (let i = 0; i < vec.length; i++) {
+        const x = vec[i];
+        norm += x * x;
+    }
+    if (norm === 0)
+        return new Float32Array(vec);
+    const inv = 1 / Math.sqrt(norm);
+    const out = new Float32Array(vec.length);
+    for (let i = 0; i < vec.length; i++) {
+        out[i] = vec[i] * inv;
+    }
+    return out;
+}
+// Mean-pool a document's chunk vectors into one vector, then L2-normalise so
+// the result lives on the unit sphere (cosine semantics).
+// Returns null when there is nothing to pool or the pooled vector is zero.
+export function meanPoolL2(vectors) {
+    if (vectors.length === 0)
+        return null;
+    const dim = vectors[0]?.length ?? 0;
+    if (dim === 0)
+        return null;
+    const sum = new Float32Array(dim);
+    let kept = 0;
+    for (const v of vectors) {
+        if (v.length !== dim)
+            continue;
+        kept += 1;
+        for (let i = 0; i < dim; i++)
+            sum[i] = sum[i] + v[i];
+    }
+    if (kept === 0)
+        return null;
+    for (let i = 0; i < dim; i++)
+        sum[i] = sum[i] / kept;
+    // If the mean is the zero vector, l2Normalize returns zeros — surface that
+    // as null so downstream callers skip the document.
+    let norm = 0;
+    for (let i = 0; i < dim; i++) {
+        const x = sum[i];
+        norm += x * x;
+    }
+    if (norm === 0)
+        return null;
+    return l2Normalize(sum);
+}
+function squaredEuclidean(a, b) {
+    let acc = 0;
+    const n = Math.min(a.length, b.length);
+    for (let i = 0; i < n; i++) {
+        const d = a[i] - b[i];
+        acc += d * d;
+    }
+    return acc;
+}
+function cosineSimilarityNormalized(a, b) {
+    let dot = 0;
+    const n = Math.min(a.length, b.length);
+    for (let i = 0; i < n; i++)
+        dot += a[i] * b[i];
+    return dot;
+}
+// Euclidean distance on the unit sphere is monotonic with cosine distance.
+// We expose it as the public distance for silhouette so the score is on the
+// same scale callers expect.
+function euclideanDistance(a, b) {
+    return Math.sqrt(squaredEuclidean(a, b));
+}
+// --- k-means++ initialisation ---------------------------------------------
+// Picks k initial centroid INDICES from `data` using the k-means++ rule:
+// the first centroid is uniform-random; each subsequent centroid is sampled
+// with probability proportional to D(x)^2, where D(x) is the squared distance
+// from x to the nearest already-chosen centroid.
+//
+// Falls back to a uniform draw if the weighted total is zero (degenerate
+// data with all duplicates) so we always return k distinct indices when
+// k ≤ data.length.
+export function kmeansPlusPlusInit(data, k, rng) {
+    const n = data.length;
+    if (k <= 0 || n === 0)
+        return [];
+    const seeds = [];
+    const taken = new Set();
+    // First centroid: uniform-random.
+    const firstIdx = Math.floor(rng() * n);
+    const first = firstIdx >= n ? n - 1 : firstIdx;
+    seeds.push(first);
+    taken.add(first);
+    // For each remaining slot, compute D(x)^2 for every point against the
+    // closest already-picked centroid and sample one index weighted by D^2.
+    const dSquared = new Float64Array(n);
+    for (let i = 0; i < n; i++) {
+        dSquared[i] = squaredEuclidean(data[i], data[first]);
+    }
+    while (seeds.length < Math.min(k, n)) {
+        let total = 0;
+        for (let i = 0; i < n; i++) {
+            if (!taken.has(i))
+                total += dSquared[i];
+        }
+        let chosen = -1;
+        if (total === 0) {
+            // All untaken points coincide with an existing centroid (or there are
+            // duplicates). Pick the first untaken index uniformly so we still
+            // return k distinct seeds.
+            for (let i = 0; i < n; i++) {
+                if (!taken.has(i)) {
+                    chosen = i;
+                    break;
+                }
+            }
+        }
+        else {
+            let target = rng() * total;
+            for (let i = 0; i < n; i++) {
+                if (taken.has(i))
+                    continue;
+                target -= dSquared[i];
+                if (target <= 0) {
+                    chosen = i;
+                    break;
+                }
+            }
+            if (chosen === -1) {
+                // Numeric drift across the loop; pick the last untaken candidate.
+                for (let i = n - 1; i >= 0; i--) {
+                    if (!taken.has(i)) {
+                        chosen = i;
+                        break;
+                    }
+                }
+            }
+        }
+        if (chosen === -1)
+            break;
+        seeds.push(chosen);
+        taken.add(chosen);
+        // Update each point's D^2 to the nearest of the (now larger) centroid set.
+        const chosenVec = data[chosen];
+        for (let i = 0; i < n; i++) {
+            const d = squaredEuclidean(data[i], chosenVec);
+            if (d < dSquared[i])
+                dSquared[i] = d;
+        }
+    }
+    return seeds;
+}
+// Standard Lloyd's iterations until assignments stabilise or `maxIter` is
+// reached. k is clamped to data.length: clustering 4 documents into 10
+// groups is undefined; instead we just return at most data.length clusters.
+export function kmeans(data, k, rng, maxIter) {
+    const n = data.length;
+    if (n === 0)
+        return { assignments: [], centroids: [], iterations: 0 };
+    const effectiveK = Math.max(1, Math.min(k, n));
+    const dim = data[0].length;
+    const seedIdxs = kmeansPlusPlusInit(data, effectiveK, rng);
+    let centroids = seedIdxs.map((i) => {
+        const src = data[i];
+        const copy = new Float32Array(src.length);
+        for (let j = 0; j < src.length; j++)
+            copy[j] = src[j];
+        return copy;
+    });
+    const assignments = new Array(n).fill(0);
+    let iterations = 0;
+    for (let iter = 0; iter < maxIter; iter++) {
+        iterations = iter + 1;
+        let changed = false;
+        // Assign step.
+        for (let i = 0; i < n; i++) {
+            const point = data[i];
+            let bestC = 0;
+            let bestD = Number.POSITIVE_INFINITY;
+            for (let c = 0; c < centroids.length; c++) {
+                const d = squaredEuclidean(point, centroids[c]);
+                if (d < bestD) {
+                    bestD = d;
+                    bestC = c;
+                }
+            }
+            if (assignments[i] !== bestC) {
+                assignments[i] = bestC;
+                changed = true;
+            }
+        }
+        // Update step.
+        const sums = Array.from({ length: centroids.length }, () => new Float32Array(dim));
+        const counts = new Array(centroids.length).fill(0);
+        for (let i = 0; i < n; i++) {
+            const c = assignments[i];
+            counts[c] = counts[c] + 1;
+            const sum = sums[c];
+            const point = data[i];
+            for (let d = 0; d < dim; d++)
+                sum[d] = sum[d] + point[d];
+        }
+        const newCentroids = [];
+        for (let c = 0; c < centroids.length; c++) {
+            const count = counts[c];
+            if (count === 0) {
+                // Empty cluster: keep the previous centroid in place rather than
+                // re-seeding. Re-seeding mid-run would defeat determinism.
+                newCentroids.push(centroids[c]);
+                continue;
+            }
+            const sum = sums[c];
+            const next = new Float32Array(dim);
+            for (let d = 0; d < dim; d++)
+                next[d] = sum[d] / count;
+            newCentroids.push(next);
+        }
+        centroids = newCentroids;
+        if (!changed)
+            break;
+    }
+    // Final assignment pass on the converged centroids so callers don't see
+    // a stale assignment vector from before the last update step.
+    for (let i = 0; i < n; i++) {
+        const point = data[i];
+        let bestC = 0;
+        let bestD = Number.POSITIVE_INFINITY;
+        for (let c = 0; c < centroids.length; c++) {
+            const d = squaredEuclidean(point, centroids[c]);
+            if (d < bestD) {
+                bestD = d;
+                bestC = c;
+            }
+        }
+        assignments[i] = bestC;
+    }
+    return { assignments, centroids, iterations };
+}
+// --- Silhouette (k-picker) ------------------------------------------------
+// Mean silhouette over all points. For each point i:
+//   a(i) = mean distance from i to other points in the same cluster
+//   b(i) = min over other clusters C of (mean distance from i to points in C)
+//   s(i) = (b - a) / max(a, b)
+// Singleton clusters contribute 0. With only one cluster the score is 0
+// (no contrast).
+export function silhouetteScore(data, assignments) {
+    const n = data.length;
+    if (n === 0 || n !== assignments.length)
+        return 0;
+    const clusters = new Map();
+    for (let i = 0; i < n; i++) {
+        const c = assignments[i];
+        const list = clusters.get(c);
+        if (list)
+            list.push(i);
+        else
+            clusters.set(c, [i]);
+    }
+    if (clusters.size < 2)
+        return 0;
+    let total = 0;
+    for (let i = 0; i < n; i++) {
+        const ci = assignments[i];
+        const own = clusters.get(ci);
+        if (!own || own.length <= 1) {
+            // Singleton: silhouette defined as 0.
+            continue;
+        }
+        // a(i): mean distance to other own-cluster members.
+        let aSum = 0;
+        let aCount = 0;
+        for (const j of own) {
+            if (j === i)
+                continue;
+            aSum += euclideanDistance(data[i], data[j]);
+            aCount += 1;
+        }
+        const a = aSum / aCount;
+        // b(i): min over other clusters of mean distance.
+        let b = Number.POSITIVE_INFINITY;
+        for (const [cj, members] of clusters) {
+            if (cj === ci)
+                continue;
+            let s = 0;
+            for (const j of members) {
+                s += euclideanDistance(data[i], data[j]);
+            }
+            const mean = s / members.length;
+            if (mean < b)
+                b = mean;
+        }
+        const denom = Math.max(a, b);
+        if (denom === 0)
+            continue;
+        total += (b - a) / denom;
+    }
+    return total / n;
+}
+// --- Coherence (per-theme score) ------------------------------------------
+// Mean pairwise cosine similarity inside one cluster. Vectors are assumed
+// L2-normalised, so cosine reduces to a dot product. Range is [-1, 1] in
+// general; for unit-sphere embeddings produced by sentence-transformers it
+// tends to fall in [0, 1].
+export function clusterCoherence(vectors) {
+    if (vectors.length === 0)
+        return 0;
+    if (vectors.length === 1)
+        return 1;
+    let total = 0;
+    let pairs = 0;
+    for (let i = 0; i < vectors.length; i++) {
+        for (let j = i + 1; j < vectors.length; j++) {
+            total += cosineSimilarityNormalized(vectors[i], vectors[j]);
+            pairs += 1;
+        }
+    }
+    if (pairs === 0)
+        return 0;
+    return total / pairs;
+}
+// Runs k-means for each k in `candidates`, computes silhouette, and returns
+// the run with the highest score. Candidates are clamped to data.length and
+// deduped; this is what handles the "tiny vault" edge case — if the user
+// requested k ∈ {10, 15, 20, 25} but only has 8 documents, we end up running
+// k-means at k=8 and stop.
+export function pickK(data, candidates, rng, maxIter) {
+    const n = data.length;
+    const seen = new Set();
+    const ks = [];
+    for (const c of candidates) {
+        const clamped = Math.max(1, Math.min(c, n));
+        if (!seen.has(clamped)) {
+            seen.add(clamped);
+            ks.push(clamped);
+        }
+    }
+    if (ks.length === 0)
+        ks.push(Math.min(1, n));
+    let best = null;
+    for (const k of ks) {
+        const { assignments, centroids } = kmeans(data, k, rng, maxIter);
+        const score = silhouetteScore(data, assignments);
+        if (!best || score > best.silhouette) {
+            best = { k, silhouette: score, assignments, centroids };
+        }
+    }
+    // `best` is non-null because ks has at least one entry.
+    return best;
+}
+// For each doc, finds the clusters (other than its primary) whose centroid
+// is close enough that the doc plausibly belongs there too. Returns a map
+// from cluster index → ordered (by sim desc) list of secondary docs.
+//
+// This implements the "soft reporting" path on top of the hard partition
+// produced by k-means: `documentCount` still partitions by primary, but
+// the secondary list surfaces the cross-cutting documents the partition
+// hides. See `docs/architecture.md` for the rationale.
+export function selectSecondaryMemberships(vectors, assignments, centroids, options) {
+    const out = new Map();
+    const { delta, minSimilarity, maxPerDoc } = options;
+    if (vectors.length === 0 || centroids.length < 2 || maxPerDoc <= 0)
+        return out;
+    for (let i = 0; i < vectors.length; i++) {
+        const vec = vectors[i];
+        const primary = assignments[i];
+        const primaryCentroid = centroids[primary];
+        if (!primaryCentroid)
+            continue;
+        const primarySim = cosineSimilarityNormalized(vec, primaryCentroid);
+        // Score every non-primary cluster; collect those passing both bars.
+        const candidates = [];
+        for (let c = 0; c < centroids.length; c++) {
+            if (c === primary)
+                continue;
+            const cv = centroids[c];
+            if (!cv)
+                continue;
+            const sim = cosineSimilarityNormalized(vec, cv);
+            if (sim < minSimilarity)
+                continue;
+            if (sim < primarySim - delta)
+                continue;
+            candidates.push({ cluster: c, sim });
+        }
+        if (candidates.length === 0)
+            continue;
+        // Take the doc's top `maxPerDoc` secondaries (highest-sim wins ties
+        // first; stable cluster index for a deterministic ordering otherwise).
+        candidates.sort((a, b) => b.sim - a.sim || a.cluster - b.cluster);
+        const top = candidates.slice(0, maxPerDoc);
+        for (const { cluster, sim } of top) {
+            const list = out.get(cluster);
+            const entry = { docIndex: i, sim };
+            if (list)
+                list.push(entry);
+            else
+                out.set(cluster, [entry]);
+        }
+    }
+    // Order each cluster's secondaries by sim desc; stable on docIndex so the
+    // map serialises deterministically across runs.
+    for (const list of out.values()) {
+        list.sort((a, b) => b.sim - a.sim || a.docIndex - b.docIndex);
+    }
+    return out;
+}
+//# sourceMappingURL=clustering.js.map

package/dist/themes/clustering.js.map

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package/dist/tools/read.js

@@ -10,9 +10,9 @@ import { listStaleFiles } from "../curation/staleness.js";
 import { DEFAULT_TENSION_STATUS, listTensions } from "../curation/tension.js";
 import { parseDocument } from "../frontmatter/parser.js";
 import { DOMAINS, err, ok, STATUSES, } from "../frontmatter/types.js";
+import { getProvider } from "../search/vector.js";
 import { countDimMismatches, openIndexDb } from "../storage/index-db.js";
 import { listFiles, readFile, resolveVaultPath } from "../storage/local.js";
-import { getProvider } from "../search/vector.js";
 import { sha256Hex } from "../utils/hash.js";
 export async function vaultRead(vaultRoot, path, access) {
     if (typeof path !== "string" || path.length === 0) {

package/dist/tools/read.js.map

@@ -1 +1 @@
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package/dist/tools/search.d.ts

@@ -2,7 +2,10 @@ import { type AccessContext } from "../access/rbac.js";
 import { type Result } from "../frontmatter/types.js";
 import { type HybridSearchResult, type RelatedSearchResult } from "../search/hybrid.js";
 import { type ReindexResult } from "../search/reindex.js";
+import { type IndexDb } from "../storage/index-db.js";
 import type { ToolDefinition } from "./read.js";
+export declare function openIndexForActiveProvider(vaultRoot: string): Result<IndexDb, Error>;
+export declare function ensureIndexReady(vaultRoot: string): Promise<Result<void, Error>>;
 export declare function vaultSearch(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<HybridSearchResult, Error>>;
 export declare function vaultSearchRelated(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<RelatedSearchResult, Error>>;
 export interface VaultReindexResult extends ReindexResult {

package/dist/tools/search.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/tools/search.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,KAAK,aAAa,EAAW,MAAM,mBAAmB,CAAC;AAChE,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAEL,KAAK,kBAAkB,EAGvB,KAAK,mBAAmB,EAEzB,MAAM,qBAAqB,CAAC;AAQ7B,OAAO,EAAE,KAAK,aAAa,EAAgB,MAAM,sBAAsB,CAAC;AAExE,OAAO,EAAiB,KAAK,OAAO,EAAe,MAAM,wBAAwB,CAAC;AAClF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AAShD,wBAAgB,0BAA0B,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAC,OAAO,EAAE,KAAK,CAAC,CAEpF;AAgBD,wBAAsB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAsBtF;AA+BD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CA2B5C;AAMD,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CA2B7C;AAMD,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CAahG;AAgBD,eAAO,MAAM,WAAW,EAAE,cAAc,EA2DvC,CAAC"}

package/dist/tools/search.js

@@ -16,7 +16,10 @@ import { documentCount, openIndexDb } from "../storage/index-db.js";
 // table matches the embeddings the search will query. A read-only tool
 // that opens after a provider switch would otherwise face a vec table
 // sized for the *previous* provider's vectors.
-function openIndexForActiveProvider(vaultRoot) {
+//
+// Exported so other index-backed tools (vault_themes) reuse the same
+// dim-aware open path.
+export function openIndexForActiveProvider(vaultRoot) {
     return openIndexDb(vaultRoot, getProvider().dim);
 }
 // Gate every index-backed tool on the current indexing state.
@@ -30,7 +33,10 @@ function openIndexForActiveProvider(vaultRoot) {
 //   through main(), or a vault whose .daftari directory was wiped) trigger
 //   a synchronous reindex so search still works without an explicit
 //   --reindex step.
-async function ensureIndexReady(vaultRoot) {
+//
+// Exported so other index-backed tools (vault_themes) reuse the same
+// readiness gate.
+export async function ensureIndexReady(vaultRoot) {
     const status = getIndexStatus();
     if (status.status === "indexing") {
         return err(new Error(indexingBusyMessage(status)));

package/dist/tools/search.js.map

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package/dist/tools/themes.d.ts

@@ -0,0 +1,21 @@
+import { type AccessContext } from "../access/rbac.js";
+import { type Result } from "../frontmatter/types.js";
+import type { ToolDefinition } from "./read.js";
+export interface VaultTheme {
+    label: string;
+    documentCount: number;
+    coherence: number | null;
+    representativeDocs: string[];
+    secondaryDocs: string[];
+    relatedTags: string[];
+}
+export interface VaultThemesResult {
+    themes: VaultTheme[];
+    totalDocuments: number;
+    skippedDocuments: number;
+    selectedK: number;
+    clusteredAt: string;
+}
+export declare function vaultThemes(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<VaultThemesResult, Error>>;
+export declare const themesTools: ToolDefinition[];
+//# sourceMappingURL=themes.d.ts.map

package/dist/tools/themes.d.ts.map

@@ -0,0 +1 @@
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