causantic 0.7.2 → 0.8.0

package/dist/cli/commands/reindex.js

@@ -0,0 +1,143 @@
+/**
+ * CLI command: re-embed all chunks with the configured embedding model.
+ *
+ * Usage: npx causantic reindex [--batch-size N] [--dry-run]
+ */
+import { getDb } from '../../storage/db.js';
+import { Embedder } from '../../models/embedder.js';
+import { getModel } from '../../models/model-registry.js';
+import { loadConfig, toRuntimeConfig } from '../../config/loader.js';
+import { serializeEmbedding } from '../../utils/embedding-utils.js';
+/**
+ * Get or create a progress tracking table and return the last completed batch.
+ */
+function getLastCompletedBatch(db, modelId) {
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS reindex_progress (
+      model_id TEXT PRIMARY KEY,
+      last_batch INTEGER NOT NULL DEFAULT 0,
+      started_at TEXT DEFAULT CURRENT_TIMESTAMP,
+      updated_at TEXT DEFAULT CURRENT_TIMESTAMP
+    )
+  `);
+    const row = db
+        .prepare('SELECT last_batch FROM reindex_progress WHERE model_id = ?')
+        .get(modelId);
+    return row?.last_batch ?? 0;
+}
+function updateProgress(db, modelId, batch) {
+    db.prepare('INSERT OR REPLACE INTO reindex_progress (model_id, last_batch, updated_at) VALUES (?, ?, CURRENT_TIMESTAMP)').run(modelId, batch);
+}
+function clearProgress(db, modelId) {
+    db.prepare('DELETE FROM reindex_progress WHERE model_id = ?').run(modelId);
+}
+export const reindexCommand = {
+    name: 'reindex',
+    description: 'Re-embed all chunks with the configured embedding model',
+    usage: 'causantic reindex [--batch-size N] [--dry-run]',
+    handler: async (args) => {
+        if (args.includes('--help') || args.includes('-h')) {
+            console.log('Usage: causantic reindex [--batch-size N] [--dry-run]');
+            console.log('');
+            console.log('Re-embeds all chunks using the configured embedding model.');
+            console.log('Processes in batches with progress tracking for safe resumption.');
+            console.log('');
+            console.log('Options:');
+            console.log('  --batch-size N  Chunks per batch (default: 100)');
+            console.log('  --dry-run       Show what would be done without making changes');
+            return;
+        }
+        const dryRun = args.includes('--dry-run');
+        let batchSize = 100;
+        const batchIdx = args.indexOf('--batch-size');
+        if (batchIdx !== -1 && args[batchIdx + 1]) {
+            batchSize = parseInt(args[batchIdx + 1], 10);
+            if (isNaN(batchSize) || batchSize < 1) {
+                console.error('Error: --batch-size must be a positive integer');
+                process.exit(1);
+            }
+        }
+        const config = toRuntimeConfig(loadConfig());
+        const targetModel = config.embeddingModel;
+        const modelConfig = getModel(targetModel);
+        console.log(`Reindex target: ${targetModel} (${modelConfig.dims}D)`);
+        const db = getDb();
+        // Count chunks that need re-embedding
+        const totalRow = db.prepare('SELECT COUNT(*) as count FROM chunks').get();
+        const totalChunks = totalRow.count;
+        if (totalChunks === 0) {
+            console.log('No chunks to reindex.');
+            return;
+        }
+        // Count existing vectors for the target model
+        const existingRow = db
+            .prepare('SELECT COUNT(*) as count FROM vectors WHERE model_id = ?')
+            .get(targetModel);
+        // Count vectors with different model
+        const otherModelRow = db
+            .prepare('SELECT COUNT(*) as count FROM vectors WHERE model_id != ?')
+            .get(targetModel);
+        console.log(`Chunks: ${totalChunks}`);
+        console.log(`Existing vectors (${targetModel}): ${existingRow.count}`);
+        if (otherModelRow.count > 0) {
+            console.log(`Vectors (other models): ${otherModelRow.count} (will be replaced)`);
+        }
+        const totalBatches = Math.ceil(totalChunks / batchSize);
+        const lastBatch = getLastCompletedBatch(db, targetModel);
+        if (lastBatch > 0) {
+            console.log(`Resuming from batch ${lastBatch + 1}/${totalBatches}`);
+        }
+        if (dryRun) {
+            console.log(`\nDry run: would process ${totalChunks} chunks in ${totalBatches} batches`);
+            return;
+        }
+        // Load the embedder
+        const embedder = new Embedder();
+        await embedder.load(modelConfig);
+        const insertStmt = db.prepare('INSERT OR REPLACE INTO vectors (id, embedding, orphaned_at, last_accessed, model_id) VALUES (?, ?, NULL, CURRENT_TIMESTAMP, ?)');
+        const deleteOldStmt = db.prepare('DELETE FROM vectors WHERE id = ? AND model_id != ?');
+        // Process in batches
+        const allChunks = db
+            .prepare('SELECT id, content FROM chunks ORDER BY created_at ASC')
+            .all();
+        let processed = lastBatch * batchSize;
+        const startTime = Date.now();
+        for (let batch = lastBatch; batch < totalBatches; batch++) {
+            const start = batch * batchSize;
+            const end = Math.min(start + batchSize, allChunks.length);
+            const batchChunks = allChunks.slice(start, end);
+            // Embed all chunks in this batch
+            const embeddings = [];
+            for (const chunk of batchChunks) {
+                const result = await embedder.embed(chunk.content, false);
+                embeddings.push({ id: chunk.id, embedding: result.embedding });
+            }
+            // Write to DB in a transaction
+            db.transaction(() => {
+                for (const { id, embedding } of embeddings) {
+                    const blob = serializeEmbedding(embedding);
+                    insertStmt.run(id, blob, targetModel);
+                    // Remove old-model vectors for this chunk
+                    deleteOldStmt.run(id, targetModel);
+                }
+            })();
+            processed += batchChunks.length;
+            updateProgress(db, targetModel, batch + 1);
+            const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
+            const pct = Math.round((processed / allChunks.length) * 100);
+            process.stdout.write(`\r  [${pct}%] ${processed}/${allChunks.length} chunks (${elapsed}s)`);
+        }
+        console.log(''); // newline after progress
+        // Clean up progress tracker
+        clearProgress(db, targetModel);
+        // Clean up any remaining vectors from other models that don't correspond to chunks
+        const cleanedUp = db.prepare('DELETE FROM vectors WHERE model_id != ?').run(targetModel);
+        if (cleanedUp.changes > 0) {
+            console.log(`Cleaned up ${cleanedUp.changes} orphaned vectors from other models`);
+        }
+        await embedder.dispose();
+        const duration = ((Date.now() - startTime) / 1000).toFixed(1);
+        console.log(`Reindex complete: ${processed} chunks re-embedded with ${targetModel} in ${duration}s`);
+    },
+};
+//# sourceMappingURL=reindex.js.map

package/dist/cli/commands/reindex.js.map

@@ -0,0 +1 @@
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package/dist/cli/index.js

@@ -4,10 +4,8 @@
  *
  * Usage: npx causantic <command> [options]
  */
-import { readFileSync } from 'node:fs';
-import { dirname, resolve } from 'node:path';
-import { fileURLToPath } from 'node:url';
-import { initCommand } from './commands/init.js';
+import { VERSION } from '../utils/version.js';
+import { initCommand } from './commands/init/index.js';
 import { serveCommand } from './commands/serve.js';
 import { ingestCommand, batchIngestCommand } from './commands/ingest.js';
 import { recallCommand } from './commands/search.js';
@@ -20,9 +18,7 @@ import { exportCommand, importCommand } from './commands/archive.js';
 import { uninstallCommand } from './commands/uninstall.js';
 import { dashboardCommand } from './commands/dashboard.js';
 import { benchmarkCollectionCommand } from './commands/benchmark-collection.js';
-const __dirname = dirname(fileURLToPath(import.meta.url));
-const pkg = JSON.parse(readFileSync(resolve(__dirname, '../../package.json'), 'utf-8'));
-const VERSION = pkg.version;
+import { reindexCommand } from './commands/reindex.js';
 const commands = [
     initCommand,
     serveCommand,
@@ -40,6 +36,7 @@ const commands = [
     uninstallCommand,
     dashboardCommand,
     benchmarkCollectionCommand,
+    reindexCommand,
 ];
 function showHelp() {
     console.log('Causantic');

package/dist/cli/index.js.map

@@ -1 +1 @@
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package/dist/clusters/cluster-manager.d.ts

@@ -54,6 +54,10 @@ export interface ClusteringOptions {
     clusterThreshold?: number;
     /** Clear existing clusters before reclustering. Default: true. */
     clearExisting?: boolean;
+    /** Project ID for persisting HDBSCAN model (incremental clustering). */
+    projectId?: string;
+    /** Embedding model ID for model-aware persistence. Default: 'jina-small'. */
+    embeddingModel?: string;
 }
 /**
  * Cluster manager for running HDBSCAN and managing cluster assignments.
@@ -64,6 +68,25 @@ export declare class ClusterManager {
      * Run HDBSCAN on all chunks and create clusters.
      */
     recluster(options?: ClusteringOptions): Promise<ClusteringResult>;
+    /**
+     * Incrementally assign new chunks to existing clusters using a persisted HDBSCAN model.
+     *
+     * Falls back to full recluster if:
+     * - No persisted model exists
+     * - Embedding model has changed (model invalidation)
+     * - New chunk ratio exceeds incrementalClusterThreshold
+     *
+     * @returns Result from either incremental assignment or full recluster
+     */
+    incrementalAssign(newChunkIds: string[], options: {
+        projectId: string;
+        embeddingModel?: string;
+        incrementalThreshold?: number;
+    }): Promise<{
+        assigned: number;
+        noise: number;
+        usedFullRecluster: boolean;
+    }>;
     /**
      * Assign a new chunk to existing clusters based on angular distance.
      * Returns IDs of clusters the chunk was assigned to.

package/dist/clusters/cluster-manager.d.ts.map

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package/dist/clusters/cluster-manager.js

@@ -7,6 +7,8 @@ import { upsertCluster, assignChunksToClusters, getAllClusters, clearAllClusters
 import { angularDistance } from '../utils/angular-distance.js';
 import { getConfig } from '../config/memory-config.js';
 import { generateId } from '../storage/db.js';
+import { predictLabels } from './hdbscan/incremental.js';
+import { saveModel, loadModel } from './hdbscan-model-store.js';
 /**
  * Match new clusters to old clusters by Jaccard overlap, returning
  * a map of newClusterId → matched old snapshot. Uses greedy best-match
@@ -188,6 +190,12 @@ export class ClusterManager {
             }
         }
         const noiseCount = rawNoiseCount - reassignedNoiseIds.size;
+        // Save the HDBSCAN model for incremental assignment
+        const hdbscanModel = hdbscan.getModel();
+        if (hdbscanModel && options.projectId) {
+            const embeddingModel = options.embeddingModel ?? 'jina-small';
+            saveModel(options.projectId, embeddingModel, hdbscanModel, vectors.length);
+        }
         return {
             numClusters: clusterMembers.size,
             assignedChunks: assignments.length + noiseAssignments.length,
@@ -198,6 +206,132 @@ export class ClusterManager {
             durationMs: Date.now() - startTime,
         };
     }
+    /**
+     * Incrementally assign new chunks to existing clusters using a persisted HDBSCAN model.
+     *
+     * Falls back to full recluster if:
+     * - No persisted model exists
+     * - Embedding model has changed (model invalidation)
+     * - New chunk ratio exceeds incrementalClusterThreshold
+     *
+     * @returns Result from either incremental assignment or full recluster
+     */
+    async incrementalAssign(newChunkIds, options) {
+        const embeddingModel = options.embeddingModel ?? 'jina-small';
+        const clusterThreshold = options.incrementalThreshold ?? this.config.clusterThreshold;
+        // Try to load persisted model
+        const stored = loadModel(options.projectId, embeddingModel);
+        if (!stored) {
+            // No model or model mismatch — full recluster
+            await this.recluster({
+                projectId: options.projectId,
+                embeddingModel,
+            });
+            return { assigned: newChunkIds.length, noise: 0, usedFullRecluster: true };
+        }
+        // Check if threshold exceeded: too many new chunks since last recluster
+        const currentCount = await vectorStore.count();
+        const newSinceRecluster = currentCount - stored.chunkCount;
+        const ratio = stored.chunkCount > 0 ? newSinceRecluster / stored.chunkCount : 1;
+        if (ratio > this.config.incrementalClusterThreshold) {
+            // Too many new chunks — full recluster
+            await this.recluster({
+                projectId: options.projectId,
+                embeddingModel,
+            });
+            return { assigned: newChunkIds.length, noise: 0, usedFullRecluster: true };
+        }
+        // Get embeddings for new chunks
+        const newEmbeddings = [];
+        const validChunkIds = [];
+        for (const id of newChunkIds) {
+            const embedding = await vectorStore.get(id);
+            if (embedding) {
+                newEmbeddings.push(embedding);
+                validChunkIds.push(id);
+            }
+        }
+        if (newEmbeddings.length === 0) {
+            return { assigned: 0, noise: 0, usedFullRecluster: false };
+        }
+        // Load all embeddings for core distance computation
+        const allVectors = await vectorStore.getAllVectors();
+        const allEmbeddings = allVectors.map((v) => v.embedding);
+        // Reconstruct a full model with current embeddings for predictLabels
+        const fullModel = {
+            ...stored.model,
+            embeddings: allEmbeddings,
+        };
+        // Run incremental assignment
+        const labels = predictLabels(newEmbeddings, fullModel, this.config.minClusterSize, 'angular');
+        // Process assignments
+        const assignments = [];
+        let noiseCount = 0;
+        for (let i = 0; i < labels.length; i++) {
+            const label = labels[i];
+            if (label >= 0) {
+                // Find the cluster with this label's centroid
+                const centroid = stored.model.centroids.get(label);
+                if (centroid) {
+                    const distance = angularDistance(newEmbeddings[i], centroid);
+                    // Find matching cluster by centroid distance
+                    const clusters = getAllClusters();
+                    let bestCluster = null;
+                    let bestDist = Infinity;
+                    for (const cluster of clusters) {
+                        if (!cluster.centroid)
+                            continue;
+                        const d = angularDistance(centroid, cluster.centroid);
+                        if (d < bestDist) {
+                            bestDist = d;
+                            bestCluster = cluster;
+                        }
+                    }
+                    if (bestCluster && bestDist < 0.1) {
+                        assignments.push({
+                            chunkId: validChunkIds[i],
+                            clusterId: bestCluster.id,
+                            distance,
+                        });
+                    }
+                    else {
+                        noiseCount++;
+                    }
+                }
+                else {
+                    noiseCount++;
+                }
+            }
+            else {
+                noiseCount++;
+            }
+        }
+        // Assign noise points to nearest cluster (fallback)
+        if (noiseCount > 0) {
+            for (let i = 0; i < labels.length; i++) {
+                if (labels[i] >= 0)
+                    continue; // Already assigned
+                // Check if already assigned via the block above
+                if (assignments.some((a) => a.chunkId === validChunkIds[i]))
+                    continue;
+                const assigned = await this.assignChunkToClusters(validChunkIds[i], newEmbeddings[i], {
+                    threshold: clusterThreshold,
+                });
+                if (assigned.length > 0) {
+                    noiseCount--;
+                }
+            }
+        }
+        if (assignments.length > 0) {
+            assignChunksToClusters(assignments);
+            await this.updateCentroids();
+        }
+        return {
+            assigned: assignments.length + (validChunkIds.length - noiseCount - assignments.length),
+            noise: noiseCount,
+            usedFullRecluster: false,
+        };
+    }
     /**
      * Assign a new chunk to existing clusters based on angular distance.
      * Returns IDs of clusters the chunk was assigned to.

package/dist/clusters/cluster-manager.js.map

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package/dist/clusters/hdbscan-model-store.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Persistence layer for HDBSCAN models.
+ *
+ * Serializes/deserializes HDBSCANModel to SQLite BLOB for incremental clustering.
+ * Maps are converted to [key, value][] arrays for JSON.stringify (bare stringify produces {}).
+ * Excludes model.embeddings from the blob — too large. Load from vector store on demand.
+ */
+import type { HDBSCANModel } from './hdbscan/types.js';
+/**
+ * Serialize an HDBSCANModel to a JSON blob, excluding embeddings.
+ */
+declare function serializeModel(model: HDBSCANModel): Buffer;
+/**
+ * Deserialize a JSON blob back to an HDBSCANModel (embeddings will be empty).
+ */
+declare function deserializeModel(blob: Buffer): Omit<HDBSCANModel, 'embeddings'>;
+/**
+ * Save an HDBSCAN model for a project.
+ */
+export declare function saveModel(projectId: string, embeddingModel: string, model: HDBSCANModel, chunkCount: number): void;
+/**
+ * Load an HDBSCAN model for a project.
+ *
+ * Returns null if:
+ * - No model exists for this project
+ * - Stored embedding_model doesn't match currentEmbeddingModel (model invalidation)
+ */
+export declare function loadModel(projectId: string, currentEmbeddingModel: string): {
+    model: Omit<HDBSCANModel, 'embeddings'>;
+    chunkCount: number;
+} | null;
+/**
+ * Delete saved model for a project.
+ */
+export declare function deleteModel(projectId: string): void;
+export { serializeModel as _serializeModel, deserializeModel as _deserializeModel };
+//# sourceMappingURL=hdbscan-model-store.d.ts.map

package/dist/clusters/hdbscan-model-store.d.ts.map

@@ -0,0 +1 @@
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package/dist/clusters/hdbscan-model-store.js

@@ -0,0 +1,73 @@
+/**
+ * Persistence layer for HDBSCAN models.
+ *
+ * Serializes/deserializes HDBSCANModel to SQLite BLOB for incremental clustering.
+ * Maps are converted to [key, value][] arrays for JSON.stringify (bare stringify produces {}).
+ * Excludes model.embeddings from the blob — too large. Load from vector store on demand.
+ */
+import { getDb } from '../storage/db.js';
+/**
+ * Serialize an HDBSCANModel to a JSON blob, excluding embeddings.
+ */
+function serializeModel(model) {
+    const serialized = {
+        coreDistances: model.coreDistances,
+        labels: model.labels,
+        centroids: Array.from(model.centroids.entries()),
+        exemplars: Array.from(model.exemplars.entries()),
+        lambdaValues: model.lambdaValues,
+        clusterMaxLambda: Array.from(model.clusterMaxLambda.entries()),
+    };
+    return Buffer.from(JSON.stringify(serialized));
+}
+/**
+ * Deserialize a JSON blob back to an HDBSCANModel (embeddings will be empty).
+ */
+function deserializeModel(blob) {
+    const parsed = JSON.parse(blob.toString('utf-8'));
+    return {
+        coreDistances: parsed.coreDistances,
+        labels: parsed.labels,
+        centroids: new Map(parsed.centroids),
+        exemplars: new Map(parsed.exemplars),
+        lambdaValues: parsed.lambdaValues,
+        clusterMaxLambda: new Map(parsed.clusterMaxLambda),
+    };
+}
+/**
+ * Save an HDBSCAN model for a project.
+ */
+export function saveModel(projectId, embeddingModel, model, chunkCount) {
+    const db = getDb();
+    const blob = serializeModel(model);
+    db.prepare(`INSERT OR REPLACE INTO hdbscan_models (project_id, embedding_model, model_blob, chunk_count, created_at)
+     VALUES (?, ?, ?, ?, CURRENT_TIMESTAMP)`).run(projectId, embeddingModel, blob, chunkCount);
+}
+/**
+ * Load an HDBSCAN model for a project.
+ *
+ * Returns null if:
+ * - No model exists for this project
+ * - Stored embedding_model doesn't match currentEmbeddingModel (model invalidation)
+ */
+export function loadModel(projectId, currentEmbeddingModel) {
+    const db = getDb();
+    const row = db
+        .prepare('SELECT model_blob, embedding_model, chunk_count FROM hdbscan_models WHERE project_id = ? AND embedding_model = ?')
+        .get(projectId, currentEmbeddingModel);
+    if (!row) {
+        return null;
+    }
+    const model = deserializeModel(row.model_blob);
+    return { model, chunkCount: row.chunk_count };
+}
+/**
+ * Delete saved model for a project.
+ */
+export function deleteModel(projectId) {
+    const db = getDb();
+    db.prepare('DELETE FROM hdbscan_models WHERE project_id = ?').run(projectId);
+}
+// Re-export for testing
+export { serializeModel as _serializeModel, deserializeModel as _deserializeModel };
+//# sourceMappingURL=hdbscan-model-store.js.map

package/dist/clusters/hdbscan-model-store.js.map

@@ -0,0 +1 @@
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package/dist/config/loader.d.ts

@@ -14,6 +14,8 @@ export interface ExternalConfig {
     clustering?: {
         threshold?: number;
         minClusterSize?: number;
+        /** Ratio of new chunks (vs total) that triggers a full recluster. Default: 0.3. */
+        incrementalThreshold?: number;
     };
     traversal?: {
         maxDepth?: number;
@@ -29,6 +31,8 @@ export interface ExternalConfig {
     llm?: {
         clusterRefreshModel?: string;
         refreshRateLimitPerMin?: number;
+        /** Enable LLM-based cluster labelling. Requires Anthropic API key. Default: true. */
+        enableLabelling?: boolean;
     };
     encryption?: {
         enabled?: boolean;
@@ -45,6 +49,8 @@ export interface ExternalConfig {
     embedding?: {
         /** Device for embedding inference: 'auto' | 'coreml' | 'cuda' | 'cpu' | 'wasm'. Default: 'auto'. */
         device?: string;
+        /** Embedding model ID from model registry. Default: 'jina-small'. */
+        model?: string;
     };
     maintenance?: {
         /** Hour of day (0-23) to run reclustering. Default: 2. */
@@ -53,6 +59,8 @@ export interface ExternalConfig {
     retrieval?: {
         /** MMR lambda: 0 = pure diversity, 1 = pure relevance. Default: 0.7 */
         mmrLambda?: number;
+        /** Feedback weight for cluster expansion scoring. Default: 0.1 */
+        feedbackWeight?: number;
     };
     recency?: {
         /** Amplitude of the time-decay boost (multiplied by exp decay). Default: 0.3 */