superlocalmemory 2.8.6 → 3.0.1

package/src/graph/edge_builder.py

@@ -1,162 +0,0 @@
-#!/usr/bin/env python3
-# SPDX-License-Identifier: MIT
-# Copyright (c) 2026 SuperLocalMemory (superlocalmemory.com)
-"""Edge building for the graph engine.
-
-Builds similarity edges between memories based on entity overlap
-and TF-IDF vector cosine similarity. Supports HNSW-accelerated
-edge building for large datasets.
-"""
-import sqlite3
-import json
-from pathlib import Path
-from typing import List
-
-import numpy as np
-
-from graph.constants import logger, cosine_similarity
-
-
-class EdgeBuilder:
-    """Build similarity edges between memories based on entity overlap."""
-
-    def __init__(self, db_path: Path, min_similarity: float = 0.3):
-        """
-        Initialize edge builder.
-
-        Args:
-            db_path: Path to SQLite database
-            min_similarity: Minimum cosine similarity to create edge
-        """
-        self.db_path = db_path
-        self.min_similarity = min_similarity
-
-    def build_edges(self, memory_ids: List[int], vectors: np.ndarray,
-                   entities_list: List[List[str]]) -> int:
-        """
-        Build edges between similar memories.
-
-        Args:
-            memory_ids: List of memory IDs
-            vectors: TF-IDF vectors (n x features)
-            entities_list: List of entity lists per memory
-
-        Returns:
-            Number of edges created
-        """
-        if len(memory_ids) < 2:
-            logger.warning("Need at least 2 memories to build edges")
-            return 0
-
-        # Try HNSW-accelerated edge building first (O(n log n))
-        use_hnsw = False
-        try:
-            from hnsw_index import HNSWIndex
-            if len(memory_ids) >= 50:  # HNSW overhead not worth it for small sets
-                use_hnsw = True
-        except ImportError:
-            pass
-
-        edges_added = 0
-        conn = sqlite3.connect(self.db_path)
-        cursor = conn.cursor()
-
-        try:
-            if use_hnsw:
-                logger.info("Using HNSW-accelerated edge building for %d memories", len(memory_ids))
-                try:
-                    dim = vectors.shape[1]
-                    hnsw = HNSWIndex(dimension=dim, max_elements=len(memory_ids))
-                    hnsw.build(vectors, memory_ids)
-
-                    for i in range(len(memory_ids)):
-                        neighbors = hnsw.search(vectors[i], k=min(20, len(memory_ids) - 1))
-                        for neighbor_id, similarity in neighbors:
-                            if neighbor_id == memory_ids[i]:
-                                continue  # Skip self
-                            # Only process each pair once (lower ID first)
-                            if memory_ids[i] > neighbor_id:
-                                continue
-                            if similarity >= self.min_similarity:
-                                # Find indices for entity lookup
-                                j = memory_ids.index(neighbor_id)
-                                entities_i = set(entities_list[i])
-                                entities_j = set(entities_list[j])
-                                shared = list(entities_i & entities_j)
-                                rel_type = self._classify_relationship(similarity, shared)
-
-                                cursor.execute('''
-                                    INSERT OR REPLACE INTO graph_edges
-                                    (source_memory_id, target_memory_id, relationship_type,
-                                     weight, shared_entities, similarity_score)
-                                    VALUES (?, ?, ?, ?, ?, ?)
-                                ''', (
-                                    memory_ids[i], neighbor_id, rel_type,
-                                    float(similarity), json.dumps(shared), float(similarity)
-                                ))
-                                edges_added += 1
-
-                except Exception as e:
-                    logger.warning("HNSW edge building failed, falling back to O(n²): %s", e)
-                    use_hnsw = False  # Fall through to O(n²) below
-
-            if not use_hnsw:
-                # Fallback: O(n²) pairwise cosine similarity
-                similarity_matrix = cosine_similarity(vectors)
-
-                for i in range(len(memory_ids)):
-                    for j in range(i + 1, len(memory_ids)):
-                        sim = similarity_matrix[i, j]
-
-                        if sim >= self.min_similarity:
-                            entities_i = set(entities_list[i])
-                            entities_j = set(entities_list[j])
-                            shared = list(entities_i & entities_j)
-                            rel_type = self._classify_relationship(sim, shared)
-
-                            cursor.execute('''
-                                INSERT OR REPLACE INTO graph_edges
-                                (source_memory_id, target_memory_id, relationship_type,
-                                 weight, shared_entities, similarity_score)
-                                VALUES (?, ?, ?, ?, ?, ?)
-                            ''', (
-                                memory_ids[i], memory_ids[j], rel_type,
-                                float(sim), json.dumps(shared), float(sim)
-                            ))
-                            edges_added += 1
-
-            conn.commit()
-            logger.info(f"Created {edges_added} edges")
-            return edges_added
-
-        except Exception as e:
-            logger.error(f"Edge building failed: {e}")
-            conn.rollback()
-            return 0
-        finally:
-            conn.close()
-
-    def _classify_relationship(self, similarity: float, shared_entities: List[str]) -> str:
-        """
-        Classify edge type based on similarity and shared entities.
-
-        Args:
-            similarity: Cosine similarity score
-            shared_entities: List of shared entity strings
-
-        Returns:
-            Relationship type: 'similar', 'depends_on', or 'related_to'
-        """
-        # Check for dependency keywords
-        dependency_keywords = {'dependency', 'require', 'import', 'use', 'need'}
-        has_dependency = any(
-            any(kw in entity.lower() for kw in dependency_keywords)
-            for entity in shared_entities
-        )
-
-        if similarity > 0.7:
-            return 'similar'
-        elif has_dependency:
-            return 'depends_on'
-        else:
-            return 'related_to'

package/src/graph/entity_extractor.py

@@ -1,95 +0,0 @@
-#!/usr/bin/env python3
-# SPDX-License-Identifier: MIT
-# Copyright (c) 2026 SuperLocalMemory (superlocalmemory.com)
-"""Entity extraction and cluster naming for the graph engine.
-
-Provides TF-IDF based entity extraction from memory content
-and cluster naming utilities.
-"""
-from typing import List, Tuple
-from collections import Counter
-
-import numpy as np
-
-from graph.constants import logger, TfidfVectorizer
-
-
-class EntityExtractor:
-    """Extract key entities/concepts from memory content using TF-IDF."""
-
-    def __init__(self, max_features: int = 20, min_df: int = 1):
-        """
-        Initialize entity extractor.
-
-        Args:
-            max_features: Top N keywords to extract per memory
-            min_df: Minimum document frequency (ignore very rare terms)
-        """
-        self.max_features = max_features
-        self.vectorizer = TfidfVectorizer(
-            max_features=max_features,
-            stop_words='english',
-            ngram_range=(1, 2),  # Unigrams + bigrams
-            min_df=min_df,
-            lowercase=True,
-            token_pattern=r'(?u)\b[a-zA-Z][a-zA-Z0-9_-]*\b'  # Alphanumeric tokens
-        )
-
-    def extract_entities(self, contents: List[str]) -> Tuple[List[List[str]], np.ndarray]:
-        """
-        Extract entities from multiple contents.
-
-        Args:
-            contents: List of memory content strings
-
-        Returns:
-            Tuple of (entities_per_content, tfidf_vectors)
-        """
-        if not contents:
-            return [], np.array([])
-
-        try:
-            # Fit and transform all contents
-            vectors = self.vectorizer.fit_transform(contents)
-            feature_names = self.vectorizer.get_feature_names_out()
-
-            # Extract top entities for each content
-            all_entities = []
-            for idx in range(len(contents)):
-                scores = vectors[idx].toarray()[0]
-
-                # Get indices of top features
-                top_indices = np.argsort(scores)[::-1]
-
-                # Extract entities with score > 0
-                entities = [
-                    feature_names[i]
-                    for i in top_indices
-                    if scores[i] > 0.05  # Minimum threshold
-                ][:self.max_features]
-
-                all_entities.append(entities)
-
-            return all_entities, vectors.toarray()
-
-        except Exception as e:
-            logger.error(f"Entity extraction failed: {e}")
-            return [[] for _ in contents], np.zeros((len(contents), 1))
-
-
-class ClusterNamer:
-    """Enhanced cluster naming with optional LLM support (future)."""
-
-    @staticmethod
-    def generate_name_tfidf(entities: List[str]) -> str:
-        """Generate name from entity list (TF-IDF fallback)."""
-        if not entities:
-            return "Unnamed Cluster"
-
-        entity_counts = Counter(entities)
-        top_entities = [e for e, _ in entity_counts.most_common(2)]
-
-        if len(top_entities) >= 2:
-            return f"{top_entities[0].title()} & {top_entities[1].title()}"
-        else:
-            return f"{top_entities[0].title()} Contexts"

package/src/graph/graph_core.py

@@ -1,226 +0,0 @@
-#!/usr/bin/env python3
-# SPDX-License-Identifier: MIT
-# Copyright (c) 2026 SuperLocalMemory (superlocalmemory.com)
-"""GraphEngine - Main orchestrator for the knowledge graph.
-
-Coordinates entity extraction, edge building, community detection,
-and graph traversal operations. All processing is local.
-"""
-import sqlite3
-import json
-import time
-from pathlib import Path
-from typing import List, Dict
-
-import numpy as np
-
-from graph.constants import (
-    logger, MEMORY_DIR, DB_PATH, IGRAPH_AVAILABLE, cosine_similarity
-)
-from graph.entity_extractor import EntityExtractor
-from graph.edge_builder import EdgeBuilder
-from graph.cluster_builder import ClusterBuilder
-from graph.schema import ensure_graph_tables
-from graph.build_helpers import apply_sampling, clear_profile_graph_data
-from graph.graph_search import (
-    get_related as _get_related,
-    get_cluster_members as _get_cluster_members,
-    get_stats as _get_stats,
-)
-
-
-class GraphEngine:
-    """Main graph engine coordinating all graph operations."""
-
-    def __init__(self, db_path: Path = DB_PATH):
-        """Initialize graph engine."""
-        self.db_path = db_path
-        self.entity_extractor = EntityExtractor(max_features=20)
-        self.edge_builder = EdgeBuilder(db_path)
-        self.cluster_builder = ClusterBuilder(db_path)
-        self._ensure_graph_tables()
-
-    def _get_active_profile(self) -> str:
-        """Get the currently active profile name from config."""
-        config_file = MEMORY_DIR / "profiles.json"
-        if config_file.exists():
-            try:
-                with open(config_file, 'r') as f:
-                    config = json.load(f)
-                return config.get('active_profile', 'default')
-            except (json.JSONDecodeError, IOError):
-                pass
-        return 'default'
-
-    def _ensure_graph_tables(self):
-        """Create graph tables if they don't exist, or recreate if schema is incomplete."""
-        ensure_graph_tables(self.db_path)
-
-    def build_graph(self, min_similarity: float = 0.3) -> Dict[str, any]:
-        """
-        Build complete knowledge graph from all memories.
-
-        Args:
-            min_similarity: Minimum cosine similarity for edge creation
-
-        Returns:
-            Dictionary with build statistics
-        """
-        start_time = time.time()
-        logger.info("Starting full graph build...")
-        conn = sqlite3.connect(self.db_path)
-        cursor = conn.cursor()
-
-        try:
-            # Check required tables
-            cursor.execute("SELECT name FROM sqlite_master WHERE type='table'")
-            existing_tables = {row[0] for row in cursor.fetchall()}
-            missing = {'memories', 'graph_edges', 'graph_nodes', 'graph_clusters'} - existing_tables
-            if missing:
-                logger.error(f"Missing required tables: {missing}")
-                return {'success': False, 'error': 'database_not_initialized',
-                        'message': f"Database not initialized. Missing tables: {', '.join(missing)}",
-                        'fix': "Run 'superlocalmemoryv2-status' first to initialize the database, or add some memories."}
-
-            active_profile = self._get_active_profile()
-            logger.info(f"Building graph for profile: {active_profile}")
-            memories = cursor.execute(
-                'SELECT id, content, summary FROM memories WHERE profile = ? ORDER BY id',
-                (active_profile,)).fetchall()
-
-            if len(memories) == 0:
-                return {'success': False, 'error': 'no_memories',
-                        'message': 'No memories found in database.',
-                        'fix': "Add some memories first: superlocalmemoryv2-remember 'Your content here'"}
-            if len(memories) < 2:
-                return {'success': False, 'error': 'insufficient_memories',
-                        'message': 'Need at least 2 memories to build knowledge graph.',
-                        'memories': len(memories),
-                        'fix': "Add more memories: superlocalmemoryv2-remember 'Your content here'"}
-
-            memories = apply_sampling(cursor, memories, active_profile)
-            clear_profile_graph_data(cursor, conn, memories, active_profile)
-
-            logger.info(f"Processing {len(memories)} memories")
-            memory_ids = [m[0] for m in memories]
-            contents = [f"{m[1]} {m[2] or ''}" for m in memories]
-            entities_list, vectors = self.entity_extractor.extract_entities(contents)
-
-            for memory_id, entities, vector in zip(memory_ids, entities_list, vectors):
-                cursor.execute('''
-                    INSERT INTO graph_nodes (memory_id, entities, embedding_vector)
-                    VALUES (?, ?, ?)
-                ''', (memory_id, json.dumps(entities), json.dumps(vector.tolist())))
-            conn.commit()
-            logger.info(f"Stored {len(memory_ids)} graph nodes")
-
-            edges_count = self.edge_builder.build_edges(memory_ids, vectors, entities_list)
-            clusters_count = self.cluster_builder.detect_communities()
-            hierarchical_stats = self.cluster_builder.hierarchical_cluster()
-            subclusters = hierarchical_stats.get('subclusters_created', 0)
-            summaries = self.cluster_builder.generate_cluster_summaries()
-            elapsed = time.time() - start_time
-
-            stats = {
-                'success': True, 'memories': len(memories), 'nodes': len(memory_ids),
-                'edges': edges_count, 'clusters': clusters_count, 'subclusters': subclusters,
-                'max_depth': hierarchical_stats.get('depth_reached', 0),
-                'summaries_generated': summaries, 'time_seconds': round(elapsed, 2)
-            }
-            if not IGRAPH_AVAILABLE:
-                stats['warning'] = 'igraph/leidenalg not installed — graph built without clustering. Install with: pip3 install python-igraph leidenalg'
-            logger.info(f"Graph build complete: {stats}")
-            return stats
-
-        except Exception as e:
-            logger.error(f"Graph build failed: {e}")
-            conn.rollback()
-            return {'success': False, 'error': str(e)}
-        finally:
-            conn.close()
-
-    def extract_entities(self, memory_id: int) -> List[str]:
-        """Extract entities for a single memory."""
-        conn = sqlite3.connect(self.db_path)
-        cursor = conn.cursor()
-        try:
-            memory = cursor.execute(
-                'SELECT content, summary FROM memories WHERE id = ?', (memory_id,)
-            ).fetchone()
-            if not memory:
-                return []
-            content = f"{memory[0]} {memory[1] or ''}"
-            entities_list, _ = self.entity_extractor.extract_entities([content])
-            return entities_list[0] if entities_list else []
-        finally:
-            conn.close()
-
-    def get_related(self, memory_id: int, max_hops: int = 2) -> List[Dict]:
-        """Get memories connected to this memory via graph edges (active profile only)."""
-        return _get_related(self.db_path, memory_id, max_hops)
-
-    def get_cluster_members(self, cluster_id: int) -> List[Dict]:
-        """Get all memories in a cluster (filtered by active profile)."""
-        return _get_cluster_members(self.db_path, cluster_id)
-
-    def add_memory_incremental(self, memory_id: int) -> bool:
-        """Add single memory to existing graph (incremental update)."""
-        conn = sqlite3.connect(self.db_path)
-        cursor = conn.cursor()
-        try:
-            memory = cursor.execute(
-                'SELECT content, summary FROM memories WHERE id = ?', (memory_id,)
-            ).fetchone()
-            if not memory:
-                return False
-
-            content = f"{memory[0]} {memory[1] or ''}"
-            entities_list, vector = self.entity_extractor.extract_entities([content])
-            if not entities_list:
-                return False
-
-            new_entities, new_vector = entities_list[0], vector[0]
-            cursor.execute('''
-                INSERT OR REPLACE INTO graph_nodes (memory_id, entities, embedding_vector)
-                VALUES (?, ?, ?)
-            ''', (memory_id, json.dumps(new_entities), json.dumps(new_vector.tolist())))
-
-            active_profile = self._get_active_profile()
-            existing = cursor.execute('''
-                SELECT gn.memory_id, gn.embedding_vector, gn.entities
-                FROM graph_nodes gn JOIN memories m ON gn.memory_id = m.id
-                WHERE gn.memory_id != ? AND m.profile = ?
-            ''', (memory_id, active_profile)).fetchall()
-
-            edges_added = 0
-            for existing_id, ev_json, ee_json in existing:
-                ev = np.array(json.loads(ev_json))
-                sim = cosine_similarity([new_vector], [ev])[0][0]
-                if sim >= self.edge_builder.min_similarity:
-                    ee = json.loads(ee_json)
-                    shared = list(set(new_entities) & set(ee))
-                    rel_type = self.edge_builder._classify_relationship(sim, shared)
-                    cursor.execute('''
-                        INSERT OR REPLACE INTO graph_edges
-                        (source_memory_id, target_memory_id, relationship_type,
-                         weight, shared_entities, similarity_score)
-                        VALUES (?, ?, ?, ?, ?, ?)
-                    ''', (memory_id, existing_id, rel_type,
-                          float(sim), json.dumps(shared), float(sim)))
-                    edges_added += 1
-
-            conn.commit()
-            logger.info(f"Added memory {memory_id} to graph with {edges_added} edges")
-            if edges_added > 5:
-                logger.info("Significant graph change - consider re-clustering")
-            return True
-        except Exception as e:
-            logger.error(f"Incremental add failed: {e}")
-            conn.rollback()
-            return False
-        finally:
-            conn.close()
-
-    def get_stats(self) -> Dict[str, any]:
-        """Get graph statistics for the active profile."""
-        return _get_stats(self.db_path)