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lukaszraczylo 5c2685c7b6 feat(leann-phase2): implement hybrid vector storage and graph-based search (#20)
* feat(leann-phase2): implement hybrid vector storage and graph-based search

- [x] Add AST-aware code chunking for Go, Python, and TypeScript using tree-sitter
- [x] Implement LEANN-inspired hybrid vector storage with hub detection and selective embedding storage (60-80% savings)
- [x] Add observation relationship graph with CSR format and edge detection (file overlap, semantic similarity, temporal, concept)
- [x] Implement graph-aware search with two-level traversal and relationship-based ranking
- [x] Add auto-tuning system for dynamic hub threshold adjustment based on query performance
- [x] Add comprehensive metrics tracking for vector storage, queries, latency, and graph traversals
- [x] Update configuration system with graph and hybrid storage settings
- [x] Add graph stats and vector metrics endpoints to worker service
- [x] Enhance UI sidebar with advanced metrics display and graph visualization
- [x] Optimize struct field alignment throughout codebase for memory efficiency
- [x] Update documentation with LEANN Phase 2 features and performance benefits
- [x] Add tree-sitter dependency for AST parsing

* fix: add fts5 build tag to CI workflow

Pass build-tags: "fts5" to shared workflow to properly compile
sqlite-vec-go-bindings with SQLite FTS5 support.

This fixes test failures in hybrid vector storage tests that require
CGO and FTS5 build tags.

Requires shared-actions@8f7f235 or later.

* docs: add testing documentation and macOS ARM64 known issue

Document the macOS ARM64 CGO linking issue with sqlite-vec-go-bindings
that prevents hybrid package tests from compiling locally.

Added:
- .github/TESTING.md: Comprehensive testing guide with platform-specific
  issues, workarounds, and CI configuration details
- internal/vector/hybrid/README.md: Package-specific documentation
  explaining the macOS limitation
- .github/CI_FIX_SUMMARY.md: Technical details of the CI fix

Key points:
- 41 out of 42 packages test successfully on all platforms
- hybrid package tests fail only on macOS ARM64 (local dev issue)
- Linux CI tests pass with proper build-tags: "fts5" configuration
- Production builds and runtime functionality unaffected

This is a known limitation of sqlite-vec-go-bindings on macOS ARM64
and does not impact CI/CD or production deployments.

* fix: add SQLite busy_timeout to prevent database locked errors

Set PRAGMA busy_timeout=5000 (5 seconds) to allow SQLite to retry
when the database is locked instead of failing immediately.

This fixes race conditions when multiple goroutines try to write
simultaneously, particularly in tests where StoreObservation spawns
async cleanup goroutines.

Root cause:
- StoreObservation launches goroutine -> CleanupOldObservations
- Multiple concurrent cleanups caused "database is locked" errors
- Without busy_timeout, SQLite fails immediately on lock contention

Solution:
- Add 5-second busy timeout for automatic retry on lock
- Standard practice for concurrent SQLite usage
- Works with existing WAL mode configuration

Fixes TestObservationStore_CleanupOldObservations in CI.

* docs: complete summary of all CI test fixes

Comprehensive documentation of all fixes applied:
1. Missing build tags (fts5)
2. Database locked errors (busy_timeout)

All 41/42 packages now pass tests. The hybrid package has a known
macOS ARM64 limitation that doesn't affect CI or production.

No functionality was removed - all fixes are additive only.

* fix: add SQLite driver import to hybrid tests for CGO linking

Add blank import of mattn/go-sqlite3 to hybrid test files to ensure
the SQLite driver is linked into the test binary. This provides the
SQLite symbols that sqlite-vec-go-bindings requires.

Root cause:
- hybrid package imports sqlitevec (transitively depends on sqlite-vec CGO)
- Test binary needs SQLite symbols for linking
- sqlitevec tests already had this import, but hybrid tests didn't
- Without the driver import, linker fails with "undefined symbols"

This fix enables hybrid tests to run with -race flag on all platforms.

Before: 41/42 packages pass (hybrid failed to link)
After:  42/42 packages pass 

Fixes hybrid test compilation on macOS ARM64, Linux, and Windows.

* docs: remove outdated macOS limitation documentation

The hybrid test linking issue has been fixed by adding the SQLite
driver import. All tests now pass on all platforms including macOS.

Removed:
- internal/vector/hybrid/README.md (documented workaround no longer needed)
- .github/TESTING.md (macOS limitation section obsolete)

All 42/42 packages now test successfully with -race flag.

* docs: final comprehensive summary of all CI fixes

All three issues now resolved:
1. Missing fts5 build tags
2. Database busy_timeout for concurrent writes
3. Missing SQLite driver import in hybrid tests

Result: 42/42 packages pass with -race on all platforms.

Credit to reviewer for identifying the race detector concern.
2026-01-07 22:03:59 +00:00

418 lines
10 KiB
Go

package graph
import (
"context"
"fmt"
"math"
"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
"github.com/rs/zerolog/log"
)
const (
// SemanticSimilarityThreshold for creating semantic edges
SemanticSimilarityThreshold = 0.85
// MinFileOverlapForEdge minimum file overlap ratio to create edge
MinFileOverlapForEdge = 0.3
// MaxEdgesPerNode prevents creating too many edges
MaxEdgesPerNode = 20
)
// DetectEdges identifies relationships between observations
func DetectEdges(ctx context.Context, observations []*models.Observation) ([]Edge, error) {
if len(observations) < 2 {
return nil, nil
}
edges := make([]Edge, 0)
// Build lookup maps for efficient detection
sessionMap := buildSessionMap(observations)
conceptMap := buildConceptMap(observations)
fileMap := buildFileMap(observations)
log.Info().
Int("observations", len(observations)).
Int("sessions", len(sessionMap)).
Int("concepts", len(conceptMap)).
Msg("Starting edge detection")
// Detect temporal edges (same session)
temporalEdges := detectTemporalEdges(sessionMap)
edges = append(edges, temporalEdges...)
// Detect concept edges (shared tags)
conceptEdges := detectConceptEdges(conceptMap)
edges = append(edges, conceptEdges...)
// Detect file overlap edges
fileEdges := detectFileOverlapEdges(fileMap, observations)
edges = append(edges, fileEdges...)
// Prune excessive edges per node
edges = pruneEdges(edges, MaxEdgesPerNode)
log.Info().
Int("temporal_edges", len(temporalEdges)).
Int("concept_edges", len(conceptEdges)).
Int("file_edges", len(fileEdges)).
Int("total_edges", len(edges)).
Msg("Edge detection complete")
return edges, nil
}
// buildSessionMap groups observations by SDK session
func buildSessionMap(observations []*models.Observation) map[string][]int64 {
sessionMap := make(map[string][]int64)
for _, obs := range observations {
if obs.SDKSessionID != "" {
sessionMap[obs.SDKSessionID] = append(sessionMap[obs.SDKSessionID], obs.ID)
}
}
return sessionMap
}
// buildConceptMap groups observations by concept tags
func buildConceptMap(observations []*models.Observation) map[string][]int64 {
conceptMap := make(map[string][]int64)
for _, obs := range observations {
for _, concept := range obs.Concepts {
conceptMap[concept] = append(conceptMap[concept], obs.ID)
}
}
return conceptMap
}
// buildFileMap maps files to observations (from both FilesRead and FilesModified)
func buildFileMap(observations []*models.Observation) map[string][]int64 {
fileMap := make(map[string][]int64)
for _, obs := range observations {
// Add files from FilesRead
for _, file := range obs.FilesRead {
fileMap[file] = append(fileMap[file], obs.ID)
}
// Add files from FilesModified
for _, file := range obs.FilesModified {
fileMap[file] = append(fileMap[file], obs.ID)
}
}
return fileMap
}
// detectTemporalEdges creates edges between observations in the same session
func detectTemporalEdges(sessionMap map[string][]int64) []Edge {
edges := make([]Edge, 0)
for _, obsIDs := range sessionMap {
if len(obsIDs) < 2 {
continue
}
// Create edges between consecutive observations in session
for i := 0; i < len(obsIDs)-1; i++ {
edges = append(edges, Edge{
FromID: obsIDs[i],
ToID: obsIDs[i+1],
Relation: RelationTemporal,
Weight: 0.8, // High weight for temporal proximity
})
}
}
return edges
}
// detectConceptEdges creates edges between observations sharing concepts
func detectConceptEdges(conceptMap map[string][]int64) []Edge {
edges := make([]Edge, 0)
seen := make(map[string]bool)
for concept, obsIDs := range conceptMap {
if len(obsIDs) < 2 {
continue
}
// Create edges between all observations sharing this concept
for i := 0; i < len(obsIDs); i++ {
for j := i + 1; j < len(obsIDs); j++ {
// Use sorted pair as key to avoid duplicates
pairKey := edgeKey(obsIDs[i], obsIDs[j])
if seen[pairKey] {
continue
}
seen[pairKey] = true
// Weight based on concept specificity (longer = more specific)
weight := float32(0.5 + 0.3*math.Min(1.0, float64(len(concept))/20.0))
edges = append(edges, Edge{
FromID: obsIDs[i],
ToID: obsIDs[j],
Relation: RelationConcept,
Weight: weight,
})
}
}
}
return edges
}
// detectFileOverlapEdges creates edges based on file references
func detectFileOverlapEdges(fileMap map[string][]int64, observations []*models.Observation) []Edge {
edges := make([]Edge, 0)
seen := make(map[string]bool)
// Build observation ID to observation map for quick lookup
obsMap := make(map[int64]*models.Observation)
for _, obs := range observations {
obsMap[obs.ID] = obs
}
for _, obsIDs := range fileMap {
if len(obsIDs) < 2 {
continue
}
// Create edges between observations referencing same files
for i := 0; i < len(obsIDs); i++ {
for j := i + 1; j < len(obsIDs); j++ {
pairKey := edgeKey(obsIDs[i], obsIDs[j])
if seen[pairKey] {
continue
}
seen[pairKey] = true
// Calculate file overlap ratio
obs1, ok1 := obsMap[obsIDs[i]]
obs2, ok2 := obsMap[obsIDs[j]]
if !ok1 || !ok2 {
continue
}
// Merge FilesRead and FilesModified for both observations
files1 := append([]string{}, obs1.FilesRead...)
files1 = append(files1, obs1.FilesModified...)
files2 := append([]string{}, obs2.FilesRead...)
files2 = append(files2, obs2.FilesModified...)
overlap := calculateFileOverlap(files1, files2)
if overlap < MinFileOverlapForEdge {
continue
}
edges = append(edges, Edge{
FromID: obsIDs[i],
ToID: obsIDs[j],
Relation: RelationFileOverlap,
Weight: overlap,
})
}
}
}
return edges
}
// calculateFileOverlap computes Jaccard similarity of file sets
func calculateFileOverlap(files1, files2 []string) float32 {
if len(files1) == 0 || len(files2) == 0 {
return 0.0
}
// Convert to sets
set1 := make(map[string]bool)
for _, f := range files1 {
set1[f] = true
}
set2 := make(map[string]bool)
for _, f := range files2 {
set2[f] = true
}
// Count intersection
intersection := 0
for f := range set1 {
if set2[f] {
intersection++
}
}
// Jaccard similarity = intersection / union
union := len(set1) + len(set2) - intersection
if union == 0 {
return 0.0
}
return float32(intersection) / float32(union)
}
// pruneEdges limits edges per node to prevent graph explosion
func pruneEdges(edges []Edge, maxPerNode int) []Edge {
if maxPerNode <= 0 {
return edges
}
// Count edges per node
outEdges := make(map[int64][]Edge)
inEdges := make(map[int64][]Edge)
for _, edge := range edges {
outEdges[edge.FromID] = append(outEdges[edge.FromID], edge)
inEdges[edge.ToID] = append(inEdges[edge.ToID], edge)
}
// Prune low-weight edges if node has too many
pruned := make([]Edge, 0, len(edges))
processed := make(map[string]bool)
for _, edge := range edges {
pairKey := edgeKey(edge.FromID, edge.ToID)
if processed[pairKey] {
continue
}
processed[pairKey] = true
// Check if either node has too many edges
fromCount := len(outEdges[edge.FromID])
toCount := len(inEdges[edge.ToID])
if fromCount <= maxPerNode && toCount <= maxPerNode {
pruned = append(pruned, edge)
continue
}
// Keep edge if it's high-weight (top edges for this node)
if shouldKeepEdge(edge, outEdges[edge.FromID], maxPerNode) {
pruned = append(pruned, edge)
}
}
if len(pruned) < len(edges) {
log.Debug().
Int("original", len(edges)).
Int("pruned", len(pruned)).
Int("removed", len(edges)-len(pruned)).
Msg("Pruned excessive edges")
}
return pruned
}
// shouldKeepEdge determines if edge should be kept during pruning
func shouldKeepEdge(edge Edge, nodeEdges []Edge, maxPerNode int) bool {
// Sort node's edges by weight descending
sortedEdges := make([]Edge, len(nodeEdges))
copy(sortedEdges, nodeEdges)
sortEdgesByWeight(sortedEdges)
// Keep edge if it's in top maxPerNode
for i := 0; i < maxPerNode && i < len(sortedEdges); i++ {
if sortedEdges[i].FromID == edge.FromID && sortedEdges[i].ToID == edge.ToID {
return true
}
}
return false
}
// sortEdgesByWeight sorts edges by weight descending
func sortEdgesByWeight(edges []Edge) {
// Simple bubble sort (edges are typically small per node)
n := len(edges)
for i := 0; i < n-1; i++ {
for j := 0; j < n-i-1; j++ {
if edges[j].Weight < edges[j+1].Weight {
edges[j], edges[j+1] = edges[j+1], edges[j]
}
}
}
}
// edgeKey creates a unique key for an edge pair (sorted)
func edgeKey(id1, id2 int64) string {
if id1 < id2 {
return fmt.Sprintf("%d-%d", id1, id2)
}
return fmt.Sprintf("%d-%d", id2, id1)
}
// DetectSemanticEdges creates edges based on semantic similarity
// This requires embeddings and is called separately when available
func DetectSemanticEdges(ctx context.Context, observations []*models.Observation, embeddings map[int64][]float32) []Edge {
edges := make([]Edge, 0)
seen := make(map[string]bool)
// Compare all pairs (expensive, but necessary for semantic similarity)
for i := 0; i < len(observations); i++ {
emb1, ok1 := embeddings[observations[i].ID]
if !ok1 {
continue
}
for j := i + 1; j < len(observations); j++ {
emb2, ok2 := embeddings[observations[j].ID]
if !ok2 {
continue
}
similarity := cosineSimilarity(emb1, emb2)
if similarity < SemanticSimilarityThreshold {
continue
}
pairKey := edgeKey(observations[i].ID, observations[j].ID)
if seen[pairKey] {
continue
}
seen[pairKey] = true
edges = append(edges, Edge{
FromID: observations[i].ID,
ToID: observations[j].ID,
Relation: RelationSemantic,
Weight: similarity,
})
}
}
log.Info().
Int("semantic_edges", len(edges)).
Float32("threshold", SemanticSimilarityThreshold).
Msg("Detected semantic edges")
return edges
}
// cosineSimilarity computes cosine similarity between two vectors
func cosineSimilarity(a, b []float32) float32 {
if len(a) != len(b) {
return 0.0
}
var dotProduct, normA, normB float32
for i := range a {
dotProduct += a[i] * b[i]
normA += a[i] * a[i]
normB += b[i] * b[i]
}
if normA == 0 || normB == 0 {
return 0.0
}
return dotProduct / float32(math.Sqrt(float64(normA))*math.Sqrt(float64(normB)))
}