synaptiq 0.4.0

Graph-powered code intelligence engine — indexes codebases into a knowledge graph, exposed via MCP tools for AI agents and a CLI for developers.

Synaptiq

Graph-powered code intelligence engine — indexes your codebase into a knowledge graph and exposes it via MCP tools for AI agents and a CLI for developers.

synaptiq analyze .

Phase 1:  Walking files...               142 files found
Phase 3:  Parsing code...                142/142
Phase 5:  Tracing calls...               847 calls resolved
Phase 7:  Analyzing types...             234 type relationships
Phase 8:  Detecting communities...       8 clusters found
Phase 9:  Detecting execution flows...   34 processes found
Phase 10: Finding dead code...           12 unreachable symbols
Phase 11: Analyzing git history...       18 coupled file pairs

Done in 4.2s — 623 symbols, 1,847 edges, 8 clusters, 34 flows

Most code intelligence tools treat your codebase as flat text. Synaptiq builds a structural graph — every function, class, import, call, type reference, and execution flow becomes a node or edge in a queryable knowledge graph. AI agents using Synaptiq don't just search for keywords; they understand how your code is connected.

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Why Synaptiq?

For AI agents (Claude Code, Cursor):

• "What breaks if I change this function?" → blast radius via call graph + type references + git coupling
• "What code is never called?" → dead code detection with framework-aware exemptions
• "Show me the login flow end-to-end" → execution flow tracing from entry points through the call graph
• "Which files always change together?" → git history change coupling analysis

For developers:

• Instant answers to architectural questions without grepping through files
• Find dead code, tightly coupled files, and execution flows automatically
• Raw Cypher queries against your codebase's knowledge graph
• Watch mode that re-indexes on every save

Zero cloud dependencies. Everything runs locally — parsing, graph storage, embeddings, search. No API keys, no data leaving your machine.

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Features

11-Phase Analysis Pipeline

Synaptiq doesn't just parse your code — it builds a deep structural understanding through 11 sequential analysis phases:

Phase	What It Does
File Walking	Walks repo respecting .gitignore, filters by supported languages
Structure	Creates File/Folder hierarchy with CONTAINS relationships
Parsing	tree-sitter AST extraction — functions, classes, methods, interfaces, enums, type aliases
Import Resolution	Resolves import statements to actual files (relative, absolute, bare specifiers)
Call Tracing	Maps function calls with confidence scores (1.0 = exact match, 0.5 = fuzzy)
Heritage	Tracks class inheritance (EXTENDS) and interface implementation (IMPLEMENTS)
Type Analysis	Extracts type references from parameters, return types, and variable annotations
Community Detection	Leiden algorithm clusters related symbols into functional communities
Process Detection	Framework-aware entry point detection + BFS flow tracing
Dead Code Detection	Multi-pass analysis with override, protocol, and decorator awareness
Change Coupling	Git history analysis — finds files that always change together

Hybrid Search (BM25 + Vector + RRF)

Three search strategies fused with Reciprocal Rank Fusion:

• BM25 full-text search — fast exact name and keyword matching via KuzuDB FTS
• Semantic vector search — conceptual queries via 384-dim embeddings (BAAI/bge-small-en-v1.5)
• Fuzzy name search — Levenshtein fallback for typos and partial matches

Test files are automatically down-ranked (0.5x), source-level functions/classes boosted (1.2x).

Dead Code Detection

Finds unreachable symbols with intelligence — not just "zero callers" but a multi-pass analysis:

1. Initial scan — flags functions/methods/classes with no incoming calls
2. Exemptions — entry points, exports, constructors, test code, dunder methods, __init__.py public symbols, decorated functions, @property methods
3. Override pass — un-flags methods that override non-dead base class methods (handles dynamic dispatch)
4. Protocol conformance — un-flags methods on classes conforming to Protocol interfaces
5. Protocol stubs — un-flags all methods on Protocol classes (interface contracts)

Impact Analysis (Blast Radius)

When you're about to change a symbol, Synaptiq traces upstream through:

• Call graph — every function that calls this one, recursively
• Type references — every function that takes, returns, or stores this type
• Git coupling — files that historically change alongside this one

Community Detection

Uses the Leiden algorithm (igraph + leidenalg) to automatically discover functional clusters in your codebase. Each community gets a cohesion score and auto-generated label based on member file paths.

Execution Flow Tracing

Detects entry points using framework-aware patterns:

• Python: @app.route, @router.get, @click.command, test_* functions, __main__ blocks
• JavaScript/TypeScript: Express handlers, exported functions, handler/middleware patterns

Then traces BFS execution flows from each entry point through the call graph, classifying flows as intra-community or cross-community.

Change Coupling (Git History)

Analyzes 6 months of git history to find hidden dependencies that static analysis misses:

coupling(A, B) = co_changes(A, B) / max(changes(A), changes(B))

Files with coupling strength ≥ 0.3 and 3+ co-changes get linked. Surfaces coupled files in impact analysis.

Watch Mode

Live re-indexing powered by a Rust-based file watcher (watchfiles):

$ synaptiq watch
Watching /Users/you/project for changes...

[10:32:15] src/auth/validate.py modified → re-indexed (0.3s)
[10:33:02] 2 files modified → re-indexed (0.5s)

• File-local phases (parse, imports, calls, types) run immediately on change
• Global phases (communities, processes, dead code) batch every 30 seconds

Multi-Instance Concurrency

Synaptiq supports multiple concurrent MCP sessions (e.g., swarm sub-agents) through a primary/proxy daemon architecture:

• Primary process: Owns the database, watcher, and socket server
• Proxy processes: Forward queries over Unix socket to primary
• Automatic role detection: Each instance self-detects its role at startup

Branch Comparison

Structural diff between branches using git worktrees (no stashing required):

$ synaptiq diff main..feature

Symbols added (4):
  + process_payment (Function) -- src/payments/stripe.py
  + PaymentIntent (Class) -- src/payments/models.py

Symbols modified (2):
  ~ checkout_handler (Function) -- src/routes/checkout.py

Symbols removed (1):
  - old_charge (Function) -- src/payments/legacy.py

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Supported Languages

Language	Extensions	Parser
Python	.py	tree-sitter-python
TypeScript	.ts, .tsx	tree-sitter-typescript
JavaScript	.js, .jsx, .mjs, .cjs	tree-sitter-javascript

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Installation

# With pip
pip install synaptiq

# With uv (recommended)
uv add synaptiq

# With Neo4j backend support
pip install synaptiq[neo4j]

Requires Python 3.11+.

From Source

git clone https://github.com/scanadi/synaptiq.git
cd synaptiq
uv sync --all-extras
uv run synaptiq --help

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Quick Start

1. Index Your Codebase

cd your-project
synaptiq analyze .

2. Query It

# Search for symbols
synaptiq query "authentication handler"

# Get full context on a symbol
synaptiq context validate_user

# Check blast radius before changing something
synaptiq impact UserModel --depth 3

# Find dead code
synaptiq dead-code

# Run a raw Cypher query
synaptiq cypher "MATCH (n:Function) WHERE n.is_dead = true RETURN n.name, n.file_path"

3. Keep It Updated

# Watch mode — re-indexes on every save
synaptiq watch

# Or re-analyze manually
synaptiq analyze .

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CLI Reference

synaptiq analyze [PATH]          Index a repository (default: current directory)
    --full                       Force full rebuild (skip incremental)

synaptiq status                  Show index status for current repo
synaptiq list                    List all indexed repositories
synaptiq clean                   Delete index for current repo
    --force / -f                 Skip confirmation prompt

synaptiq query QUERY             Hybrid search the knowledge graph
    --limit / -n N               Max results (default: 20)

synaptiq context SYMBOL          360-degree view of a symbol
synaptiq impact SYMBOL           Blast radius analysis
    --depth / -d N               BFS traversal depth (default: 3)

synaptiq dead-code               List all detected dead code
synaptiq cypher QUERY            Execute a raw Cypher query (read-only)

synaptiq watch                   Watch mode — live re-indexing on file changes
synaptiq diff BASE..HEAD         Structural branch comparison

synaptiq setup                   Print MCP configuration JSON
    --claude                     For Claude Code
    --cursor                     For Cursor

synaptiq mcp                     Start the MCP server (stdio transport)
synaptiq serve                   Start the MCP server (same as synaptiq mcp)
    --watch, -w                  Enable live file watching with auto-reindex
synaptiq --version               Print version

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MCP Integration

Synaptiq exposes its full intelligence as an MCP server, giving AI agents like Claude Code and Cursor deep structural understanding of your codebase.

Setup for Claude Code

Add to your .claude/settings.json or project .mcp.json:

{
  "mcpServers": {
    "synaptiq": {
      "command": "synaptiq",
      "args": ["serve", "--watch"]
    }
  }
}

This starts the MCP server with live file watching — the knowledge graph updates automatically as you edit code. To run without watching, use "args": ["mcp"] instead.

Or run the setup helper:

synaptiq setup --claude

Claude Code Skill (Optional)

For richer Claude Code integration, copy the bundled skill into your project:

cp -r "$(python -c 'import synaptiq; import pathlib; print(pathlib.Path(synaptiq.__file__).parent.parent.parent)')"/.claude/skills/synaptiq .claude/skills/

Or manually copy .claude/skills/synaptiq/SKILL.md from the Synaptiq repo. This teaches Claude when and how to use Synaptiq's tools, the knowledge graph schema, Cypher query patterns, and investigation workflows.

Setup for Cursor

Add to your Cursor MCP settings:

{
  "synaptiq": {
    "command": "synaptiq",
    "args": ["serve", "--watch"]
  }
}

Or run:

synaptiq setup --cursor

MCP Tools

Once connected, your AI agent gets access to these tools:

Tool	Description
synaptiq_list_repos	List all indexed repositories with stats
synaptiq_query	Hybrid search (BM25 + vector + fuzzy) across all symbols
synaptiq_context	360-degree view — callers, callees, type refs, community, processes
synaptiq_impact	Blast radius — all symbols affected by changing the target
synaptiq_dead_code	List all unreachable symbols grouped by file
synaptiq_detect_changes	Map a git diff to affected symbols in the graph
synaptiq_cypher	Execute read-only Cypher queries against the knowledge graph

Every tool response includes a next-step hint guiding the agent through a natural investigation workflow:

query → "Next: Use context() on a specific symbol for the full picture."
context → "Next: Use impact() if planning changes to this symbol."
impact → "Tip: Review each affected symbol before making changes."

MCP Resources

Resource URI	Description
synaptiq://overview	Node and relationship counts by type
synaptiq://dead-code	Full dead code report
synaptiq://schema	Graph schema reference for writing Cypher queries

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Knowledge Graph Model

Nodes

Label	Description
File	Source file
Folder	Directory
Function	Top-level function
Class	Class definition
Method	Method within a class
Interface	Interface / Protocol definition
TypeAlias	Type alias
Enum	Enumeration
Community	Auto-detected functional cluster
Process	Detected execution flow

Relationships

Type	Description	Key Properties
CONTAINS	Folder → File/Symbol hierarchy	—
DEFINES	File → Symbol it defines	—
CALLS	Symbol → Symbol it calls	confidence (0.0–1.0)
IMPORTS	File → File it imports from	symbols (names list)
EXTENDS	Class → Class it extends	—
IMPLEMENTS	Class → Interface it implements	—
USES_TYPE	Symbol → Type it references	role (param/return/variable)
EXPORTS	File → Symbol it exports	—
MEMBER_OF	Symbol → Community it belongs to	—
STEP_IN_PROCESS	Symbol → Process it participates in	step_number
COUPLED_WITH	File → File that co-changes with it	strength, co_changes

Node ID Format

{label}:{relative_path}:{symbol_name}

Examples:
  function:src/auth/validate.py:validate_user
  class:src/models/user.py:User
  method:src/models/user.py:User.save

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Architecture

Source Code (.py, .ts, .js, .tsx, .jsx)
    │
    ▼
┌──────────────────────────────────────────────┐
│         Ingestion Pipeline (11 phases)        │
│                                               │
│  walk → structure → parse → imports → calls   │
│  → heritage → types → communities → processes │
│  → dead_code → coupling                       │
└──────────────────────┬───────────────────────┘
                       │
                       ▼
              ┌─────────────────┐
              │ KnowledgeGraph  │  (in-memory during build)
              └────────┬────────┘
                       │
          ┌────────────┼────────────┐
          ▼            ▼            ▼
     ┌─────────┐ ┌─────────┐ ┌─────────┐
     │ KuzuDB  │ │  FTS    │ │ Vector  │
     │ (graph) │ │ (BM25)  │ │ (HNSW)  │
     └────┬────┘ └────┬────┘ └────┬────┘
          └────────────┼────────────┘
                       │
              StorageBackend Protocol
                       │
              ┌────────┴────────┐
              ▼                 ▼
        ┌──────────┐     ┌──────────┐
        │   MCP    │     │   CLI    │
        │  Server  │     │ (Typer)  │
        │ (stdio)  │     │          │
        └────┬─────┘     └────┬─────┘
             │                │
        Claude Code      Terminal
        / Cursor         (developer)

Tech Stack

Layer	Technology	Purpose
Parsing	tree-sitter	Language-agnostic AST extraction
Graph Storage	KuzuDB	Embedded graph database with Cypher, FTS, and vector support
Graph Algorithms	igraph + leidenalg	Leiden community detection
Embeddings	fastembed	ONNX-based 384-dim vectors (~100MB, no PyTorch)
MCP Protocol	mcp SDK (FastMCP)	AI agent communication via stdio
CLI	Typer + Rich	Terminal interface with progress bars
File Watching	watchfiles	Rust-based file system watcher
Gitignore	pathspec	Full .gitignore pattern matching

Storage

Everything lives locally in your repo:

your-project/
└── .synaptiq/
    ├── kuzu/          # KuzuDB graph database (graph + FTS + vectors)
    └── meta.json      # Index metadata and stats

Add .synaptiq/ to your .gitignore.

The storage layer is abstracted behind a StorageBackend Protocol — KuzuDB is the default, with an optional Neo4j backend available via pip install synaptiq[neo4j].

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Example Workflows

"I need to refactor the User class — what breaks?"

# See everything connected to User
synaptiq context User

# Check blast radius
synaptiq impact User --depth 3

# Find which files always change with user.py
synaptiq cypher "MATCH (a:File)-[r:CodeRelation]->(b:File) WHERE a.name = 'user.py' AND r.rel_type = 'coupled_with' RETURN b.name, r.strength ORDER BY r.strength DESC"

"Is there dead code we should clean up?"

synaptiq dead-code

"What are the main execution flows in our app?"

synaptiq cypher "MATCH (p:Process) RETURN p.name, p.properties ORDER BY p.name"

"Which parts of the codebase are most tightly coupled?"

synaptiq cypher "MATCH (a:File)-[r:CodeRelation]->(b:File) WHERE r.rel_type = 'coupled_with' RETURN a.name, b.name, r.strength ORDER BY r.strength DESC LIMIT 20"

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How It Compares

Capability	grep/ripgrep	LSP	Synaptiq
Text search	Yes	No	Yes (hybrid BM25 + vector)
Go to definition	No	Yes	Yes (graph traversal)
Find all callers	No	Partial	Yes (full call graph with confidence)
Type relationships	No	Yes	Yes (param/return/variable roles)
Dead code detection	No	No	Yes (multi-pass, framework-aware)
Execution flow tracing	No	No	Yes (entry point → flow)
Community detection	No	No	Yes (Leiden algorithm)
Change coupling (git)	No	No	Yes (6-month co-change analysis)
Impact analysis	No	No	Yes (calls + types + git coupling)
AI agent integration	No	Partial	Yes (full MCP server)
Structural branch diff	No	No	Yes (node/edge level)
Watch mode	No	Yes	Yes (Rust-based, 500ms debounce)
Works offline	Yes	Yes	Yes

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Development

git clone https://github.com/scanadi/synaptiq.git
cd synaptiq
uv sync --all-extras

# Run tests
uv run pytest

# Lint
uv run ruff check src/

# Run from source
uv run synaptiq --help

See CONTRIBUTING.md for detailed contribution guidelines.

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Acknowledgments

Synaptiq was originally inspired by and built upon axon by @harshkedia177. This project has since evolved into an independent codebase with its own architecture, features, and direction.

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License

MIT — see LICENSE.