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scanadi/synaptiq

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.

PyPI version Python 3.11+ License: MIT

$ 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.


Why Synaptiq?

For AI agents (Claude Code, Cursor, agent swarms):

  • "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.


Table of Contents


🔬 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
1. File Walking Walks repo respecting .gitignore, filters by supported languages
2. Structure Creates File/Folder hierarchy with CONTAINS relationships
3. Parsing tree-sitter AST extraction — functions, classes, methods, interfaces, enums, type aliases
4. Import Resolution Resolves import statements to actual files (relative, absolute, bare specifiers)
5. Call Tracing Maps function calls with confidence scores (1.0 = exact match, 0.5 = fuzzy)
6. Heritage Tracks class inheritance (EXTENDS) and interface implementation (IMPLEMENTS)
7. Type Analysis Extracts type references from parameters, return types, and variable annotations
8. Community Detection Leiden algorithm clusters related symbols into functional communities
9. Process Detection Framework-aware entry point detection + BFS flow tracing
10. Dead Code Detection Multi-pass analysis with override, protocol, and decorator awareness
11. 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 (batched BFS — one query per depth level)
  • 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 run immediately on change — parsing happens without holding any lock
  • Global phases (communities, processes, dead code) batch every 30 seconds
  • The CPU-intensive parse step and the I/O-intensive storage write are split so locks are held for the shortest possible window

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

🌐 Supported Languages

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

📦 Installation

# With uv (recommended) — installs as a global CLI tool
uv tool install synaptiq

# With pip
pip install synaptiq

# As a project dependency
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

🚀 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 .

🖥 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 MCP server with daemon features
    --watch, -w                  Enable live file watching with auto-reindex
synaptiq --version               Print version

🤖 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.

Claude Code Plugin

For a batteries-included Claude Code experience, install the Synaptiq Claude Plugin — it bundles the MCP server, skill, setup command, and a session hook in a single install:

claude plugins add scanadi/synaptiq-claude-plugin

Then run /synaptiq:setup to install Synaptiq, index your codebase, and configure the MCP connection automatically.

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

🔄 Multi-Agent Concurrency

Synaptiq is designed for environments where multiple AI agents hit the same codebase simultaneously — Claude Code with sub-agents, Cursor with background indexing, or any swarm-of-agents setup.

Primary/Proxy Architecture

flowchart TB
    A1(["🤖 Agent 1"])
    A2(["🤖 Agent 2"])
    A3(["🤖 Agent 3"])
    AN(["🤖 Agent N"])

    subgraph PRIMARY ["🟢 Primary Instance"]
        MCP["📡 MCP Server"]
        FW["👁️ File Watcher<br/>watchfiles"]
        RWL{{"🔒 AsyncRWLock<br/>concurrent reads · exclusive writes"}}
        DB[(🗄️ KuzuDB + Pool<br/>8 read connections)]
        SOCK["🔌 Unix Socket Server<br/>16 concurrent slots"]
        MCP --> RWL
        FW --> RWL
        RWL --> DB
        SOCK --> RWL
    end

    P1["🔵 Proxy 1<br/>MCP + Socket Client"]
    P2["🔵 Proxy 2<br/>MCP + Socket Client"]
    PN["🔵 Proxy N ···"]

    A1 -->|MCP stdio| MCP
    A2 --> P1
    A3 --> P2
    AN --> PN
    P1 -->|unix socket| SOCK
    P2 -->|unix socket| SOCK
    PN -->|unix socket| SOCK

    style PRIMARY fill:#ecfdf5,stroke:#10b981,stroke-width:2px
    classDef agent fill:#fbbf24,stroke:#d97706,color:#000,stroke-width:2px
    classDef server fill:#6ee7b7,stroke:#10b981,color:#000,stroke-width:2px
    classDef lock fill:#c4b5fd,stroke:#8b5cf6,color:#000,stroke-width:2px
    classDef database fill:#67e8f9,stroke:#06b6d4,color:#000,stroke-width:2px
    classDef socket fill:#fda4af,stroke:#f43f5e,color:#000,stroke-width:2px
    classDef proxy fill:#93c5fd,stroke:#3b82f6,color:#000,stroke-width:2px

    class A1,A2,A3,AN agent
    class MCP,FW server
    class RWL lock
    class DB database
    class SOCK socket
    class P1,P2,PN proxy
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How it works:

  1. The first synaptiq serve --watch becomes the primary — it owns the database, runs the file watcher, and opens a Unix domain socket
  2. Subsequent instances detect the lock and become proxies — they forward all queries through the socket to the primary
  3. Role detection is automatic via fcntl.flock() — no configuration needed
  4. If the primary crashes, the OS releases the lock and the next instance takes over

Concurrency Model

Layer Mechanism Purpose
Storage reads Connection pool (8 kuzu.Connection objects) Multiple threads query in parallel
Storage writes Dedicated write connection + AsyncRWLock Exclusive access during index updates
MCP dispatch AsyncRWLock.reader() with 120s timeout Concurrent tool/resource calls
Socket server asyncio.Semaphore(16) backpressure Limits concurrent proxy dispatches
Socket client Request-ID multiplexing + asyncio.Future Concurrent calls on a single connection
File watcher Split parse/write pattern CPU work runs lock-free; lock held only for I/O
Process lock fcntl.flock() on .synaptiq/synaptiq.lock Primary election, auto-released on crash
Proxy recovery Auto-reconnect (3 attempts, exponential backoff) Handles primary restarts gracefully

Lock Strategy: Write-Preferring RWLock

The AsyncRWLock allows multiple readers to query simultaneously while giving priority to writers:

  • Reads (agent queries): Run concurrently — multiple agents can search, inspect context, and analyze impact at the same time
  • Writes (file watcher updates): Get exclusive access, and pending writes block new reads to prevent writer starvation
  • Timeout: All lock acquisitions have a 60-second timeout to prevent deadlocks
  • Split processing: The watcher parses files without the lock (CPU-intensive), then acquires the write lock only for the storage I/O step

macOS Compatibility

Unix domain socket paths are limited to 104 bytes on macOS. When the .synaptiq/synaptiq.sock path exceeds 100 bytes (common with deep directory nesting), Synaptiq automatically falls back to /tmp/synaptiq-<hash>.sock using a truncated SHA-256 hash of the data directory.


📊 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
  file:src/auth/validate.py:

🏗 Architecture

flowchart TB
    SRC(["📁 Source Code<br/>.py · .ts · .js · .tsx · .jsx"])

    PIPELINE["⚙️ Ingestion Pipeline — 11 Phases<br/>walk → structure → parse → imports → calls<br/>heritage → types → communities<br/>processes → dead_code → coupling"]

    KG(["🧠 KnowledgeGraph<br/>in-memory during build"])

    KUZU[(KuzuDB<br/>graph)]
    FTS[(FTS<br/>BM25)]
    VEC[(Vector<br/>HNSW)]

    PROTO["⬡ StorageBackend Protocol"]

    MCP_OUT["📡 MCP Server<br/>stdio transport"]
    CLI_OUT["⌨️ CLI<br/>Typer + Rich"]

    CLAUDE(["🤖 Claude Code · Cursor"])
    DEV(["👤 Developer Terminal"])

    SRC --> PIPELINE --> KG
    KG --> KUZU
    KG --> FTS
    KG --> VEC
    KUZU --> PROTO
    FTS --> PROTO
    VEC --> PROTO
    PROTO --> MCP_OUT
    PROTO --> CLI_OUT
    MCP_OUT --> CLAUDE
    CLI_OUT --> DEV

    classDef source fill:#d8b4fe,stroke:#a855f7,color:#000,stroke-width:2px
    classDef pipeline fill:#fed7aa,stroke:#f97316,color:#000,stroke-width:2px
    classDef kg fill:#6ee7b7,stroke:#10b981,color:#000,stroke-width:2px
    classDef store fill:#93c5fd,stroke:#3b82f6,color:#000,stroke-width:2px
    classDef proto fill:#cbd5e1,stroke:#64748b,color:#000,stroke-width:2px
    classDef iface fill:#5eead4,stroke:#14b8a6,color:#000,stroke-width:2px
    classDef user fill:#fbbf24,stroke:#d97706,color:#000,stroke-width:2px

    class SRC source
    class PIPELINE pipeline
    class KG kg
    class KUZU,FTS,VEC store
    class PROTO proto
    class MCP_OUT,CLI_OUT iface
    class CLAUDE,DEV user
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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 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
    +-- synaptiq.lock  # Process lock (present while serve is running)

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].


💡 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"

"What changed in this PR and what does it affect?"

# Structural diff
synaptiq diff main..feature

# Or pipe a git diff through detect_changes (via MCP)
git diff main | synaptiq detect-changes

⚖ 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)
Multi-agent concurrency No No Yes (RWLock + connection pool)
Structural branch diff No No Yes (node/edge level)
Watch mode No Yes Yes (Rust-based, 500ms debounce)
Works offline Yes Yes Yes

🛠 Development

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

# Run tests (581 tests)
uv run pytest

# Run only fast unit tests (skip e2e)
uv run pytest tests/core/ tests/cli/ tests/mcp/

# Lint
uv run ruff check src/ tests/

# Format
uv run ruff format src/ tests/

# Run from source
uv run synaptiq --help

Project Structure

src/synaptiq/
+-- cli/main.py                    # Typer CLI (analyze, query, serve, watch, ...)
+-- mcp/
|   +-- server.py                  # MCP server (tools + resources + dispatch)
|   +-- tools.py                   # Tool handler implementations
|   +-- resources.py               # Resource handler implementations
+-- core/
|   +-- ingestion/
|   |   +-- pipeline.py            # 11-phase pipeline orchestrator
|   |   +-- walker.py              # File discovery respecting .gitignore
|   |   +-- structure.py           # Folder/File hierarchy
|   |   +-- parser_phase.py        # tree-sitter AST extraction
|   |   +-- imports.py             # Import resolution
|   |   +-- calls.py               # Call tracing with confidence
|   |   +-- heritage.py            # Inheritance and implementation
|   |   +-- types.py               # Type reference extraction
|   |   +-- community.py           # Leiden clustering
|   |   +-- processes.py           # Entry point + flow detection
|   |   +-- dead_code.py           # Multi-pass dead code analysis
|   |   +-- coupling.py            # Git co-change analysis
|   |   +-- watcher.py             # File watcher with split parse/write
|   +-- storage/
|   |   +-- base.py                # StorageBackend protocol
|   |   +-- kuzu_backend.py        # KuzuDB implementation + connection pool
|   +-- daemon/
|   |   +-- rwlock.py              # Write-preferring AsyncRWLock
|   |   +-- lock.py                # fcntl.flock() based process lock
|   |   +-- socket_server.py       # Unix socket server (primary)
|   |   +-- socket_client.py       # Unix socket client (proxy)
|   +-- search/hybrid.py           # BM25 + vector + fuzzy fusion
|   +-- parsers/                   # Language-specific tree-sitter parsers
+-- config/
    +-- languages.py               # Language registry
    +-- ignore.py                  # Gitignore loading

See CONTRIBUTING.md for detailed contribution guidelines.


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.


License

MIT — see LICENSE.

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