Skip to content
/ Cocode Public

A codebase indexing mcp server based on Cocoindex.

License

MIT license
4 stars 0 forks Branches Tags Activity
Star
Notifications You must be signed in to change notification settings

hrayleung/Cocode

BranchesTags

Repository files navigation

Cocode

MCP server for semantic codebase search, powered by CocoIndex for real-time incremental indexing and intelligent ranking.

Search your codebase semantically without memorizing exact function names—find "HTTP error handler" and get all error handling logic, even if it doesn't contain those exact keywords.

Built on CocoIndex

Cocode leverages CocoIndex, a data transformation framework designed for AI applications. CocoIndex provides:

  • Incremental Processing: Only re-indexes changed files, not the entire codebase—real-time updates with minimal computation
  • Tree-sitter Integration: Intelligent code chunking based on syntax structure (not arbitrary line breaks) for syntactically coherent embeddings
  • Automatic Synchronization: Keeps the vector index in sync with source code changes across long time horizons
  • AI Integration: Powers code context for AI agents and development tools

This combination enables fast, accurate semantic search that stays up-to-date as your code evolves.

Key Features

Hybrid Search Architecture

  • Vector Similarity: pgvector cosine similarity for semantic understanding
  • BM25 Keyword Search: PostgreSQL full-text search for exact term matching
  • Reciprocal Rank Fusion: Intelligently combines multiple search strategies with configurable weights
  • Symbol-Level Indexing: Functions, classes, and methods indexed separately with precise line numbers

Intelligent Ranking

  • Graph-Based Centrality: PageRank algorithm identifies structurally important files (e.g., core utilities imported by many modules)
  • Category Boosting: Prioritizes implementation code over tests/docs/config (configurable weights)
  • Multi-Hop Graph Traversal: Finds related files via import dependencies (up to 3 hops by default)
  • Optional Cohere Reranking: rerank-v3.5 for improved relevance (when API key provided)

Multiple Embedding Providers

  • Jina (default): Late chunking preserves cross-chunk context
  • Mistral: Codestral Embed optimized specifically for code
  • OpenAI: text-embedding-3-large with contextual headers

Real-Time Incremental Indexing

  • File-Level Change Detection: Only re-indexes modified files based on timestamps
  • Automatic Index Updates: First search triggers indexing; subsequent searches use cached results
  • Symbol-Level Updates: UPSERT operations for functions/classes when files change
  • Graph Cache Invalidation: Import graphs automatically refresh when dependencies change

Installation

Prerequisites

  • Python 3.10+
  • PostgreSQL with pgvector (vector) extension (the server will also attempt to enable pgcrypto for UUIDs)
  • API key for at least one embedding provider
  • Rust toolchain (only required for building from source):
    • Install via rustup: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
    • Includes cargo and the Rust compiler

Quick Install (Recommended)

Install from PyPI using pip, uvx, or pipx:

# Using pip
pip install cocode-mcp

# Or using uvx (isolated environment, no global install)
uvx --from cocode-mcp cocode

# Or using pipx (isolated environment with global command)
pipx install cocode-mcp

# Verify installation
cocode --help

From Source

Standard Installation

# Clone the repository
git clone https://github.com/hrayleung/Cocode.git
cd Cocode

# Install dependencies and build Rust extensions (requires Rust toolchain)
# This single command installs Python deps and builds the Rust extension in release mode
maturin develop --release

# Create .env file
cp .env.example .env
# Edit .env with your API keys

NixOS / Nix Flakes

# Clone repository
git clone https://github.com/hrayleung/Cocode.git
cd Cocode

# Enter dev shell (includes Python 3.11, PostgreSQL 16, and dependencies)
nix develop

# Install dependencies and build Rust extensions (requires Rust toolchain)
maturin develop --release

# Create .env file (automatically copied by shellHook)
# Edit .env with your API keys

The Nix flake automatically:

  • Sets up PostgreSQL 16 (via Unix socket) in .postgres/
  • Creates a Python virtual environment in venv/
  • Activates the venv automatically
  • Copies .env.example to .env if it doesn't exist

Required Environment Variables

# PostgreSQL (requires pgvector; server also attempts to CREATE EXTENSION pgcrypto)
COCOINDEX_DATABASE_URL=postgresql://localhost:5432/cocode

# Embeddings (choose one)
OPENAI_API_KEY=sk-...          # Required unless using Jina late chunking
JINA_API_KEY=jina_...          # Can run without OpenAI if USE_LATE_CHUNKING=true
MISTRAL_API_KEY=...            # Optional (requires OPENAI_API_KEY as fallback)

# Select provider: jina, mistral, or openai (default: jina)
EMBEDDING_PROVIDER=jina
USE_LATE_CHUNKING=true

# Optional: Cohere reranking
COHERE_API_KEY=...
ENABLE_RERANKER=true  # enabled by default when COHERE_API_KEY is set

MCP Configuration

Cocode works with multiple MCP clients. Choose the setup that matches your workflow.

Claude Desktop

Claude Desktop reads its configuration from claude_desktop_config.json:

Configuration File Locations:

  • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
  • Windows: %APPDATA%\Claude\claude_desktop_config.json
  • Linux: ~/.config/Claude/claude_desktop_config.json

Configuration Example:

{
  "mcpServers": {
    "cocode": {
      "command": "cocode",
      "args": [],
      "env": {
        "COCOINDEX_DATABASE_URL": "postgresql://localhost:5432/cocode",
        "JINA_API_KEY": "jina_...",
        "EMBEDDING_PROVIDER": "jina",
        "USE_LATE_CHUNKING": "true",
        "COHERE_API_KEY": "your_cohere_key_optional"
      }
    }
  }
}

Important Notes:

  • Use absolute paths in args if needed
  • Avoid trailing commas in JSON (causes silent failures)
  • Restart Claude Desktop completely after config changes (not just close window)
  • Claude Desktop does not support ${VAR_NAME} environment variable substitution (use literal values instead). Other clients like VS Code and .mcp.json configs support ${VAR_NAME} or ${env:VAR} syntax

Alternative: Using uvx for isolation:

{
  "mcpServers": {
    "cocode": {
      "command": "uvx",
      "args": ["--from", "cocode-mcp", "cocode"],
      "env": {
        "COCOINDEX_DATABASE_URL": "postgresql://localhost:5432/cocode",
        "JINA_API_KEY": "jina_..."
      }
    }
  }
}

Note: Before PyPI publication, use "args": ["--from", "git+https://github.com/hrayleung/Cocode.git", "cocode"] to install from source.

Claude Code CLI

Option 1: Add via CLI (Recommended)

# Add to your user config (available across all projects)
claude mcp add --scope user cocode -- cocode

# Or add to current project only
claude mcp add --scope project cocode -- cocode

# With environment variables baked in
claude mcp add --scope user \
  -e COCOINDEX_DATABASE_URL=postgresql://localhost:5432/cocode \
  -e JINA_API_KEY="${JINA_API_KEY}" \
  -e EMBEDDING_PROVIDER=jina \
  -e USE_LATE_CHUNKING=true \
  cocode -- cocode

Option 2: Project Configuration

Create .mcp.json in your project root:

{
  "mcpServers": {
    "cocode": {
      "command": "cocode",
      "args": [],
      "env": {
        "COCOINDEX_DATABASE_URL": "postgresql://localhost:5432/cocode",
        "JINA_API_KEY": "${JINA_API_KEY}",
        "EMBEDDING_PROVIDER": "jina",
        "USE_LATE_CHUNKING": "true"
      }
    }
  }
}

Option 3: Run Standalone

cocode
# or
python -m src.server

Verify Installation

In Claude Code:

/mcp
VS Code (GitHub Copilot)

VS Code supports MCP servers through workspace or user settings.

Workspace Configuration (.vscode/settings.json):

{
  "github.copilot.chat.mcp.servers": {
    "cocode": {
      "command": "cocode",
      "args": [],
      "env": {
        "COCOINDEX_DATABASE_URL": "postgresql://localhost:5432/cocode",
        "JINA_API_KEY": "${env:JINA_API_KEY}",
        "EMBEDDING_PROVIDER": "jina",
        "USE_LATE_CHUNKING": "true"
      }
    }
  }
}

User Configuration (global settings):

  1. Open Command Palette (Cmd+Shift+P / Ctrl+Shift+P)
  2. Search "Preferences: Open User Settings (JSON)"
  3. Add the same github.copilot.chat.mcp.servers object

Using Input Variables for Secrets:

{
  "github.copilot.chat.mcp.servers": {
    "cocode": {
      "command": "cocode",
      "args": [],
      "env": {
        "COCOINDEX_DATABASE_URL": "${input:databaseUrl}",
        "JINA_API_KEY": "${input:jinaApiKey}"
      }
    }
  },
  "inputs": [
    {
      "id": "databaseUrl",
      "type": "promptString",
      "description": "PostgreSQL database URL"
    },
    {
      "id": "jinaApiKey",
      "type": "promptString",
      "password": true,
      "description": "Jina API Key"
    }
  ]
}
Codex CLI

Codex stores MCP server configs in ~/.codex/config.toml.

Option 1: Add via CLI (Codex)

# Add the server (stdio transport)
codex mcp add cocode \
  --env COCOINDEX_DATABASE_URL=postgresql://localhost:5432/cocode \
  --env JINA_API_KEY="${JINA_API_KEY}" \
  --env EMBEDDING_PROVIDER=jina \
  --env USE_LATE_CHUNKING=true \
  -- cocode

# Verify
codex mcp list
codex mcp get cocode

Option 2: Edit ~/.codex/config.toml

[mcp_servers.cocode]
command = "cocode"
args = []

[mcp_servers.cocode.env]
COCOINDEX_DATABASE_URL = "postgresql://localhost:5432/cocode"
JINA_API_KEY = "jina_..."
EMBEDDING_PROVIDER = "jina"
USE_LATE_CHUNKING = "true"
Warp Terminal

Warp supports MCP servers through its settings UI.

Setup Steps:

  1. Open Warp Settings via:
    • Settings > MCP Servers, or
    • Warp Drive > Personal > MCP Servers, or
    • Command Palette: search "Open MCP Servers", or
    • Settings > AI > Manage MCP servers
  2. Click + Add button
  3. Choose configuration type:
    • CLI Server (Command): For local executables
    • Streamable HTTP/SSE Server (URL): For remote servers

CLI Server Configuration:

{
  "command": "cocode",
  "args": [],
  "env": {
    "COCOINDEX_DATABASE_URL": "postgresql://localhost:5432/cocode",
    "JINA_API_KEY": "jina_...",
    "EMBEDDING_PROVIDER": "jina",
    "USE_LATE_CHUNKING": "true"
  },
  "working_directory": "/path/to/your/project"
}

Multiple Servers: Paste JSON under the mcpServers key:

{
  "mcpServers": {
    "cocode": {
      "command": "cocode",
      "args": [],
      "env": {
        "COCOINDEX_DATABASE_URL": "postgresql://localhost:5432/cocode",
        "JINA_API_KEY": "jina_..."
      }
    }
  }
}
Troubleshooting MCP Setup

Server Not Appearing

  1. Check Configuration Syntax:

    • Validate JSON (no trailing commas)
    • Use absolute paths in args if needed
    • Ensure environment variables are quoted strings

  2. Restart the Client:

    • Claude Desktop: Fully quit (not just close window)
    • VS Code: Reload window or restart
    • Warp: Restart terminal

  3. Verify Server Installation:

# Check if cocode is in PATH
which cocode

# Test server directly
cocode

Connection Failures

  1. Check PostgreSQL:
# Test database connection
psql postgresql://localhost:5432/cocode

# Verify pgvector extension
psql -d cocode -c "SELECT * FROM pg_extension WHERE extname = 'vector';"

  1. Verify API Keys:

    • Ensure keys are valid and not expired
    • Check that EMBEDDING_PROVIDER matches the key you provided
    • For Jina: USE_LATE_CHUNKING=true must be set

  2. Check Logs:

    • Claude Desktop: Check MCP logs in the application
    • VS Code: View Output panel → select "MCP" channel
    • Warp: View server logs in MCP settings

Common Errors

"Could not connect to server":

  • Verify server command is correct and in PATH
  • Check that all required environment variables are set
  • Ensure PostgreSQL is running

"Database connection failed":

  • Confirm PostgreSQL is running: pg_isready
  • Verify database URL format: postgresql://user:pass@host:port/dbname
  • Ensure database exists: createdb cocode

"Missing API key":

  • Set at least one embedding provider key
  • If using Jina: set both JINA_API_KEY and USE_LATE_CHUNKING=true
  • If using Mistral: set both MISTRAL_API_KEY and OPENAI_API_KEY (fallback)

Silent Failures:

  • Check for trailing commas in JSON configuration
  • Validate JSON with a linter
  • Review application logs for specific error messages

Performance Issues:

  • First indexing can take several minutes for large codebases
  • Check PostgreSQL memory settings if indexing is very slow
  • Consider enabling graph cache: automatically enabled by default

MCP Tools

Tool Description
codebase_retrieval_full(query, path, top_k, max_symbols, max_symbols_per_file, max_code_chars, include_dependencies) Returns key files + import dependencies + full implementations of relevant symbols (functions/classes/methods).
clear_index(path) Delete index to force re-indexing on next search.

Result Format

codebase_retrieval_full returns an object:

  • files: ranked key files (with category + line hints)
  • dependencies: import edges between returned files
  • symbols: full code implementations for the most relevant functions/classes/methods

Example Queries

"Where is user authentication implemented?"
"How does the payment processing work?"
"Find all database connection code"

How It Works

1. Indexing Phase (Automatic on First Search)

When you search a codebase for the first time, Cocode:

  1. Repository Registration: Creates metadata entry with path hash to handle duplicate folder names
  2. CocoIndex Processing:
    • Scans repository for supported file types (.py, .ts, .js, .go, .rs, etc.)
    • Intelligently chunks code using Tree-sitter AST parsing (respects function/class boundaries)
    • Generates embeddings for each chunk using your selected provider
    • Stores chunks with HNSW vector index for fast similarity search
  3. Symbol Extraction (parallel):
    • Parses functions, classes, and methods using Tree-sitter
    • Extracts signatures, docstrings, visibility, and categorization
    • Stores with precise line numbers and separate embeddings
  4. Import Graph Construction:
    • Parses import statements across all files
    • Builds bidirectional dependency graph (imports + imported_by)
    • Computes PageRank centrality scores
    • Caches graph for fast traversal

Subsequent searches reuse the index, only re-indexing files that changed (via mtime comparison).

2. Search Phase (Real-Time)

When you query the codebase:

  1. Query Embedding: Convert natural language query to vector using selected provider
  2. Parallel Search Execution (ThreadPoolExecutor with 3 workers):
    • Vector Search: pgvector cosine similarity on chunk embeddings
    • BM25 Search: PostgreSQL full-text search with ts_rank_cd scoring
    • Symbol Search: Vector + BM25 on functions/classes/methods
  3. Reciprocal Rank Fusion: Combines results with configurable weights (vector=0.6, bm25=0.4, symbol=0.7)
  4. Ranking Pipeline:
    • Centrality Boost: Amplifies scores for structurally important files (PageRank)
    • Category Boost: Prioritizes implementation > docs > config > tests
    • Cohere Rerank (optional): LLM-based reranking for improved relevance
  5. Post-Processing:
    • File Aggregation: Groups chunks by file, keeps top 3 per file
    • Graph Expansion: BFS traversal finds related files via imports (up to 3 hops)
    • Tiered Results: Top 3 with full code excerpts, remainder as compact signatures

3. Incremental Updates (Transparent)

On subsequent searches, Cocode automatically:

  1. Change Detection: Compares file modification times against last index time
  2. Selective Re-indexing: Only processes changed/new/deleted files
  3. Symbol Updates: UPSERT operations via ON CONFLICT constraints
  4. Graph Cache Refresh: Invalidates affected import relationships
  5. Centrality Recalculation: Updates PageRank scores if graph topology changed

This ensures your search results always reflect the current state of the codebase with minimal latency.

Architecture

config/
└── settings.py              # Environment-driven configuration

src/
├── server.py                # FastMCP entry point (2 tools)
│
├── indexer/                 # CocoIndex Integration
│   ├── service.py           # IndexerService singleton - orchestrates indexing
│   ├── flow.py              # CocoIndex flows for chunking/embedding
│   ├── repo_manager.py      # Repository metadata and status tracking
│   ├── symbol_indexing.py   # AST-based function/class extraction
│   └── call_graph_indexing.py # (Experimental) call edge extraction
│
├── retrieval/               # Hybrid Search Pipeline
│   ├── service.py           # SearchService singleton - orchestrates search
│   ├── hybrid.py            # RRF fusion + parallel execution
│   ├── vector_search.py     # pgvector cosine similarity
│   ├── bm25_search.py       # PostgreSQL FTS with ts_rank_cd
│   ├── symbol_search.py     # Symbol-level search (vector + BM25)
│   ├── file_categorizer.py  # Category-based score boosting
│   ├── centrality.py        # PageRank computation and boosting
│   ├── graph_expansion.py   # Multi-hop import traversal (BFS)
│   ├── graph_cache.py       # Import graph caching (30-50% faster)
│   ├── fts_setup.py         # Lazy FTS index creation
│   └── reranker.py          # Cohere rerank-v3.5 integration
│
├── parser/                  # AST-Based Code Analysis
│   ├── ast_parser.py        # Tree-sitter import parsing (8 languages)
│   ├── symbol_extractor.py  # Symbol metadata extraction (Python, Go)
│   └── call_extractor.py    # Function call extraction (Python, Go)
│
├── embeddings/              # Multi-Provider Support
│   ├── backend.py           # Provider selection + API key validation
│   ├── provider.py          # Base provider interface (singleton pattern)
│   ├── jina.py              # Jina late chunking implementation
│   ├── mistral.py           # Codestral Embed implementation
│   └── openai.py            # OpenAI embeddings implementation
│
└── storage/                 # Database Layer
    ├── schema.py            # PostgreSQL table definitions
    └── postgres.py          # Connection pooling + query helpers

Search Pipeline

Query → Embedding
         ↓
       [Parallel Search - ThreadPoolExecutor]
       ├─ Vector search (pgvector cosine)
       ├─ BM25 search (PostgreSQL FTS)
       └─ Symbol search (functions/classes)
         ↓
       Reciprocal Rank Fusion (weights: vector=0.6, bm25=0.4, symbol=0.7)
         ↓
       Centrality Boost (PageRank)
         ↓
       Category Boost (impl=1.0, docs=0.7, config=0.6, tests=0.3)
         ↓
       Cohere Rerank (optional)
         ↓
       Aggregate by File (top 3 chunks per file)
         ↓
       Graph Expansion (related files via imports)

Configuration

Embedding Providers

Variable Description
EMBEDDING_PROVIDER jina, mistral, or openai (default: jina)
JINA_API_KEY Jina late chunking - preserves cross-chunk context
USE_LATE_CHUNKING Must be true for Jina selection (default: true)
JINA_MODEL Jina model name (default: jina-embeddings-v3)
MISTRAL_API_KEY Codestral Embed - optimized for code
MISTRAL_EMBED_MODEL Mistral model name (default: codestral-embed)
OPENAI_API_KEY OpenAI embeddings (default fallback)
EMBEDDING_MODEL OpenAI embedding model (default: text-embedding-3-large)
EMBEDDING_DIMENSIONS Embedding dimensions (default: 1024; changing requires re-index)

Search Tuning

Variable Default Description
VECTOR_WEIGHT 0.6 RRF weight for vector search
BM25_WEIGHT 0.4 RRF weight for BM25
SYMBOL_WEIGHT 0.7 RRF weight for symbol search
CENTRALITY_WEIGHT 1.0 PageRank boost (0=disabled)
MAX_GRAPH_HOPS 3 Import traversal depth
MAX_GRAPH_RESULTS 30 Max related files

Indexing

Variable Default Description
CHUNK_SIZE 2000 Characters per chunk
CHUNK_OVERLAP 400 Overlap between chunks
ENABLE_SYMBOL_INDEXING true Index functions/classes

Database Schema

Global Tables (public schema)

repos - Repository metadata

  • Core: id, name, path, status (pending/indexing/ready/failed)
  • Timestamps: created_at, last_indexed
  • Stats: file_count, chunk_count
  • Errors: error_message

{repo}_centrality - PageRank scores (created on demand)

  • filename (PK), score (float)
  • Updated when import graph topology changes

Per-Repository Tables (schema = sanitized repo name)

codeindex_{repo}__{repo}_chunks - CocoIndex-managed chunk store

  • Content: filename, location (char range), content, embedding (vector)
  • Indexes: HNSW on embedding for vector search
  • BM25: content_tsv (tsvector) + GIN index added lazily on first search
  • Managed entirely by CocoIndex (incremental updates, caching)

codeindex_{repo}__cocoindex_tracking - CocoIndex internal state

  • Tracks file hashes, chunk boundaries, and behavior versions for incremental processing
  • Automatically maintained by CocoIndex

{schema}.symbols - Functions/classes/methods

  • Metadata: symbol_name, symbol_type (function/class/method), signature, docstring
  • Location: filename, line_start, line_end (1-indexed, inclusive)
  • Context: parent_symbol, visibility (public/private/internal), category (implementation/test/api/config)
  • Search: embedding (vector) + HNSW, content_tsv (tsvector) + GIN
  • Unique constraint: (filename, symbol_name, line_start) for UPSERT support
  • Timestamps: created_at, updated_at

{schema}.edges - Call graph relationships (experimental)

  • Relationships: source_symbol_id, target_symbol_id, edge_type ('calls', 'implements', etc.)
  • Location: source_file, source_line, target_file, target_line
  • Confidence: 1.0 (exact match), 0.7 (partial), 0.5 (unresolved/external)
  • Context: 'loop', 'conditional', 'recursive', etc.
  • CASCADE deletion when symbols removed

{schema}.graph_cache - Import graph cache

  • filename (PK), imports (JSONB), imported_by (JSONB)
  • Stats: symbol_count, edge_count
  • Invalidated automatically during incremental indexing
  • 30-50% faster graph queries vs. on-the-fly parsing

All table names derived from repository folder name + path hash (to handle duplicates).

Supported Languages

AST-Based Features (Tree-sitter)

Import Parsing + Graph Expansion: Python, Go, Rust, C, C++, JavaScript, TypeScript, TSX

  • Parses import/include statements to build dependency graph
  • Handles dynamic imports, conditional imports, aliased imports
  • Falls back to regex if Tree-sitter unavailable

Symbol Extraction: Python, Go

  • Extracts functions, classes, methods with signatures and docstrings
  • Detects visibility (public/private/internal)
  • Categorizes as implementation/test/api/config
  • Precise line number ranges (1-indexed, inclusive)

Indexed File Types (Chunked + Searchable)

All these extensions are chunked and embedded for semantic + keyword search:

.py .rs .ts .tsx .js .jsx .go .java .cpp .c .h .hpp .rb .php .swift .kt .scala .md .mdx

Files not matching these extensions are ignored during indexing.

Development

Running Tests

# All tests
pytest

# Verbose output with details
pytest -v

# Single test file
pytest tests/test_file_categorizer.py -v

# Single test method
pytest tests/test_file_categorizer.py::TestFileCategorizerDetection::test_python_test_files -v

# Pattern matching
pytest -k "test_python"

# With coverage
pytest --cov=src --cov-report=html

Project Structure Notes

  • Singleton Services: IndexerService and SearchService use singleton pattern to prevent duplicate connections
  • CocoIndex Integration: Chunk storage delegated to CocoIndex; symbol/graph storage managed directly
  • Thread Safety: Uses locks for concurrent search requests
  • Error Handling: Graceful fallbacks when search backends fail (e.g., vector-only if BM25 fails)

Learn More

License

MIT

Questions or issues? Open an issue on GitHub.

About

A codebase indexing mcp server based on Cocoindex.

Resources

Readme

License

MIT license
Activity

Stars

4 stars

Watchers

0 watching

Forks

0 forks
Report repository

Releases 3

v0.1.2 Latest
Jan 22, 2026
+ 2 releases

Packages

 
 
 

Contributors

Languages