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graphify

Memory server

First committed by safishamsi

Published in Graphify-Labs/graphify. Publisher page

145,900 GitHub stars

What it is

Turn any codebase, with its docs, SQL schemas, configs, and PDFs, into a queryable knowledge graph. A /graphify skill for Claude Code, Cursor, Codex, and Gemini CLI: local deterministic AST parsing, every edge explained, no vector store.
— the description by safishamsi

AutoGineer overview, from the brain’s own files

Graphify transforms complex codebases, documentation, and various file formats into a structured knowledge graph. Unlike traditional RAG systems that rely on vector embeddings, Graphify uses deterministic AST parsing via tree-sitter to map code relationships, ensuring high accuracy and transparency. It provides agents with a bird's-eye view of the project, enabling them to query specific concepts, trace paths between components, and understand system architecture without the overhead of re-reading files or relying on probabilistic vector searches. The system supports a wide range of AI coding assistants and can be extended with Graphify Cloud for continuous, cross-repo monitoring and formal verification.

How it works

Memory model: Hybrid

AutoGineer overview, from the brain’s own files

Graphify installs as a skill within your AI coding assistant. It parses your project files using tree-sitter to create a deterministic knowledge graph. Code relationships like imports, calls, and inheritance are extracted directly from the source code. For non-code assets like PDFs or documentation, it performs a semantic pass. The resulting graph is stored locally as a JSON file, which the agent can then query to explain concepts or find paths between nodes. Every connection in the graph is tagged as either explicitly extracted from the source or inferred by the system.

Folders
FolderRoleFiles
.githubagent-config13
docsdocs44
scriptsscripts1
teststests684
toolsscripts176
graphifyfolder236
workedfolder36

The agent reads

The agent writes

Requirements

Runtimes: Python >=3.10,<3.15

Databases: FalkorDB, Neo4j, PostgreSQL, SQLite

API keys (by name): ANTHROPIC_API_KEY, AZURE_OPENAI_API_KEY, DEEPSEEK_API_KEY, GEMINI_API_KEY, GOOGLE_API_KEY, MOONSHOT_API_KEY, OPENAI_API_KEY

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Google Antigravity, Kiro, OpenCode, Amp, Roo Code, Cline, JetBrains Junie, Devin (ex-Windsurf)

Set it up

  1. This brain runs code automatically: 3 scripts. Review README.md, graphify/install.py before opening the folder in Claude Code. No step below turns a hook on for you.

    • README.md: | uv *(recommended)* | any | `uv --version` | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
    • README.md: curl -LsSf https://astral.sh/uv/install.sh | sh
    • graphify/install.py: python graphify/install.py
  2. Not scanned by AutoGineerIts dependencies are installed by pip or uv when you run it and were not scanned by AutoGineer (31 declared). https://pypi.org/project/graphifyy/
  3. First committed by safishamsi. Published in Graphify-Labs/graphify. Licence: Apache License 2.0.

Usage

AutoGineer overview, from the brain’s own files

  • Querying the graph to explain specific code components.
  • Tracing the shortest path between two disparate code modules.
  • Identifying 'god nodes' or central concepts within a codebase.
  • Generating a high-level report of key concepts and connections.
  • Updating the graph incrementally after code changes.
  • Integrating with AI agents to reduce token usage by querying the graph instead of reading files.
“/graphify explain "APIRouter"”
Returns the node details for APIRouter, including its source location, community, degree, and all explicit or inferred connections.
“/graphify path "FastAPI" "ModelField"”
Displays the shortest path between the two nodes, showing the intermediate hops and the overall confidence of the path.

Documentation by safishamsi

<p align="center"> <a href="https://graphify.com"><img src="https://raw.githubusercontent.com/Graphify-Labs/graphify/v8/docs/graphify-logo.png" width="360" height="189" alt="Graphify"/></a> </p>

<p align="center"> <a href="https://trendshift.io/repositories/25296?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-25296" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/25296" alt="Graphify-Labs%2Fgraphify | Trendshift" width="250" height="55"/></a> </p>

<div align="center"> <details><summary><b>Read this in other languages</b></summary>

<a href="README.md">English</a> | <a href="docs/translations/README.zh-CN.md">简体中文</a> | <a href="docs/translations/README.ja-JP.md">日本語</a> | <a href="docs/translations/README.ko-KR.md">한국어</a> | <a href="docs/translations/README.de-DE.md">Deutsch</a> | <a href="docs/translations/README.fr-FR.md">Français</a> | <a href="docs/translations/README.es-ES.md">Español</a> | <a href="docs/translations/README.hi-IN.md">हिन्दी</a> | <a href="docs/translations/README.pt-BR.md">Português</a> | <a href="docs/translations/README.ru-RU.md">Русский</a> | <a href="docs/translations/README.ar-SA.md">العربية</a> | <a href="docs/translations/README.fa-IR.md">فارسی</a> | <a href="docs/translations/README.it-IT.md">Italiano</a> | <a href="docs/translations/README.pl-PL.md">Polski</a> | <a href="docs/translations/README.nl-NL.md">Nederlands</a> | <a href="docs/translations/README.tr-TR.md">Türkçe</a> | <a href="docs/translations/README.uk-UA.md">Українська</a> | <a href="docs/translations/README.vi-VN.md">Tiếng Việt</a> | <a href="docs/translations/README.id-ID.md">Bahasa Indonesia</a> | <a href="docs/translations/README.sv-SE.md">Svenska</a> | <a href="docs/translations/README.el-GR.md">Ελληνικά</a> | <a href="docs/translations/README.ro-RO.md">Română</a> | <a href="docs/translations/README.cs-CZ.md">Čeština</a> | <a href="docs/translations/README.fi-FI.md">Suomi</a> | <a href="docs/translations/README.da-DK.md">Dansk</a> | <a href="docs/translations/README.no-NO.md">Norsk</a> | <a href="docs/translations/README.hu-HU.md">Magyar</a> | <a href="docs/translations/README.th-TH.md">ภาษาไทย</a> | <a href="docs/translations/README.uz-UZ.md">Oʻzbekcha</a> | <a href="docs/translations/README.zh-TW.md">繁體中文</a> | <a href="docs/translations/README.fil-PH.md">Filipino</a> | <a href="docs/translations/README.he-IL.md">עברית</a>

</details> </div>

<p align="center"> <a href="https://pypi.org/project/graphifyy/"><img src="https://img.shields.io/pypi/v/graphifyy" alt="PyPI"/></a> <a href="https://github.com/Graphify-Labs/graphify/actions/workflows/ci.yml"><img src="https://github.com/Graphify-Labs/graphify/actions/workflows/ci.yml/badge.svg?branch=v8" alt="CI"/></a> <a href="LICENSE"><img src="https://img.shields.io/badge/License-Apache%202.0-blue" alt="License: Apache-2.0"/></a> <a href="https://pepy.tech/project/graphifyy"><img src="https://img.shields.io/pepy/dt/graphifyy?color=blue&label=downloads" alt="Downloads"/></a> <a href="https://docs.graphify.com"><img src="https://img.shields.io/badge/Docs-docs.graphify.com-0b7285?style=flat&logo=readthedocs&logoColor=white" alt="Docs"/></a> <a href="https://app.graphify.com/login"><img src="https://img.shields.io/badge/Graphify%20Cloud-app.graphify.com-118d4f?style=flat&logoColor=white" alt="Graphify Cloud"/></a> <a href="https://discord.gg/graphify"><img src="https://img.shields.io/badge/Discord-Join-5865F2?style=flat&logo=discord&logoColor=white" alt="Discord"/></a> <a href="https://www.youtube.com/@graphifylabs"><img src="https://img.shields.io/badge/YouTube-Graphify%20Labs-FF0000?style=flat&logo=youtube&logoColor=white" alt="YouTube"/></a> <a href="https://www.linkedin.com/company/graphify-labs"><img src="https://img.shields.io/badge/LinkedIn-Graphify%20Labs-0077B5?logo=linkedin" alt="LinkedIn"/></a> <a href="https://www.ycombinator.com/companies/graphify-labs"><img src="https://img.shields.io/badge/Y%20Combinator-S26-F0652F?style=flat&logo=ycombinator&logoColor=white" alt="YC S26"/></a> </p>

<p align="center"> <b>Cut agent token spend by 80%.</b> Graphify Cloud is always-on memory that governs your agents, keeps code quality high, and proves correctness with formal verification. <a href="https://app.graphify.com/login"><b>Start a free 14-day trial &rarr;</b></a> </p>

Type /graphify in your AI coding assistant and it maps your entire project (code, docs, PDFs, images, videos) into a knowledge graph you can query instead of grepping through files.

  • Code maps for free, fully local. Code is parsed with tree-sitter AST: deterministic, no LLM, nothing leaves your machine. (Docs, PDFs, images and video use your assistant's model, or a configured API key, for a semantic pass.)

  • Every edge is explained. Each connection is tagged EXTRACTED (explicit in the source) or INFERRED (resolved by graphify), so you can tell what was read directly from what was inferred.

  • Not a vector index. No embeddings, no vector store: a real graph you traverse. Ask a question, trace the path between two things, or explain one concept.

NOTE
Want this always-on? Graphify Cloud keeps the graph live across your entire SDLC: monorepo and cross-repo support, formal verification, and code review with a bird's-eye view of your SDLC, plus connectors for Sentry, Jira, and more so incidents and tickets sit in the same graph as your code. Start a free 14-day trial at app.graphify.com.

<p align="center"> <img src="https://raw.githubusercontent.com/Graphify-Labs/graphify/v8/docs/graph-hero.png" alt="graphify's interactive graph.html showing the FastAPI codebase as a force-directed knowledge graph with a legend of detected communities" width="900"> </p> <p align="center"> <em>The FastAPI codebase mapped by graphify. Every node is a concept, colors are detected communities, and the whole thing is clickable in graph.html.</em> </p>

Get started (30 seconds). Needs Python 3.10+ and uv (or pipx):

uv tool install graphifyy      # install the CLI (or: pipx install graphifyy)
graphify install               # detects your assistant and registers the skill

Then, in your AI assistant:

/graphify .

That's it. You get three files:

graphify-out/
├── graph.html       open in any browser: click nodes, filter, search
├── GRAPH_REPORT.md  the highlights: key concepts, surprising connections, suggested questions
└── graph.json       the full graph: query it anytime without re-reading your files

The persisted graph includes graph.schema_version so integrations can detect incompatible format changes, plus graph.graphify_version identifying the Graphify release that produced it.

One install, any assistant, any OS. Claude Code, Cursor, Codex, Gemini CLI, GitHub Copilot, and 20+ more, on macOS, Linux, and Windows: pick your platform.


See it in action

<p align="center"> <img src="https://raw.githubusercontent.com/Graphify-Labs/graphify/v8/docs/demo-path.svg" alt="graphify path query: a terminal asks for the shortest path between FastAPI and ModelField, and the answer lights up hop by hop across the knowledge graph" width="900"> </p>

Once the graph is built you query it instead of reading files. Real output, graphify run on the FastAPI codebase shown above:

$ graphify explain "APIRouter"
Node: APIRouter
  Source:    routing.py L2210
  Community: 2
  Degree:    47

Connections (47):
  --> RequestValidationError [uses] [INFERRED]
  --> Dependant [uses] [INFERRED]
  --> .get() [method] [EXTRACTED]
  <-- __init__.py [imports] [EXTRACTED]
  ...

$ graphify path "FastAPI" "ModelField"
Shortest path (3 hops):
  FastAPI --uses--> DefaultPlaceholder <--references-- get_request_handler() --references--> ModelField

Every edge carries a confidence tag (EXTRACTED = explicit in the source, INFERRED = derived by resolution), so you can tell what was read directly from what was inferred. graphify query "<question>" returns a scoped subgraph for a plain-language question, and graphify path A B traces how any two things connect, ending with the path's overall confidence: that of its weakest hop.


What it does

What you get out of the box:

CapabilityWhat you get
God nodesThe most-connected concepts, so you see what everything flows through
CommunitiesThe graph split into subsystems (Leiden), with LLM-free labels
Cross-file linkscalls / imports / inherits / mixes_in resolved across ~40 languages via tree-sitter AST
Query, path, explainAsk a question, trace the path between two things, or explain one concept, all against graph.json
Rationale + doc refs# NOTE: / # WHY: comments and ADR/RFC citations become first-class nodes linked to the code
Beyond codeDocs, PDFs, images, and video/audio all map into the same graph
Local-firstCode is parsed locally with tree-sitter (no LLM, nothing leaves your machine); only the semantic pass over docs/media calls a backend, and only if you configure one

TIP
Running this across many repos or a monorepo? Graphify Cloud does it continuously and cuts agent token spend by 80%, with cross-repo links, SDLC-wide code review, formal verification, and Sentry/Jira connectors. Start a free 14-day trial &rarr;


Benchmarks: 0.497 recall@10, 0 LLM credits

BenchmarkMetricgraphifyField
LOCOMO (n=300)recall@100.497mem0 0.048, supermemory 0.149
LOCOMO (n=300)QA accuracy45.3%supermemory 49.7%, mem0 27.3%
LongMemEval-S (n=50)QA accuracy76%tied with dense RAG
ERPNext cross-tool (n=6)key-fact coverage82.0%grep/read baseline 70.8%
Graph buildLLM credits0per-token for most systems

Every system ran on the same harness with the same model and budgets, scored by a judge blind-validated against a second judge (90.6% agreement, Cohen's kappa 0.81). Full per-system tables, the code-intelligence result, and reproduction commands: BENCHMARKS.md.


Documentation

Full guides and reference live at docs.graphify.com:


Prerequisites

RequirementMinimumCheckInstall
Python3.10+python --versionpython.org
uv (recommended)anyuv --versioncurl -LsSf https://astral.sh/uv/install.sh | sh
pipx (alternative)anypipx --versionpip install pipx

macOS quick install (Homebrew):

brew install [email protected] uv

Windows quick install:

winget install astral-sh.uv

Ubuntu/Debian:

# uv manages its own Python, so this is the only step you need:
curl -LsSf https://astral.sh/uv/install.sh | sh
# or use the system Python with pipx:
sudo apt install python3 python3-pip pipx

Install

IMPORTANT
Official package: The PyPI package is graphifyy (double-y). Other graphify* packages on PyPI are not affiliated. The CLI command is still graphify.

The official source repository is Graphify-Labs/graphify.

The two-command quickstart is at the top of this README. This section covers the install methods, project-scoped installs, and every supported platform.

Install methods (pick one):

uv tool install graphifyy   # recommended, isolated env (if 'graphify' isn't found after, run: uv tool update-shell)
pipx install graphifyy      # alternative
pip install graphifyy       # may need PATH setup, see Troubleshooting below

Then run graphify install once. It detects which assistant you run and registers the skill, so there is no per-assistant setup. Open your AI assistant and type /graphify .

To install the assistant skill into the current repository instead of your user profile, add --project:

graphify install --project
graphify install --project --platform codex

Project-scoped installs write under the current directory, for example .claude/skills/graphify/SKILL.md or .agents/skills/graphify/SKILL.md (plus a references/ sidecar the skill loads on demand), and print a git add hint for files that can be committed. Per-platform commands that support project-scoped installs accept the same flag, for example graphify claude install --project or graphify codex install --project.

TIP
Hitting command not found, a pip-on-Mac/Windows issue, PowerShell quoting, uvx usage, git-hook PATH quirks, or strict mode? See Installation and Troubleshooting.

<details> <summary><b>Pick your platform</b> (20+ assistants, click to expand)</summary>

PlatformInstall command
Claude Code (Linux/Mac)graphify install
Claude Code (Windows)graphify install (auto-detected) or graphify install --platform windows
CodeBuddygraphify install --platform codebuddy
Codexgraphify install --platform codex
OpenCodegraphify install --platform opencode
Kilo Codegraphify install --platform kilo
GitHub Copilot CLIgraphify install --platform copilot
VS Code Copilot Chatgraphify vscode install
Aidergraphify install --platform aider
OpenClawgraphify install --platform claw
Factory Droidgraphify install --platform droid
Traegraphify install --platform trae
Trae CNgraphify install --platform trae-cn
Gemini CLIgraphify install --platform gemini
Hermesgraphify install --platform hermes
Kimi Codegraphify install --platform kimi
Ampgraphify amp install
Agent Skills (cross-framework)graphify install --platform agents (alias --platform skills)
Kiro IDE/CLIgraphify kiro install
Pi coding agentgraphify install --platform pi, plus graphify pi guard install for the native guard
Cursorgraphify cursor install
Devin CLIgraphify devin install
Google Antigravitygraphify antigravity install
Google Antigravity (Windows)graphify antigravity install (auto-detected on Windows)

Codex users also need multi_agent = true under [features] in ~/.codex/config.toml for parallel extraction. CodeBuddy uses the same Agent tool and PreToolUse hook mechanism as Claude Code. Factory Droid uses the Task tool for parallel subagent dispatch. OpenClaw and Aider use sequential extraction (parallel agent support is still early on those platforms). Trae uses the Agent tool for parallel subagent dispatch and does not support PreToolUse hooks, so AGENTS.md is the always-on mechanism.

--platform agents (alias --platform skills) targets the generic cross-framework Agent-Skills locations: the spec's user-global ~/.agents/skills/ (read by npx skills and spec-compliant frameworks) for a global install, and ./.agents/skills/ for a project (--project) install. The bare graphify install stays single-platform (Claude Code) by design: use the named agents platform when you want the skill discoverable by any framework that reads .agents/skills.

Claude Code's graphify install --project --strict makes Read and dedicated Grep share one denial per session unless a recent graph query has oriented the agent (default 30 minutes). A Grep over a directory needs no indexed-file match; a Grep pinned to a single file is denied only when the graph indexes that file, as with Read. External and graph-output Grep targets produce neither a deny nor a nudge, in soft mode as well as strict mode, matching Read's scope. A graph marked needs_update never triggers a Grep denial. Bash searches and Glob stay advisory. GRAPHIFY_HOOK_STRICT=1 enables the policy without reinstalling; GRAPHIFY_HOOK_STRICT=0 disables it even when installed with --strict. Existing strict installs need a reinstall to add the search hook's --strict flag, or the environment override. Soft nudges are capped per session (GRAPHIFY_HOOK_NUDGE_CAP, default 5). After a context compaction, a SessionStart hook (matcher compact) resets that budget, the subagents' budgets and the strict denial, since the compacted context no longer holds the earlier nudges.

Pi has no PreToolUse hook, so graphify pi guard install registers a native Pi extension (via Pi's own pi install <package directory>) that runs the installed graphify hook-guard before Pi's read, grep, find and search-style bash calls. Fresh/stale graph decisions and the GRAPHIFY_HOOK_STRICT=1 once-per-session denial shared by indexed Read and dedicated Grep come from that same policy, so Pi matches Claude Code's hook behavior; Bash and file listing remain advisory. Guidance arrives as a <system-reminder source="graphify"> steering message. It needs Pi 0.58.4 or newer: earlier versions let a steering message skip the rest of a parallel tool-call batch. The package ships inside the Graphify installation, so install Graphify persistently (uv tool install graphifyy or pipx install graphifyy, not uvx), restart Pi after installing or upgrading, and remove it with graphify pi guard uninstall. Only local file targets are inspected; the hook needs graphify on an absolute PATH entry outside the project, is bounded to a two-second, 256 KiB-in/64 KiB-out call, and fails open. The same package also loads in Oh My Pi: omp plugin install "$(graphify pi guard path)". The registered path contains the Python version and venv, so re-run graphify pi guard install after changing either, and remove the old entry with pi remove <old path>.

Codex uses $graphify instead of /graphify.

</details>

<details> <summary><b>Optional extras</b> (install only what you need)</summary>

ExtraWhat it addsInstall
pdfPDF extractionuv tool install "graphifyy[pdf]"
office.docx and .xlsx supportuv tool install "graphifyy[office]"
googleGoogle Sheets renderinguv tool install "graphifyy[google]"
videoVideo/audio transcription (faster-whisper + yt-dlp)uv tool install "graphifyy[video]"
mcpMCP stdio serveruv tool install "graphifyy[mcp]"
watchAuto-rebuild on file changes (graphify watch)uv tool install "graphifyy[watch]"
neo4jNeo4j push supportuv tool install "graphifyy[neo4j]"
falkordbFalkorDB push supportuv tool install "graphifyy[falkordb]"
svgSVG graph exportuv tool install "graphifyy[svg]"
leidenLeiden community detection (graspologic on Python < 3.13; native backend on 3.13+)uv tool install "graphifyy[leiden]"
ollamaOllama local inferenceuv tool install "graphifyy[ollama]"
openaiOpenAI / OpenAI-compatible APIsuv tool install "graphifyy[openai]"
geminiGoogle Gemini APIuv tool install "graphifyy[gemini]"
anthropicAnthropic Claude API (--backend claude, uses ANTHROPIC_API_KEY)uv tool install "graphifyy[anthropic]"
bedrockAWS Bedrock (uses IAM, no API key)uv tool install "graphifyy[bedrock]"
azureAzure OpenAI Service (--backend azure, uses AZURE_OPENAI_API_KEY + AZURE_OPENAI_ENDPOINT)uv tool install "graphifyy[openai]"
sqlSQL schema extractionuv tool install "graphifyy[sql]"
postgresLive PostgreSQL introspection (--postgres DSN)uv tool install "graphifyy[postgres]"
dmBYOND DreamMaker .dm/.dme AST extraction (may need a C compiler + python3-dev if no wheel matches your platform)uv tool install "graphifyy[dm]"
terraformTerraform / HCL .tf/.tfvars/.hcl AST extractionuv tool install "graphifyy[terraform]"
pascalPascal / Delphi .pas/.dpr/.dpk/.inc AST extraction (more accurate calls/inherits edges; falls back to a regex extractor when absent)uv tool install "graphifyy[pascal]"
ocamlOCaml .ml/.mli AST extractionuv tool install "graphifyy[ocaml]"
commonlispCommon Lisp .lisp/.cl/.lsp/.asd AST extractionuv tool install "graphifyy[commonlisp]"
robotRobot Framework .robot/.resource extraction (suites, test cases, keywords, keyword-call and resource/library import edges)uv tool install "graphifyy[robot]"
chineseChinese query segmentation (jieba)uv tool install "graphifyy[chinese]"
allEverything aboveuv tool install "graphifyy[all]"

</details>


Make your assistant always use the graph

Run this once in your project after building a graph:

Run graphify <platform> install once in your project, for example graphify claude install or graphify codex install (or graphify install --platform <name>).

This writes a small config file that tells your assistant to consult the knowledge graph for codebase questions, preferring scoped queries like graphify query "<question>" over reading the full report or grepping raw files.

  • Hook platforms (Claude Code, Gemini CLI): a hook fires automatically before search-style tool calls (and, on Claude Code, before reading source files one by one via the Read/Glob tools, or via cat, head, tail, sed -n and similar readers in Bash) and nudges your assistant toward the graph path.

  • Instruction-file platforms (Codex, OpenCode, Cursor, etc.): persistent instruction files (AGENTS.md, .cursor/rules/, etc.) provide the same query-first guidance.

GRAPH_REPORT.md is still available for broad architecture review.

Exactly which files each platform writes (CodeBuddy's CODEBUDDY.md + PreToolUse hooks, Codex's AGENTS.md, Kilo's native .kilo plugin, Cursor's alwaysApply rule, and so on) is covered in Always-on setup.

To remove graphify from all platforms at once: graphify uninstall (add --purge to also delete graphify-out/). Or use the per-platform command (e.g. graphify claude uninstall).

CLI skills or MCP instructions?

The instructions installed by graphify install and those supplied with a Graphify MCP connection describe different ways to query a graph:

SetupGuidance to useQuery access
Local CLI and installed assistant skillThe platform instructions written by graphify installRun graphify query, graphify path, and graphify explain against the local graph (graphify-out/ by default).
Connected Graphify MCP serverThe connection's instructions and the tools listed by that serverCall the listed MCP tools against the graph served by that connection. Tool names and descriptions come from the server.

Both encourage scoped graph queries before broad source searches. Choose the instructions that match the tools your assistant can actually access; neither block establishes a universal precedence rule for your assistant's instruction files. If you use both integrations, identify which graph each queries and choose a primary query path instead of copying two unconditional instruction blocks into AGENTS.md.

graphify install installs the local assistant integration; it does not establish an MCP connection. An MCP client does not need to run local CLI queries to use its connected server. A locally hosted server still needs its own Graphify installation and graph, while a hosted connection may serve a graph that is not present in the client's working directory. If the expected tools are missing, check the relevant CLI installation or MCP connection rather than treating the other setup's instructions as interchangeable.


What's in the report

GRAPH_REPORT.md summarizes the god nodes, communities, and key paths for broad architecture review. How the graph is built and what it contains: How graphify works.


What files it handles: ~40 languages

graphify parses ~40 programming languages locally with tree-sitter AST, and maps docs, PDFs, images, and audio/video through an optional semantic pass. Full list: Supported inputs.


Common commands

/graphify .                        # build graph for current folder
/graphify ./docs --update          # re-extract only changed files
/graphify . --cluster-only         # rerun clustering without re-extracting
/graphify . --cluster-only --resolution 1.5      # more granular communities
/graphify . --cluster-only --exclude-hubs 99     # suppress utility super-hubs from god-node rankings
/graphify . --no-viz               # skip the HTML, just the report + JSON
/graphify . --wiki                 # build a markdown wiki from the graph
graphify export callflow-html      # Mermaid architecture/call-flow HTML (auto-regenerates on every git commit if hook is installed)

/graphify query "what connects auth to the database?"
/graphify path "UserService" "DatabasePool"
/graphify explain "RateLimiter"

/graphify add https://arxiv.org/abs/1706.03762   # fetch a paper and add it
/graphify add <youtube-url>                       # transcribe and add a video

graphify hook install              # auto-rebuild on commit + branch checkout (run `graphify update .` after `git pull`: see "Recommended workflow" below)
graphify merge-graphs a.json b.json              # combine two graphs

graphify prs                       # PR dashboard: CI state, review status, worktree mapping
graphify prs 42                    # deep dive on PR #42 with graph impact
graphify prs --triage              # AI ranks your review queue (uses whatever backend is configured)
graphify prs --conflicts           # PRs sharing graph communities: merge-order risk

See the full command reference below.


Labeling and rendering limits

  • --batch-size: 100 communities per labeling call by default, sized for a ~16k-token context (~150 tokens/community). Use --batch-size 40 for an 8k window. Context overflow is not split-retried; failed batches keep hub-derived names.

  • --missing-only: label --missing-only keeps existing labels and names only unnamed / Community N entries. Use label (full relabel) to refresh names after the community set changes.

  • .graphify_labels.json.sig: records the community membership signature; labels survive a re-cluster only while it matches.

  • export html: 5,000-node default; above it graphify renders an aggregated community view. Use --node-limit N. GRAPHIFY_VIZ_NODE_LIMIT / .graphifyrc viz_node_limit=N apply to cluster-only, update, watch, and hooks, not export html.

  • Leiden fallback: without the leiden extra, clustering silently uses networkx Louvain. Switching later reshuffles every community, so plan a full relabel.


Ignoring files

graphify honors .gitignore and supports --exclude patterns and a project .graphifyignore. Details: Configuration.

graphify extract reports paths skipped by ignore rules, with up to three sorted examples relative to the scan root. Each pruned directory counts once; its contents are not enumerated. Default noise directories such as node_modules are excluded from this summary. If source is missing, review the ignore rules. --no-gitignore bypasses VCS ignore rules only; .graphifyignore and --exclude remain effective.

Project configuration

Create a .graphifyrc in the scan root for settings that belong to the project rather than to one run. One key=value per line; lines beginning with # are comments.

Ambiguous extensions. Some extensions mean different languages in different projects: .inc is PHP on pfSense, Pascal in a Delphi tree, SQL or assembly elsewhere; .h is C or C++; .m is Objective-C or MATLAB. graphify has to pick one global default, and when it picks wrong the file does not fail: it parses as the wrong language and yields a handful of incidental nodes, so the graph looks populated while the real symbols are missing. Declare what the extension means in your repo:

# .graphifyrc
# A language name:
language.inc=php
# Or an extension graphify already knows:
language.tpl=.ts
# Baked into the git hooks (see Team setup):
viz_node_limit=0

The declaration flows through classification, extractor selection, grammar and resolution, imports, graphify watch, and the AST cache (a file re-parsed under a different language never reuses the old entry), and the same .graphifyrc is read by extract, update, the hooks, the MCP server, and the /graphify skill. A typo is reported once on stderr and the scan continues with the defaults. How declarations interact with caching, incremental rebuilds, and import resolution: Configuration.

Query defaults. Set query_budget to a positive integer and query_depth to an integer from 1 to 6:

query_budget=4000
query_depth=3

For graphify query, explicit --budget N / --budget=N and --depth N / --depth=N override these settings independently. Without a project setting or explicit option, the defaults remain budget 2000 and depth 2. These keys do not change the MCP server's defaults.

Settings come from the project owning the selected --graph, even when the command runs from another directory. An existing absolute directory in the graph's sibling .graphify_root marker identifies that project. Otherwise a matching relative GRAPHIFY_OUT suffix identifies it; absolute, empty, traversal-containing or nonmatching output paths fall back to the graph file's directory. Relative markers are ignored.

The query command always reads that project's .graphifyrc. An invalid recognized setting or an unreadable file produces one stderr warning and discards all project settings for that query; explicit options still apply. The settings parser stays strict for its other callers. Existing explicit budget values retain their behavior; persisted query_budget values must be positive.


Team setup

Commit or share the graph so your whole team queries the same context, and review pull requests with graph context. See Share context with your team and Review pull requests.


Using the graph directly

Beyond your AI assistant, query graph.json straight from the CLI with graphify query, graphify path, and graphify explain. A name that matches several nodes is refused with the candidates listed rather than guessed. Scripts can read the outcome from the exit code: 0 an answer, 3 an ambiguous name, 4 no matching node. See Ask better graph questions and the query reference.


Environment variables

Backends, API keys, hook behavior, and tuning are controlled by environment variables. Full table: Configuration.

  • Claude API prompt caching: GRAPHIFY_CLAUDE_PROMPT_CACHE controls system-prompt caching for --backend claude. Unset or blank keeps caching enabled; 1, true, yes, or on explicitly enables it, and 0, false, no, or off disables it (case-insensitive, surrounding whitespace ignored). Invalid values raise an error before sending a request. For example, run GRAPHIFY_CLAUDE_PROMPT_CACHE=0 graphify extract . --backend claude when an Anthropic-compatible endpoint rejects cache_control. Disabling sends the original plain-text system prompt. The setting applies equally to official Anthropic and custom ANTHROPIC_BASE_URL / ANTHROPIC_MODEL endpoints, including deep mode; it does not affect Bedrock, Claude CLI, or Graphify's local extraction cache. Enabling requests caching but cannot guarantee cache hits: the endpoint/model must support it and the prompt must meet its minimum length. Unsupported caching errors are not silently retried without caching.

  • Claude CLI model: GRAPHIFY_CLAUDE_CLI_MODEL overrides the model for the claude-cli backend (default: Opus). haiku or sonnet are usually enough for community naming; the semantic extraction pass benefits from a larger model.


Privacy

  • Code files: processed locally via tree-sitter. Nothing leaves your machine. A code-only corpus requires no API key: graphify extract runs fully offline. On a mixed repo, add --code-only to index just the code and skip the docs/PDFs/images that would otherwise need an LLM.

  • Video / audio: transcribed locally with faster-whisper. Nothing leaves your machine.

  • Docs, PDFs, images: sent to your AI assistant for semantic extraction (via the /graphify skill, using whatever model your IDE session runs). Headless graphify extract requires GEMINI_API_KEY / GOOGLE_API_KEY (Gemini), MOONSHOT_API_KEY (Kimi), ANTHROPIC_API_KEY (Claude), OPENAI_API_KEY (OpenAI), DEEPSEEK_API_KEY (DeepSeek), a running Ollama instance (OLLAMA_BASE_URL), AWS credentials via the standard provider chain (Bedrock - no API key needed, uses IAM), or the claude CLI binary (Claude Code - no API key needed, uses your Claude subscription). The --dedup-llm flag uses the same key.

  • Data residency: graphify extract auto-detects which provider to use based on which API key is set (priority: Gemini → Kimi → Claude → OpenAI → DeepSeek → Azure → Bedrock → Ollama). When it auto-detects, it prints the exact environment variable that chose the provider, so a run is never a surprise. To choose explicitly, pass --backend, or set GRAPHIFY_BACKEND=<name>; set GRAPHIFY_BACKEND=none to disable all LLM backends (semantic extraction and the claude -p labeling fallback) and keep a code-only graph. For code with data-residency requirements, use GRAPHIFY_BACKEND=ollama / --backend ollama (fully local). Kimi (MOONSHOT_API_KEY) routes to Moonshot AI servers in China.

  • No telemetry, no usage tracking, no analytics.

  • Query logging: every graphify query, graphify path, graphify explain, and MCP query_graph call is logged to ~/.cache/graphify-queries.log in JSON Lines format (timestamp, question, corpus, nodes returned, duration). Full subgraph responses are not stored by default. Set GRAPHIFY_QUERY_LOG_DISABLE=1 to opt out, or GRAPHIFY_QUERY_LOG=/dev/null to silence without disabling the code path.


Troubleshooting

Common install and extraction issues and their fixes: Troubleshooting.


Full command reference

Every command and flag, with examples: CLI reference.


Learn more


Graphify Cloud

Graphify Cloud is the always-on layer built on top of graphify. Instead of a graph you rebuild on demand per folder, it keeps one live graph across your entire software development lifecycle:

  • 80% fewer tokens: always-on memory means your agents stop re-reading and re-explaining the codebase every session.

  • Monorepo and cross-repo: one connected graph across every service and repository, not a graph per folder.

  • Formal verification: check architectural and dependency invariants against the live graph.

  • Code review with a bird's-eye view of your SDLC: see how a change ripples across the whole system before you merge.

  • SDLC connectors: pull in Sentry, Jira, and more, so incidents, tickets, and code live in one graph.

  • Always-on: updates continuously in the background across code, docs, and meetings.

Start a free 14-day trial at app.graphify.com &rarr;


Contributing

Contributions are welcome. See CONTRIBUTING.md for the development setup, the test and CI-parity commands, the git workflow, and what makes a strong contribution (worked examples and extraction bug reports are the most useful). Architecture and how to add a language: ARCHITECTURE.md.

New here? Say hi on Discord or in GitHub Discussions.


Contributors

<a href="https://github.com/Graphify-Labs/graphify/graphs/contributors"> <img src="https://contrib.rocks/image?repo=Graphify-Labs/graphify" alt="graphify contributors" /> </a>

Made with contrib.rocks.


Translations

The README is available in 32 languages. Use the language switcher at the top of this file to read it in yours, or browse docs/translations/. To improve a translation or add a new one, open a pull request against the matching file there.


Building on graphify

Building something in the graphify ecosystem? That is encouraged. If your project uses "graphify" in its name (for example graphify-dashboard or graphify-action), please add a short note to your README clarifying that it is community-built and not affiliated with or endorsed by Graphify Labs. "graphify" and the graphify logo are marks of Graphify Labs; please do not use them in a way that implies official status.


<p align="center"> <a href="https://graphify.com"><img src="https://img.shields.io/badge/Website-graphify.com-4c1?style=flat&logo=googlechrome&logoColor=white" alt="Website"/></a> <a href="https://discord.gg/graphify"><img src="https://img.shields.io/badge/Discord-Join-5865F2?style=flat&logo=discord&logoColor=white" alt="Discord"/></a> <a href="https://x.com/graphify"><img src="https://img.shields.io/badge/X-graphify-000000?logo=x&logoColor=white" alt="X"/></a> <a href="https://www.youtube.com/@graphifylabs"><img src="https://img.shields.io/badge/YouTube-Graphify%20Labs-FF0000?style=flat&logo=youtube&logoColor=white" alt="YouTube"/></a> <a href="https://github.com/sponsors/safishamsi"><img src="https://img.shields.io/badge/sponsor-safishamsi-ea4aaa?logo=github-sponsors" alt="Sponsor"/></a> <a href="https://safishamsi.gumroad.com/l/qetvlo"><img src="https://img.shields.io/badge/Book-The%20Memory%20Layer-2ea44f?style=flat&logo=gitbook&logoColor=white" alt="The Memory Layer"/></a> </p>

CONTRIBUTING.md

Contributing to Graphify

Graphify is a graph-building system whose correctness depends on preserving provenance, deterministic extraction, and safe incremental updates. A contribution is not complete because the new code works on the happy path; it is complete when the relevant invariant is explicit, tested, and preserved across rebuilds.

Before You Start

  • Read ARCHITECTURE.md

  • Read SECURITY.md when relevant

  • Understand v8 is the active development branch

  • Use graphify-out/GRAPH_REPORT.md for repository orientation

What We Value

  1. Preserve correctness, not merely successful execution. A failed, partial, smaller, or differently keyed extraction must not overwrite valid persisted state or poison incremental caches.

  2. Preserve provenance; incidental richness is not evidence. A real source-backed record must not lose to a richer sourceless stub. A location without a corresponding source file is not sufficient provenance.

  3. Keep deterministic extraction deterministic. AST extraction, symbol identity, traversal order, merge behavior, and other structural passes must not depend on filesystem ordering, ambient environment state, network calls, or nondeterministic model output.

  4. Keep inference visibly separate from extracted fact. Never turn uncertainty into false certainty just because a richer result looks better. Preserve the distinction between extracted fact, inference, and ambiguity.

  5. Prefer fail-closed behavior over guessed relationships.

  6. Treat persistent graph/cache state as data that can be corrupted.

  7. Make bug fixes prove the old failure with a regression test. Demonstrate the old failure, not merely exercise the new code.

  8. Keep PRs narrow and reviewable. Small, auditable diffs beat clever broad fixes.

  9. Document heuristic boundaries and unsupported cases.

  10. Never hand-edit generated artifacts. Edit the source fragment, run the generator, and run the corresponding verification checks.

  11. Do not let ambient environment state affect tests. Tests must be deterministic with respect to the contributor's shell environment.

  12. Treat paths, source text, model output, URLs, and generated commands as untrusted. Never construct shell commands or Python source by interpolating free text.

  13. Check cross-platform behavior when touching filesystem/process/install logic. A change is not considered cross-platform-safe merely because it passes on Linux.

  14. Update documentation when behavior or invariants change. Documentation is part of the behavior contract.

  15. Use Graphify itself to understand Graphify, except when the graph is the thing being debugged.

Repository Architecture

  • Pipeline: detect() → extract() → build() → cluster() → analyze() → report.generate() → export.to_*()

  • Where extractors live: graphify/extractors/

  • Generated skills vs source fragments: Skill files in graphify/ are generated from fragments in tools/skillgen/.

  • What is generated and what is authoritative: tools/skillgen/fragments/ is authoritative.

Development Setup

# Fork and clone the repository
git clone https://github.com/<your-username>/graphify.git
cd graphify
git remote add upstream https://github.com/Graphify-Labs/graphify.git
git fetch upstream
git checkout -b my-feature-branch upstream/v8  # Always branch off upstream v8, never commit directly to v8

# Set up the environment (--all-extras installs the optional grammars and SDKs,
# matching CI; without it the tests that need them are skipped)
uv sync --all-extras
uv run pre-commit install

# Run the test suite to confirm your setup
uv run pytest tests/ -q

# Run linters and type checkers before pushing
uv run ruff check .
uv run pyright
  • Python versions: 3.10+

  • uv: We use uv for dependency management.

Working on the Codebase

  • Use graphify itself: Before making non-trivial architectural changes, use graphify query ... to navigate the codebase rather than blind grepping. Do not use the graph as evidence when the task concerns the graph's own correctness.

  • Update graph after code changes: graphify update .

  • Root/path invariants: Paths resolve relative to the calling module or scan root.

  • Cache considerations: Be aware of relative/absolute path caching across rebuilds.

  • Generated skill files: Regenerate with uv run python -m tools.skillgen --bless. Never hand-edit the generated files directly.

  • Corpus boundaries: Do not create a second interpretation of the corpus boundary. Reuse the existing detection/ignore semantics whenever another pass walks project files (e.g. .graphifyignore).

  • Cross-platform: Windows portability is a first-class contribution concern. Path separators, symlinks, absolute/relative paths, hash seeds, and shell interpolation must work correctly on Windows.

Making a Change

  1. Find or create an issue

  2. Reproduce

  3. Identify invariant

  4. Make smallest fix

  5. Add regression test

  6. Run targeted tests

  7. Run full suite (uv run pytest tests)

  8. Run lint/type checks (uv run ruff check ., uv run pyright)

  9. Regenerate artifacts if you touched their sources (uv run python -m tools.skillgen --bless).

Tests

  • pytest: The primary test runner.

  • Fixture conventions: New language extractors need fixtures under tests/fixtures/ and tests in tests/test_languages.py.

  • Environment isolation: Tests must not accidentally depend on the contributor's ambient environment. When writing backend/provider tests, explicitly isolate or clear environment variables (e.g., OPENAI_API_KEY, OLLAMA_HOST).

  • Deterministic tests: Ensure tests don't rely on ambient state or ordering.

  • Regression-test expectations: Test must fail on pre-fix and pass on post-fix.

Language Extractors

  • Extractor module: Defines logic for each language AST.

  • Dispatch table: Registers the parser and language.

  • Tree-sitter dependency: Use ASTs where possible.

  • Fixture: Ensure comprehensive test cases in tests/fixtures/.

  • Cross-file resolution considerations: Resolution stays local to AST paths.

Generated Skills and Monoliths

  • Source fragments are authoritative.

  • Run skillgen (uv run python -m tools.skillgen --bless).

  • Never casually edit generated artifacts.

  • Sanctioned round-trip changes only.

  • Preserve multiset checks.

Data Integrity Rules

  • Zero-node guard: Must run before writes.

  • Shrink guard: Must not persist smaller corrupt graphs. (Note: forced writes can bypass this).

  • to_json before report side effects.

  • Cache consistency: Must be maintained across absolute/relative paths. (e.g., The Windows absolute-path issue taught us that earlier side effects that persist bad absolute-path entries into the semantic cache are still data loss, even if the final graph write passes the shrink guard).

  • Provenance: Must be preserved.

  • Cross-file edges: Must be preserved during incremental updates, even if node count is unchanged.

Security

  • Review SECURITY.md.

  • Any change touching generated skill instructions, shell commands, subprocesses, URL ingestion, path handling, prompts, or serialization must be reviewed as a security-sensitive change.

  • Never interpolate untrusted content into shell/Python.

Commit Messages

Use a conventional-commit prefix (e.g., fix:, feat:, docs:, fix(extract):) and make the subject describe the change. Explain why in the body when the change is non-trivial. Reference the relevant issue/PR.

  • AI Authorship Disclosure: If an AI coding assistant materially contributed to the implementation, disclose it in the commit metadata according to the repository's authorship convention (e.g., Co-Authored-By: Claude <[e-mail address on the upstream page](https://github.com/Graphify-Labs/graphify/blob/35d1d2038b9e9d470f117bf8f2473d415b5f5358/CONTRIBUTING.md)>). Do not attribute code to a model that did not contribute.

Pull Requests

  • One concern per PR.

  • No unrelated changes.

  • Describe problem / implementation / verification.

  • List commands actually run.

  • Document limitations / unsupported cases.

  • Keep description synchronized with final implementation.

  • Rebase/resolve conflicts before requesting final review.

Working with AI Coding Agents

AI assistants are welcome, but every rule in this guide applies to the code they write, and you remain the author of the PR.

  • Point your agent at this file and ARCHITECTURE.md before it changes anything.

  • Branch off upstream/v8, keep the PR to one concern, and never let an agent hand-edit generated skill files.

  • For bug fixes, confirm the regression test fails without the fix, not only that it passes with it.

  • Run the checks yourself before opening the PR: uv run pytest tests, uv run ruff check ., uv run pyright.

  • Disclose material AI help with a Co-Authored-By: trailer, as described under Commit Messages.

  • Write the PR description yourself, and list the commands you actually ran.

Issue Reports

Bugs

Include exact version/commit, environment, minimal reproduction, expected vs actual, logs, graph/cache artifacts where relevant, and whether a clean checkout reproduced it.

Feature Requests

Focus on the problem first, proposed behavior, alternatives, and compatibility considerations.

Review Expectations

  • Correctness, regression coverage, scope, determinism, provenance, security, and documentation.

Release / Generated Artifacts

  • What gets regenerated: Skill files via skillgen, HTML exports.

  • What should not be committed: Local cache (.graphify_cached.json), generated node artifacts outside of the expected outputs.

Getting Help

  • Discord: Join the Graphify Discord for questions and discussion.

  • Issues: Search existing issues before opening a new one.

  • Discussions: Use GitHub issues for bugs and feature requests, Discord for open-ended questions.

Further Reading

512 files · 494 not served here

Advantages

  • Deterministic parsing using tree-sitter ensures no LLM is required for code structure extraction. evidence: README.md
  • Reduces agent token spend by providing a queryable graph instead of requiring full file reads. evidence: README.md
  • Provides explicit confidence tags for every edge, distinguishing between extracted and inferred connections. evidence: README.md

Limitations

  • Semantic passes for non-code assets like PDFs or images may require a configured API key or the assistant's model. evidence: README.md
  • Requires manual or automated updates to the graph after significant code changes to maintain accuracy. evidence: AGENTS.md

Security

Risk level: Medium risk

This brain runs

Git hooks (2)

  • .pre-commit-config.yaml: python -m tools.skillgen --check
  • .pre-commit-config.yaml: pre-commit hooks from https://github.com/astral-sh/ruff-pre-commit at v0.15.14 (contributor tooling: runs only after pre-commit install) · uses the network

Agent instructions that run or fetch something (1)

  • AGENTS.md: After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)

Install scripts (3)

  • README.md: | uv *(recommended)* | any | `uv --version` | `curl -LsSf https://astral.sh/uv/install.sh \| sh` | · uses the network
  • README.md: curl -LsSf https://astral.sh/uv/install.sh | sh · uses the network
  • graphify/install.py: python graphify/install.py
  • Medium risk: runs-git-hook-remote-exec (.pre-commit-config.yaml:18)
  • Medium risk: runs-install-script-remote-exec (README.md:163)
  • Medium risk: runs-install-script-remote-exec (README.md:179)
  • Medium risk: unicode-zero-width (graphify/install.py:495)
  • Low risk: scripts-present (graphify/install.py)

Attribution and licence

First committed by
GitHub avatar of safishamsisafishamsi
Publisher
Graphify Labs (Community)
Source
Graphify-Labs/graphify · commit 35d1d20
Licence
Apache License 2.0 (files served here)
  • ATTRIBUTION.md (written by AutoGineer)
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Contributors
safishamsi, xRedLeader, Deepjyoti-Sarmah, rohit-jsfreaky, Adityakk9031

AutoGineer is not affiliated with or endorsed by safishamsi or Graphify Labs.

Install from source

494 of its files are not served here, so there is no ZIP. Graphify-Labs/graphify at 35d1d20