Graphify-Labs

    Graphify-Labs/graphify

    #231 this week

    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.

    llm
    ai-agents
    antigravity
    ast
    claude-code
    code-analysis
    Python
    Apache-2.0
    97.0K stars
    9.4K forks
    97.0K GitHub watchers
    Updated 7/27/2026
    View on GitHub

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    Use Cases & Benefits

    • Transforms any folder of code, scripts, documents, images, or videos into a queryable knowledge graph integrating app code, database schema, and infrastructure.
    • Enables unified, AI-assisted querying across diverse project assets, reducing manual search and improving understanding of complex codebases and documentation.
    • Use for exploring and understanding large, multi-language codebases with linked documentation and infrastructure in a single interactive graph.
    • Use for integrating AI coding assistants with your project to answer architecture and code questions contextually using the generated knowledge graph.
    • Use for automating project onboarding and review by generating visual reports and call-flow diagrams that highlight key concepts and surprising connections.

    About graphify

    Graphify

    🇺🇸 English | 🇨🇳 简体中文 | 🇯🇵 日本語 | 🇰🇷 한국어 | 🇩🇪 Deutsch | 🇫🇷 Français | 🇪🇸 Español | 🇮🇳 हिन्दी | 🇧🇷 Português | 🇷🇺 Русский | 🇸🇦 العربية | 🇮🇷 فارسی | 🇮🇹 Italiano | 🇵🇱 Polski | 🇳🇱 Nederlands | 🇹🇷 Türkçe | 🇺🇦 Українська | 🇻🇳 Tiếng Việt | 🇮🇩 Bahasa Indonesia | 🇸🇪 Svenska | 🇬🇷 Ελληνικά | 🇷🇴 Română | 🇨🇿 Čeština | 🇫🇮 Suomi | 🇩🇰 Dansk | 🇳🇴 Norsk | 🇭🇺 Magyar | 🇹🇭 ภาษาไทย | 🇺🇿 Oʻzbekcha | 🇹🇼 繁體中文 | 🇵🇭 Filipino

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    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.

    Works in Claude Code, Codex, OpenCode, Kilo Code, Cursor, Gemini CLI, GitHub Copilot CLI, VS Code Copilot Chat, Aider, Amp, OpenClaw, Factory Droid, Trae, Hermes, Kimi Code, Kiro, Pi, Devin CLI, and Google Antigravity.

    /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
    

    For a readable architecture page with Mermaid call-flow diagrams, run:

    graphify export callflow-html
    

    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:

    sudo apt install python3.12 python3-pip pipx
    # or install uv:
    curl -LsSf https://astral.sh/uv/install.sh | sh
    

    Install

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

    Step 1 — install the package:

    # Recommended (uv puts graphify on PATH automatically):
    uv tool install graphifyy
    
    # Alternatives:
    pipx install graphifyy
    pip install graphifyy  # may need PATH setup — see note below
    

    Step 2 — register the skill with your AI assistant:

    graphify install
    

    That's it. 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.

    PowerShell note: Use graphify . not /graphify . — the leading slash is a path separator in PowerShell.

    graphify: command not found? Use uv tool install graphifyy or pipx install graphifyy — both put the CLI on PATH automatically. With plain pip, add ~/.local/bin (Linux) or ~/Library/Python/3.x/bin (Mac) to your PATH, or run python -m graphify.

    Avoid pip install on Mac/Windows if possible. The skill resolves Python at runtime from graphify-out/.graphify_python; if that points to a different environment than where pip installed the package, you'll get ModuleNotFoundError: No module named 'graphify'. uv tool install and pipx install isolate the package in their own env and avoid this entirely.

    Git hooks and uv tool / pipx: graphify hook install embeds the current interpreter path directly into the hook scripts at install time, so the post-commit hook fires correctly even in GUI git clients and CI runners where ~/.local/bin is not on PATH. If you reinstall or upgrade graphify, re-run graphify hook install to refresh the embedded path.

    Pick your platform

    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
    Cursorgraphify cursor install
    Devin CLIgraphify devin install
    Google Antigravitygraphify antigravity install

    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 — 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.

    Codex uses $graphify instead of /graphify.

    Optional extras

    Install only what you need:

    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]"
    neo4jNeo4j push supportuv tool install "graphifyy[neo4j]"
    falkordbFalkorDB push supportuv tool install "graphifyy[falkordb]"
    svgSVG graph exportuv tool install "graphifyy[svg]"
    leidenLeiden community detection (Python < 3.13 only)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]"
    chineseChinese query segmentation (jieba)uv tool install "graphifyy[chinese]"
    allEverything aboveuv tool install "graphifyy[all]"

    Make your assistant always use the graph

    Run this once in your project after building a graph:

    PlatformCommand
    Claude Codegraphify claude install
    CodeBuddygraphify codebuddy install
    Codexgraphify codex install
    OpenCodegraphify opencode install
    Kilo Codegraphify kilo install
    GitHub Copilot CLIgraphify copilot install
    VS Code Copilot Chatgraphify vscode install
    Aidergraphify aider install
    OpenClawgraphify claw install
    Factory Droidgraphify droid install
    Traegraphify trae install
    Trae CNgraphify trae-cn install
    Cursorgraphify cursor install
    Gemini CLIgraphify gemini install
    Hermesgraphify hermes install
    Kimi Codegraphify install --platform kimi
    Ampgraphify amp install
    Agent Skills (cross-framework)graphify agents install (alias graphify skills install)
    Kiro IDE/CLIgraphify kiro install
    Pi coding agentgraphify pi install
    Devin CLIgraphify devin install
    Google Antigravitygraphify antigravity install

    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. On platforms that support payload-bearing hooks (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) and nudges your assistant toward the graph path. On the others (Codex, OpenCode, Cursor, etc.), the persistent instruction files (AGENTS.md, .cursor/rules/, etc.) provide the same query-first guidance. GRAPH_REPORT.md is still available for broad architecture review.

    CodeBuddy does the same two things as Claude Code: writes a CODEBUDDY.md section telling CodeBuddy to read graphify-out/GRAPH_REPORT.md before answering architecture questions, and installs PreToolUse hooks (.codebuddy/settings.json) that fire before Bash search commands and file reads, nudging toward graphify query instead.

    Codex writes to AGENTS.md and also installs a PreToolUse hook in .codex/hooks.json that fires before every Bash tool call — same always-on mechanism as Claude Code.

    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).


    Kilo Code installs the Graphify skill to ~/.config/kilo/skills/graphify/SKILL.md and a native /graphify command to ~/.config/kilo/command/graphify.md. graphify kilo install also writes AGENTS.md plus a native tool.execute.before plugin (.kilo/plugins/graphify.js + .kilo/kilo.json or .kilo/kilo.jsonc registration) so Kilo gets the same always-on graph reminder behavior through native .kilo config.

    Cursor writes .cursor/rules/graphify.mdc with alwaysApply: true — Cursor includes it in every conversation automatically, no hook needed.

    What's in the report

    • God nodes — the most-connected concepts in your project. Everything flows through these.
    • Surprising connections — links between things that live in different files or modules. Ranked by how unexpected they are.
    • The "why" — inline comments (# NOTE:, # WHY:, # HACK:), docstrings, and design rationale from docs are extracted as separate nodes linked to the code they explain.
    • Suggested questions — 4–5 questions the graph is uniquely positioned to answer.
    • Confidence tags — every inferred relationship is marked EXTRACTED, INFERRED, or AMBIGUOUS. You always know what was found vs guessed.

    What files it handles

    TypeExtensions
    Code (36 tree-sitter grammars).py .ts .js .jsx .tsx .mjs .go .rs .java .c .cpp .h .hpp .cu .cuh .rb .cs .kt .scala .php .swift .lua .luau .zig .ps1 .psm1 .ex .exs .m .mm .jl .vue .svelte .astro .groovy .gradle .dart .v .sv .svh .sql .f .f90 .f95 .f03 .f08 .pas .pp .dpr .dpk .lpr .inc .dfm .lfm .lpk .sh .bash .json .dm .dme .dmi .dmm .dmf .sln .slnx .csproj .fsproj .vbproj .xaml .razor .cshtml (.dm/.dme requires uv tool install graphifyy[dm]; CUDA .cu/.cuh reuse the C++ grammar)
    Salesforce Apex.cls .trigger (regex-based; classes, interfaces, enums, methods, triggers, SOQL/DML edges)
    Terraform / HCL.tf .tfvars .hcl (requires uv tool install graphifyy[terraform])
    MCP configs.mcp.json mcp.json mcp_servers.json claude_desktop_config.json — extracts server nodes, package refs, env var requirements
    Package manifestsapm.yml pyproject.toml go.mod pom.xml — one canonical package node per package (by name) plus depends_on edges, so a package referenced from many manifests is a single hub
    Docs.md .mdx .qmd .html .txt .rst .yaml .yml (markdown [text](./other.md) links and [[wikilinks]] become references edges between docs)
    Office.docx .xlsx (requires uv tool install graphifyy[office])
    Google Workspace.gdoc .gsheet .gslides (opt-in; requires gws auth and --google-workspace; Sheets need uv tool install graphifyy[google])
    PDFs.pdf
    Images.png .jpg .webp .gif
    Video / Audio.mp4 .mov .mp3 .wav and more (requires uv tool install graphifyy[video])
    YouTube / URLsany video URL (requires uv tool install graphifyy[video])

    Code is extracted locally with no API calls (AST via tree-sitter). Everything else goes through your AI assistant's model API.

    Google Drive for desktop .gdoc, .gsheet, and .gslides files are shortcut pointers, not document content. To include native Google Docs, Sheets, and Slides in a headless extraction, install and authenticate the gws CLI, then run:

    uv tool install "graphifyy[google]"  # needed for Google Sheets table rendering
    gws auth login -s drive
    graphify extract ./docs --google-workspace
    

    You can also set GRAPHIFY_GOOGLE_WORKSPACE=1. Graphify exports shortcuts into graphify-out/converted/ as Markdown sidecars, then extracts those files.


    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 git commit
    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.


    Ignoring files

    Create a .graphifyignore in your project root — same syntax as .gitignore, including ! negation.

    .gitignore is respected automatically. graphify reads the .gitignore in each directory. If a .graphifyignore is also present, the two are merged.graphifyignore patterns are evaluated last, so they win on conflicts (including ! negations). Adding a .graphifyignore only ever excludes more; it never re-includes a file your .gitignore already excluded. Subdirectory scoping works the same way as git — an ignore file only affects its own subtree.

    # .graphifyignore
    node_modules/
    dist/
    *.generated.py
    
    # only index src/, ignore everything else
    *
    !src/
    !src/**
    

    Team setup

    graphify-out/ is meant to be committed to git so everyone on the team starts with a map.

    Recommended .gitignore additions:

    graphify-out/cost.json        # local only
    # graphify-out/cache/         # optional: commit for speed, skip to keep repo small
    

    manifest.json is now portable — keys are stored as relative paths and re-anchored on load, so committing it is safe and avoids a full rebuild on first checkout.

    Workflow:

    1. One person runs /graphify . and commits graphify-out/.
    2. Everyone pulls — their assistant reads the graph immediately.
    3. Run graphify hook install to auto-rebuild after each commit (AST only, no API cost). This also sets up a git merge driver so graph.json is never left with conflict markers — two devs committing in parallel get their graphs union-merged automatically.
    4. When docs or papers change, run /graphify --update to refresh those nodes.

    Using the graph directly

    # query the graph from the terminal
    graphify query "show the auth flow"
    graphify query "what connects DigestAuth to Response?" --graph graphify-out/graph.json
    
    # expose the graph as an MCP server (for repeated tool-call access)
    python -m graphify.serve graphify-out/graph.json
    python -m graphify.serve --graph graphify-out/graph.json  # --graph flag also accepted
    
    # register with Kimi Code:
    kimi mcp add --transport stdio graphify -- python -m graphify.serve graphify-out/graph.json
    
    # or serve over HTTP so a whole team points at one URL (no local graphify needed):
    python -m graphify.serve graphify-out/graph.json --transport http --port 8080
    python -m graphify.serve graphify-out/graph.json --transport http --host 0.0.0.0 --api-key "$SECRET"
    

    The MCP server gives your assistant structured access: query_graph, get_node, get_neighbors, shortest_path, list_prs, get_pr_impact, triage_prs.

    Shared HTTP server

    --transport stdio (the default) spawns one local server per developer. --transport http serves the same tools over the MCP Streamable HTTP transport, so a single shared process can serve the graph for the whole team — clients point their IDE MCP config at http://<host>:8080/mcp instead of running graphify locally.

    FlagDefaultPurpose
    --transport {stdio,http}stdioTransport to serve on
    --host127.0.0.1HTTP bind host (use 0.0.0.0 to expose beyond localhost)
    --port8080HTTP bind port
    --api-keyenv GRAPHIFY_API_KEYRequire Authorization: Bearer <key> (or X-API-Key)
    --path/mcpHTTP mount path
    --json-responseoffReturn plain JSON instead of SSE streams
    --statelessoffNo per-session state (for load-balanced / CI deployments)
    --session-timeout3600Reap idle stateful sessions after N seconds (0 disables)

    The default 127.0.0.1 bind is loopback-only. Set --host 0.0.0.0 and --api-key together when exposing on a shared host. Run it in a container:

    docker build -t graphify .
    docker run -p 8080:8080 -v "$(pwd)/graphify-out:/data" graphify \
      /data/graph.json --transport http --host 0.0.0.0 --api-key "$SECRET"
    

    WSL / Linux note: Ubuntu ships python3, not python. Use a venv to avoid conflicts:

    python3 -m venv .venv && .venv/bin/pip install "graphifyy[mcp]"
    

    Environment variables

    These are only needed for headless / CI extraction (graphify extract). When running via the /graphify skill inside your IDE, the model API is provided by your IDE session — no extra keys needed.

    VariableUsed forWhen required
    ANTHROPIC_API_KEYClaude (Anthropic) backend--backend claude
    ANTHROPIC_BASE_URLAnthropic-compatible endpoint URL (LiteLLM proxy, gateways, ...)--backend claude (default: https://api.anthropic.com)
    ANTHROPIC_MODELModel name for the Claude backend — for custom endpoints, use the model name/alias your server exposes--backend claude (default: claude-sonnet-4-6)
    GEMINI_API_KEY or GOOGLE_API_KEYGoogle Gemini backend--backend gemini
    OPENAI_API_KEYOpenAI or OpenAI-compatible APIs--backend openai (local servers accept any non-empty value)
    OPENAI_BASE_URLOpenAI-compatible server URL (llama.cpp, vLLM, LM Studio, ...)--backend openai (default: https://api.openai.com/v1)
    OPENAI_MODELModel name for the OpenAI backend — for self-hosted servers, use the model name/alias your server exposes (check its /v1/models endpoint), e.g. LFM2.5-8B-A1B-UD-Q4_K_XL for llama.cpp--backend openai (default: gpt-4.1-mini)
    DEEPSEEK_API_KEYDeepSeek backend--backend deepseek
    MOONSHOT_API_KEYKimi Code backend--backend kimi
    OLLAMA_BASE_URLOllama local inference URL--backend ollama (default: http://localhost:11434)
    OLLAMA_MODELOllama model name--backend ollama (default: auto-detect)
    GRAPHIFY_OLLAMA_NUM_CTXOverride Ollama KV-cache window sizeoptional — auto-sized by default
    GRAPHIFY_OLLAMA_KEEP_ALIVEMinutes to keep Ollama model loadedoptional — set 0 to unload after each chunk
    AZURE_OPENAI_API_KEYAzure OpenAI Service backend--backend azure
    AZURE_OPENAI_ENDPOINTAzure resource endpoint URL--backend azure (required alongside API key)
    AZURE_OPENAI_API_VERSIONAzure API version overrideoptional — default 2024-12-01-preview
    AZURE_OPENAI_DEPLOYMENT or GRAPHIFY_AZURE_MODELAzure deployment nameoptional — default gpt-4o
    AWS_* / ~/.aws/credentialsAWS Bedrock — standard credential chain--backend bedrock (no API key, uses IAM)
    GRAPHIFY_MAX_WORKERSAST parallelism thread countoptional — also --max-workers flag
    GRAPHIFY_MAX_OUTPUT_TOKENSRaise output cap for dense corporaoptional — e.g. 32768 for large files
    GRAPHIFY_API_TIMEOUTPer-call timeout in seconds for HTTP, claude-cli, and Anthropic SDK backends (default: 600)optional — also --api-timeout flag
    GRAPHIFY_FORCEForce graph rebuild even with fewer nodesoptional — also --force flag
    GRAPHIFY_GOOGLE_WORKSPACEAuto-enable Google Workspace exportoptional — set to 1
    GRAPHIFY_TRIAGE_BACKENDBackend for graphify prs --triageoptional — auto-detected from available keys
    GRAPHIFY_TRIAGE_MODELModel override for triageoptional — e.g. claude-opus-4-7
    GRAPHIFY_QUERY_LOGOverride query log path (default: ~/.cache/graphify-queries.log)optional — set to empty or /dev/null to silence
    GRAPHIFY_QUERY_LOG_DISABLESet to 1 to disable query logging entirelyoptional
    GRAPHIFY_QUERY_LOG_RESPONSESSet to 1 to also log full subgraph responses (off by default)optional
    GRAPHIFY_MAX_GRAPH_BYTESOverride the 512 MiB graph.json size cap — e.g. 700MB, 2GB, or plain bytesoptional — useful for very large corpora
    GRAPHIFY_LLM_TEMPERATUREOverride LLM temperature for semantic extraction — e.g. 0.7, or none to omitoptional — auto-omitted for o1/o3/o4/gpt-5 reasoning models

    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.
    • 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 residencygraphify extract auto-detects which provider to use based on which API key is set (priority: Gemini → Kimi → Claude → OpenAI → DeepSeek → Azure → Bedrock → Ollama). For code with data-residency requirements, use --backend ollama (fully local) or pass an explicit --backend flag. 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

    graphify: command not found after pip install graphifyy pip installs scripts to a user bin directory that may not be on your PATH. Fix:

    • macOS: add ~/Library/Python/3.x/bin to your PATH in ~/.zshrc
    • Linux: add ~/.local/bin to your PATH in ~/.bashrc
    • Or use uv tool install graphifyy / pipx install graphifyy — both manage PATH automatically.

    python -m graphify works but graphify command doesn't Your shell's PATH doesn't include the Python scripts directory. Use uv or pipx instead of plain pip.

    /graphify . causes "path not recognized" in PowerShell PowerShell treats a leading / as a path separator. Use graphify . (no slash) on Windows.

    Graph has fewer nodes after --update or rebuild If a refactor deleted files, the old nodes linger. Pass --force (or set GRAPHIFY_FORCE=1) to overwrite even when the rebuild has fewer nodes.

    Graph has duplicate nodes for the same entity (ghost duplicates) Ghost duplicates (same symbol appearing twice — once from AST extraction with a source location, once from semantic extraction without) are now automatically merged at build time. If you see this in a graph built before v0.8.33, run a full re-extract to clean up:

    graphify extract . --force
    

    Ollama runs out of VRAM / context window exceeded The KV-cache window is auto-sized but may be too large for your GPU. Reduce it:

    GRAPHIFY_OLLAMA_NUM_CTX=8192 graphify extract ./docs --backend ollama --token-budget 4000
    

    LLM returned invalid JSON / Unterminated string warnings The model's JSON response hit its output-token limit and was cut off mid-string. graphify auto-recovers (it splits the chunk and re-extracts the halves, and an oversized single document is first sliced at heading/paragraph boundaries so the whole file is still covered), so these warnings are noisy but not data loss. To reduce the churn, raise the output cap or shrink each chunk's output:

    GRAPHIFY_MAX_OUTPUT_TOKENS=16384 graphify extract . --mode deep   # lift the cap
    graphify extract . --mode deep --token-budget 4000                # smaller input chunks -> smaller output
    

    With a cloud gateway like OpenRouter, prefer --backend openai (set OPENAI_BASE_URL) over the Ollama shim — it's a cleaner OpenAI-compatible path. If the model has its own max-output ceiling, lowering --token-budget is the reliable lever.

    Graph HTML is too large to open in a browser (>5000 nodes) Skip HTML generation and use the JSON directly:

    graphify cluster-only ./my-project --no-viz
    graphify query "..."
    

    graph.json has conflict markers after two devs commit at once Run graphify hook install — it sets up a git merge driver that union-merges graph.json automatically so conflicts never happen.

    Extraction returns empty nodes/edges for docs or PDFs Docs, PDFs, and images require an LLM call — code-only corpora need no key. Check that your API key is set and the backend is correct:

    ANTHROPIC_API_KEY=sk-... graphify extract ./docs --backend claude
    

    Skill version mismatch warning in your IDE Your installed graphify version is different from the skill file. Update:

    uv tool upgrade graphifyy
    graphify install  # overwrites the skill file
    

    Full command reference

    /graphify                          # run on current directory
    /graphify ./raw                    # run on a specific folder
    /graphify ./raw --mode deep        # more aggressive relationship extraction
    /graphify ./raw --update           # re-extract only changed files
    /graphify ./raw --directed         # preserve edge direction
    /graphify ./raw --cluster-only     # rerun clustering on existing graph
    /graphify ./raw --no-viz           # skip HTML visualization
    /graphify ./raw --obsidian         # generate Obsidian vault
    /graphify ./raw --wiki             # build agent-crawlable markdown wiki
    /graphify ./raw --svg              # export graph.svg
    /graphify ./raw --graphml          # export for Gephi / yEd
    /graphify ./raw --neo4j            # generate cypher.txt for Neo4j
    /graphify ./raw --neo4j-push bolt://localhost:7687
    /graphify ./raw --falkordb         # generate cypher.txt for FalkorDB
    /graphify ./raw --falkordb-push falkordb://localhost:6379
    /graphify ./raw --watch            # auto-sync as files change
    /graphify ./raw --mcp              # start MCP stdio server
    
    /graphify add https://arxiv.org/abs/1706.03762
    /graphify add <video-url>
    /graphify add https://... --author "Name" --contributor "Name"
    
    /graphify query "what connects attention to the optimizer?"
    /graphify query "..." --dfs --budget 1500
    /graphify path "DigestAuth" "Response"
    /graphify explain "SwinTransformer"
    
    graphify save-result --question "Q" --answer "A" --nodes Foo Bar --outcome useful   # record how a Q&A turned out (work memory; outcome ∈ useful|dead_end|corrected)
    graphify reflect                   # aggregate graphify-out/memory/ outcomes into reflections/LESSONS.md
    graphify reflect --if-stale        # no-op when LESSONS.md is already newer than every input (cheap to run each session)
    graphify reflect --out docs/LESSONS.md    # write the lessons doc somewhere else
    graphify reflect --graph graphify-out/graph.json  # also group lessons by community
    
    graphify uninstall                 # remove from all platforms in one shot
    graphify uninstall --purge         # also delete graphify-out/
    graphify uninstall --project --platform codex  # remove project-scoped install files only
    
    graphify hook install              # post-commit + post-checkout hooks
    graphify hook uninstall
    graphify hook status
    
    # always-on assistant instructions - platform-specific
    graphify claude install            # CLAUDE.md + PreToolUse hook (Claude Code)
    graphify claude uninstall
    graphify codebuddy install         # CODEBUDDY.md + PreToolUse hook (CodeBuddy)
    graphify codebuddy uninstall
    graphify codex install             # AGENTS.md + PreToolUse hook in .codex/hooks.json (Codex)
    graphify opencode install          # AGENTS.md + tool.execute.before plugin (OpenCode)
    graphify kilo install              # native Kilo skill + /graphify command + AGENTS.md + .kilo plugin
    graphify kilo uninstall
    graphify cursor install            # .cursor/rules/graphify.mdc (Cursor)
    graphify cursor uninstall
    graphify gemini install            # GEMINI.md + BeforeTool hook (Gemini CLI)
    graphify gemini uninstall
    graphify copilot install           # skill file (GitHub Copilot CLI)
    graphify copilot uninstall
    graphify aider install             # AGENTS.md (Aider)
    graphify aider uninstall
    graphify claw install              # AGENTS.md (OpenClaw)
    graphify claw uninstall
    graphify droid install             # AGENTS.md (Factory Droid)
    graphify droid uninstall
    graphify trae install              # AGENTS.md (Trae)
    graphify trae uninstall
    graphify trae-cn install           # AGENTS.md (Trae CN)
    graphify trae-cn uninstall
    graphify hermes install             # AGENTS.md + ~/.hermes/skills/ (Hermes)
    graphify hermes uninstall
    graphify amp install               # skill file (Amp)
    graphify amp uninstall
    graphify agents install            # ~/.agents/skills/ + AGENTS.md (cross-framework; alias: graphify skills)
    graphify agents uninstall
    graphify kiro install               # .kiro/skills/ + .kiro/steering/graphify.md (Kiro IDE/CLI)
    graphify kiro uninstall
    graphify pi install                # skill file (Pi coding agent)
    graphify pi uninstall
    graphify devin install             # skill file + .windsurf/rules/graphify.md (Devin CLI)
    graphify devin uninstall
    graphify antigravity install       # .agents/rules + .agents/workflows (Google Antigravity)
    graphify antigravity uninstall
    
    graphify extract ./docs                        # headless LLM extraction for CI (no IDE needed)
    graphify extract ./docs --backend gemini       # explicit backend: gemini, kimi, claude, openai, deepseek, ollama, bedrock, or claude-cli
    graphify extract ./docs --backend gemini --model gemini-3.1-pro-preview
    graphify extract ./docs --backend ollama       # local Ollama (set OLLAMA_BASE_URL / OLLAMA_MODEL) - no API key needed for loopback
    OPENAI_BASE_URL=http://localhost:8080/v1 OPENAI_MODEL=my-model graphify extract ./docs --backend openai   # any OpenAI-compatible server (llama.cpp, vLLM, LM Studio)
    ANTHROPIC_BASE_URL=http://localhost:4000 ANTHROPIC_MODEL=my-model graphify extract ./docs --backend claude   # any Anthropic-compatible endpoint (LiteLLM proxy, gateways)
    GRAPHIFY_OLLAMA_NUM_CTX=32768 graphify extract ./docs --backend ollama   # override KV-cache window (auto-sized by default)
    GRAPHIFY_OLLAMA_KEEP_ALIVE=0 graphify extract ./docs --backend ollama    # unload model after each chunk (saves VRAM on small GPUs)
    graphify extract ./docs --backend bedrock      # AWS Bedrock via IAM - no API key, uses AWS credential chain
    graphify extract ./docs --backend claude-cli   # route through Claude Code CLI - no API key, uses your Claude subscription
    graphify extract ./docs --backend azure        # Azure OpenAI (set AZURE_OPENAI_API_KEY + AZURE_OPENAI_ENDPOINT)
    graphify extract ./docs --max-workers 16       # AST parallelism (also GRAPHIFY_MAX_WORKERS)
    graphify extract --postgres "postgresql://user:pass@host/db"   # introspect live PostgreSQL schema directly
    graphify extract ./my-workspace --cargo        # introspect Rust Cargo workspace dependencies directly
    graphify extract ./docs --token-budget 30000   # smaller semantic chunks for local/small models
    graphify extract ./docs --max-concurrency 2    # fewer parallel LLM calls (useful for local inference)
    graphify extract ./docs --api-timeout 900      # longer HTTP timeout for slow local models (default 600s)
    graphify extract ./docs --google-workspace     # export .gdoc/.gsheet/.gslides via gws before extraction
    graphify extract ./docs --mode deep            # richer semantic extraction via extended system prompt
    graphify extract ./docs --no-cluster           # raw extraction only, skip clustering
    graphify extract ./docs --force                # overwrite graph.json even if new graph has fewer nodes (use after refactors or to clear ghost duplicates)
    graphify extract ./docs --dedup-llm            # LLM tiebreaker for ambiguous entity pairs (uses same API key)
    graphify extract ./docs --global --as myrepo   # extract and register into the cross-project global graph
    GRAPHIFY_MAX_OUTPUT_TOKENS=32768 graphify extract ./docs --backend claude  # raise output cap for dense corpora
    
    graphify export callflow-html                       # graphify-out/<project>-callflow.html
    graphify export callflow-html --max-sections 8      # cap generated architecture sections
    graphify export callflow-html --output docs/arch.html
    graphify export callflow-html ./some-repo/graphify-out
    
    graphify global add graphify-out/graph.json myrepo   # register a project graph into ~/.graphify/global.json
    graphify global remove myrepo                         # remove a project from the global graph
    graphify global list                                  # show all registered repos + node/edge counts
    graphify global path                                  # print path to the global graph file
    
    graphify prs                              # PR dashboard: CI, review, worktree, graph impact
    graphify prs 42                           # deep dive on PR #42
    graphify prs --triage                     # AI triage ranking (auto-detects backend from env)
    graphify prs --worktrees                  # worktree → branch → PR mapping
    graphify prs --conflicts                  # PRs sharing graph communities (merge-order risk)
    graphify prs --base main                  # filter to PRs targeting a specific base branch
    graphify prs --repo owner/repo            # run against a different GitHub repo
    GRAPHIFY_TRIAGE_BACKEND=kimi graphify prs --triage   # use a specific backend for triage
    
    graphify clone https://github.com/karpathy/nanoGPT
    graphify merge-graphs a.json b.json --out merged.json
    graphify --version                                    # print installed version
    graphify watch ./src
    graphify check-update ./src
    graphify update ./src
    graphify update ./src --no-cluster  # skip reclustering, write raw AST graph only
    graphify update ./src --force       # overwrite even if new graph has fewer nodes
    graphify cluster-only ./my-project
    graphify cluster-only ./my-project --graph path/to/graph.json  # custom graph location
    graphify cluster-only ./my-project --max-concurrency 16 --batch-size 200  # parallel community labeling (large graphs)
    graphify cluster-only ./my-project --resolution 1.5            # more, smaller communities
    graphify cluster-only ./my-project --exclude-hubs 99           # exclude p99 degree nodes from partitioning
    graphify cluster-only ./my-project --no-label                  # keep "Community N" placeholders
    graphify cluster-only ./my-project --backend=gemini            # backend for community naming
    graphify cluster-only ./my-project --backend=gemini --model gemini-2.5-pro  # specific model
    graphify label ./my-project                                    # (re)name communities with the configured backend
    graphify label ./my-project --backend=openai --model gpt-4o   # force a specific backend and model
    

    Community names: inside an agent (Claude Code, Gemini CLI) the agent names communities itself. When you run the bare CLI, cluster-only auto-names them with the configured backend (built-in or custom OpenAI-compatible provider) — pass --no-label to keep Community N, or run graphify label to (re)generate names on demand.


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    Contributing

    Development setup

    The project uses uv for dev workflow. Install it once, then:

    git clone https://github.com/safishamsi/graphify.git
    cd graphify
    git checkout v8                        # active development branch
    
    # Create the project venv and install graphify + all extras + the dev group
    # (pytest). uv installs the dev dependency group by default; pass --no-dev to
    # skip it.
    uv sync --all-extras
    

    Verify the editable install:

    uv run graphify --version
    uv run python -c "import graphify; print(graphify.__file__)"
    

    Running tests

    uv run pytest tests/ -q                # run the full suite
    uv run pytest tests/test_extract.py -q # one module
    uv run pytest tests/ -q -k "python"    # filter by name
    

    macOS note: the test suite includes both sample.f90 and sample.F90 fixtures. These collide on case-insensitive HFS+ / APFS file systems. Run on Linux or in a Docker container if you need to test both Fortran variants simultaneously.

    Git workflow

    • Active development happens on the v8 branch.
    • Commit style: fix: <description> / feat: <description> / docs: <description>
    • Before opening a PR, run uv run pytest tests/ -q and confirm it passes.
    • Add a fixture file to tests/fixtures/ and tests to tests/test_languages.py for any new language extractor.

    What to contribute

    Worked examples are the most useful contribution. Run /graphify on a real corpus, save the output to worked/{slug}/, write an honest review.md covering what the graph got right and wrong, and open a PR.

    Extraction bugs — open an issue with the input file, the cache entry (graphify-out/cache/), and what was missed or wrong.

    See ARCHITECTURE.md for module responsibilities and how to add a language.

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