Graphify

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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.

• 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.

Want this always-on, updating in the background across your code, docs, and meetings rather than only on demand? That is what we are building at graphify.com. You can join the waitlist there.

Get started (30 seconds):

uv tool install graphifyy      # install the CLI (or: pipx install graphifyy)
graphify install               # register the skill with your AI assistant

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

Works in Claude Code, Cursor, Codex, Gemini CLI, GitHub Copilot, and 15+ more — pick your platform.

See it in action

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.

What it does

What you get out of the box:

Benchmarks

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.

Prerequisites

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 (isolated env; if 'graphify' isn't found after, run: uv tool update-shell):
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? uv tool install / pipx install put the graphify command in their tool bin dir (~/.local/bin). If your shell can't find it right after install — common on a fresh macOS + zsh setup — that dir isn't on your PATH yet: run uv tool update-shell (or pipx ensurepath), then open a new terminal. With plain pip, add ~/.local/bin (Linux) or ~/Library/Python/3.x/bin (Mac) to your PATH, or run python -m graphify.

Running with uvx / uv tool run instead of installing? Name the package, not the command: uvx --from graphifyy graphify install. Plain uvx graphify … fails (No solution found … no versions of graphify) because uv tool run reads the first word as a package, and the package is graphifyy — the graphify command lives inside it.

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.

Strict mode (Claude Code): graphify install --project --strict makes the assistant actually use the graph. The default install nudges it to run graphify query before reading files; strict mode blocks the first raw source read of a session and redirects it to the graph, then reverts to the nudge (so it fires at most once per session and never gets stuck). Toggle at runtime with GRAPHIFY_HOOK_STRICT=1/0; the default install is unchanged (soft nudge).

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.

Codex uses $graphify instead of /graphify.

Make your assistant always use the graph

Run this once in your project after building a graph:

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) 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.

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, which is what actually carries the always-on graph guidance on this platform. graphify codex install also registers a PreToolUse hook in .codex/hooks.json (graphify hook-check), but that entry is deliberately a no-op: Codex Desktop rejects hookSpecificOutput.additionalContext on PreToolUse, so emitting a nudge there would break Bash tool calls. Unlike Claude Code, where the hook (graphify hook-guard) does the nudging, on Codex the hook fires and intentionally does nothing, and AGENTS.md is the always-on mechanism.

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, so Cursor includes it in every conversation automatically, no hook needed.

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).

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

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.

Pass --no-gitignore to graphify extract when git-ignored generated or transpiled code belongs in the graph. This disables .gitignore and .git/info/exclude; .graphifyignore still applies.

# .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.

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.

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). 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 installing The CLI is installed but its bin directory isn't on your shell's PATH. Pick the fix for how you installed:

• uv (uv tool install graphifyy): the command lands in uv's tool bin dir (~/.local/bin), which a fresh macOS/zsh setup often doesn't have on PATH. Run uv tool update-shell, then open a new terminal. (Find the dir with uv tool dir --bin.)
• pipx (pipx install graphifyy): run pipx ensurepath, then open a new terminal.
• pip (pip install graphifyy): pip installs scripts to a user bin dir that may not be on PATH — add ~/Library/Python/3.x/bin (macOS) or ~/.local/bin (Linux) to your PATH in ~/.zshrc/~/.bashrc, or just run python -m graphify.

uvx graphify … or uv tool run graphify … fails to resolve graphify The PyPI package is graphifyy; graphify is only the command it provides. uv tool run treats the first word as a package name, so it looks for a package called graphify and reports No solution found … no versions of graphify. Name the package explicitly: uvx --from graphifyy graphify install (same as uv tool run --from graphifyy graphify install). Or uv tool install graphifyy once and then call graphify directly.

uv run --with graphifyy python -m graphify silently runs an older install uv run uses your system Python, so if an older graphifyy also lives there (e.g. a past pip install graphifyy), Python can find that copy first on sys.path and --with graphifyy won't override it. It runs with no error, but you get the old version's behavior — e.g. env overrides like OPENAI_BASE_URL are silently ignored, so requests hit the default endpoint and fail with a 401 that looks like a bad key. The fingerprint is a warning: skill is from graphify <newer>, package is <older> line — that means a different install was loaded, not just a stale skill. Check which copy actually loaded:

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

Then run the installed command directly (it uses the uv-managed copy), or drop the stale system copy:

uvx --from graphifyy graphify extract . --backend openai   # names the package explicitly
pip uninstall graphifyy                                    # or remove the old system install

python -m graphify works but graphify command doesn't Your shell's PATH doesn't include the bin directory the command was installed to. Prefer uv tool install / pipx install over plain pip, then run uv tool update-shell / pipx ensurepath and open a new terminal (see the install notes above).

/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.

extract exits with "extraction was incomplete ... refusing to overwrite" When an extraction pass crashes or a walk can't fully read the corpus, the run would be smaller than a complete one, so graphify extract refuses to overwrite a larger existing graph with the partial result (protecting your graph.json). Fix the underlying failure and re-run, or pass --allow-partial to overwrite anyway.

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