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Troubleshooting

Quick reference for common install/setup problems

Four issues account for most support questions. Check these first:

1. Hooks use a matcher + hooks array error in .claude/settings.json

You're on a pre-v2.2.3 release. v2.2.1 and v2.2.2 shipped a broken hook schema — flat {matcher, command, timeout} entries without the required nested hooks: [] array, timeouts in milliseconds instead of seconds, and a PreCommit event that isn't a real Claude Code event. PR #208 (shipped in v2.2.3) rewrote the generator to emit the correct v1.x+ schema.

Fix:

pip install --upgrade code-review-graph   # → v2.2.4 or later
cd /path/to/your/project
code-review-graph install                 # rewrites .claude/settings.json

The re-install merge-replaces the entire broken hooks block with the new nested format and drops a real git pre-commit hook into the hooks directory resolved via git rev-parse --git-path hooks — typically .git/hooks/pre-commit, but linked worktrees and core.hooksPath (husky) setups are handled too. That's where "check before commit" lives in v2.2.3+, not in Claude Code settings.

Valid Claude Code hook events are: PreToolUse, PostToolUse, UserPromptSubmit, Stop, SubagentStop, SessionStart, SessionEnd, PreCompact, Notification. There is no PreCommit.

2. code-review-graph: command not found after pip install

pip install put the console script into a bin/ directory that isn't on your $PATH. Four fixes, in order of recommendation:

Option 1 — Use pipx (cleanest):

pip uninstall code-review-graph
pipx install code-review-graph

pipx installs CLI tools in an isolated venv. If the command is not found afterwards, run pipx ensurepath or add ~/.local/bin to your PATH.

Option 2 — Use uvx (no install needed):

uvx code-review-graph install
uvx code-review-graph build

Option 3 — Run it as a Python module (always works):

python -m code_review_graph install
python -m code_review_graph build

Option 4 — Fix PATH manually:

pip show code-review-graph | grep Location
# Find the sibling `bin/` directory; on macOS user installs this is
# typically ~/Library/Python/3.X/bin. Add it to your shell rc:
echo 'export PATH="$HOME/Library/Python/3.12/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

3. Is code-review-graph project-scoped or user-scoped?

Both — four different pieces, each scoped differently:

Piece Scope Where
The Python package User-scoped Install once via pip/pipx/uvx
The graph database Project-scoped .code-review-graph/graph.db inside each project
MCP server config (.mcp.json) Project-scoped Claude Code launches one MCP server per project, with cwd=<project>
Multi-repo registry User-scoped ~/.code-review-graph/registry.json (only for cross_repo_search)

TL;DR: install the tool once, then run code-review-graph install && code-review-graph build inside each project you want graph-aware reviews in.

4. Using a venv? You must update settings.json manually

Claude Code hooks and MCP tool paths in .claude/settings.json are hardcoded at install time. If you switch to (or create) a virtual environment after running code-review-graph install, the paths will still point to the old interpreter and the server will silently fail or use the wrong Python.

Fix — update the command/args in .mcp.json and any hook commands in .claude/settings.json to match your venv:

// .mcp.json — point to your venv's Python or uvx inside the venv
{
  "mcpServers": {
    "code-review-graph": {
      "command": "/path/to/your/venv/bin/uvx",
      "args": ["code-review-graph", "serve"]
    }
  }
}

Or simply re-run code-review-graph install from within the activated venv so the paths are regenerated correctly:

source .venv/bin/activate          # activate your venv first
code-review-graph install          # rewrites .mcp.json and hook paths

Then fully quit and reopen Claude Code so it picks up the new config.

5. "I built the graph but Claude Code doesn't see it in a new session"

Most likely causes, ranked:

  1. You didn't restart Claude Code after install. Claude Code reads .mcp.json at startup — if you ran install in one session, fully quit and reopen Claude Code for the MCP server to register.
  2. New session's cwd is a different directory. The MCP server is launched with cwd=<project> and it reads .code-review-graph/graph.db from there. If your new session opened in a parent folder or a different project, it won't find the graph you built.
  3. You ran build but not install. build creates graph.db; install is what registers the MCP server with Claude Code via .mcp.json. You need both.
  4. MCP server is crashing on startup. Run /mcp inside Claude Code to see server status, or check ~/Library/Logs/Claude/mcp*.log on macOS.

Quick checklist:

cd /path/to/your/project
code-review-graph status    # should print Files/Nodes/Edges from the built graph
ls .mcp.json                # should exist
cat .mcp.json               # should reference `code-review-graph serve`
# then: fully quit Claude Code and reopen it inside this project

If status shows the graph but /mcp in the new session doesn't list code-review-graph, the .mcp.json isn't in the session's cwd — re-run code-review-graph install from the correct project root.

Database lock errors

The graph uses SQLite with WAL mode. If you see lock errors:

  • Ensure only one build process runs at a time
  • The database auto-recovers; just retry
  • Delete .code-review-graph/graph.db-wal and .code-review-graph/graph.db-shm if corrupt

Large repositories (>10k files)

  • First build may take 30-60 seconds
  • Subsequent incremental updates are fast (<2s)
  • Add more ignore patterns to .code-review-graphignore: 
    generated/**
vendor/**
*.min.js

Missing nodes after build

  • Check that the file's language is supported (see FEATURES.md)
  • Check that the file isn't matched by an ignore pattern
  • Run with full_rebuild=True to force a complete re-parse

Graph seems stale

  • Hooks auto-update on edit/commit
  • If stale, run /code-review-graph:build-graph manually
  • Check that hooks are configured in .claude/settings.json (re-run code-review-graph install to regenerate)

Embeddings not working

  • Install with: pip install code-review-graph[embeddings]
  • Run embed_graph_tool to compute vectors
  • First embedding run downloads the model (~90MB, one time)

MCP server won't start

  • Verify uv is installed (uv --version; install with pip install uv or brew install uv)
  • Check that uvx code-review-graph serve runs without errors
  • If using a custom .mcp.json, ensure it uses "command": "uvx" with "args": ["code-review-graph", "serve"]
  • Re-run code-review-graph install to regenerate the config

Windows / WSL

  • Upgrade to v2.3.6+ if daemon status crashes with WinError 87 (#511) or CLI detect-changes maps 0 functions on Windows (#528) — both are fixed there
  • Use forward slashes in paths when passing repo_root to MCP tools
  • In WSL, ensure uv is installed inside WSL (not the Windows version): curl -LsSf https://astral.sh/uv/install.sh | sh
  • If uv is not found after install, add ~/.cargo/bin to your PATH
  • File watching (code-review-graph watch) may have delays on WSL1 due to filesystem event limitations; WSL2 is recommended
  • On Windows native (non-WSL), long path support may need to be enabled: git config --system core.longpaths true

Community detection requires igraph

  • Install with: pip install code-review-graph[communities]
  • Without igraph, community detection falls back to file-based grouping (less precise but functional)

Wiki generation with LLM summaries

  • Install with: pip install code-review-graph[wiki]
  • Requires a running Ollama instance for LLM-powered summaries
  • Without Ollama, wiki pages are generated with structural information only (no prose summaries)

Optional dependency groups

If a tool returns an ImportError, install the relevant optional group:

  • pip install code-review-graph[embeddings] for semantic search
  • pip install code-review-graph[google-embeddings] for Google Gemini embeddings
  • OpenAI-compatible and MiniMax embeddings use stdlib HTTP clients and require only their environment variables
  • pip install code-review-graph[communities] for igraph-based community detection
  • pip install code-review-graph[enrichment] for Python call-resolution enrichment via Jedi
  • pip install code-review-graph[eval] for evaluation benchmarks (matplotlib)
  • pip install code-review-graph[wiki] for wiki LLM summaries (ollama)
  • pip install code-review-graph[all] for everything