# Phase 3 Plan 1: Graph Store (NetworkX + PPR + Protocol Abstraction) Summary
**One-liner:** NetworkX-backed graph store with Protocol abstraction, Personalized PageRank, and JSON persistence
## What Was Built
- `GraphStore` Protocol (runtime_checkable) with 10 methods covering CRUD, PPR, counts, and serialization
- `NetworkXGraphStore` implementation using `nx.DiGraph[str]` with dict-based node/edge storage
- Personalized PageRank using `nx.pagerank()` with proper full-graph personalization vector and seed exclusion
- JSON persistence via `nx.node_link_data` / `nx.node_link_graph(directed=True)`
- 11 test cases covering all methods, edge cases, performance (1300-node PPR < 200ms), and protocol conformance
## Tasks Completed
| # | Task | Commit | Key Files |
|---|------|--------|-----------|
| 1 | Add networkx + create GraphStore Protocol and NetworkXGraphStore | f395d72 | `src/skill_retriever/memory/graph_store.py` |
| 2 | Write 11 graph store tests | f395d72 | `tests/test_graph_store.py` |
## Decisions Made
| Decision | Rationale |
|----------|-----------|
| `Any` type annotations for NX edge/node iteration results | NetworkX stubs return Unknown types; explicit `Any` + str casts cleanest approach |
| `pyright: ignore` for `node_link_data`/`node_link_graph` | NX stubs incomplete for serialization functions; no clean workaround |
| Sorted neighbor IDs in `get_neighbors` | Deterministic output for testing and downstream consumers |
| scipy added as dependency | NX 3.6 delegates `pagerank()` to scipy internally; required at runtime |
## Deviations from Plan
### Auto-fixed Issues
**1. [Rule 3 - Blocking] Added scipy>=1.15 dependency**
- **Found during:** Task 2 (running PPR tests)
- **Issue:** `nx.pagerank()` in NetworkX 3.6 delegates to `_pagerank_scipy()` which imports scipy
- **Fix:** Added `scipy>=1.15` to pyproject.toml dependencies
- **Files modified:** `pyproject.toml`, `uv.lock`
## Verification
```
uv run pytest tests/test_graph_store.py -v → 11 passed
uv run pyright src/skill_retriever/memory/graph_store.py → 0 errors
uv run ruff check src/skill_retriever/memory/ → All checks passed
```
## Metrics
- **Duration:** ~7 minutes
- **Completed:** 2026-02-03
- **Tests:** 11 passed, 0 failed
## Tech Stack
- **Added:** networkx 3.6.1, scipy 1.15+
- **Patterns:** Protocol-based abstraction for graph store backends, dict-based NX storage with Pydantic reconstruction on read
## Key Files
### Created
- `src/skill_retriever/memory/graph_store.py` — GraphStore Protocol + NetworkXGraphStore implementation
- `tests/test_graph_store.py` — 11 test cases
### Modified
- `src/skill_retriever/memory/__init__.py` — Exports GraphStore, NetworkXGraphStore (auto-updated by linter)
## Next Phase Readiness
Graph store ready for integration with ComponentMemory (Plan 03-03). PPR tuning will need validation query-component pairs as noted in STATE.md blockers.
