feat: semantic query via sentence-transformers embeddings

[juhii31]

Closes #1

What this does

Adds semantic embedding support to graphify query using
sentence-transformers with all-MiniLM-L6-v2 (80MB, local,
no API key required).

Changes

• graphify/embed.py — new module with embed_graph() function

  • Embeds all node labels + docstrings using all-MiniLM-L6-v2
  • Computes pairwise cosine similarity matrix
  • Adds semantically_similar_to edges above configurable
    threshold (default 0.82)
  • Tags edges as INFERRED with confidence_score = cosine similarity
  • Caches embedding vectors in graphify-out/cache/embeddings.json
  • Re-runs only embed new/changed nodes via SHA256 cache key

• tests/test_embed.py — 3 tests covering:

  • Similar nodes get connected
  • Cache file is created on first run
  • No duplicate edges on repeated runs

Notes

• Works fully offline, zero API cost after model download
• All 393 applicable tests passing (symlink and git hook
  tests skipped — Windows privilege limitation, pre-existing)

[juhii31]

This PR adds the embedding engine, caching, and edge creation. Query wiring into main.py and pyproject.toml optional dependency coming in the next commit before merge.

[juhii31]

Updated , query wiring into main.py and pyproject.toml optional dependency now included. graphify query "question" --embeddings uses semantic cosine similarity ranking instead of BFS keyword match. Fully closes #1.

[Qodo-Free-For-OSS]

Hi, embed_graph() sets an edge attribute named "source", which collides with NetworkX node-link JSON’s reserved edge endpoint key and can corrupt exported graph.json edge endpoints.

Severity: action required | Category: correctness

How to fix: Rename edge attribute "source"

Agent prompt to fix - you can give this to your LLM of choice:

Issue description

embed_graph() adds an edge attribute source="embeddings". NetworkX’s node-link JSON format uses source/target for edge endpoints, so this attribute name can collide and corrupt exported graphs.

Issue Context

The repo exports graphs via json_graph.node_link_data(...) in graphify/export.py, which emits edge endpoint keys named source and target.

Fix Focus Areas

• graphify/embed.py[60-66]
• graphify/export.py[282-297]

Suggested change

Rename the edge attribute from source to something non-reserved (e.g., edge_source, provenance, or inferred_by).

We noticed a couple of other issues in this PR as well - happy to share if helpful.

---

Qodo code review - free for open-source.

[juhii31]

Hi, embed_graph() sets an edge attribute named "source", which collides with NetworkX node-link JSON’s reserved edge endpoint key and can corrupt exported graph.json edge endpoints.

Severity: action required | Category: correctness

How to fix: Rename edge attribute "source"

Agent prompt to fix - you can give this to your LLM of choice:

Issue description

embed_graph() adds an edge attribute source="embeddings". NetworkX’s node-link JSON format uses source/target for edge endpoints, so this attribute name can collide and corrupt exported graphs.

Issue Context

The repo exports graphs via json_graph.node_link_data(...) in graphify/export.py, which emits edge endpoint keys named source and target.

Fix Focus Areas

• graphify/embed.py[60-66]
• graphify/export.py[282-297]

Suggested change

Rename the edge attribute from source to something non-reserved (e.g., edge_source, provenance, or inferred_by).

We noticed a couple of other issues in this PR as well - happy to share if helpful.

Qodo code review - free for open-source.

hi , Fixed — renamed source to provenance in embed.py to avoid NetworkX node-link JSON collision. Happy to see the other issues too