feat(vectors)!: default to the sqlite vector store and never start Docker without embeddings

[vitali87]

Summary

• --no-embeddings never starts Docker for Qdrant. Before this change, cgr start --update-graph --clean --no-embeddings on the default embedded graph exited with docker is installed but the daemon is not responding. The cause was the docker-compose.yaml that a Memgraph-era cgr start left in CGR_HOME, which made cgr start the stack's Qdrant. --no-embeddings was never checked. Now a run that writes no embeddings (--no-embeddings or CGR_SKIP_EMBEDDINGS) starts no Qdrant. On Memgraph it starts only Memgraph.
• Breaking: CGR_VECTOR_STORE_BACKEND now defaults to sqlite instead of qdrant. Vectors go to ~/.cgr/vectors.sqlite, next to the embedded graph, with no server and no Docker. The semantic extra now installs sqlite-vec; its wheels cover every platform torch ships wheels for. Qdrant is still available with CGR_VECTOR_STORE_BACKEND=qdrant.
• Making the switch safe for existing installs:
  • Refill after the switch. Each project records which backend holds its vectors, so the first sync after the backend changes re-embeds the project into the new store, even on an unchanged checkout. Without this, semantic search would return nothing until some file changed.
  • Upgrade notice. An install that sets QDRANT_URL or QDRANT_DB_PATH without choosing a backend logs a one-time notice.
  • Pythons that can't load SQLite extensions (e.g. pyenv builds). Semantic search is turned off with a single warning. Otherwise every sync would owe the embeddings pass again and --clean would raise after the graph was wiped.

Breaking change

Installs that never set CGR_VECTOR_STORE_BACKEND move from Qdrant to the SQLite file:

• Each project is re-embedded once into ~/.cgr/vectors.sqlite on its next sync.
• Vectors already in Qdrant (the embedded ./.qdrant_code_embeddings or the stack's Qdrant) are left in place, not migrated, and no longer searched.
• To keep Qdrant, set CGR_VECTOR_STORE_BACKEND=qdrant.
• pip installs need the semantic extra again to pick up sqlite-vec; uv tool and pipx upgrades keep their extras.
• The standalone sqlite-vec extra (for CGR_EMBEDDING_PROVIDER=openai without torch) installs only where sqlite-vec has wheels: not on musl/Alpine or Windows ARM. Qdrant is the option there.

The upgrade path is documented under Upgrade → From Qdrant to the sqlite vector store in docs/getting-started/installation.md.

Demo

The command from the report, run in a CGR_HOME that holds a leftover docker-compose.yaml, with a docker on PATH whose daemon does not answer:

$ cgr start --repo-path . --update-graph --clean --no-embeddings -y

# main
docker is installed but the daemon is not responding. Start Docker and retry.
exit: 1

# this branch
INFO | Skipping semantic embedding generation (--no-embeddings / CGR_SKIP_EMBEDDINGS)
Knowledge graph sync done for 'repo__b116146a' in 8.68s.
Graph update completed!
exit: 0

Type of Change

• Bug fix
• New feature
• Performance improvement
• Refactoring (no functional changes)
• Documentation
• CI/CD or tooling
• Dependencies

Related Issues

None filed. Reported directly: cgr start --update-graph --clean --no-embeddings asked for Docker on the embedded-graph default.

Test Plan

• Unit tests pass (uv run pytest -n auto -m "not integration"): 23085 passed. Two failures in test_oracle_toolchain_guards.py::TestCsharpGuard fail identically on unmodified main in this environment (local .NET SDK), so they are unrelated.
• New tests added:
  • stack start under --no-embeddings (flag and setting), Memgraph-only starts, --no-embeddings reaching the stack start
  • the default config not routing vectors to Docker even with a leftover compose file
  • sqlite as the default, and the upgrade notice (noted once; not noted once a backend is chosen)
  • a switched backend refilled on an unchanged checkout, and a pre-stamp checkout owing one pass
  • the extension-loading gate
• Integration tests pass (make test-integration, requires Docker)
• Manual testing: the before/after run above
• Existing tests that model Qdrant now pin it in conftest.py, as the graph tests pin Memgraph.

Checklist

• PR title follows Conventional Commits format
• All pre-commit checks pass (make pre-commit): ruff check and format are clean. ty reports only the pre-existing unresolved imports of optional extras (pymilvus, transformers) not installed locally.
• No hardcoded strings in non-config/non-constants files
• No # type: ignore, cast(), Any, or object type hints
• New comments and docstrings explain why, not what (see Comment Policy)

🤖 Generated with Claude Code

https://claude.ai/code/session_014fL7it5rTxfGMgcX1qZVe6

Summary by CodeRabbit

• New Features
  • Semantic search now uses a local SQLite vector store by default, with no separate server or Docker required. Qdrant and Milvus remain available as alternatives.
• Behavior Changes
  • Projects are re-embedded on their next sync after a vector-store backend change. Existing vectors remain in the previous store but are no longer searched.
  • Docker services start only when needed for the selected graph and vector-store backends. A notice appears when Qdrant settings are set without explicitly selecting a backend.
• Documentation
  • Updated setup and configuration guidance to reflect the SQLite default and available backend options.

[chatgpt-codex-connector]

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-19T11:15:06.100936Z	c7cf4a7	PR opened

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• codebase_rag/tests/test_embedding_sync_retry.py
• pyproject.toml

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📝 Walkthrough

SQLite is now the default vector store. The change adds extension-load checks, tracks the backend used for project embeddings, adjusts stack startup, and updates configuration, dependency, and user documentation.

Changes: SQLite vector-store default

Layer / File(s)	Summary
Select and initialize the default store .env.example, PYPI_README.md, codebase_rag/config.py, codebase_rag/constants/providers.py, codebase_rag/exceptions.py, codebase_rag/logs.py, codebase_rag/utils/dependencies.py, codebase_rag/vector_store.py, codebase_rag/tests/conftest.py, codebase_rag/tests/test_bundled_qdrant_default.py, codebase_rag/tests/test_sqlite_vector_store.py, pyproject.toml, docs/architecture/security.md, docs/getting-started/*, docs/guide/interactive-querying.md, docs/sdk/semantic-search.md	Configuration now defaults to SQLite. SQLite vector-store checks require loadable extensions, and legacy Qdrant settings without an explicit backend trigger a notice. Tests and documentation describe the default and supported alternatives.
Track backend changes during project sync codebase_rag/constants/core.py, codebase_rag/graph_updater.py, codebase_rag/tests/test_embedding_sync_retry.py, docs/getting-started/installation.md, docs/sdk/semantic-search.md	A missing or mismatched project backend stamp now makes embeddings outstanding. A settled embedding pass records the selected backend. Tests cover backend changes, missing stamps, and skipped embeddings.
Choose stack services for the selected backends codebase_rag/cli.py, codebase_rag/tests/test_embedded_graph_default.py, codebase_rag/tests/test_start_update_graph_flags.py	Stack startup now uses the embeddings-skip option and selects services based on graph backend, vector backend, and whether embeddings are skipped.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant ProjectSync
  participant GraphUpdater
  participant VectorStore
  ProjectSync->>GraphUpdater: Check backend stamp and pending markers
  GraphUpdater-->>ProjectSync: Request embeddings pass when stamp is missing or differs
  ProjectSync->>VectorStore: Write embeddings for selected backend
  ProjectSync->>GraphUpdater: Record settled embeddings pass
  GraphUpdater->>GraphUpdater: Save selected backend stamp

Loading

Suggested reviewers: claude

Merge Risk: ⚪ Minimal · up to 36f81

No actionable merge risk remains from the reviewed changes. SQLite refill tests skip when extensions cannot load, and sync can refill when support becomes available.

Pre-merge checks: 4

Check name	Status	Explanation
Title check		The title clearly and concisely describes both primary changes: SQLite becomes the default vector store, and Docker does not start when embeddings are disabled.
Description check		The description follows the required template and provides a complete summary, demo, change type, issue context, test results, limitations, and checklist status.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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[chatgpt-codex-connector]

💡 Codex Review

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Reviewed commit: c7cf4a7a7f

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[chatgpt-codex-connector]

Exclude musl Linux from the sqlite-vec dependency marker

On Alpine/musl with an x86_64 or aarch64 machine, this marker evaluates true even though the locked sqlite-vec release has only manylinux wheels and no source distribution (as shown by its wheel-only entry in uv.lock). Consequently, installing the documented semantic extra fails during dependency resolution rather than skipping sqlite-vec and allowing users to select Qdrant as intended; use a marker or packaging strategy that excludes musl environments.

Useful? React with 👍 / 👎.

[vitali87]

Not changing the marker. I traced the failure path, and it already exists on main. semantic also requires torch. The locked torch 2.14.0 has no sdist and ships wheels only for macosx_14_0_arm64, manylinux_2_28_{x86_64,aarch64} and win_amd64, so pip install 'code-graph-rag[semantic]' already fails to resolve on Alpine/musl before sqlite-vec is considered. sqlite-vec's wheels cover every platform torch ships for, so wherever the extra installs at all, sqlite-vec installs too. PEP 508 also has no marker that tells musl from glibc, so excluding musl isn't possible in the marker itself.

The next push corrects the pyproject.toml comment to say this, and I'm correcting the PR description, which wrongly said the extra skips sqlite-vec on musl.

---

Generated by Claude Code

[greptile-apps]

Confidence Score: 5/5

[Medium impact] The PR appears safe to merge; no blocking defects were found.

Summary

Makes SQLite the default vector store and avoids starting Qdrant when embeddings are skipped.

• Graph sync skips Docker when it does not need the stack's Qdrant.
• Semantic search stores vectors in SQLite by default and refills projects after a backend switch.
• SQLite semantic search turns off when Python cannot load its extension.

No actionable blocking issues were found.

Intentional changes acknowledged by vitali87:

• Runs without embeddings never start Qdrant, even if a later search would need the stopped server.
• Existing Qdrant vectors are no longer searched after the default changes to SQLite. Set CGR_VECTOR_STORE_BACKEND=qdrant to keep using them.

_{Reviews (1) · Last reviewed commit: "feat(vectors)!: default to the sqlite ve..." · Reviewed by Greptile}

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Actionable comments posted: 1

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Inline comments:
Review comments at @codebase_rag/tests/test_embedding_sync_retry.py:
- Line 403: Update the SQLite refill test’s skip condition to also skip when
extensions_loadable() is false, while retaining the existing has_sqlite_vec()
check.

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📥 Commits

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⛔ Files ignored due to path filters: 1

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📒 Files selected for processing: 23

• .env.example
• PYPI_README.md
• codebase_rag/cli.py
• codebase_rag/config.py
• codebase_rag/constants/core.py
• codebase_rag/constants/providers.py
• codebase_rag/exceptions.py
• codebase_rag/graph_updater.py
• codebase_rag/logs.py
• codebase_rag/tests/conftest.py
• codebase_rag/tests/test_bundled_qdrant_default.py
• codebase_rag/tests/test_embedded_graph_default.py
• codebase_rag/tests/test_embedding_sync_retry.py
• codebase_rag/tests/test_sqlite_vector_store.py
• codebase_rag/tests/test_start_update_graph_flags.py
• codebase_rag/utils/dependencies.py
• codebase_rag/vector_store.py
• docs/architecture/security.md
• docs/getting-started/configuration.md
• docs/getting-started/installation.md
• docs/guide/interactive-querying.md
• docs/sdk/semantic-search.md
• pyproject.toml

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