acatome-store

Persistent storage, deduplication, metadata queries, and semantic search for scientific paper bundles.

Features

• SQLAlchemy ORM — portable across SQLite, Postgres, MySQL
• Refs + Papers split — identity table (refs) separate from ingested content (papers)
• Citation graph — directed citing → cited edges, works for ingested + stub papers
• Supplements — ingest supplementary PDFs with scoped block retrieval
• Retractions — flag papers as retracted with notes
• Vector search — ChromaDB (default) or pgvector (zero text duplication)
• CLI — acatome-store command for ingest, reingest, query, retract, and stats
• Schema management — reset_schema() and reingest --drop for clean rebuilds

Installation

uv pip install -e .

With Postgres support:

uv pip install -e ".[postgres]"

Usage

from acatome_store import Store

store = Store()
ref_id = store.ingest(bundle_path)
paper = store.get(ref_id)
results = store.search_text("transformer attention", top_k=5)
# hits include paper info, block summaries, and text

CLI

acatome-store ingest /path/to/bundle.acatome    # single bundle
acatome-store ingest /path/to/dir/               # directory of bundles
acatome-store reingest                            # re-ingest all from ~/.acatome/papers/
acatome-store reingest --drop                     # drop schema + re-ingest (confirm prompt)
acatome-store reingest --path /other/dir          # custom bundle directory
acatome-store stats
acatome-store search "CO2 capture"
acatome-store list
acatome-store info doi:10.1234/example
acatome-store retract doi:10.1234/fake --note "Fabricated data"

Schema Reset

If the database schema drifts from the model (e.g. after upgrading acatome-store), use reingest --drop to drop all tables, recreate from the current SQLAlchemy model, and re-ingest all .acatome bundles. No data is lost since bundles are the source of truth.

acatome-store reingest --drop
# prompts for confirmation, then:
# 1. Drops all tables (refs, blocks, papers, links, etc.)
# 2. Recreates schema from current model
# 3. Re-ingests all bundles from ~/.acatome/papers/

Programmatically:

store = Store()
store.reset_schema()  # drop + recreate tables

Testing

uv run python -m pytest tests/ -v

License

LGPL-3.0-or-later — see LICENSE.