gbanyan 63e3cccd3c fix: implement real checkpoint persistence for literature layer ...

Previously checkpoints only logged a message but never wrote to DuckDB,
causing all progress to be lost on process kill. Now every batch_size
genes (default 500) are persisted to a literature_partial table.
On restart the CLI loads partial results and resumes from where it
left off. The partial table is cleaned up after successful completion.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-02-13 21:14:16 +08:00

..

api_clients

feat(01-01): create base API client with retry and caching

2026-02-11 16:25:46 +08:00

cli

fix: implement real checkpoint persistence for literature layer

2026-02-13 21:14:16 +08:00

config

feat(04-01): implement known gene compilation and ScoringWeights validation

2026-02-11 20:41:31 +08:00

evidence

fix: implement real checkpoint persistence for literature layer

2026-02-13 21:14:16 +08:00

gene_mapping

fix: resolve runtime bugs for pipeline execution on Python 3.14 + latest deps

2026-02-13 03:44:01 +08:00

output

feat(05-02): implement reproducibility report module with JSON and Markdown output

2026-02-12 04:00:21 +08:00

persistence

feat(03-03): implement protein evidence layer with UniProt/InterPro integration

2026-02-11 19:07:30 +08:00

scoring

feat(06-03): comprehensive validation report and CLI validate command

2026-02-12 04:48:25 +08:00

__init__.py

feat(01-01): create Python package scaffold with config system

2026-02-11 16:24:35 +08:00