4 Commits

Author	SHA1	Message	Date
admin	fcbde7c689	Restructured src to more logical heirachy	2026-02-09 16:22:05 +00:00
Andrew Charlwood	76838887e6	refactor: reorganize repository to src/ layout ... Move 6 packages (core, config, data_processing, analysis, visualization, cli) into src/ to reduce root clutter. Merge tools/data.py into data_processing/transforms.py. Move docs to docs/. Path resolution via .pth file (setup_dev.py), pytest pythonpath config, and sys.path bootstrap in rxconfig.py and CLI entry points. Clean up pyproject.toml deps (remove stale pins, add snowflake-connector-python). Fix tomllib import for Python 3.10 compatibility. All 113 tests pass.	2026-02-06 12:03:48 +00:00
Andrew Charlwood	c6e426e36c	fix: increase network timeout and batch size for GP lookup queries (Task 3.2) ... Dry run test revealed GP lookup queries timing out at 30s (connection_timeout in snowflake.toml). Increased to 600s. Also increased batch_size from 500 to 5000 — query time is ~40s regardless of batch size (CTE compilation overhead), so larger batches reduce total time from ~50min to ~6min for 36K patients. Dry run results: 91.8% GP match rate, 49.3% drug-indication match rate, 42,072 modified UPIDs, 1,846 pathway nodes across 6 date filters.	2026-02-05 23:55:12 +00:00
Andrew Charlwood	fdd33a67af	Initial commit before Ralph loop	2026-02-04 13:04:29 +00:00