3 Commits

Author	SHA1	Message	Date
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	778ed99ef6	refactor: slim pathways.db from 351 MB to 3.5 MB by removing unused tables ... Drop fact_interventions (440K rows), mv_patient_treatment_summary (35K rows), ref_drug_snomed_mapping (144K rows), and processed_files — all unused since the app moved to pre-computed pathway_nodes. Key changes: - Rewrite load_data() to source from pathway_nodes + pathway_refresh_log - Remove 7 dead methods and 8 dead state vars from pathways_app.py - Delete patient_data.py, load_snomed_mapping.py, test_large_dataset_performance.py - Remove SQLiteDataLoader (depended on fact_interventions) - Remove file tracking schema (processed_files tracked fact_interventions loads) - Remove legacy diagnosis functions from diagnosis_lookup.py - Add source_row_count migration for pathway_refresh_log - Clean all cross-references in __init__.py, data_source.py, migrate.py	2026-02-06 08:51:03 +00:00
Andrew Charlwood	fdd33a67af	Initial commit before Ralph loop	2026-02-04 13:04:29 +00:00