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5 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 1581b1d3dd docs: update CLAUDE.md to reflect slimmed database architecture 
Remove references to deleted tables (fact_interventions,
mv_patient_treatment_summary, ref_drug_snomed_mapping, processed_files),
deleted files (patient_data.py, load_snomed_mapping.py), and removed
classes (SQLiteDataLoader). Update package structure, data loaders,
database schema, fallback chain, and AppState descriptions.
 2026-02-06 09:39:19 +00:00
Andrew Charlwood fed909481e docs: update CLAUDE.md with indication chart architecture and CLI docs (Task 5.2) 2026-02-05 20:50:01 +00:00
Andrew Charlwood 76e0d64820 docs: complete Task 4.3 Documentation 
Update CLAUDE.md with new pathway data architecture:
- Add Pathway Data Architecture section with date filter table
- Update package structure with cli/ and pathway_pipeline.py
- Add CLI module and pathway pipeline documentation
- Update data flow diagrams (pre-computed vs legacy)
- Add pathway tables to database schema section
- Add CLI commands section with usage examples
- Add Breaking Changes section documenting:
  - Date filter changes (pickers -> dropdowns)
  - Data refresh model (real-time -> pre-computed)
  - State variable changes
  - Icicle chart enhancements

Mark all Task 4.3 subtasks complete in IMPLEMENTATION_PLAN.md
Update completion criteria status
 2026-02-05 00:56:34 +00:00
Andrew Charlwood fdd33a67af Initial commit before Ralph loop 2026-02-04 13:04:29 +00:00