3 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	092fdbba5a	feat: add CLI refresh command for pathway data (Task 2.1) ... Add cli/refresh_pathways.py with: - refresh_pathways() main function for full pipeline orchestration - insert_pathway_records() for SQLite insertion - log_refresh_start/complete/failed() for refresh tracking - CLI with --minimum-patients, --provider-codes, --dry-run, --verbose Uses existing pipeline functions: - fetch_and_transform_data() from pathway_pipeline.py - process_all_date_filters() for 6 date filter combinations - Schema helpers from data_processing/schema.py	2026-02-04 23:30:11 +00:00