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Repository Guidelines

Project Structure & Module Organization

  • Core orchestration lives in code/; main_handler.py coordinates task-level QC flows.
  • Domain logic sits in code/data_processing/ (CC, MEM, PS, WL modules plus utilities for plotting and persistence).
  • Raw exports belong in data/ (data/int/ stores intermediates); aggregated CSVs auto-save to meta/.
  • Visual artifacts render into group/plots/; keep derived notebooks or experiments outside tracked dirs unless reproducible.

Build, Test, and Development Commands

  • python -m venv .venv && source .venv/bin/activate (or nix develop) prepares the toolchain.
  • pip install -r requirements.txt installs runtime dependencies; prefer dev-only extras in a separate file if needed.
  • python code/main_handler.py <TASK> runs QC for a specific task (AF, WL, etc.); use all to replicate the scheduled GitHub Action.
  • python -m flake8 code enforces lint rules; resolve warnings before committing.

Coding Style & Naming Conventions

  • Target Python 3.10+ features compatible with the flake environment; keep indentation at four spaces and follow PEP 8 layout.
  • Modules and functions use snake_case (save_utils.py, qc_cc_dfs), while orchestration classes remain PascalCase (Handler, CCqC).
  • Constants stay UPPER_SNAKE_CASE; include concise docstrings when adding new data loaders or plotters.

Testing Guidelines

  • Pytest is available in CI; place new tests under tests/ mirroring the package tree (tests/data_processing/test_wl_qc.py).
  • Name tests test_<behavior>() and rely on fixtures for representative CSV payloads; store them in tests/fixtures/.
  • Run pytest locally before opening a PR; aim for coverage on threshold logic and file outputs, using temp dirs to assert artifact names.

Commit & Pull Request Guidelines

  • History favors short, imperative titles (e.g., Add WL QC persistence); keep subjects ≤72 chars and add context in the body when behavior shifts.
  • PRs should summarize intent, list commands run (pytest, flake8, task processors), and call out any data schema or visualization changes with screenshots from group/plots/.
  • Link related tickets or issues and flag breaking changes early so downstream analysts can adjust schedules.

Security & Configuration Notes

  • Never commit credentials or real tokens—parameterize secrets via environment variables and document expectations in README.md.
  • Large or sensitive CSV exports stay in meta/ (tracked aggregations) or ignored paths; update .gitignore when introducing new temp output folders.
  • When adding config flags, reflect them in run.py usage examples and surface defaults in module-level constants.