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Repository Guidelines

Project Structure & Modules

  • bacformer/: Python package (modeling, preprocessing, TL). Entry modules live under modeling/, pp/, and tl/.
  • tests/: Pytest suite organized by area (modeling/, tl/, pp/).
  • tutorials/: Jupyter notebooks demonstrating core tasks.
  • scripts/: Small utilities used during development.
  • files/: Sample assets (e.g., pao1.gbff, images).
  • ai_docs/, .claude/: Design and agent notes (keep synced with code).

Build, Test, and Dev Commands

  • Install (dev + tests): pip install .[dev,test] (Python >= 3.10).
  • Lint/format: ruff check . and ruff format . (or pre-commit run -a).
  • Tests: pytest -q (or with coverage: pytest --cov=bacformer).
  • Build wheel: hatch build (uses Hatchling per pyproject.toml).
  • Pre-commit: pre-commit install then commit; CI expectations mirror hooks.

Coding Style & Naming

  • Formatter/linter: Ruff (120 char lines, import sorting, numpy-style docstrings). No nb formatting in CI.
  • Indentation: 4 spaces; UTF-8; Unix line endings.
  • Naming: snake_case for modules/functions, PascalCase for classes, UPPER_SNAKE_CASE for constants.
  • Public APIs live in bacformer/__init__.py and subpackage __init__.py; keep imports explicit.

Testing Guidelines

  • Framework: Pytest; tests under tests/; name files test_*.py and functions test_*.
  • Coverage: target meaningful lines in bacformer/; avoid testing tutorials and data assets (see coverage omit in pyproject.toml).
  • Use small, deterministic fixtures; prefer CPU paths when possible.

Commit & Pull Request Guidelines

  • Style: Conventional prefixes (feat, fix, refactor, docs, test, chore); keep subject imperative and concise.
  • Commits should be focused; include brief rationale when non-obvious.
  • PRs: clear description, linked issues (Fixes #123), test updates, before/after notes for behavior, and any performance/memory impact.
  • Run pre-commit run -a and pytest locally before opening the PR.

Security & Configuration Tips

  • GPU is optional; CPU tests should pass. Flash-Attn and FAESM are optional extras.
  • Pin heavy deps only when required; prefer feature flags/extras (.[faesm]).