# Byte-compiled / cache
__pycache__/
*.py[cod]
*$py.class
.pytest_cache/
.mypy_cache/
.ruff_cache/
.ipynb_checkpoints/

# Distribution / build
build/
dist/
*.egg-info/
.eggs/
wheels/

# Environments
.venv/
venv/
env/
ENV/

# Coverage / tooling
.coverage
.coverage.*
htmlcov/
coverage.xml
.tox/
.nox/
.hypothesis/

# OS / editor
.DS_Store
Thumbs.db
.idea/
.vscode/
*.swp

# Machine-local agent/tool settings
.claude/settings.local.json

# Internal working documents. The technical review is kept locally rather than
# published; its conclusions live in CHANGELOG.md. Move it under docs/ if you
# decide to publish it.
*_Technical Review.md

# --- Project-specific -------------------------------------------------------

# Vendored rENA reference material. rENA is a large third-party GPL-3 project with
# its own upstream; see reference/README.md for how to obtain it. Keep the man pages
# and manifest that ARE tracked, and exclude everything else.
rENA-main/
rENA-main*.zip
reference/rENA/*
!reference/rENA/man/
!reference/rENA/man/**
pyENA-*-internal-alpha/
pyENA-*-internal-alpha.zip

# Local research data. ENA inputs are often transcripts containing personal data;
# keep them out of the repository by default.
data/local/
*.local.csv
