allelix/.gitignore at main · dial481/allelix · GitHub

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# Claude / AI tooling
CLAUDE.md
GITHUB_WORKFLOW.md
.claude/

# Virtual environments
.venv/
venv/
env/
ENV/

# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
*.egg
MANIFEST
pip-log.txt
pip-delete-this-directory.txt

# Testing / coverage
.pytest_cache/
.coverage
.coverage.*
htmlcov/
.tox/
.nox/
coverage.xml
*.cover
.hypothesis/

# Linting / type checking
.ruff_cache/
.mypy_cache/
.dmypy.json
dmypy.json
.pyre/
.pytype/

# Local database cache (downloaded at runtime, project root only)
/data/
!/data/.gitkeep

# Private genotype files — NEVER commit
# CC0 openSNP test fixtures are hosted as release assets (see scripts/fetch_testdata.sh)
MHG.txt
# Genotype data — NEVER commit private genetic data
*.vcf
*.vcf.gz
*.vcf.gz.tbi
/*.txt
/*.csv
!README.txt
!CHANGELOG.txt
# Synthetic test fixtures are committed
!tests/fixtures/*.vcf
!tests/fixtures/*.vcf.gz
!tests/fixtures/*.txt

# IDE / editor
.idea/
.vscode/
*.swp
*.swo
*~
.DS_Store

# OS
Thumbs.db
desktop.ini

# Jupyter
.ipynb_checkpoints/
*.ipynb

# Environment / secrets
.env
.env.local
.env.*.local
*.pem
*.key

# Test data library (committed fixtures; downloads stay gitignored)
test_data/databases/
test_data/baselines_local/
test_data/gwas_catalog*
test_data/gwas-catalog*
test_data/data/
test_data.tar.gz