# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
dist/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
coverage.lcov
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
Pipfile.lock

# PEP 582
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

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

# OS
.DS_Store
Thumbs.db

# Project-specific (keep local only)
CLAUDE.md

# docs/ used to be ignored wholesale, which made every design doc and plan in the
# repo invisible to collaborators and made a docs site unbuildable. Only build
# artefacts are ignored now.
docs/_build/
docs/site/

# Scripts that ship with the examples are tracked; only the Dropbox packaging
# helper stays local (it encodes personal paths).
examples/hgdp_1kgp/package_data_for_dropbox.sh

# Binary tools and data
bin/
data/
logs/
examples/_shared/tools/

# Example outputs
examples/hgdp_1kgp/outputs/
examples/ukbb/*/outputs/
examples/aou/*/outputs/

# Controlled-access genetic data must never be committed.
# Binary genotype/dosage formats (PLINK, BGEN) - never belong in git
*.bed
*.bim
*.fam
*.bgen
*.pgen
*.psam
*.sample
*.bcf
*.vcf
*.vcf.gz

# Local-only data/output staging dirs (e.g. data_old/, outputs_old/, figures/)
**/data_old/
**/outputs_old/
**/data/
**/figures/

# Files holding real sample IDs / private path mappings
*_private*
*mappings_private*
*_labels.csv
*_samples.txt
# Synthetic test fixtures (SAMPLE_### IDs, no private data) must stay tracked
!tests/fixtures/cross_cohort/fit_labels.csv
!tests/fixtures/cross_cohort/project_labels.csv
examples/CaG/
examples/ukbb/60k_random/data/
examples/ukbb/60k_random/outputs/

# Local-only working dirs: superseded code kept for reference, and stray run
# output. Neither is part of the package; kept out of git rather than deleted.
deprecated/
admixture_outputs/
