# Temp files
.DS_Store
*~
buck-out/
node_modules/
playground/
data/
temp/

# Compiled files
.venv/
__pycache__/
.mypy_cache/
.ruff_cache/

# Distribution / packaging
/build/
/dist/
/*.egg-info/

# Tests and coverage
/.pytest_cache/
/.cache/
/data/

# docs
/docs/generated/
/docs/_build/
# mkdocs build output
site/

# pixi
.pixi/

# IDEs
/.idea/
/.vscode/
.ipynb_checkpoints/
tests/check.ipynb

# training
rune/*
**/wandb/
**/*.json
# exclude all pt / joblib / json, but always keep the committed package data
# assets under src/bolero/pkg_data (motif clusters, gene regions, etc.)
**/*.pt
!src/bolero/pkg_data/**/*.pt
**/*.joblib
!src/bolero/pkg_data/**/*.joblib
**/*.ckpt
!src/bolero/pkg_data/**

# images
**/*.jpg

# inference reult
**/*.npy
**/*.txt

paper/
working_dir
working_dir/

# In docs/tutorials keep only prose + notebooks; ignore every generated data
# artifact (h5ad/h5mu/feather/model dirs/... produced by running the notebooks).
docs/tutorials/**
!docs/tutorials/**/
!docs/tutorials/**/*.md
!docs/tutorials/**/*.ipynb
# ...but never track notebook checkpoints
docs/tutorials/**/.ipynb_checkpoints/
