.gitignore

# Misc
workflow/.snakemake
workflow/logs/*
!workflow/logs/.gitkeep
*ignore*
archive/
explore
sandbox
*.html
.env
*.h5ad
*.zarr
*.explorer

# OS related
.DS_Store

# Documentation
site

# Code Ocean
code
results

# Logs
outputs
multirun
lightning_logs
checkpoints
run.log

# Jupyter Notebook
.ipynb_checkpoints
exploration/*
*.ipynb
!docs/tutorials/**/**.ipynb
!notebooks/*.ipynb

# pyenv
.python-version

# VisualStudioCode
.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
!.vscode/launch.json
!.vscode/extensions.json
*.code-workspace
**/.vscode

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

# C extensions
*.so

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

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.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
*.cover
*.py,cover
.hypothesis/
.pytest_cache/