#dev
# NOTE: For .gitignore, order matters. The last match wins. meaning if you want to ignore a folder but keep something in the folder, first ignore the folder, then unignore the file.
.venv
conda
token
# input/output is designed as a generic folder for input files if the config isn't adjusted. Because of this we want to ensure it's documented out. As it'll be an empty folder a .gitkeep file is used for git to maintain the structure.
input/*
!input/.gitkeep
!input/example_samplesheet.tsv
output/*
!output/.gitkeep
# The config folder is intended to keep multiple program configs, these are sensitive to the system, a default is included for people to work off of while the others are hidden
config/*
# If you are using pypi integration
.pypirc
logs/*
!logs/.gitkeep

_proc/
# The following files ignored are part of a standard python project with minor additions
_docs/

*.bak
.gitattributes
.last_checked
.gitconfig
*.bak
*.log
*~
~*
_tmp*
tmp*
tags
*.pkg

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

# C extensions
*.so

# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# 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/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# pyenv
.python-version

# celery beat schedule file
celerybeat-schedule

# SageMath parsed files
*.sage.py

# dotenv
.env

# virtualenv
.venv
venv/
ENV/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/

*.swp

# osx generated files
.DS_Store
.DS_Store?
.Trashes
ehthumbs.db
Thumbs.db
.idea

# pytest
.pytest_cache

# tools/trust-doc-nbs
docs_src/.last_checked

# symlinks to fastai
docs_src/fastai
tools/fastai

# link checker
checklink/cookies.txt

# .gitconfig is now autogenerated
.gitconfig

# Quarto installer
.deb
.pkg

# Quarto
.quarto
