.gitignore

_docs/
_proc/

*.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/

.vscode
*.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

# ===========================================================================
# Project files and folders to exclude from tracking and GitHub

# Secrets, keys, ...
secrets/

# General resources
resources/

# wandb local directories
*/wandb/*
**/artifacts/*

# Data
# Track all files in the top level directory data/ 
# Ignore all files in the subdirectories data/xxx
data/*/

# Package Development Files
# Output files of Art-Illumina in data_dev
nbs-dev/data_dev/*.fq
nbs-dev/data_dev/*.aln
nbs-dev/data_dev/*.sam
nbs-dev/data_dev/paired*


# Work notebooks (nbs) excluded from tracking, i.e. all files in work-nbs subdirectory
nbs/*/work-nbs

# dataset files created by nbs
nbs/*_ds 
nbs/*/*_ds 
nbs/*/*/*_ds 

# art output files created with nbs
nbs/reads
nbs/*/reads
nbs/*/*/reads

# Any file marked as WIP
wip.*.ipynb
nbs/wip.*.ipynb
nbs/*/wip.*.ipynb

# Any html version of notebooks
nbs/*.html
nbs/*/*.html
nbs/*/*/*.html

# Any database file with extension .db
nbs-dev/data_dev/*.db
nbs-dev/data_dev/*/*.db
nbs-dev/data_dev/*/*/*.db
nbs-dev/data_dev/*/*/*/*.db