.gitignore

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

# C extensions
*.so

# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.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

# Translations
*.mo
*.pot

# Django stuff:
*.log

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# DotEnv configuration
.env

# Database
*.db
*.rdb

# Pycharm
.idea

# VS Code
.vscode/

# Spyder
.spyproject/

# Jupyter NB Checkpoints
.ipynb_checkpoints/

# Mac OS-specific storage files
.DS_Store

# vim
*.swp
*.swo

# Mypy cache
.mypy_cache/

# Vim settings
.vim/

# Ignore top level data (actual .csv, .xml etc) but track the folder structure and src/data/ scripts 
data/raw/*
data/interim/*
data/processed/*
data/external/*
data/meta/*

data/raw/.gitkeep
data/interim/.gitkeep
data/processed/.gitkeep
data/external/.gitkeep

# Data that I don't need to upload, large uncompressed files
organoid_T.tsv
primary_T.tsv
remote/*
*/lightning_logs/*
notebooks/poster*
notebooks/*/*.png
notebooks/*.png
credentials
src/visualization/*.png
wandbcreds
wandb/*
*.ckpt
*/wandb/*
data/mouse/*
src/data/converter_chunks/*
data
credentials
*.npy
lightning_logs/