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

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
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/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

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

# JetBrains
.idea/

# Data & Models
*.h5
*.tar
*.tar.gz

# Lightning-Hydra-Template
configs/local/default.yaml
/data/*
!/data/.gitkeep
/logs/*
!/logs/.gitkeep
.env

# Aim logging
.aim

# WandB logger
/wandb/

# Jupyter Notebook
.ipynb_checkpoints

# pyaging
tutorials/pyaging_data/
tutorials/artifacts/
tutorials/logs/
tutorials/dependencies/

# Feather files
*.feather
*.arrow

# VS Code Profile
CpGPT.code-profile

# CSV
*.csv

# Checkpoints
*.ckpt

# Dependencies
/dependencies/*
!/dependencies/.gitkeep

# Gzip
*.gz

# numpy
*.npy

# macOS
.DS_Store

# Cookies
cookies.txt
analysis/GSE*
analysis/logs/
analysis/tmp/
analysis/figures/svg/
analysis/supplementary/
analysis/ComputAge/
analysis/benchdata/
tutorials/CpGPT-submission-package

# Python testing and linting
.ruff_cache/
.pytest_cache/

# Lightning logs
lightning_logs/

# Pyaging data
pyaging_data/

# Pickle files
*.pkl

# Public ignores
/revision/
CLAUDE.md
AGENTS.md
/analysis/
/scripts/
/tests/
/tutorials/*
!/tutorials/attend.ipynb
!/tutorials/convert_array.ipynb
!/tutorials/denoise.ipynb
!/tutorials/finetune.ipynb
!/tutorials/generate.ipynb
!/tutorials/impute.ipynb
!/tutorials/predict_mortality.ipynb
!/tutorials/quick_setup copy.ipynb
!/tutorials/quick_setup.ipynb
!/tutorials/reference_map.ipynb
/docker/
# Keep private CI config out of the public repo, except the PyPI
# trusted-publishing workflow which must exist here to publish releases.
/.github/*
!/.github/workflows/
/.github/workflows/*
!/.github/workflows/release.yaml
/configs/data/*
!/configs/data/default.yaml
/configs/experiment/*
!/configs/experiment/template.yaml
.pre-commit-config.yaml
Makefile
.DS_Store
.coveragerc
