# ======================
# Python Standard Ignore 
# ======================

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

# Distribution / packaging
.Python
wandb/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
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/
cover/

# 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
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

.pdm.toml
.pdm-python
.pdm-build/

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

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.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/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# pycache files
**/__pycache__/
*.pyc

# ======================
# PDFBench Ignore 
# ======================

# EvoLlama, ProTrek and EvoLlama Folder
src/metrics/alignment/.deepgo2
src/metrics/alignment/.ProTrek
src/metrics/alignment/.EvoLlama

# test
**/test/
**/.test/
**/test_*
**/temp/
**/temp_*

# vscode
**/.vscode/

# example evaluation output
example/output/**/*.json
example/output/**/logs/
example/output/**/pdb_cache_dir/

# tools
tools/MMseqs/*
tools/InterProScan/*
tools/Foldseek/*
tools/TMScore/*

# weights
weights/*