MutationScan/.gitignore at main · vihaankulkarni29/MutationScan · GitHub

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# Snakemake State
.snakemake/

# Dynamic Data & Results (Strict quarantine)
data/local_genomes/*
!data/local_genomes/.gitkeep
data/output/*
!data/output/.gitkeep
data/results/*
!data/results/.gitkeep
data/ligands/*
!data/ligands/.gitkeep

# IDE & Python Caches
__pycache__/
*.pyc
.vscode/
.idea/

# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.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

# Virtual environments
venv/
ENV/
env/
.venv

# IDE
.vscode/
.idea/
*.swp
*.swo
*~
.DS_Store
*.sublime-project
*.sublime-workspace

# Testing and coverage
.pytest_cache/
.coverage
.coverage.*
htmlcov/
.tox/
.hypothesis/

# Type checking
.mypy_cache/
.dmypy.json
dmypy.json

# IDE specific
.pylintrc
.flake8

# Project specific Data & Caches
data/genomes/*
!data/genomes/.gitkeep
data/output/*
!data/output/.gitkeep
data/databases/*
!data/databases/.gitkeep
data/interim/*
!data/interim/.gitkeep
data/results/*
!data/results/.gitkeep
data/proteins/*
!data/proteins/.gitkeep
data/refs/*
!data/refs/.gitkeep
data/raw/*
!data/raw/.gitkeep
data/ligands/*
!data/ligands/.gitkeep

# Global ignores for dynamic biophysics and data files
*.csv
*.pdb
*.pdbqt
*.fasta
*.faa
*.fna

# Downloaded tools/binaries
datasets.exe
*.exe

# Logs
logs/
*.log

# Cache
.cache/
*.pkl
*.pickle

# Temporary files
*.tmp
*.bak
*.backup
temp_data_collection/
filter_modern_strains.py
get_refs.py

# OS specific
Thumbs.db
.DS_Store
.AppleDouble
.LSOverride

# Docker
docker-compose.override.yml

# CI/CD
.github/workflows/*.backup