darwin-pbpk-platform/.gitignore at main · agourakis82/darwin-pbpk-platform · GitHub

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# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Virtual environments
venv/
ENV/
env/
.venv/

# IDE
.idea/
.vscode/
*.swp
*.swo
*~

# Jupyter
.ipynb_checkpoints/

# Testing
.pytest_cache/
.coverage
htmlcov/

# Julia
*.jl.cov
*.jl.*.cov
*.jl.mem
Manifest.toml

# Large data files (use Zenodo/DVC for these)
data/embeddings/*.npy
data/embeddings/*.npz
data/embeddings/*.pkl
data/embeddings/*.parquet
data/external_datasets/*.zip
julia-migration/data/zenodo/*.zip
julia-migration/data/zenodo/wget-log
*.h5
*.hdf5
*.pt
*.pth
*.onnx

# Keep README in embeddings
!data/embeddings/README.md

# OS
.DS_Store
Thumbs.db

# Logs
*.log
logs/

# Secrets
.env
.env.local
*.pem
*.key

# Temporary
tmp/
temp/
*.tmp
*.zip
darwin-pbpk-datasets-*.zip
.env
-e
# API keys
julia-migration/scripts/data_import/.env

# Large data files (>100MB) - Use external storage (Zenodo/DVC)
julia-migration/scripts/data_import/raw_data/cpic/diplotypes.json
**/raw_data/**/*.json

# OBO Foundry ontologies (download via scripts)
julia-migration/data/ontologies/*.owl
julia-migration/data/ontologies/*.obo
julia-migration/data/ontologies/*.json