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

# Environments
.venv/
venv/
env/
.conda/

# Jupyter
.ipynb_checkpoints/

# OS / Editor
.DS_Store
Thumbs.db
.vscode/
.idea/

# Logs
*.log
nohup.out

# Large binary artifacts (distributed via Zenodo)
*.pkl
*.pt
*.pth
*.bin
*.safetensors
*.h5
*.npy
*.npz

# Model checkpoints are distributed separately
checkpoints/

# Data directory (populated from Zenodo)
/data/

# Training outputs (not committed)
pretrain_output/
finetune_output/
models/
outputs/

# MMseqs2 raw alignment outputs (distributed via Zenodo data/model archive)
similarity_audit/results/run*/alignment_results.tsv

# Temporary files
*.tmp
*.temp
