bionemo-framework/bionemo-recipes/interpretability/sparse_autoencoders/.gitignore at c936525214249e833f912d6c5d2b324d43fac817 · NVIDIA/bionemo-framework · 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/
venv/
ENV/
env/

# UV package manager
.python-version

# Jupyter Notebooks
.ipynb_checkpoints/

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

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/
.nox/

# Weights & Biases
wandb/

# Node.js
node_modules/
npm-debug.log*
yarn-debug.log*
yarn-error.log*
.npm
.yarn

# Model weights and checkpoints
*.pt
*.pth
*.ckpt
*.safetensors
*.bin
checkpoints/

# Data files (large)
*.parquet
*.arrow
*.h5
*.hdf5
*.fasta
*.fasta.gz
*.tsv.gz
features.json
interpretations.json
cluster_labels.json

# Activation stores
activations_store/
**/activations_store/

# Output directories
outputs/
**/outputs/
**/outputs_*/
analysis_output/
**/analysis_output/

# Data directories (but not source code data/ modules)
/data/
datasets/
recipes/*/data/
!**/src/**/data/

# Viewer public data (generated)
**/public/features.json
**/public/features_atlas.parquet
**/public/*.parquet
**/public/features/
**/public/features/*.json

# Logs
*.log
logs/

# Temporary files
*.tmp
*.temp
.cache/

# Environment variables
.env
.env.local
.env.*.local

# Keep specific files
!recipes/**/configs/**
!**/config.yaml
# Note: uv.lock is NOT ignored - it's useful for reproducibility