| # Foundational Libraries (core dependencies) | |
| setuptools==59.5.0 | |
| numpy==1.23.5 # Pin numpy to ensure compatibility | |
| scipy==1.9.3 # Install scipy after numpy | |
| pandas==1.5.3 # Pin pandas to avoid dask incompatibilities | |
| # Libraries dependent on numpy, pandas, or scipy | |
| numba==0.58.1 | |
| dask==2023.4.1 # Use a stable version compatible with pandas==1.5.3 | |
| scikit-learn==1.2.2 | |
| imageio==2.34.0 | |
| matplotlib==3.7.1 | |
| seaborn==0.12.2 | |
| wordcloud==1.9.3 | |
| # Machine Learning and Deep Learning | |
| torchmetrics==0.10.3 | |
| pytorch-lightning==1.9.5 | |
| transformers==4.29.2 | |
| deepspeed==0.9.2 | |
| accelerate==0.19.0 | |
| diffusers==0.16.1 | |
| optuna==3.1.1 | |
| fair-esm==2.0.0 | |
| # Specialized Libraries | |
| lightning-flash==0.8.2 | |
| axial-positional-embedding==0.2.1 | |
| linear-attention-transformer==0.19.1 | |
| linformer==0.2.3 | |
| # Bioinformatics | |
| biopython==1.79 | |
| # General Utilities | |
| tqdm==4.65.0 | |
| pynvml==11.5.0 | |