| # Conda environment shared across the molecule, peptide, and language experiments. | |
| # Create with: | |
| # conda env create -f environment.yml | |
| # conda activate a2d2 | |
| # | |
| # NOTE: flash-attn is hardware-specific and must be built against your installed torch | |
| # and CUDA, so it is not listed below. It is imported by the shared transformer backbone | |
| # (model/casual_transformer.py, model/rotary.py) and is required for all experiments. | |
| # After creating the env, install it with: | |
| # pip install flash-attn==2.8.3 --no-build-isolation | |
| # Adjust pytorch-cuda below to match your CUDA toolkit / GPU. | |
| name: a2d2 | |
| channels: | |
| - pytorch | |
| - nvidia | |
| - conda-forge | |
| dependencies: | |
| - python=3.11 | |
| - pip | |
| - pytorch | |
| - pytorch-cuda=12.1 | |
| - rdkit=2023.9.6 | |
| - jupyterlab # for demo/quality_inference_demo.ipynb | |
| - pip: | |
| # --- core scientific / DL stack --- | |
| - numpy==1.26.4 | |
| - scipy==1.17.1 | |
| - pandas==2.1.4 | |
| - scikit-learn==1.8.0 | |
| - pytorch-lightning==2.6.0 | |
| - lightning==2.6.1 | |
| - transformers==4.55.4 | |
| - tokenizers==0.21.4 | |
| - safetensors==0.7.0 | |
| - accelerate==0.33.0 | |
| - peft==0.15.1 # LoRA adapters (language experiment) | |
| - datasets==2.19.2 | |
| - huggingface-hub==0.36.2 | |
| - einops==0.8.2 | |
| - timm==1.0.26 | |
| - omegaconf==2.3.0 | |
| - wandb==0.26.1 | |
| # --- molecule experiment --- | |
| - safe-mol==0.1.14 | |
| - datamol==0.12.5 | |
| - PyTDC==1.1.15 | |
| # --- peptide experiment --- | |
| - SmilesPE==0.0.3 | |
| - fair-esm==2.0.0 | |
| - xgboost==3.2.0 | |
| # --- plotting / utilities --- | |
| - matplotlib==3.10.6 | |
| - seaborn==0.13.2 | |
| - tqdm==4.67.1 | |
| - joblib==1.5.3 | |
| - loguru==0.7.3 | |
| - fsspec==2024.3.1 |