| # Note if using Conda it is recommended to install torch separately. | |
| # For most of testing the following commands were run to set up the environment | |
| # This was tested with torch==1.12.1 | |
| # conda create -n ti-env python=3.10 | |
| # conda activate ti-env | |
| # pip install torch==1.12.1+cu113 torchvision==0.13.1+cu113 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu113 | |
| # pip install -r requirements.txt | |
| # --------- pytorch --------- # | |
| torch>=1.11.0,<2.0.0 | |
| torchvision>=0.11.0 | |
| pytorch-lightning==1.8.3.post2 | |
| torchmetrics==0.11.0 | |
| # --------- hydra --------- # | |
| hydra-core==1.2.0 | |
| hydra-colorlog==1.2.0 | |
| hydra-optuna-sweeper==1.2.0 | |
| # hydra-submitit-launcher | |
| # --------- loggers --------- # | |
| wandb | |
| # neptune-client | |
| # mlflow | |
| # comet-ml | |
| # --------- others --------- # | |
| black | |
| isort | |
| flake8 | |
| Flake8-pyproject # for configuration via pyproject | |
| pyrootutils # standardizing the project root setup | |
| pre-commit # hooks for applying linters on commit | |
| rich # beautiful text formatting in terminal | |
| pytest # tests | |
| # sh # for running bash commands in some tests (linux/macos only) | |
| # --------- pkg reqs -------- # | |
| lightning-bolts | |
| matplotlib | |
| numpy | |
| scipy | |
| scikit-learn | |
| scprep | |
| scanpy | |
| timm | |
| torchdyn>=1.0.5 # 1.0.4 is broken on pypi | |
| pot | |
| # --------- notebook reqs -------- # | |
| seaborn>=0.12.2 | |
| pandas>=2.2.2 | |