runner-requirements.txt

# 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<2.0.0 # Due to pandas incompatibility
scipy
scikit-learn
scprep
scanpy
timm
torchdyn>=1.0.5   # 1.0.4 is broken on pypi
pot<0.9.5

# --------- notebook reqs -------- #
seaborn>=0.12.2
pandas