requirements.txt

# --------- pytorch --------- #
torch==2.5.1
torchvision==0.20.1
lightning==2.5.2
torchmetrics==1.8.0

# --------- hydra --------- #
hydra-core==1.3.2
hydra-colorlog==1.2.0
hydra-optuna-sweeper==1.2.0

# --------- loggers --------- #
wandb==0.21.0
# neptune-client
# mlflow
# comet-ml
# aim>=3.16.2  # no lower than 3.16.2, see https://github.com/aimhubio/aim/issues/2550

# --------- others --------- #
rootutils==1.0.7  # standardizing the project root setup
pre-commit==4.0.1      # hooks for applying linters on commit
rich==13.9.4            # beautiful text formatting in terminal
pytest==8.1.1  # tests
sh==2.2.2  # for running bash commands in some tests (linux/macos only)
transformers==4.54.1
polars==1.12.0
xformers==0.0.28.post3 --index-url https://download.pytorch.org/whl/cu124
ninja==1.11.1.1
einops==0.8.0
ipython-autotime==0.3.2
seaborn==0.13.2
lru-dict==1.3.0
datasets==4.0.0
scanpy==1.11.3
pyfaidx==0.8.1.4
biopython==1.85
peft==0.15.2
fiddle==0.3.0