LucaOneTasks/requirements_dnabert2.txt at master · LucaOne/LucaOneTasks · GitHub

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deepspeed==0.5.9
sentencepiece==0.1.97
sacremoses==0.0.53
datasets==2.12.0
h5py==3.8.0
biopython==1.80
biotite==0.35.0
brotlipy==0.7.0
numpy==1.24.2
obonet==0.3.1
pandas==1.5.3
pickle5==0.0.11
Pillow==9.3.0
scikit-learn==1.2.1
scipy==1.10.1
seaborn==0.12.2
six==1.16.0
subword-nmt==0.3.8
tensorboard==2.11.2
tensorboardX==2.5.1
tensorflow==2.11.0
tensorflow-estimator==2.11.0
tfrecord==1.14.1
tokenizers==0.13.2
# tokenizers==0.19.1
torch==1.13.1
torchaudio==0.13.1
torchvision==0.14.1
# torch==1.12.1
# torchaudio==0.12.1
# torchvision==0.13.1
tqdm==4.64.1
transformers==4.29.0
# transformers==4.41.2
matplotlib==3.6.3
Werkzeug==2.2.2
wget==3.2
wrapt==1.14.1
xgboost==1.7.3
zipp==3.12.0
lightgbm==3.3.5
xgboost==1.7.3
BeautifulSoup4==4.11.1
requests==2.24.0
gemmi==0.5.8
networkx==3.0
statsmodels==0.14.0
pymysql==0.10.1
charset-normalizer==3.1.0
fairscale==0.4.13
fair-esm[esmfold]
# OpenFold and its remaining dependency
dllogger @ git+https://github.com/NVIDIA/dllogger.git
rdkit==2023.9.4
timm==0.9.12
apex  # better install it from source: https://github.com/NVIDIA/apex
fire==0.5.0
fsspec==2023.5.0
peft==0.8.2
openpyxl==3.1.2
pynvml==11.5.0
fairscale==0.4.13