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Update requirements.txt

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  1. requirements.txt +17 -24
requirements.txt CHANGED
@@ -1,41 +1,34 @@
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  # deep learning
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  # Install with conda
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- torch>=2.1.0
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- torch_geometric
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- lightning>=2.1.0
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  torchmetrics
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  transformers
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  scikit-learn
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  dgl
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- dglgo
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  dgllife
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  # configuration and utilities
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  hydra-core
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- # hydra-colorlog
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- # hydra-optuna-sweeper
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- # hydra-submitit-launcher
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  pandas
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- swifter
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- # pre-commit
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- # rich
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- # pytest
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- # tensorboard
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-
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- # feature extraction
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- biopython
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- rdkit
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- networkx>=3.2.0
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- mhfp
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- # tmap
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  # model-specific requirements
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- # subword-nmt # MONN
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  tape_proteins # TransformerCPI2
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- gensim # TransformerCPI
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  fair-esm # CoaDTI-pro
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  # apex # recommended by TAPE-BERT
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- # data visualization utilities
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- seaborn
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- plotly
 
 
 
 
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  # deep learning
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  # Install with conda
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+ # torch>=2.0
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+ # torch_geometric
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+ lightning>=2.0
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  torchmetrics
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  transformers
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  scikit-learn
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  dgl
 
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  dgllife
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  # configuration and utilities
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  hydra-core
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+ hydra-colorlog
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+ hydra-optuna-sweeper
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+ hydra-submitit-launcher
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  pandas
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+ pre-commit
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+ rich
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+ pytest
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+ tensorboard
 
 
 
 
 
 
 
 
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  # model-specific requirements
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+ subword-nmt # MolTrans
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  tape_proteins # TransformerCPI2
 
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  fair-esm # CoaDTI-pro
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  # apex # recommended by TAPE-BERT
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+ # feature extraction
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+ rdkit
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+ mordred
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+ networkx>=3.0
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+ mhfp
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+ # tmap