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igematberkeley / NLPChemExtractor

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getting git to integrate with some portion of Savio data #25

Open mrunalimanj opened 3 years ago

mrunalimanj commented 3 years ago

would be neat if we could sync some things of Savio work to GitHub, so it's easier to follow updates on data?

reverts might be hard because of permission issues, though. maybe I can do a few subfolders onto a separate branch for now or something

mrunalimanj commented 3 years ago

git clone --branch scibert --single-branch --depth 1 --filter=blob:none --no-checkout https://github.com/arjunchandran1999/NLPChemExtractor.git gets me onto the scibert branch, with no files! don't have to bother with extra directories, can just add my own

git sparse-checkout init --cone git sparse-checkout set savio_mimic

had to unstage all the deletions?? git reset HEAD -- . pushed to the scibert folder, will work on stuff there + push continually as needed.

mrunalimanj commented 3 years ago

`conda config --set env_prompt '(scibert_env_NER)' conda install nltk, pandas, transformers

VVV is maybe an alternatives to requirements.txt?

NLPChemExtractor mrunali$ pip install torch==1.2.0 torchvision==0.4.0 -f https://download.pytorch.org/whl/torch_stable.html --target=savio_mimic/software/scibert_env_NER/bin CFLAGS=-stdlib=libc++ pip3 install allennlp --target=savio_mimic/software/scibert_env_NER/bin