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extract chemprot requirements from main setup.cfg (PyPI disallows direct dependency links) #168

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Aug 3, 2023
Merged

extract chemprot requirements from main setup.cfg (PyPI disallows direct dependency links) #168

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2 changes: 1 addition & 1 deletion examples/chemprot/README.md
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Expand Up @@ -5,7 +5,7 @@

2. Unzip the folder and each of the contents in the folder. Make sure that each folder starts with `chemprot_`. For example, train data folder should have a name of `chemprot_training`.

3. Run ```pip install scispacy https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz``` to get dependencies for the preprocessing tokenization and sentence splitting.
3. Run ```pip install -r chemprot_requirements.txt``` to get dependencies for the preprocessing tokenization and sentence splitting.

4. Preprocess the data with ```python -m cnlpt.data.transform_prot data/ChemProt_Corpus/ data/scispacy_chemprot/ chemprot```. Note, this only gives us {train,dev}.tsv in `data/scispacy_chemprot` since there are no gold labels for the test data.

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3 changes: 3 additions & 0 deletions examples/chemprot/chemprot_requirements.txt
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en-core-sci-sm @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz
scispacy==0.5.1
spacy~=3.4.0
3 changes: 0 additions & 3 deletions setup.cfg
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Expand Up @@ -38,9 +38,6 @@ install_requires =
torch~=1.5
transformers~=4.15
uvicorn[standard]~=0.16.0
en-core-sci-sm @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz ; platform_machine!='arm64' and platform_machine!='aarch64' and sys_platform=='linux'
scispacy==0.5.1; platform_machine!='arm64' and platform_machine!='aarch64' and sys_platform=='linux'
spacy~=3.4.0; platform_machine!='arm64' and platform_machine!='aarch64' and sys_platform=='linux'

[options.entry_points]
console_scripts =
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