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rxn4chemistry / rxnfp

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).
https://rxn4chemistry.github.io/rxnfp/
MIT License
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Higher Python version compatibility #20

Open xuchunqiu opened 1 year ago

xuchunqiu commented 1 year ago

If anyone else want to run rxnfp on a higher Python version (for me its 3.9), the only thing you need to do is install rxnfp with --no-deps:


conda create -n rxnfp python=3.9 -y
conda activate rxnfp
pip install rxnfp==0.1.0 --no-deps
pip install scipy torch tqdm transformers rdkit  # enough for gen fingerprint

# some error message when installing, obviously you need other packages to draw reaction atlas
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
rxnfp 0.1.0 requires faerun==0.3.20, which is not installed.
rxnfp 0.1.0 requires matplotlib==3.2.2, which is not installed.
rxnfp 0.1.0 requires scikit-learn==0.23.1, which is not installed.
rxnfp 0.1.0 requires scipy==1.4.1, but you have scipy 1.11.1 which is incompatible.

The main problem here is the compatibility of scipy==1.4.1 with python=3.9. Full error message has been mentioned at intel/dffml/issues/1334.

AslantheAslan commented 9 months ago

Thanks a lot, it worked well!