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ersilia-os / eos1pu1

GNU General Public License v3.0
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PR for entry model incorporation task #1

Closed kurysauce closed 3 months ago

kurysauce commented 3 months ago

First PR for eos1pu1 cardiotoxicity model

GemmaTuron commented 3 months ago

Hi @kurysauce

Good, a few comments:

We try to avoid Git LFS tracking if not necessary. Are you sure the current files listed in gitattributes require the minimum size to be git lfs? I would think at least the .csv files do not, nor others maybe? Also, the mock.txt file is not needed, please delete.

From main.py, please change the last bit:

   save_output(output_file, probabilities, include_predictions=True, predictions=predictions)
   print("Threshold for Cardiotoxicity: 0.64\n")
   for prob, pred in zip(probabilities, predictions):
       print(f"Predicted DICTrank probability: {np.round(prob, 2)}, Prediction: {pred}")

As I said, we prefer to keep the structure of the template, so do not use the save_output function and instead leave that code chunk in the main.py parsing the results to the csv output. Will make it much easier to debug and/or change in the future

Also, small issue in the license name, see the action failure

GemmaTuron commented 3 months ago

@kurysauce

That looks good! Can you simply remove the .gitattributes file if it is empty, so it won't initialise GitLFS?