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ersilia-os / eos6tg8

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Clean UP & Dockerization eos6tg8 #2

Closed GemmaTuron closed 1 year ago

GemmaTuron commented 1 year ago

@samuelmaina It seems you deleted your fork? Let me know what stage you are in so I can help if needed

samuelmaina commented 1 year ago

Hi @GemmaTuron , I am getting this error https://github.com/ersilia-os/eos6tg8/pull/3#issuecomment-1636755213 . I thought it was due to GitHub quota limit or a tracking error on my side. I deleted the repo which automatically closed the PR. I can not push the code to the new fork due to the same error.

samuelmaina commented 1 year ago

@GemmaTuron , This PR https://github.com/ersilia-os/eos6tg8/pull/5 passed the tests. The issue stems from changing from *.pkl filter=lfs diff=lfs merge=lfs -text to *.pt filter=lfs diff=lfs merge=lfs -text in the .gitignore . The checkpoints files are in the .pt extension and wondered how they were being tracked earlier. It a wierd behavior but I don't know how to explain it.

GemmaTuron commented 1 year ago

Hi @samuelmaina

A few points:

I guess you are referring to the .gitattributes file. If the *.pt files were not tracked it is because they were not large enough, otherwise we could not have pushed them. If you open one from the original repo, indeed you will see it does not say anywhere "tracked by Git LFS".

I would move the files to the checkpoints folder as you did but not track them, nor *.pkl files of course

Regarding the main.py, I am unsure which file you modified. The Main.py should be in the root of the /code folder, not inside other folders. Did you write it from scratch or which file you modified? I see the get_fps.py is missing... I guess its that one. Please do not touch the original code by the authors, simply create a main.py and call the relevant functions there. I hope these pointers are clear!

samuelmaina commented 1 year ago

The LFS file is 60mb so I thought it was big enough. Onwards, if something is not tracked I will not track it. I modified the get_fp file inside the model nfps folder due to the importation error I was getting when I was calling the one function from the main.py in the code folder..

samuelmaina commented 1 year ago

Changing the path from code/neural_npfp/neural_npfp/main.py $2 $3 -s smiles to code/main.py changes the overall relative path, I was getting no module named utils After wording the problem differently on Google, I was able to find the solution at stackoverfow One need to from .utils import * instead of from utils import *.