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ersilia-os / eos2b6f

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Clean UP & Dockerization eos2b6f #2

Closed GemmaTuron closed 1 year ago

GemmaTuron commented 1 year ago

Please check that the model is working and refactor it model to the latest eos-template structure. The workflows have already been updated, you can start by checking if the Actions have run successfully or changes need to be made

ZakiaYahya commented 1 year ago

Hello @GemmaTuron I have made PR on it, kindly check it. Thanks.

GemmaTuron commented 1 year ago

Hi @ZakiaYahya The tests are failing, please check

ZakiaYahya commented 1 year ago

Hello @GemmaTuron Yes, i just check it.

ZakiaYahya commented 1 year ago

Hello @GemmaTuron @DhanshreeA The model is failing at ModuleNotFoundError: No module named 'rdkit'. In my opinion This model is also installing rdkit with conda-forge which normally causes problem in models what i observed plus this model also uses the same version of rdkit as model eos9sa2. And i'm experiencing this exact same problem with model eos9sa2 as well. That's why we switched to rdkit version 2022.3.1b1 using pip because this version has same descriptors plus same len of descriptors.

What i propose: We need to switch to rdkit version 2022.3.1b1 in this case as well and let see that's working or not at push test in github actions. What you suggest @GemmaTuron Thanks.

GemmaTuron commented 1 year ago

Hi @ZakiaYahya

If the changes you are doing work on your system first (meaning, at --repo_path fetching with the modified dockerfile) you can open a PR. if the modifications to not work on your system then we will need to further dig into it. Please, attach the log of the error, since the ModuleNotFound only is not that informative, there can be other underlying issues.

ZakiaYahya commented 1 year ago

Hi @GemmaTuron Right, i'll try it. From error log of https://github.com/ersilia-os/eos2b6f/actions/runs/5369315556/jobs/9740655367 what i understand that it has dependancy issue with rdkit version, by going into detail i got to know that it's the same rdkit version that causes problem in model eos9sa2. I'll test it if it will work then i'll open PR on it. Thanks

GemmaTuron commented 1 year ago

@ZakiaYahya

Try the pip install of RDKIT, that should work. Regarding the issue with the fingerprints, you'll only encounter it again if the rdkit specific fps are being used for featurizing the molecules, in many cases they are not so it should be safe to upgrade version

ZakiaYahya commented 1 year ago

@GemmaTuron Yes i'm trying pip install rdkit-pypi==2022.3.1b1 version. Let see if it's working or not. Thanks.

ZakiaYahya commented 1 year ago

Hi @GemmaTuron I have changed RDkit version from conda-forge rdkit==2021.3.4 to rdkit-pypi==2022.3.1b1 and the model is working inside ersilia with --repo-path. I've open PR on it, kindly check it.