Update 2023

[kabu00002]

Description

Update packages and adapt new changes from the KinaseFocusedFragmentLibrary update

Todos

Notable points that this PR has either accomplished or will accomplish.

• Update README
• Update packages
• Add updated fragment library
• Resolve KinFragLib dataset update #52
• Resolve List of publications using KinFragLib data #46
• Resolve Add CITATION.cff #51
• Rerun notebooks
• Get CI running CI fixes #62

Questions

Status

• Ready to go

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[PaulaKramer]

Thanks @kabu00002! I have reviewed all files except the jupyter notebooks - I will do that in ReviewNB :)

[review-notebook-app]

View / edit / reply to this conversation on ReviewNB

PaulaKramer commented on 2023-12-20T16:22:17Z
----------------------------------------------------------------

This is missing the .to_html, if this is needed, check in all notebooks that it's consistent.

[review-notebook-app]

View / edit / reply to this conversation on ReviewNB

PaulaKramer commented on 2023-12-20T16:22:20Z
----------------------------------------------------------------

This list probably changed, we might have to look into that.

kabu00002 commented on 2024-01-24T14:57:00Z
----------------------------------------------------------------

There maybe something added but not deleted (?)

[review-notebook-app]

View / edit / reply to this conversation on ReviewNB

PaulaKramer commented on 2023-12-20T16:22:20Z
----------------------------------------------------------------

Check the warning, I think re-running the cell should already fix it.

[kabu00002]

There maybe something added but not deleted (?)

---

View entire conversation on ReviewNB

[dominiquesydow]

Hi @PaulaKramer and @AndreaVolkamer,

Thanks a lot for this update!!

I may have missed this in one of the files - could you please add prominently to the README of this repo the timestamp of the dataset that you used for this update?

Which rdkit and Python version did you use to run this?
From the env file it seems you used python=3.8 and rdkit=2020.03.3

• Re rdkit: Is there a reason for using the quite old version? If so, I would add that as a comment to the env file.
• Re python: For the next update, we should move to the latest stable Python version (3.8 is almost deprecated).

I did not go through every notebook, do you have any specific questions regarding the notebooks? Happy to take a deep dive in that case.

[dominiquesydow]

@AndreaVolkamer I would drop Python 3.7 in the CI and only focus on 3.8 (as it is the Python version you used for the update afaiu).

[PaulaKramer]

Hi @dominiquesydow, thanks a lot for your comments!

We used rdkit=2021.09 (there were some changes with the dummy atom labels in the newer versions if I remember correctly, so we used the older version - @kabu00002 maybe you can add a comment regarding that). The rdkit version should be the same as in the KFFL repository.

I started working on the CI here: #62 (I haven't merged it yet). I removed python 3.7 and included 3.8 and 3.9 for ubuntu and mac, which seems to work. The CI is currently still failing for a few notebooks because the new combinatorial library is not on zenodo yet.

[PaulaKramer]

Hi @dominiquesydow,
we adapted the readmes and updated the CI in case you would like to have another look before we merge it :)

[dominiquesydow]

Hi @PaulaKramer, many thanks for your work on this update — this looks great! :)