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prody / ProDy

A Python Package for Protein Dynamics Analysis
http://prody.csb.pitt.edu
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Python 3.12 Support #1915

Open xavierholt opened 1 month ago

xavierholt commented 1 month ago

Is there a plan to support Python 3.12?

Ubuntu 24.04 is out now, and it only comes with Python 3.12; none of the older Python versions are available in the official APT repos. It would be great if I could install ProDy on a new Ubuntu box, but I've seen several comments to the effect that it isn't compatible with Python 3.12 (and my attempts to install it via pip have all failed with some sort of build system error).

I might be able to help out with this - is there a list of changes that would be required for 3.12 support?

jamesmkrieger commented 1 month ago

First of all, compatibility with the latest numpy and scipy, I think. I think there were some changes to installation too. @atbogetti, do you know?

help would be great. Thanks. Just remember to keep back compatibility with python 3.9 and 2.x

Are you sure you can’t get earlier python with anaconda? Lots of things don’t support python 3.11 or 3.12 yet.

lenny-mavs commented 1 month ago

I am having compatibility issues when trying to install ProDy and MDAnalysis in the same Anaconda environment, as downgrading all of the mutual dependencies causes one or the other to not work correctly. I would greatly appreciate a version that can use the more recent releases of numpy, scipy, biopython, etc.

jamesmkrieger commented 1 month ago

Could you maybe use an older version of mdanalysis?

lenny-mavs commented 1 month ago

Yes, that solved the issue quite quickly!

jamesmkrieger commented 1 month ago

Great. Glad to hear

diogomart commented 1 month ago

@xavierholt @jamesmkrieger me and @sforli took a look and the C extension dynamics/rtbtools seems to be a culprit. One guess are the numpy headers needing updating to 1.26 or later. Not sure this helps much but may be a start. If we continue looking into it and make progress we will post here.