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MDAnalysis / UserGuide

User Guide for MDAnalysis
https://userguide.mdanalysis.org
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Recommend mamba over conda #361

Closed lilyminium closed 3 months ago

lilyminium commented 10 months ago

The user guide recommends conda -- I haven't been keeping up with its development but mamba still really seems the way to go instead.

mikemhenry commented 5 months ago

Yes, here is the latest https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html Miniforge is definitely the way to go in 2024.

orbeckst commented 4 months ago

Our USer Guide installation instructions recommend installing mamba inside the mda env

conda create --name mdanalysis
conda activate mdanalysis
conda install -c conda-forge mamba

but this is not recommended in the official mamba instructions for mamba with existing conda where it is explicitly said

WARNING: Installing mamba into any other environment than base is not supported.

Therefore, we should also update the UG Installation Instructions.

RMeli commented 4 months ago

I agree with @mikemhenry. I've had a very smooth experience with Miniforge, from my laptop to HPC clusters. I think it would be best to suggest to use Miniforge directly.

IAlibay commented 4 months ago

Yeah we shouldn't be advocating for conda at all nowadays - it's blocked at most pharma companies.

orbeckst commented 4 months ago

I think we still need to mention "conda" because that's what people know who do not deal with the details of the python ecosystem, and it's even in the name "conda-forge".

mikemhenry commented 4 months ago

I think its fine to mention conda, then say mamba is a drop in replacement (so the same commands that worked with conda will work with mamba) is better, and the best way to install it is from Miniforge. Hopefully that isn't too much to overwhelm learners while still pointing them to the best solution

jennaswa commented 3 months ago

Hi all - thanks for your efforts and thoughts on this issue. What is the current status on updating the installation instructions in the User Guide? I'm wondering if this something we want to try to prioritize getting done before the UGM, especially so folks can reference it during the hackathon?

orbeckst commented 3 months ago

This looks like a "nice to have" for me – mamba/conda, potato/potatoe. If anyone feels strongly about it, please change it.

The much more pressing issue is updating installation instructions for develop #368 (EDIT: because we need them for the UGM!)