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macOS python3.11 fails to install mdanalysis[all]
from git branch directly (not always though)
#4586
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I ran into a similar(?) issue with I am trying to install the development version (actually, the dask-0 branch from the parallelization PR), following the instructions in the user guide https://userguide.mdanalysis.org/stable/contributing_code.html#creating-a-development-environment but creating a Python 3.11 environment (on macOS) with the packages from https://userguide.mdanalysis.org/stable/contributing_code.html#id1 When doing pip install it complains about absolute paths and I get this error:
Note that I didn't want an editable install pip install -e, which actually works. p.s.: If my issue is different from @marinegor 's then I can also open a new issue. |
@orbeckst and @marinegor do your python install environments have a base setuptool / pip installl? Also @orbeckst could you confirm your macos version? |
@IAlibay how do I check for that? I'm working inside a standard |
My env has
|
Not sure 😅, does |
🤷♂️🤷♂️🤷♂️ |
@orbeckst This seems a bit fishy. Is there a tilde in your file path? I think Python does not handle paths with tildes very well. I cannot reproduce the error with my mac (sonoma 14.4). My output for this line is |
No, that was me manually sanitizing paths before posting. These are full absolute paths in the real output. |
That's what I suspected :) What if you remove the |
@yuxuanzhuang I deleted the existing
Thank you very much — my problem is solved. |
Expected behavior
I want to install full MDAnalysis package from
dask-0
branch on macOS laptop.Actual behavior
I get following log:
Code to reproduce the behavior
Current version of MDAnalysis
I also noticed something weird -- after the first time I got the bug, I couldn't reproduce it, i.e. the code above worked when I tested it while writing the issue, so I'm not sure how to reproduce it anymore. Anyway, raising it, since there might be something
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