Installing MDAnalysis using conda

[Ashi Agrawal]

Hi, 

I've run all the lines below, in order, as followed: 

conda install -c conda-forge mdanalysis 

conda config --add channels conda-forge 

conda update --yes conda

conda create --yes -n mdaenv python=3.6

source activate mdaenv

conda install --yes -n mdaenv MDAnalysis MDAnalysisTests

python -c 'import MDAnalysis as mda; print(mda.__version__)'

-- upon completing the last step, I get an output of '1.0.0'

I then run 

pytest --disable-pytest-warnings --pyargs MDAnalysisTests

and it comes up with 142 errors in 5 seconds. Does anyone have any advice?

Thank you, 

Ashi

[Shubham Anand]

Hi,

That is because of the latest version of matplotlib. Try to degrade the version of matplotlib to 3.2.1 then run it again.

Regards,

Shubham

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[Ashi Agrawal]

Hi Shubham, 

Thank you for your reply - I've checked and I have version 3.3.2 . How would I go about degrading the version?

Regards, 

Ashi

[Shubham Anand]

pip install matplotlib == 3.2.1 

Just check it once on google

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[Oliver Beckstein]

Hi Ashi,

Please see https://github.com/MDAnalysis/mdanalysis/issues/2938 for a workaround.

We should have 1.0.1 out soon, which fixes this issue.

Oliver

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Oliver Beckstein (he/his/him)

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[Suliman Sharif]

Yeah I came across this as well,

I honestly just deleted the warn flag in the MDAnalysis source code when I pip installed it while retaining my matplotlib version. Still running okay without it - it was easier to deal with than the mess of dependencies I have in my conda env that rely on higher versions of matplotlib. 

-Sul

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Suliman Sharif

M.Sc Medicinal Chemistry | University of California, Riverside

B.Sc. Biochemistry | University of Texas at Austin

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