I am unable to import MDAnalysis tests

[sindhura duddela]

Something simple which  I am missing and it looks some installation issue. but I have installed all pre requisites. Could you please any one help on this. I have attached exception screen shot for your reference. 

[Oliver Beckstein]

Hello Sindhura Duddela,

Welcome to the MDAnalysis list!

This looks like incompatibility between linked and installed numpy.

1) How did you install MDAnalysis and the dependencies? Copy and paste the commands.

2) Are you using conda or venv virtual environments?

3) Which versions of Python, MDAnalysis, numpy are you using and installing?

4) Did you install jupyter/ipython INSIDE the same virtual environment as MDAnalysis? If not then do this and try again.

If it’s not 4) then your answers to 1 and 2 might help us to narrow down the problem.

Oliver

On Jun 5, 2021, at 1:35 PM, sindhura duddela <sindhura...@gmail.com> wrote:

Something simple which  I am missing and it looks some installation issue. but I have installed all pre requisites. Could you please any one help on this. I have attached exception screen shot for your reference. 

--

Oliver Beckstein (he/his/him)

email: orbe...@mdanalysis.org
twitter: @orbeckst

MDAnalysis – a NumFOCUS fiscally sponsored project

https://www.mdanalysis.org/

[sindhura duddela]

Hi Oliver,

Thanks for your email and swift response on this.

Please find my in-line comments below ,

1) How did you install MDAnalysis and the dependencies? Copy and paste the commands. - Yes , I copied and pasted commands from MDAnalysis installation list then ran in my CONDA command prompt. 

2) Are you using conda or venv virtual environments? - i am using CONDA from their launching jupiter notebook in browser which is python 3. Actually , I am using my Windows personal computer for Python. 

3) Which versions of Python, MDAnalysis, numpy are you using and installing?  - I have attached version details for your reference by extracting from Conds list and Pip list commands in conda command prompt.

4) Did you install jupyter/ipython INSIDE the same virtual environment as MDAnalysis? If not then do this and try again. - Yes it is installed. 

Version details :

Conda list:

 

numpy                     1.20.3                   pypi_0    pypi
numpy-base                1.18.5           py38hc3f5095_0
numpydoc                  1.1.0                      py_1    conda-forge

    

    python                    3.8.3                he1778fa_2

    mdanalysis                1.1.1            py38h885f38d_0    conda-forge

    mdanalysistests           1.1.1            py38haa244fe_0    conda-forge

    ipython                   7.24.1           py38h43734a8_0    conda-forge
    ipython_genutils          0.2.0                      py_1    conda-forge

As per your 4th point ,  jupyter/ipython already isntalled in my machine.

Hope this helps and appreciated your support to resolve this issue. 

 

Thansk in advance.

Regards,

Sindhura 

[Oliver Beckstein]

Hi Sindhura,

I would guess that your problem is that you are mixing numpy packages:

numpy                     1.20.3                   pypi_0    pypi

numpy-base                1.18.5           py38hc3f5095_0

That will almost certainly lead to problems.

pip uninstall numpy

Then

conda install numpy

Maybe that will help.

Oliver

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<Conda_list.txt><Pip_list.txt>

[sindhura duddela]

Hi Oliver,

I hope you are well.

I had sent an email earlier regarding MdAnalysis installation issue while running in Jupiter Notebook

But now I am facing a similar issue while running .py file in Anaconda terminal as per the screen shot.

I tried to uninstall MDAnalysis through pip and tried using conda which didn't work.

Could you please advise ? 

I Appreciate your support.

Regards,

sindhura 

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/CD5C6A15-4660-40E5-B3DA-D7ED916FE501%40mdanalysis.org.

["ROPÓN-PALACIOS G."]

Check if your jupyter notebook use same PATH to where MDAnalyis instale with Python using as kernel into notebook. 

Enviado desde mi iPhone

El 6 jul. 2021, a la(s) 6:10 p. m., sindhura duddela <sindhura...@gmail.com> escribió:



Hi Oliver,

I hope you are well.

I had sent an email earlier regarding MdAnalysis installation issue while running in Jupiter Notebook

But now I am facing a similar issue while running .py file in Anaconda terminal as per the screen shot.

I tried to uninstall MDAnalysis through pip and tried using conda which didn't work.

Could you please advise ? 

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/CAOhtPTf0DnA839qka51Xd70AgsqUtZfLfMOqhuLLm8HmRVPVaA%40mail.gmail.com.