Installing MDAlaysis+ MDAnalysisTests

[hanahg]

HI
I am installing MDAalysis and after following command I got the errors.
mamba install -c conda-forge MDAnalysisTests
I tried to install the versions of python required but the problem did not solved yet.
Please help me to solve the problem.

Thank you

The anaconda version is 23.9.0

The error:

looking for: ['mdanalysistests']

pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
bioconda/noarch                                               No change
bioconda/linux-64                                             No change
conda-forge/noarch                                  12.8MB @   5.5MB/s  2.7s
conda-forge/linux-64                               @   7.6MB/s  5.1s

Pinned packages:
  - python 3.12.*

warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
└─ mdanalysistests is installable with the potential options
   ├─ mdanalysistests 0.15.0 would require
   │  └─ mdanalysis 0.15.0 , which does not exist (perhaps a missing channel);
   ├─ mdanalysistests 0.16.0 would require
   │  └─ mdanalysis 0.16.0 , which does not exist (perhaps a missing channel);
   ├─ mdanalysistests 0.16.1 would require
   │  └─ mdanalysis 0.16.1 , which does not exist (perhaps a missing channel);
   ├─ mdanalysistests [0.16.2|0.17.0|...|0.20.1] would require
   │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
   ├─ mdanalysistests [0.17.0|0.18.0] would require
   │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
   ├─ mdanalysistests 0.17.0 would require
   │  └─ python 3.6* , which can be installed;
   ├─ mdanalysistests [0.18.0|0.19.0|...|2.0.0] would require
   │  └─ python >=3.6,<3.7.0a0 , which can be installed;
   ├─ mdanalysistests [0.19.2|0.20.1|...|2.1.0] would require
   │  └─ python >=3.7,<3.8.0a0 , which can be installed;
   ├─ mdanalysistests [0.20.1|1.0.0|...|2.2.0] would require
   │  └─ python >=3.8,<3.9.0a0 , which can be installed;
   ├─ mdanalysistests [2.0.0|2.1.0|2.2.0] would require
   │  └─ python >=3.9,<3.10.0a0 , which can be installed;
   ├─ mdanalysistests [2.1.0|2.2.0] would require
   │  └─ python >=3.10,<3.11.0a0 , which can be installed;
   ├─ mdanalysistests [2.2.0|2.3.0] would require
   │  └─ python >=3.8,<=3.10 , which can be installed;
   ├─ mdanalysistests [2.4.1|2.4.2|2.4.3] would require
   │  └─ python >=3.8,<=3.11 , which can be installed;
   └─ mdanalysistests [2.5.0|2.6.1] would require
      └─ python >=3.9,<=3.11 , which can be installed.

[IAlibay]

@hanahg - am I correct in understanding that you are using Python 3.12?

Unfortunately MDAnalysis does not have a py3.12 compatible release yet, you would have to downgrade to py3.11.

[hanahg]

Thanks for your reply. I didn't notice that. I will install the correct version of python. Sent from Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Irfan Alibay ***@***.***> Sent: Monday, December 4, 2023 4:43:29 PM To: MDAnalysis/mdanalysis ***@***.***> Cc: hanahg ***@***.***>; Mention ***@***.***> Subject: Re: [MDAnalysis/mdanalysis] Installing MDAlaysis+ MDAnalysisTests (Issue #4350) @hanahg<https://github.com/hanahg> - am I correct in understanding that you are using Python 3.12? Unfortunately MDAnalysis does not have a py3.12 compatible release yet, you would have to downgrade to py3.11. — Reply to this email directly, view it on GitHub<#4350 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI5LF6434WUS24NVS4RBXPLYHXVSDAVCNFSM6AAAAABAGFVQZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZYHEYTKNZQGQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[hanahg]

Hi,
I have reinstalled Anaconda and I have found that Python 3.12 is installed with this version of Anaconda3-2023.09. If not the Python version of my system is 3.11. I installed python 3.11 on Anaconda and again installed MDAnalysis. However, for this command I received this message "mamba install -c conda-forge mdanalysis
Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba." and I don't know what should I do then.
I uninstalled all and I am trying by pip.

[RMeli]

Hi @hanahg, please have a look at @IAlibay suggestion below. You likely used the Anaconda installer which bundles Python 3.12, and this will be the version of Python in your base environment. You can create a new environment with Python 3.11 as suggested below by @IAlibay. Using environments instead of installing everything in the base environment is strongly recommended.

[hanahg]

I did not find his discussion.
Could you please send the link?

Thanks

[IAlibay]

@hanahg it's just below on the page, here's the link just in case: #4358 (comment)

[IAlibay]

@hanahg Unfortunately it's unclear to me as to what specific steps you took to get this mamba error. May I suggest reaching out on discord where folks can more interactively respond to your questions?

The general approach with anaconda is to use environments which let you define a specific python version & packages.

You can see more about this here: https://userguide.mdanalysis.org/stable/installation.html#conda

Your typical usage pattern would be something like:

conda create --name mdanalysis python=3.11 MDAnalysis
conda activate mdanalysis

[hanahg]

Thank you very much

[IAlibay]

@hanahg Given that we've moved to github discussions, please disregard my comment about discord. This is a good place to workshop your installation issues.