Skip to content

"Building MDAnalysis" in the "Contributing to the main codebase" tutorial breaks when installing optional dependencies #416

Open

Description

@FNNunes

Describe the bug
When following the tutorial in
Contributing Code when installing the optional dependencies clustwal2.1 is not found, and the package duecredit-0.10.0-pyhd8ed1ab_0 fails to install because no citeproc-py >=0.4
version can be found.
The command in the tutorial, raised these errors:

Collecting package metadata (repodata.json): done
Solving environment: / warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides requested clustalw 2.1**
  - package duecredit-0.10.0-pyhd8ed1ab_0 requires citeproc-py >=0.4, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ clustalw 2.1**  does not exist (perhaps a typo or a missing channel);
├─ duecredit is installable and it requires
│  └─ citeproc-py >=0.4  with the potential options
│     ├─ citeproc-py 0.6.0 would require
│     │  └─ python >=3.10,<3.11.0a0 , which can be installed;
│     ├─ citeproc-py 0.6.0 would require
│     │  └─ python >=3.11,<3.12.0a0 , which can be installed;
│     ├─ citeproc-py 0.6.0 would require
│     │  └─ python >=3.7,<3.8.0a0 , which can be installed;
│     ├─ citeproc-py 0.6.0 would require
│     │  └─ python >=3.8,<3.9.0a0 , which can be installed;
│     ├─ citeproc-py 0.6.0 would require
│     │  └─ python >=3.9,<3.10.0a0 , which can be installed;
│     └─ citeproc-py 0.6.0 would require
│        └─ python >=3.12,<3.13.0a0 , which can be installed;
└─ pin-1 is not installable because it requires
   └─ python 3.13.* , which conflicts with any installable versions previously reported.

I am using conda and not mamba so that could be the reason for this.

Nonetheless, if I force the python version to be python3.12, I solve the duecredit-0.10.0-pyhd8ed1ab_0 dependency problem. And to solve the clustalw=2.1 I have added new channels to conda, being bioconda the one that has clustalw 2.1

Desktop (please complete the following information):

  • OS:Ubuntu 22.04
  • Which version of MDAnalysis? UserGuide Version 2.8.0
  • Which version of Python (python -V)? Python 3.13.2

Activity

  1. lilyminium commented on Mar 27, 2025

    @lilyminium
    Member

    Thanks for raising this, @FNNunes -- clustalw is indeed not available on conda-forge.

    I'm surprised citeproc-py can't install on 3.13, that might need some looking into.

  2. FNNunes commented on Mar 27, 2025

    @FNNunes
    Author

    @lilyminium you are most welcome!

    Is there a problem if I try and fix it, I am new to git and GitHub and trying out pulls and pull requests seems daunting.
    So, doing it in something easier would soften the learning curve.

  3. lilyminium commented on Mar 28, 2025

    @lilyminium
    Member

    No please go ahead @FNNunes , very welcome to! There is a guide for user guide contributors in the user guide as well 😃

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    defectbugdeveloper-docsDocs for new contributors and developers.

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions