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

[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

[lilyminium]

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.

[FNNunes]

@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.

[lilyminium]

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