Oliver Beckstein

CI suggests to filter warnings: ``` WARNING: >>>------------------------------------------------------------------------- Warning in /home/runner/work/UserGuide/UserGuide/doc/source/reading_and_writing.rst at block ending on line 225 Specify :okwarning: as an option in the ipython:: block to suppress this message...

CI shows various issues with link targets ``` /home/runner/work/UserGuide/UserGuide/doc/source/contributing.rst:18: ERROR: Unknown target name: "github discussions". /home/runner/work/UserGuide/UserGuide/doc/source/index.rst:42: ERROR: Unknown target name: "mdnalysis-discussion". /home/runner/work/UserGuide/UserGuide/doc/source/index.rst:58: ERROR: Unknown target name: "mdnalysis-discussion". ```

## Is your feature request related to a problem? ## We are lacking clear installation instructions for developers on how to install the *develop* branch for hacking and testing, see...

replace doc footer of all authors with link to AUTHORS

2

Over the last 2 years or so we had discussions about how to represent the effort of all authors. One point was that we should replace the "all author footer"...

Check that the new versioningit properly works with the release tags and that installed packages have the proper version associated with them.

testing codecov

1

Test different versions of `codecov.yml` to see if anything solves #287 Validate with ``` curl --data-binary @codecov.yml https://codecov.io/validate ```

The following error is now failing Windows CI runners (e.g. https://github.com/alchemistry/alchemlyb/actions/runs/11134663073/job/30943263819?pr=417 ) ``` Installing pip packages: alchemtest @ https://github.com/alchemistry/alchemtest/archive/master.zip '"C:\Users\runneradmin\micromamba\condabin\micromamba"' is not recognized as an internal or external command, operable...

With #71 published, we should add the paper citation - [ ] README: add citation and use badge ``` Markdown: [](https://doi.org/10.21105/joss.06934) HTML: reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.06934/status.svg :target: https://doi.org/10.21105/joss.06934 - [...

- [ ] Upgrade to Trusted Publishing: Trusted Publishers allows publishing packages to PyPI from automated environments like GitHub Actions without needing to use username/password combinations or API tokens to...

I manually checked coverage with ``` pytest -n 4 -v --cov=alchemlyb --pyargs alchemlyb.tests ``` and found a few files with (relatively) low coverage: ``` --------- coverage: platform darwin, python 3.10.14-final-0...