Change bibliography to footbibliography

[lilyminium]

Fixes #12

Changes made in this Pull Request:

• Changes bibliography directive to footbibliography

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #13 (41e6699) into main (87290ae) will not change coverage.
The diff coverage is n/a.

Additional details and impacted files

[lilyminium]

This is more to show what I mean and the content that let me render what's in #12 -- it may make more sense to just have a global bibliography instead.

[orbeckst]

The RTD build https://readthedocs.org/projects/mdaencore/builds/21702726/ fails with

ModuleNotFoundError: No module named 'mdaencore.cutils'

[orbeckst]

Building locally make html and having installed with pip install -e .

1. mdaencore.data.files is not found:

   Failed to import mdaencore.data.files.
   Possible hints:
   * ModuleNotFoundError: No module named 'mdaencore.data.files'
   * AttributeError: module 'mdaencore.data' has no attribute 'files'
   WARNING: [autosummary] failed to import mdaencore.data.files.
   Possible hints:
   * ModuleNotFoundError: No module named 'mdaencore.data.files'
   * AttributeError: module 'mdaencore.data' has no attribute 'files'
   

2. Some footnote issues

   ~/MDAnalysis/mdaencore/docs/source/autosummary/mdaencore.rst:38:<autosummary>:1: ERROR: Too many autonumbered footnote references: only 0 corresponding footnotes available.
   ~/MDAnalysis/mdaencore/docs/source/autosummary/mdaencore.rst:38:<autosummary>:1: ERROR: Unknown target name: "footcite-lindorfflarsen2009".
   

On the plus side, the RTD build is working again.

[orbeckst]

I forgot to merge main into the branch before editing and had independently moved danalysis-sphinx-theme from pip to conda... and then I grouped it with other sphinx things.

[orbeckst]

same here... doubled up on work that was already in main

[lilyminium]

@orbeckst I could reproduce the footnote issue but not the missing .data.files -- does that still occur to you with the merge of main?

The footnotes issue was because it was in the first sentence of the module docstring, which was then reproduced in the autosummary table but without a corresponding local bibliography to link to.

[orbeckst]

I generally agree with @lilyminium that a global bibliography makes a lot of sense for this kit. However, the current PR is strictly improvement over the previous approach so let's merge it.

There's the one issue with missing(??) citation in the autosummary generated page

~/MDAnalysis/mdaencore/docs/source/autosummary/mdaencore.rst:38:<autosummary>:1: ERROR: Too many autonumbered footnote references: only 0 corresponding footnotes available.
~/MDAnalysis/mdaencore/docs/source/autosummary/mdaencore.rst:38:<autosummary>:1: ERROR: Unknown target name: "footcite-lindorfflarsen2009".

which I don't understand (and I am not a fan of autosummary in general...).

[orbeckst]

Thanks for fixing the footnote bib!

[orbeckst]

data files is still missing for me

...
building [html]: targets for 21 source files that are out of date
updating environment: [new config] 21 added, 0 changed, 0 removed
reading sources... [100%] index
WARNING: autodoc: failed to import module 'files' from module 'mdaencore.data'; the following exception was raised:
No module named 'mdaencore.data.files'
looking for now-outdated files... none found
pickling environment... done
checking consistency... ~/MDAnalysis/mdaencore/docs/source/autosummary/mdaencore.data.rst: WARNING: document isn't included in any toctree
~/MDAnalysis/mdaencore/docs/source/autosummary/mdaencore.data.files.rst: WARNING: document isn't included in any toctree
done
...

[orbeckst]

If RTD build then please merge whenever you want to @lilyminium .

[lilyminium]

Ah you might need to delete the autosummary directory and rebuild docs to get rid of the warning -- mdaencore.data.files was removed as a path, so it wouldn't be included in toctrees anymore, but if you built docs prior to its removal then its rst file would still be lying around.

Oh weird, I don't get the autodoc warning.

[orbeckst]

I see. I assumed (wrongly) that make clean would be sufficient. But I also had to rm -rf source/autosummary/. Now it worked without issues. Thanks for the tip.

(See, I am justified in not liking autosummary ;-) ).

[orbeckst]

The setup-miniconda job step timed out for two runners. Maybe change to uses: mamba-org/setup-micromamba@v1 (although that also requires some option changing)... issue for another day.