Fix docs builds

[mattwthompson]

Description

Partially resolves #318

Todos

Notable points that this PR has either accomplished or will accomplish.

• Explicitly indicate docs configuration file
• Resolve docs build errors

Status

• Ready to go

[mattwthompson]

https://about.readthedocs.com/blog/2024/12/deprecate-config-files-without-sphinx-or-mkdocs-config/

[j-wags]

Thanks @mattwthompson!

[j-wags]

Oh, I see the docs builds are hitting some other errors. Well this is still a clear improvement to me. This can be merged as-is, and I've updated the description to clarify that it's a partial resolution, and I'll leave #318 open and in current iteration on zenhub.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.63%. Comparing base (c298486) to head (ddad3aa).
Report is 1 commits behind head on main.

Additional details and impacted files

[mattwthompson]

This surfaced several long-standing, not all of which I am able to resolve in an hour and half or so of work:

• An old version of Sphinx is used
• Sphinx config was not passed to .readthedocs.yaml
• openff.qcsubmit.results.caching was built
• ResultRecordFilter and ResultRecordGroupFilter were referenced
• ClientHandler was referenced
• Broken MolSSI links were referenced Broken link in docs MolSSI/QCFractal#894
• Sphinx complains about repeated sub-headings in release notes
• Sphinx complains - reasonably so - about distinct classes with common names (compare

  openff-qcsubmit/openff/qcsubmit/results/filters.py

  Line 580 in c298486

  class ChargeFilter(CMILESResultFilter):

  and

  openff-qcsubmit/openff/qcsubmit/workflow_components/filters.py

  Line 702 in c298486

  class ChargeFilter(ToolkitValidator, CustomWorkflowComponent):

  )

See remaining warnings: https://app.readthedocs.org/projects/openff-qcsubmit/builds/27150302/

I think these should be dealt with later since this still fixes the original issue (that docs were not building at all) and just adds in more fixes for free