Fix docs CI fails

[dominiquesydow]

Description

Currently, our docs CI fails (docs can be built locally though) due to some warnings:

• In docs notebook structure_pocket.ipynb: WARNING: Content block expected for the "raw" directive; none found. - was introduced with nbsphinx 0.8.8 and already fixed in https://github.com/spatialaudio/nbsphinx/pull/621 - pin version 0.8.7 until this fix is part of their next release
• MDA warning
• opencadd warning

Not quite sure if all warnings lead to the CI fail or only the docs notebook - fix all of them anyways :)

Todos

• [x] Pin setuptools <60 in test_env.yml in order to remove warning until the latest MDA release contains the fix - see full description here: https://github.com/volkamerlab/opencadd/issues/136
• [x] Fix opencadd warning, check out: https://adamj.eu/tech/2020/06/18/why-does-python-syntaxwarning-for-assertion-is-always-true/
• [x] Off-topic: Add black line between text and list in structure_pocket.ipynb to fix list rendering on RTD
• [x] Pin nbsphinx <0.8.8

Status

• [ ] Ready to go

[codecov-commenter]

Codecov Report

Merging #137 (f79a3aa) into master (37714e6) will increase coverage by 0.00%. The diff coverage is 100.00%.

[dominiquesydow]

Alternative: Do not turn warnings into errors in our docs CI.

Check our RTD config: Does not fail on warnings (compare to RTD docs)

Sync this behaviour with our docs CI? Remove -W --keep-going: https://github.com/volkamerlab/opencadd/blob/master/.github/workflows/ci.yaml#L154

Check out sphinx options: https://www.sphinx-doc.org/en/master/man/sphinx-build.html#options

EDIT: Dropped this alternative - better to be made aware of errors big time and fix them :)