docs: Fix numpy types for Python 3.12

[joverlee521]

Scheduled docs-ci failed with warning for numpy types

<unknown>:1: WARNING: py:class reference target not found: numpy._typing._array_like.GenericAlias [ref.class]

This is not an issue in our RTD build since we are using Python 3.11, but will cause different renderings in Python 3.12. We're ignoring the warning for now, but would be good to eventually fix when moving RTD build to Python 3.12.

[joverlee521]

Hmm, numpy's stable docs still point to 2.4 and we use it for the interphinx_mapping

augur/docs/conf.py

Line 167 in 5396f59

'numpy': ('https://numpy.org/doc/stable', None),

Likely will resolve once numpy's stable docs get updated to 2.5.

[joverlee521]

Numpy's stable docs have been updated to 2.5 since yesterday, but today's scheduled docs ci still ran into the same warnings about numpy types.

I'm wondering if there's something going on with Sphinx/napoleon/autodoc_typehints?
We can suppress the warning by adding it to the list of ignored with the downside the there would be no hyperlink to the numpy type in the developer API docs.

[victorlin]

Weird, I can't reproduce this locally. I'm fine with ignoring for now.

[joverlee521]

I was expecting differences in the docs preview for #2020 , but there are no visible changes compared to prod. Our use of Python 3.11 for RTD pins Sphinx to 9.0 and sphinx-autodoc-typehints to 3.6.1. which do not produce the warning when running locally.

I am able to reproduce the warning in a fresh environment with Python 3.12, which is the default Python version in GH Actions ubuntu-latest/ubuntu-24.04 that we use for docs-ci.

If we ignore the warning in Python 3.12, it does have differences in the docs