Legacy editable installs are deprecated

[genehack]

Current Behavior

Slack context

Copying the deprecation message from there:

DEPRECATION: Legacy editable install of nextstrain-augur[dev]==25.2.0 from 
file:///home/tom/nextstrain/augur (setup.py develop) is deprecated. pip 25.0 
will enforce this behaviour change. A possible replacement is to add a 
pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the 
resulting installation is not behaving as expected, try using 
--config-settings editable_mode=compat. Please consult the setuptools 
documentation for more information. Discussion can be found at 
https://github.com/pypa/pip/issues/11457

Possible solution

We should discuss and standardize on which of the options we want to go with, create additional issues in other affected projects, and then fix things.