Expand test matrix to include Python 3.9 to 3.12

[caufieldjh]

No description provided.

[caufieldjh]

Errors in flake8 caused by this: https://stackoverflow.com/questions/74558565/flake8-error-code-supplied-to-ignore-option-does-not-match-a-z1-30

[caufieldjh]

Some dependency is trying to use scipy 1.13.1 but scipy is only compatible with Python 3.13 as of 1.14.1 - https://scipy.org/news/#scipy-1141-released

[caufieldjh]

Hrm, poetry really wants to install numpy 2.0.0rc1 instead of 2.1, but the former won't work with Python 3.13.
scikit-learn may be the culprit.

[caufieldjh]

This is strange - the builds other than Python 3.13 aren't even requiring scikit-learn as a dependency (they don't install it) but that's what 3.13 appears to be failing on, because it's trying to install scikit-learn and that wants numpy 2.0.0rc1, which doesn't exist.

This may instead be referring to sqlalchemy 2.0.0rc1 as sqlalchemy is an upstream dependency for packages like oaklib, but what is trying to install that specific version if that's the case?

[caufieldjh]

OK, so numpy 2.0.0rc1 may have existed at some point, and some scikit-learn versions built against that when it was the most recent numpy 2 available (see scikit-learn/scikit-learn#29360).
So the real issue here is forcing numpy >=2. Will try a slightly different config here

[caufieldjh]

Now it's an issue with tiktoken. Trying a more generous pin as there's a new version of that out as of last month

[caufieldjh]

That's the dependencies handled but now tests are failing on 3.13, mostly because of ImportError: cannot import name 're' from 'typing', and that happens because linkml_runtime does it

[caufieldjh]

Blocked by linkml/linkml#2420

[caufieldjh]

Since 3.9 to 3.12 work, I will restrict the test matrix to those versions and support 3.13 once linkml allows.