fix: Cython>=3.0 and Python 3.13 compatibility

[davecwright3]

Description

This PR migrates the Cython utilities to Cython 3.0. It mostly is just additional flags for exceptions.

The PR also makes holodeck compatible with Python 3.13. This was a simple fix in cyutils.sam_poisson_gwb. long is no longer exposed in the C API in Python 3.13, but calling int is the same thing and is backwards compatible.

Todos

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

• Migrate to Cython 3.0
• Bumps NumPy lower bound to a version compatible with Cython 3.0
• Add Python 3.13 compatibility

Status

• Builds (fails tests but tests were already failing)
• Confirmed locally that all builds 3.9-3.13 work on linux
• Tests from Mac users
• Tests from Windows users

As the status above suggests, I'd like to get some Mac and Windows users to check that the builds work.

[kayhangultekin]

Does this override #121 ?

[kayhangultekin]

I can confirm it works on my macOS 15.7.2 (Sequoia) Intel Xeon W iMac (from 2017). I will test on my M1 laptop next.

[kayhangultekin]

Can confirm it runs on my macOS 26.0.1 (Tahoe) Apple M2 laptop.

[kayhangultekin]

@jjohnpeter , Can you see if this PR (1) works for you on your windows set up and (2) does it fix the long long int issue you saw in #121 ?

[jjohnpeter]

@jjohnpeter , Can you see if this PR (1) works for you on your windows set up and (2) does it fix the long long int issue you saw in #121 ?

I tested the PR on my Windows setup, and it compiles and builds successfully without errors. It does not fix the long long int mismatch I was seeing in #121 though.

[kayhangultekin]

Thanks @jjohnpeter!

I see no reason not to merge this. @davecwright3 is building and running a single SAM notebook sufficient testing for you?

I will return to #121.

[davecwright3]

@kayhangultekin I forgot to add Python 3.13 tests. I'll add them in the next few days to this pull request.

[davecwright3]

The force push was a rebase onto dev. This should be good to go. Although, we could merge #124 first, then I can rebase again so that we can run the tests on this via GitHub actions.