pybigtools: NumPy 2.0

[nvictus]

Numpy just released its 2.0, which includes ABI breaks, and a migration guide. We should check that nothing breaks or pin numpy < 2 until migration is complete.

[nvictus]

Re: ABI compatibility

https://numpy.org/doc/stable/dev/depending_on_numpy.html#numpy-2-0-specific-advice

When you build wheels for your package using a NumPy 2.x version at build time, those will work with NumPy 1.xx.

So for pybigtools, we want a numpy 2.x dependency at build time. i.e.:

[build-system]
requires = ["maturin>=1.0,<2.0",  "numpy>=2.0,<3.0"]
build-backend = "maturin"
...

[jackh726]

That seems fine - I did a bit of testing and didn't encounter any problems.

[nvictus]

I take it back. For pyO3-based bindings, the build time dependency that matters is rust-numpy.

[nvictus]

It's still not clear to me whether or not there could be ABI incompatibility between pybigtools and a Python environment that uses numpy 2.0. However, pybigtools currently depends on rust-numpy 0.19, which are bindings to the NumPy 1.xx C API.

We should probably bump rust-numpy to 0.22 or later, which supports NumPy 2.0 which supports both ABIs.

[jackh726]

I've upgraded to rust-numpy 0.22 on master.

[jackh726]

The pybigtools v0.2.4 release contains rust-numpy 0.22, so closing this.