Fix CI and other issues

[Billyzhang1229]

• Pin pandas <3.0 in requirements and pyproject (Dask/pandas 3.0 not fully supported yet)
• Split NumPy constraints by sys_platform (Apple ARM uses NumPy >=2.3.5)
• Drop Python 3.10 and NumPy 1.x support (requirements + CI workflows + docs)
• Make xr.concat data_vars explicit to silence FutureWarning
• Expand Zarr error regex to accept “contains data”
• Ignore .hypothesis in pytest collection
• Filter known runtime warnings (Numba correlation_reduce_cpu, Zarr v3 dtype warning)
• Fix Windows CI: conda only for msprime, pip for requirements (PEP 508 markers)
• Docs: update xarray intersphinx link and use PEP 604 unions to avoid typing.Union nitpicks
• Temporary disable notebook execution due to missing link
• Update mergify Python targets

#1338

[jeromekelleher]

This all LGTM - thanks @Billyzhang1229!

[jeromekelleher]

We could also consider dropping Mergify - the built in GitHub support has been working well over in tskit-dev.

[jeromekelleher]

LGTM!

[Billyzhang1229]

The only failing job is the Cubed workflow.

The Cubed workflow explicitly installs dev builds from GitHub, overriding the pinned dependencies in requirements.txt. In .github/workflows/cubed.yml it runs:

python -m pip install -U git+https://github.com/cubed-dev/cubed.git -U git+https://github.com/cubed-dev/cubed-xarray.git -U git+https://github.com/pydata/xarray.git

The Cubed failure is due to an upstream FutureWarning / behavior change related to tuple-based chunk specification in xarray 2026.1.1.dev18.

[tomwhite]

The only failing job is the Cubed workflow.

It would be OK to skip this until we can fix it.

[Billyzhang1229]

Cool, I’ll go ahead and squash the commits.

[jeromekelleher]

These commits all seem like they do something well specified, so no need to squash from my perspective

[Billyzhang1229]

There are a couple of small dev commits (15c21ad, 27d6a19) where I iterated on the same change. I’ll tidy those up / revert the redundant bits to keep the history clean, but otherwise I’ll leave the commits as-is rather than squashing.

[Billyzhang1229]

I’ve tidied things up a bit now. removed the dev commits.