Test on Python 3.11

[tomwhite]

• Fixes Test on Python 3.11 #915
• User visible changes (including notable bug fixes) are documented in changelog.rst

[tomwhite]

From https://github.com/pystatgen/sgkit/actions/runs/4870994546/jobs/8687416800?pr=1080:

Successfully built callee scikit-allel msprime bed-reader cbgen asv feedgen asciitree

We should open I have opened upstream issues for Python 3.11 wheels for msprime, bed-reader, and cbgen.

The failure is in Numba - something that seems to only happen on Python 3.11. Worth reporting @timothymillar?

_______ test_pedigree_inverse_kinship__raise_on_singular_kinship_matrix ________

    def test_pedigree_inverse_kinship__raise_on_singular_kinship_matrix():
        ds = sg.simulate_genotype_call_dataset(n_variant=1, n_sample=4, n_ploidy=4, seed=1)
        ds.sample_id.values  # doctest: +NORMALIZE_WHITESPACE
        ds["parent_id"] = ["samples", "parents"], [
            [".", "."],
            [".", "."],
            ["S0", "S0"],
            ["S1", "S2"],
        ]
        ds["stat_Hamilton_Kerr_tau"] = ["samples", "parents"], [
            [1, 1],
            [1, 1],
            [2, 2],
            [2, 2],
        ]
        ds["stat_Hamilton_Kerr_lambda"] = xr.zeros_like(ds["stat_Hamilton_Kerr_tau"], float)
        # check kinship is singular
        K = pedigree_kinship(ds, method="Hamilton-Kerr").stat_pedigree_kinship.values
        with pytest.raises(np.linalg.LinAlgError, match="Singular matrix"):
            np.linalg.inv(K)
        # check sgkit message
        with pytest.raises(ValueError, match="Singular kinship matrix"):
>           pedigree_inverse_kinship(ds, method="Hamilton-Kerr").compute()

sgkit/tests/test_pedigree.py:1340: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/xarray/core/dataset.py:900: in compute
    return new.load(**kwargs)
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/xarray/core/dataset.py:734: in load
    evaluated_data = da.compute(*lazy_data.values(), **kwargs)
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/base.py:599: in compute
    results = schedule(dsk, keys, **kwargs)
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/threaded.py:89: in get
    results = get_async(
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/local.py:511: in get_async
    raise_exception(exc, tb)
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/local.py:319: in reraise
    raise exc
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/local.py:224: in execute_task
    result = _execute_task(task, data)
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/core.py:119: in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/core.py:119: in <genexpr>
    return func(*(_execute_task(a, cache) for a in args))
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/core.py:119: in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/optimization.py:990: in __call__
    return core.get(self.dsk, self.outkey, dict(zip(self.inkeys, args)))
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/core.py:149: in get
    result = _execute_task(task, cache)
/opt/hostedtoolcache/Python/3.11.3/x64/lib/python3.11/site-packages/dask/core.py:119: in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   raise ValueError("Singular kinship matrix")
E   AssertionError: Unreachable condition reached (op code RERAISE executed)
E   -------------------------------------------------------------------------------
E   This should not have happened, a problem has occurred in Numba's internals.
E   You are currently using Numba version 0.57.0.
E   
E   Please report the error message and traceback, along with a minimal reproducer
E   at: https://github.com/numba/numba/issues/new?template=bug_report.md
E   
E   If more help is needed please feel free to speak to the Numba core developers
E   directly at: https://gitter.im/numba/numba
E   
E   Thanks in advance for your help in improving Numba!

[timothymillar]

@tomwhite looks like it's already reported numba/numba#8845

[tomwhite]

I excluded the failing Numba test on Python 3.11, since no fix seems forthcoming in Numba.

The Windows build is now failing due to #1109