Handle SciPy and libpysal deprecations

[martinfleis]

The CI is currently showing a deprecations from SciPy, libpysal and a few others that would be good to tackle. See https://github.com/pysal/pointpats/actions/runs/4287451301/jobs/7468323178

/Users/runner/work/pointpats/pointpats/pointpats/geometry.py:134: DeprecationWarning: Please use `ConvexHull` from the `scipy.spatial` namespace, the `scipy.spatial.qhull` namespace is deprecated.

/Users/runner/micromamba-root/envs/test/lib/python3.11/site-packages/libpysal/cg/shapes.py:1208: FutureWarning: Objects based on the `Geometry` class will deprecated and removed in a future version of libpysal.

[jGaboardi]

@martinfleis @sjsrey et al

This scipy warning have been taken care of for quite some time and I have taken care of the other while addressing #200, but the libpysal ones remain.

~libpysal/cg/shapes.py:1208: FutureWarning: Objects based on the `Geometry` class will deprecated and removed in a future version of libpysal.

Should we:

1. start moving away from the PySAL native geometries;
2. 2 suppress the warning in CI
3. both
4. other?

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• xref items for deprecation libpysal#484

[martinfleis]

Is there anything that requires PySAL geometries? At least the parts I touched support them but alongside shapely geometries. I guess we can just drop the support of PySAL geoms then, no?

[jGaboardi]

I have not done a comprehensive review of everything, but for example window.py relies entirely on native libpysal geometries.

[martinfleis]

Hmm, then that needs to be refactored to work on top of shapely but with some transition period during which it supports both.