drop unmaintained pygeos for shapely 2.0

[omsai]

The requirement pygeos fails to install with python 3.12 with the error described here: pygeos/pygeos#463

The maintainer explains that pygeos is no longer maintained and has been merged into the shapley 2.0 dependency of geopandas. Since version 0.14, geopandas uses shapley instead of pygeos: https://geopandas.org/en/stable/docs/user_guide/pygeos_to_shapely.html

Therefore, the PR drops the unmaintained pygeos and requires geopandas >= 0.14 to ensure the default shapley version is used instead.

[clwgg]

(Issue tracked here: #432)

[giovp]

thanks @omsai for this PR, I wonder we could probably also remove this right https://github.com/scverse/spatialdata/blob/main/src/spatialdata/_compat.py#L1 ?

[omsai]

@giovp Indeed; I've dropped that as well.

[giovp]

thank you @omsai , I think it should be fine to not have it backward compatible, would like to have other devs chime in

[LucaMarconato]

Thanks for the PR! I have also tested it, with Python 3.12, and all works as expected.

Minor comment, I have removed the line os.environ["USE_PYGEOS"] = "0" from spatialdata/tests/conftest.py (and from other scripts in the ecosystem) because now it'd not needed anymore. Some notebooks still have it, so if we see it let's remove it (but no rush, that line currently has no effect).

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.55%. Comparing base (b73f3a8) to head (0acc495).
Report is 91 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #545      +/-   ##
==========================================
+ Coverage   92.53%   92.55%   +0.01%     
==========================================
  Files          43       42       -1     
  Lines        6003     6000       -3     
==========================================
- Hits         5555     5553       -2     
+ Misses        448      447       -1     

Files	Coverage Δ
src/spatialdata/__init__.py	100.00% <ø> (ø)

... and 2 files with indirect coverage changes

[LucaMarconato]

codecov woke up after 3 months 😅