pandas 3.0 support

[LucaMarconato]

• Support for pandas 3.0. Currently uses the latest anndata and geopandas from GitHub main (they are not released yet).
• Restore test against pre-release versions, and ensure support for all of them. Specifically:

 - colorcet==3.1.0
 + colorcet==3.1.1a1
 - pandas==2.3.3
 + pandas==3.0.0rc0
 - pytz==2025.2
 - scikit-image==0.25.2
 + scikit-image==0.26.0rc1
 - scipy==1.16.3
 + scipy==1.17.0rc1

• Improve uv support for pre-release versions.
• Bump min Python to 3.12.

[LucaMarconato]

The pre-release job should fail with a few hundreds red tests. Most of them fail with the latest geopandas geopandas-1.1.1, but are green with the latest geopandas main.

[codecov]

Codecov Report

❌ Patch coverage is 87.50000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 92.19%. Comparing base (d013fe0) to head (84ca1e0).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata/models/models.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1034   +/-   ##
=======================================
  Coverage   92.19%   92.19%           
=======================================
  Files          49       49           
  Lines        7545     7549    +4     
=======================================
+ Hits         6956     6960    +4     
  Misses        589      589           

Files with missing lines	Coverage Δ
src/spatialdata/_core/operations/rasterize_bins.py	93.79% <100.00%> (ø)
src/spatialdata/_io/io_shapes.py	94.66% <100.00%> (+0.30%)	⬆️
src/spatialdata/models/models.py	88.61% <50.00%> (ø)

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[LucaMarconato]

Both geopandas and anndata had a release. I'll looking into merging this now.

[LucaMarconato]

Ah no, https://github.com/scverse/anndata/pull/2133/changes#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711 is still unreleased.

[LucaMarconato]

I reverted the min python version to be 3.11 (in the incoming anndata release it will be 3.12, as for SPEC-0). I also modified the pre-release CI job to only include specific packages that we want to test against.

[LucaMarconato]

I'll modify the test.yaml workflow at a later point in a follow-up PR: #1039