Replace pip with uv for test workflow

[LucaMarconato]

Giving a try to using uv instead of pip for the test workflow. I did't edit the release and docker workflows since they are run rarely and trying to make them faster would not pay off.

I took inspiration from https://github.com/vitessce/vitessce-python/pull/390/files. Note that I removed the pip caching mechanism in this commit fac7848. It could be that having uv + caching leads to better results.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.91%. Comparing base (4df1912) to head (ef7d357).
Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   91.91%   91.91%           
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  Files          48       48           
  Lines        7388     7388           
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  Hits         6791     6791           
  Misses        597      597           

[LucaMarconato]

uv without caching is already faster!

• with uv: (around 30s) https://github.com/scverse/spatialdata/actions/runs/13289302024/job/37105692929?pr=877
• with pip + caching: (around 2m) https://github.com/scverse/spatialdata/actions/runs/13270423075/job/37048312124

I'll give a try to uv + caching now.

[LucaMarconato]

I'm having problems with optional dependencies. It seems that they are not correctly cached.

[LucaMarconato]

Ok I made it work. Caching doesn't help with pre-built wheels, re-downloading every time is as fast (also explained here https://github.com/astral-sh/setup-uv#disable-cache-pruning).

I will disable the cache. This PR will still bring a 4-fold decrease in the time required to setup the env.

[LucaMarconato]

I tried using uv instead of pip in readthedocs using the approach described here: astral-sh/uv#10074, but it didn't seem to speed up things (strange tbh, but ok, 2 min is already fast compared to the time to run tests).

• pip run: https://readthedocs.org/projects/scverse-spatialdata/builds/27168628/
• uv run: https://readthedocs.org/projects/scverse-spatialdata/builds/27168689/

I therefore went back to pip for readthedocs.

[LucaMarconato]

CC @timtreis (worth moving to uv also in spatialdata-plot etc). It's very easy to move to uv (I did many experiments with caching here, but in the end what I recommend is what shown in the PR diff).