Rework perturbation spaces around a perturbation-level API

[Zethson]

Reworks pertpy's perturbation space module so that every space returns one observation per perturbation and the spaces compose with each other, and adds distance/embedding spaces plus combination and dose analyses.

• MLPClassifierSpace averages its penultimate-layer activations per perturbation (was one embedding per cell).
• Classifiers default to target_col="perturbation" and emit the label under target_col with perturbation-named obs_names, so classifier → distance/cluster/neighbors chains work.
• Reproducible random_state accepting int | Generator | RandomState | None (new RandomStateLike in pertpy/_types.py).
• Sparse-aware JAXDataset (per-batch densification), shared obs-carry helpers, and typing cleanup (str | None, dropped # type: ignores).
• DistanceSpace — wraps Distance.pairwise into a perturbation space (matrix in .X and .obsp["distances"]), feeding clustering/neighbors directly.
• PerturbationSpace.nearest_perturbations — rank perturbations by proximity (mechanism-of-action lookup).
• PerturbationSpace.plot_similarity — clustered heatmap of perturbation distances.
• EmbeddingSpace — ingest an external per-perturbation embedding (e.g. scGPT/Geneformer gene embeddings).
• evaluate_combinations — score an additive model (effect(A)+effect(B)) against the measured combination effect.
• dose_response — effect size of each perturbation versus dose.
• DBSCANSpace → HDBSCANSpace (sklearn HDBSCAN).

Breaking changes (clean break, no shims)

• Classifier target_col default "perturbations" → "perturbation"; output column follows target_col instead of the hardcoded "perturbations".
• MLPClassifierSpace returns perturbation-level (not cell-level) embeddings.
• DBSCANSpace removed in favor of HDBSCANSpace.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 86.24339% with 26 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.99%. Comparing base (31b2fe9) to head (28caf3e).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...y/tools/_perturbation_space/_perturbation_space.py	83.33%	15 Missing ⚠️
.../_perturbation_space/_discriminator_classifiers.py	85.41%	7 Missing ⚠️
pertpy/tools/_perturbation_space/_simple.py	91.83%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1032      +/-   ##
==========================================
- Coverage   78.00%   77.99%   -0.02%     
==========================================
  Files          50       50              
  Lines        6557     6694     +137     
==========================================
+ Hits         5115     5221     +106     
- Misses       1442     1473      +31     

Files with missing lines	Coverage Δ
pertpy/_types.py	100.00% <100.00%> (ø)
pertpy/tools/__init__.py	78.37% <ø> (ø)
pertpy/tools/_perturbation_space/_simple.py	93.38% <91.83%> (+1.72%)	⬆️
.../_perturbation_space/_discriminator_classifiers.py	80.65% <85.41%> (-1.32%)	⬇️
...y/tools/_perturbation_space/_perturbation_space.py	87.67% <83.33%> (-3.17%)	⬇️

... and 2 files with indirect coverage changes

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