fix: restore the test suite on Python 3.12 (pandas 3, anndata 0.13)

[Marius1311]

The Test workflow is red on main for both 3.12 legs and has been since mid-June — the scheduled run of 2026-08-15 reports 27 failed, 732 passed identically on ubuntu and macOS. The 3.11 leg stays green because it resolves older anndata/pandas. Two unrelated breakages, both dependency drift:

1. Positional indexing of a pandas.Series (24 failures)

src/moscot/base/problems/_mixins.py:288 and :312:

v = np.array(tm_batch.argmax(0))
out.extend(source_df[annotation_label][v[i]] for i in range(len(v)))

v holds positions, while source_df[annotation_label] is a Series indexed by observation names. series[np.int64(0)] therefore relied on pandas' positional fallback for non-integer indexes, which pandas 2 deprecated and pandas 3 removed:

E   KeyError: np.int64(0)
pandas/_libs/index.pyx:583: KeyError

Every test_annotation_mapping case (mapping_mode="max", across the space, time and cross-modality mixins) hits this. Fixed with .iloc, which is exactly what the fallback used to do — so the behaviour is unchanged on older pandas too.

This one is a genuine bug in moscot rather than a test artefact: any user calling annotation_mapping(..., mapping_mode="max") on pandas 3 gets the same KeyError.

2. AnnData.concatenate was removed (3 failures)

tests/problems/base/test_general_problem.py used the long-deprecated method, giving AttributeError: 'AnnData' object has no attribute 'concatenate' in the three test_set_graph_xy cases. Replaced with anndata.concat([...]).

Verification

Full suite on Python 3.12 with anndata 0.13.2 and pandas 3.0.5: 759 passed, 1 skipped, 0 failed (was 732 passed / 27 failed — exactly the 27 restored). black, isort, ruff clean.

Independent of #848 (lint) and #846 (sparsify); together the three take CI back to green.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.62%. Comparing base (e7a0567) to head (56801ee).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #849   +/-   ##
=======================================
  Coverage   76.62%   76.62%           
=======================================
  Files          36       36           
  Lines        4175     4175           
  Branches      670      670           
=======================================
  Hits         3199     3199           
  Misses        679      679           
  Partials      297      297           

Files with missing lines	Coverage Δ
src/moscot/base/problems/_mixins.py	88.61% <100.00%> (ø)

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[Marius1311]

@selmanozleyen, let me know whether I can merge this.

[selmanozleyen]

Thanks looks good