ci: unbreak the lint jobs (mypy python_version, dead doc links)

[Marius1311]

Both legs of the Lint workflow have been failing on main since 2026-07-27, at the same SHA and for reasons unrelated to any code change — the last green run was 2026-07-06. Neither failure is caused by moscot code. The Test workflow is separately red on 3.12 (see below).

Lint code

The mypy hook aborts inside numpy's own stubs:

numpy/__init__.pyi:737:45: error: Type statement is only supported in Python 3.12 and greater  [syntax]
Found 1 error in 1 file (errors prevented further checking)

numpy's stubs now use PEP 695 (type X = …), which needs python_version >= 3.12, while [tool.mypy] still pins python_version = "3.10". mypy therefore never reaches any moscot source — it has effectively not type-checked the project for a month.

• Bump to python_version = "3.12". The project requires >=3.11, so this only means checking under 3.12 semantics; no supported interpreter is dropped.
• Drop plugins = "numpy.typing.mypy_plugin", deprecated in NumPy 2.3 and slated for removal.

With mypy actually running again, five type: ignore comments are reported as unnecessary (warn_unused_ignores = true) — three in __init__.py, one in base/cost.py (only the type-var code was stale, arg-type is kept), one in problems/time/_mixins.py. They are removed, after checking moscot.__version__/__author__ still resolve. mypy src is then clean: no issues found in 50 source files.

The hook's environment installs only numpy (additional_dependencies: [numpy>=1.25.0]), so this is exactly what CI checks. Running mypy in a fully populated environment surfaces ~140 further errors from third-party stubs; that is a separate discussion and this PR does not touch it.

Lint docs

lint-docs builds with SPHINXOPTS = -W -q --keep-going, so anything that warns fails it. Two causes:

1. Dead links. make linkcheck reported two upstream 404s — muon.atac.tl.lsi and an openproblems dataset page — both from 600_tutorial_translation.ipynb, which lives in the docs/notebooks submodule and so cannot be fixed here. They join the existing linkcheck_ignore list, in its established commented style.
2. Nine broken references. Every remaining warning was py:func reference target not found: scanpy.read. These come from dataset docstrings saying "Keyword arguments for :func:scanpy.read" — but _load_dataset_from_url forwards **kwargs to anndata.read_h5ad (or mudata.read_h5mu), never to scanpy.read, which scanpy also no longer documents. Retargeted to :func:~anndata.io.read_h5ad, which fixes a factual error in the docs as well as the build. (pancreas_multiome already documented the right functions and is untouched.)

After this, the job has no broken links and no warnings left to trip -W.

Not fixed here

The Test workflow fails on ubuntu-3.12 and macOS-3.12 with 27 failures (3.11 passes) in test_annotation_mapping and test_set_graph_xy. Those are pre-existing and orthogonal to lint: this PR touches only mypy config, linkcheck_ignore and docstrings, and reproduces the identical 27 failures. I also reproduced them locally with and without an unrelated source change and got identical counts. Worth its own issue.

Verification

• mypy src under the hook's exact dependency set (mypy 1.15.0 + numpy only): clean.
• black, isort, ruff, rstcheck, doc8 and the remaining hooks: pass (prettier needs Node, which I don't have locally — untouched by this diff).
• pytest tests/solvers tests/utils: 56 passed.
• anndata.io.read_h5ad confirmed present in anndata's intersphinx inventory.

Split out of #846, which is blocked on the same red lint.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 76.62%. Comparing base (915643e) to head (e2bcc57).

Files with missing lines	Patch %	Lines
src/moscot/base/cost.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #848   +/-   ##
=======================================
  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/datasets.py	61.00% <ø> (ø)
src/moscot/problems/time/_mixins.py	63.84% <100.00%> (ø)
src/moscot/base/cost.py	75.00% <0.00%> (ø)

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[Marius1311]

@selmanozleyen, merging this, it's just linting stuff.