docs: make ReadTheDocs build deps-free and reliable (D6)

[nceglia]

Summary

The RTD build did pip install . (pulling the full ML stack — torch, scvi-tools, scanpy, pyro…) and then let autodoc import it. That's slow and OOM-prone on RTD's runners, and it never actually worked with the D11 autodoc. This rebuilds the API reference from source with the heavy deps mocked, so RTD installs almost nothing.

Changes

• conf.py — autodoc_mock_imports: torch, pyro, scvi, sklearn, scanpy, anndata, scipy, matplotlib, seaborn, mpltern, umap, tqdm, daft, gseapy. autodoc still reads TCRi's own real signatures/docstrings; only third-party imports are stubbed. numpy/pandas kept real so intersphinx resolves their types.
• conf.py — autodoc_class_signature = 'separated': without it, TCRIModel renders as TCRIModel(*args, **kwargs) because the mocked scvi BaseModelClass injects a __new__(*args, **kwargs) that shadows the real __init__. With it, autodoc reads __init__ directly and the real constructor signature (n_latent=128, …) renders.
• conf.py — version: prefer installed metadata, fall back to parsing pyproject.toml (so the version is right even without an install).
• .readthedocs.yaml: Python 3.9 → 3.12 (pyproject requires >=3.10); drop the pip install . step; HTML-only.
• docs/requirements.txt: trimmed to the Sphinx toolchain + numpy/pandas; pinned sphinx>=7,<9, sphinx-rtd-theme>=2.0, myst-parser>=2.0.
• Deleted the stale duplicate docs/.readthedocs.yaml (RTD uses the repo-root file).

Verification

Sphinx's mock finder shadows the locally-installed torch/scvi, so a local build genuinely reproduces the deps-free RTD path:

• python -m sphinx -b html docs <out> → build succeeded, 0 warnings, 0 import failures.
• Real API renders: joint_distribution_posterior, save_tcri_session, and TCRIModel.__init__(adata, n_latent=128, …). Version resolves to 0.1.0.

Needs RTD-side confirmation

The mocked-build path is verified locally, but the actual RTD environment (network install + RTD resource limits) can only be confirmed by a real RTD build — please trigger/check one after merge. If a mocked module turns out to need un-mocking, it's a one-line edit to autodoc_mock_imports.

Closes Notion D6.

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