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docs: overhaul nitpick-ignore rules and fix broken cross-references - #46

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docs: overhaul nitpick-ignore rules and fix broken cross-references#46
AVHopp wants to merge 2 commits into
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docs/fix-doc-references

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@AVHopp AVHopp commented Aug 11, 2026

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Layer 1 of a 4-PR stack decoupling linkcheck from the docs pipeline (rebased onto latest main).

Replaces the catch-all nitpick_ignore_regex (which suppressed every non-baybe reference, and thereby also hid broken internal cross-refs) with targeted, categorized ignore patterns, and fixes the internal references, admonition, and docstrings this exposed. Also suppresses the unavoidable forward-reference/guarded-import warnings from lazy-loaded heavy deps.

Stack (bottom → top):

  1. docs/fix-doc-references ← this PR (base: main)
  2. docs/separate-linkcheck
  3. docs/refactor-apidoc
  4. docs/docs-py311

Replace the catch-all nitpick_ignore_regex (which suppressed every
non-baybe reference and thereby also hid broken internal cross-refs)
with targeted, categorized ignore patterns. Fix the internal references,
admonition, and docstrings this exposed, and suppress the unavoidable
forward-reference/guarded-import warnings from lazy-loaded heavy deps.
Fix pre-existing issues surfaced by the nitpicky (`-n -W`) build that
the strict nitpick rules newly expose:

- Change the `MeanFactoryProtocol` cross-reference in the GP surrogate
  docstring from `:class:` to `:obj:`. The runtime type alias only exposes
  a `py:obj` target, so the `:class:` role failed to resolve.
- Drop the invalid `:hidden:` option from the `autosummary` directive in
  `docs/index.md`, which raised "unknown option: hidden".
- Add the `GPyTorchKernel` and `GPyTorchMean` TYPE_CHECKING-only aliases to
  the nitpick-ignore list alongside their sibling `GPyTorchLikelihood`. All
  three appear in `GaussianProcessSurrogate.from_preset`'s signature and
  cannot be resolved by Sphinx.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
@AVHopp
AVHopp force-pushed the docs/fix-doc-references branch from 00a5924 to 651d4a5 Compare August 17, 2026 13:42
@AVHopp AVHopp closed this Aug 18, 2026
@AVHopp
AVHopp deleted the docs/fix-doc-references branch August 18, 2026 07:19
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