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docs: fix broken intersphinx links #442

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Merged
BorisMuzellec merged 2 commits into from
Apr 14, 2026
+13 −3
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docs: fix broken intersphinx links #442

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7116990
docs: fix broken intersphinx links for pandas and numpy
Ekin-Kahraman Apr 8, 2026
77987f4
docs: suppress pandas.core.frame.DataFrame nitpick warning
Ekin-Kahraman Apr 11, 2026
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16 changes: 13 additions & 3 deletions docs/source/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,13 @@
"Inference": ":class:`Inference <pydeseq2.inference.Inference>`",
"DefaultInference": ":class:`DefaultInference "
"<pydeseq2.default_inference.DefaultInference>`",
# numpy short forms
"ndarray": ":class:`numpy.ndarray`",
"np.ndarray": ":class:`numpy.ndarray`",
# pandas short forms
"pd.DataFrame": ":class:`pandas.DataFrame`",
"pd.Series": ":class:`pandas.Series`",
"pandas.Index": ":class:`pandas.Index`",
}

# Add any paths that contain templates here, relative to this directory.
Expand Down Expand Up @@ -228,10 +235,13 @@
# documentation for each type specified
# The following elements are the link that auto doc were not able to do
nitpick_ignore = [
("py:class", "pd.Series"),
("py:class", "pd.DataFrame"),
# anndata re-exports AnnData from a private submodule; autodoc resolves the
# runtime path for base-class references which intersphinx cannot remap.
("py:class", "anndata._core.anndata.AnnData"),
# pandas re-exports DataFrame from pandas.core.frame, but intersphinx only
# knows the public path (pandas.DataFrame). autodoc resolves type annotations
# like `pd.DataFrame` to the internal module path at runtime.
("py:class", "pandas.core.frame.DataFrame"),
("py:class", "ndarray"),
("py:class", "numpy._typing._generic_alias.ScalarType"),
("py:class", "pydantic.main.BaseModel"),
("py:class", "torch.nn.modules.module.Module"),
Expand Down
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