Apply qualname_overrides in more circumstances

.vscode/settings.json

@@ -1,9 +1,7 @@
 {
     "python.analysis.typeCheckingMode": "strict",
     "python.testing.pytestArgs": ["-vv", "--color=yes"],
-    "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
-    "python.terminal.activateEnvironment": false,
     "[python]": {
         "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.formatOnSave": true,

src/scanpydoc/elegant_typehints/__init__.py

@@ -68,7 +68,10 @@ def x() -> Tuple[int, float]:
     from collections.abc import Callable
 
     from sphinx.config import Config
+    from docutils.nodes import TextElement, reference
+    from sphinx.addnodes import pending_xref
     from sphinx.application import Sphinx
+    from sphinx.environment import BuildEnvironment
 
 
 __all__ = [
@@ -113,6 +116,24 @@ class PickleableCallable:
     __call__ = property(lambda self: self.func)
 
 
+# https://www.sphinx-doc.org/en/master/extdev/event_callbacks.html#event-missing-reference
+def _last_resolve(
+    app: Sphinx,
+    env: BuildEnvironment,
+    node: pending_xref,
+    contnode: TextElement,
+) -> reference | None:
+    if "sphinx.ext.intersphinx" not in app.extensions:
+        return None
+
+    from sphinx.ext.intersphinx import resolve_reference_detect_inventory
+
+    if (qualname := qualname_overrides.get(node["reftarget"])) is None:
+        return None
+    node["reftarget"] = qualname
+    return resolve_reference_detect_inventory(env, node, contnode)
+
+
 @_setup_sig
 def setup(app: Sphinx) -> dict[str, Any]:
     """Patches :mod:`sphinx_autodoc_typehints` for a more elegant display."""
@@ -123,6 +144,8 @@ def setup(app: Sphinx) -> dict[str, Any]:
     app.add_config_value("qualname_overrides", default={}, rebuild="html")
     app.add_config_value("annotate_defaults", default=True, rebuild="html")
     app.connect("config-inited", _init_vars)
+    # Add 1 to priority to run after sphinx.ext.intersphinx
+    app.connect("missing-reference", _last_resolve, priority=501)
 
     from ._formatting import typehints_formatter
 

tests/test_elegant_typehints.py

@@ -12,12 +12,14 @@
 
 import pytest
 
+from scanpydoc.elegant_typehints import _last_resolve, qualname_overrides
 from scanpydoc.elegant_typehints._formatting import typehints_formatter
 
 
 if TYPE_CHECKING:
     from types import ModuleType
     from typing import Protocol
+    from collections.abc import Generator
 
     from sphinx.application import Sphinx
 
@@ -32,6 +34,12 @@ def __call__(  # noqa: D102
 NONE_RTYPE = ":rtype: :sphinx_autodoc_typehints_type:`\\:py\\:obj\\:\\`None\\``"
 
 
+@pytest.fixture(autouse=True)
+def _reset_qualname_overrides() -> Generator[None, None, None]:
+    yield
+    qualname_overrides.clear()
+
+
 @pytest.fixture
 def testmod(make_module: Callable[[str, str], ModuleType]) -> ModuleType:
     return make_module(
@@ -240,6 +248,40 @@ def fn_test(m: object) -> None:  # pragma: no cover
     ]
 
 
+def test_resolve(app: Sphinx) -> None:
+    """Test that qualname_overrides affects _last_resolve as expected."""
+    from docutils.nodes import TextElement, reference
+    from sphinx.addnodes import pending_xref
+    from sphinx.ext.intersphinx import InventoryAdapter
+
+    app.setup_extension("sphinx.ext.intersphinx")
+
+    # Inventory contains documented name
+    InventoryAdapter(app.env).main_inventory["py:class"] = {
+        "test.Class": ("TestProj", "1", "https://x.com", "Class"),
+    }
+    # Node contains name from code
+    node = pending_xref(refdomain="py", reftarget="testmod.Class", reftype="class")
+
+    resolved = _last_resolve(app, app.env, node, TextElement())
+    assert isinstance(resolved, reference)
+    assert resolved["refuri"] == "https://x.com"
+    assert resolved["reftitle"] == "(in TestProj v1)"
+
+
+@pytest.mark.parametrize("qualname", ["testmod.Class", "nonexistent.Class"])
+def test_resolve_failure(app: Sphinx, qualname: str) -> None:
+    from docutils.nodes import TextElement
+    from sphinx.addnodes import pending_xref
+
+    app.setup_extension("sphinx.ext.intersphinx")
+    node = pending_xref(refdomain="py", reftarget=qualname, reftype="class")
+
+    resolved = _last_resolve(app, app.env, node, TextElement())
+    assert resolved is None
+    assert node["reftarget"] == qualname_overrides.get(qualname, qualname)
+
+
 # These guys aren’t listed as classes in Python’s intersphinx index:
 @pytest.mark.parametrize(
     "annotation",