Ensure submodules are unique in sphinx.ext.apidoc

CHANGES

@@ -72,6 +72,8 @@ Features added
 Bugs fixed
 ----------
 
+* #10200: apidoc: Duplicated submodules are shown for modules having both .pyx
+  and .so files
 * #10279: autodoc: Default values for keyword only arguments in overloaded
   functions are rendered as a string literal
 * #10280: autodoc: :confval:`autodoc_docstring_signature` unexpectedly generates

sphinx/ext/apidoc.py

@@ -117,6 +117,7 @@ def create_package_file(root: str, master_package: str, subroot: str, py_files:
     submodules = [sub.split('.')[0] for sub in py_files
                   if not is_skipped_module(path.join(root, sub), opts, excludes) and
                   not is_initpy(sub)]
+    submodules = sorted(set(submodules))
     submodules = [module_join(master_package, subroot, modname)
                   for modname in submodules]
     options = copy(OPTIONS)

tests/test_ext_apidoc.py

@@ -4,6 +4,7 @@
 
 import pytest
 
+import sphinx.ext.apidoc
 from sphinx.ext.apidoc import main as apidoc_main
 from sphinx.testing.path import path
 
@@ -639,3 +640,31 @@ def test_namespace_package_file(tempdir):
                        "   :members:\n"
                        "   :undoc-members:\n"
                        "   :show-inheritance:\n")
+
+
+def test_no_duplicates(rootdir, tempdir):
+    """Make sure that a ".pyx" and ".so" don't cause duplicate listings.
+
+    We can't use pytest.mark.apidoc here as we use a different set of arguments
+    to apidoc_main
+    """
+
+    original_suffixes = sphinx.ext.apidoc.PY_SUFFIXES
+    try:
+        # Ensure test works on Windows
+        sphinx.ext.apidoc.PY_SUFFIXES += ('.so',)
+
+        package = rootdir / 'test-apidoc-duplicates' / 'fish_licence'
+        outdir = tempdir / 'out'
+        apidoc_main(['-o', outdir, "-T", package, "--implicit-namespaces"])
+
+        # Ensure the module has been documented
+        assert (outdir / 'fish_licence.rst').isfile()
+
+        # Ensure the submodule only appears once
+        text = (outdir / 'fish_licence.rst').read_text(encoding="utf-8")
+        count_submodules = text.count(r'fish\_licence.halibut module')
+        assert count_submodules == 1
+
+    finally:
+        sphinx.ext.apidoc.PY_SUFFIXES = original_suffixes