From 78697caacc9caf1eb8ab85774951fe9fc7fc9b46 Mon Sep 17 00:00:00 2001
From: Shurong Cao <170531907+CAOShurong@users.noreply.github.com>
Date: Mon, 24 Aug 2026 14:48:36 +0800
Subject: [PATCH] Normalize paths when matching manifest entries to package
 dirs in build_py

Manifest/SOURCES.txt paths use forward slashes while get_package_dir
emits OS-native separators; on Windows the mismatch made analyze_manifest
overshoot the package dir, emitting a false 'Package is absent from the
packages configuration' warning and misclassifying extension sources
(e.g. .pyx files written in the documented Unix form) as parent-package
data. Normalize both sides before comparison.

Fixes #5093
---
 newsfragments/5093.bugfix.rst     |  5 +++
 setuptools/command/build_py.py    |  6 ++-
 setuptools/tests/test_build_py.py | 66 +++++++++++++++++++++++++++++++
 3 files changed, 75 insertions(+), 2 deletions(-)
 create mode 100644 newsfragments/5093.bugfix.rst

diff --git a/newsfragments/5093.bugfix.rst b/newsfragments/5093.bugfix.rst
new file mode 100644
index 0000000000..9d0f76b385
--- /dev/null
+++ b/newsfragments/5093.bugfix.rst
@@ -0,0 +1,5 @@
+Fixed a Windows-only false ``Package '...' is absent from the `packages`
+configuration`` warning (and the resulting misclassification of the file as
+package data) that occurred when an ``Extension`` source path written with
+forward slashes (the documented, portable form) lived inside a subpackage:
+manifest paths and package directories are now normalized before comparison.
diff --git a/setuptools/command/build_py.py b/setuptools/command/build_py.py
index 3c7c2d1bd6..b3dac06c2c 100644
--- a/setuptools/command/build_py.py
+++ b/setuptools/command/build_py.py
@@ -181,7 +181,9 @@ def analyze_manifest(self) -> None:
         src_dirs: dict[str, str] = {}
         for package in self.packages or ():
             # Locate package source directory
-            src_dirs[assert_relative(self.get_package_dir(package))] = package
+            src_dirs[
+                os.path.normpath(assert_relative(self.get_package_dir(package)))
+            ] = package
 
         if (
             self.existing_egg_info_dir
@@ -198,7 +200,7 @@ def analyze_manifest(self) -> None:
 
         check = _IncludePackageDataAbuse()
         for path in self._filter_build_files(files, egg_info_dir):
-            d, f = os.path.split(assert_relative(path))
+            d, f = os.path.split(assert_relative(os.path.normpath(path)))
             prev = None
             oldf = f
             while d and d != prev and d not in src_dirs:
diff --git a/setuptools/tests/test_build_py.py b/setuptools/tests/test_build_py.py
index 62ed408f3c..fd7816243c 100644
--- a/setuptools/tests/test_build_py.py
+++ b/setuptools/tests/test_build_py.py
@@ -479,3 +479,69 @@ def get_outputs(build_py):
         os.path.relpath(x, build_dir).replace(os.sep, "/")
         for x in build_py.get_outputs()
     }
+
+
+def test_analyze_manifest_mixed_separators(tmpdir_cwd):
+    """
+    A subpackage source path written with forward slashes (the documented,
+    portable form for ``Extension`` sources) must not be misclassified as
+    package data of the parent package on Windows due to a separator mismatch
+    between manifest paths and package dirs.
+
+    Regression test for #5093.
+    """
+    jaraco.path.build({
+        "setup.cfg": DALS(
+            """
+                [metadata]
+                name = mypkg
+                version = 42
+
+                [options]
+                include_package_data = True
+                packages =
+                    mypkg
+                    mypkg.lib
+                """
+        ),
+        "mypkg": {
+            "__init__.py": "",
+            "lib": {"__init__.py": "", "say.pyx": "# dummy"},
+        },
+        "MANIFEST.in": DALS(
+            """
+                recursive-include mypkg *.pyx
+                prune dist
+                prune build
+                prune *.egg-info
+                """
+        ),
+    })
+    from setuptools.extension import Extension
+
+    dist = Distribution({"script_name": "%PEP 517%"})
+    dist.parse_config_files()
+    dist.ext_modules = [Extension("mypkg.lib.say", ["mypkg/lib/say.pyx"])]
+
+    egg_info = dist.get_command_obj("egg_info")
+    dist.run_command("egg_info")
+
+    build_py = dist.get_command_obj("build_py")
+    build_py.finalize_options()
+    build_py.existing_egg_info_dir = egg_info.egg_info
+
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always")
+        build_py.analyze_manifest()
+
+    offending = [
+        w
+        for w in caught
+        if issubclass(w.category, SetuptoolsDeprecationWarning)
+        and "mypkg.lib" in str(w.message)
+        and "absent" in str(w.message)
+    ]
+    assert not offending, (
+        "Subpackage whose extension source is written in Unix form was "
+        "misclassified as data of the parent package (mixed path separators)"
+    )