fix include/exclude compiled_src order as described in README.md

src/hatch_cython/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2023-present joshua-auchincloss <joshua.auchincloss@proton.me>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.6.0"
+__version__ = "0.6.1"

src/hatch_cython/plugin.py

@@ -427,7 +427,10 @@ def autogenerated_files(self) -> RelAbsPathMap:
     def inclusion_map(self):
         include = {}
         for compl in list(self.compiled_files.keys()):
-            include[compl] = compl
+            dest = compl
+            if self.is_src and dest.startswith("src/"):
+                dest = dest[4:]  # strip "src/" for correct wheel placement
+            include[compl] = dest
         self.app.display_debug("Derived inclusion map")
         self.app.display_debug(include)
         return include
@@ -565,7 +568,25 @@ def should_drop(member_name: str) -> bool:
                 return False
 
             # IMPORTANT: use your existing pathspec-based matchers
-            return self.path_is_excluded_compiled_src(name) and not self.path_is_included_compiled_src(name)
+            # For src-layout, config patterns may use "src/" prefix
+            # but wheel paths don't have it. Try both.
+            is_excluded = self.path_is_excluded_compiled_src(name)
+            is_included = self.path_is_included_compiled_src(name)
+            if self.is_src:
+                src_name = f"src/{name}"
+                is_excluded = is_excluded or self.path_is_excluded_compiled_src(src_name)
+                is_included = is_included or self.path_is_included_compiled_src(src_name)
+
+            # Mirror path_is_wanted_excluded_compiled_src: when include_all_compiled_src
+            # is False, treat every compiled .py as excluded (unless in include_compiled_src)
+            if not self.options.include_all_compiled_src:
+                is_compiled = self.path_is_wanted(name)
+                if self.is_src:
+                    is_compiled = is_compiled or self.path_is_wanted(f"src/{name}")
+                if is_compiled:
+                    is_excluded = True
+
+            return is_excluded and not is_included
 
         tmp_fd, tmp_path = tempfile.mkstemp(suffix=".whl")
         os.close(tmp_fd)

test_libraries/namespace_structure/hatch.toml

@@ -0,0 +1,12 @@
+[build]
+ignore-vcs = true
+
+[build.hooks.custom]
+dependencies = ["Cython", "setuptools", "hatch"]
+path = "../../src/hatch_cython/devel.py"
+
+[build.hooks.custom.options]
+src = "org/myproject"
+
+[build.targets.wheel]
+packages = ["src/org"]

test_libraries/namespace_structure/pyproject.toml

@@ -0,0 +1,11 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling", "Cython", "setuptools"]
+
+[project]
+name = "org-myproject"
+dynamic = ["version"]
+requires-python = ">=3.8"
+
+[tool.hatch.version]
+path = "src/org/myproject/__about__.py"

test_libraries/namespace_structure/src/org/myproject/__about__.py

@@ -0,0 +1 @@
+__version__ = "0.0.1"

test_libraries/namespace_structure/src/org/myproject/core.pyx

@@ -0,0 +1,2 @@
+def hello():
+    return "hello from org.myproject"

tests/test_plugin.py

@@ -1,5 +1,8 @@
 import gc
+import io
 import shutil
+import tempfile
+import zipfile
 from os import getcwd, path
 from pathlib import Path
 from sys import path as syspath
@@ -38,6 +41,73 @@ def new_src_proj(tmp_path):
     return project_dir
 
 
+@pytest.fixture
+def new_namespace_proj(tmp_path):
+    project_dir = tmp_path / "app"
+    project_dir.mkdir()
+    (project_dir / "pyproject.toml").write_text(read("test_libraries/namespace_structure/pyproject.toml"))
+    (project_dir / "hatch.toml").write_text(read("test_libraries/namespace_structure/hatch.toml"))
+    (project_dir / "LICENSE.txt").write_text("")
+    shutil.copytree(join("test_libraries/namespace_structure", "src"), (project_dir / "src"))
+    return project_dir
+
+
+def test_namespace_build_hook(new_namespace_proj):
+    with override_dir(new_namespace_proj):
+        syspath.insert(0, str(new_namespace_proj))
+        build_config = load(new_namespace_proj / "hatch.toml")["build"]
+        cython_config = build_config["hooks"]["custom"]
+        builder = WheelBuilder(root=str(new_namespace_proj))
+        hook = CythonBuildHook(
+            new_namespace_proj,
+            cython_config,
+            WheelBuilderConfig(
+                builder=builder,
+                root=str(new_namespace_proj),
+                plugin_name="cython",
+                build_config=build_config,
+                target_config=build_config["targets"]["wheel"],
+            ),
+            SimpleNamespace(name="org-myproject"),
+            directory=new_namespace_proj,
+            target_name="wheel",
+        )
+
+        assert hook.is_src
+        assert hook.dir_name == "org/myproject"
+        assert hook.project_dir == "src/org/myproject"
+
+        assert sorted(hook.precompiled_globs) == sorted(
+            [
+                "src/org/myproject/*.py",
+                "src/org/myproject/**/*.py",
+                "src/org/myproject/*.pyx",
+                "src/org/myproject/**/*.pyx",
+                "src/org/myproject/*.pxd",
+                "src/org/myproject/**/*.pxd",
+            ]
+        )
+
+        assert sorted(hook.normalized_included_files) == sorted(
+            [
+                "src/org/myproject/__about__.py",
+                "src/org/myproject/__init__.py",
+                "src/org/myproject/core.pyx",
+            ]
+        )
+
+        assert sorted(
+            [{**ls, "files": sorted(ls.get("files"))} for ls in hook.grouped_included_files],
+            key=lambda x: x.get("name"),
+        ) == [
+            {"name": "org.myproject.__about__", "files": ["src/org/myproject/__about__.py"]},
+            {"name": "org.myproject.__init__", "files": ["src/org/myproject/__init__.py"]},
+            {"name": "org.myproject.core", "files": ["src/org/myproject/core.pyx"]},
+        ]
+
+    syspath.remove(str(new_namespace_proj))
+
+
 @pytest.mark.parametrize("include_all_compiled_src", [None, True, False])
 def test_wheel_build_hook(new_src_proj, include_all_compiled_src: bool | None):
     with override_dir(new_src_proj):
@@ -238,3 +308,71 @@ def make_hook():
         assert len(so_files_after) == 0, f"compiled extension files not removed by clean(): {so_files_after}"
 
     syspath.remove(str(new_src_proj))
+
+
+def test_finalize_drops_compiled_src_when_include_all_false(new_src_proj):
+    """finalize() must remove compiled .py files from the wheel when include_all_compiled_src=False.
+
+    Files listed in include_compiled_src should survive; everything else that was
+    compiled should be dropped.
+    """
+    with override_dir(new_src_proj):
+        syspath.insert(0, str(new_src_proj))
+        build_config = load(new_src_proj / "hatch.toml")["build"]
+        cython_config = build_config["hooks"]["custom"]
+        cython_config["options"]["include_all_compiled_src"] = False
+
+        builder = WheelBuilder(root=str(new_src_proj))
+        hook = CythonBuildHook(
+            new_src_proj,
+            cython_config,
+            WheelBuilderConfig(
+                builder=builder,
+                root=str(new_src_proj),
+                plugin_name="cython",
+                build_config=build_config,
+                target_config=build_config["targets"]["wheel"],
+            ),
+            SimpleNamespace(name="example_lib"),
+            directory=new_src_proj,
+            target_name="wheel",
+        )
+
+        # Wheel paths use no "src/" prefix (hatchling strips it for src-layout).
+        # These are all compiled files; normal_include_compiled_src.py is the only
+        # one listed in include_compiled_src and should survive.
+        wheel_py_files = [
+            "example_lib/__about__.py",
+            "example_lib/__init__.py",
+            "example_lib/normal.py",
+            "example_lib/normal_exclude_compiled_src.py",
+            "example_lib/normal_include_compiled_src.py",
+        ]
+        record_name = "example_lib-0.1.0.dist-info/RECORD"
+
+        # Build a minimal fake wheel zip
+        with tempfile.NamedTemporaryFile(suffix=".whl", delete=False) as tmp:
+            whl_path = tmp.name
+        with zipfile.ZipFile(whl_path, "w") as zf:
+            for f in wheel_py_files:
+                zf.writestr(f, b"# placeholder")
+            zf.writestr(record_name, "")
+
+        build_data: dict = {"artifacts": [], "force_include": {}}
+        hook.finalize("0.1.0", build_data, whl_path)
+
+        with zipfile.ZipFile(whl_path) as zf:
+            names = set(zf.namelist())
+
+        # normal_include_compiled_src.py is in include_compiled_src → must stay
+        assert "example_lib/normal_include_compiled_src.py" in names
+        # all other compiled .py files must be dropped
+        for dropped in [
+            "example_lib/__about__.py",
+            "example_lib/__init__.py",
+            "example_lib/normal.py",
+            "example_lib/normal_exclude_compiled_src.py",
+        ]:
+            assert dropped not in names, f"{dropped!r} should have been dropped from wheel"
+
+    syspath.remove(str(new_src_proj))