fix: Prevent clobbering of generated sources

Ensure that sources generated from modules with the same file name but
located in different packages do not clobber each other.

For example, generating sources from the following files will
now work as expected:

```
<src_dir>/package1/module.pyx
<src_dir>/package1/package2/module.pyx
```

This will generate the following files in the build directory:

```
<bld_dir>/package1/module.c
<bld_dir>/package1/module.c.dep
<bld_dir>/package1/package2/module.c
<bld_dir>/package1/package2/module.c.dep
```

Additionally, source files configured outside of the source tree and now
properly supported by computing the relative path and replacing "." with "_".

For example, given the following project structure:

```
<src_dir>/package1/__init__.py
<src_dir>/package1/module1.pyx
<src_dir>/package3/__init__.py
module3.pyx
```

the following will be generated:

```
<bld_dir>/package1/module1.c
<bld_dir>/package1/module1.c.dep
<bld_dir>/__/module3.c
<bld_dir>/__/module3.c.dep
```

Author: jcfr

src/cython_cmake/cmake/UseCython.cmake

@@ -135,11 +135,16 @@ function(Cython_compile_pyx)
         ${CMAKE_SOURCE_DIR} ${_source_file})
     set(comment "Generating ${_language} source '${generated_file_relative}' from '${source_file_relative}'")
 
+    # Get output directory to ensure its exists
+    get_filename_component(output_directory "${generated_file}" DIRECTORY)
+
     get_source_file_property(pyx_location ${_source_file} LOCATION)
 
     # Add the command to run the compiler.
     add_custom_command(
       OUTPUT ${generated_file}
+      COMMAND
+        ${CMAKE_COMMAND} -E make_directory ${output_directory}
       COMMAND
         ${_cython_command}
         ${_language_arg}
@@ -169,7 +174,19 @@ function(Cython_compile_pyx)
     # cmake_path(GET _input_file STEM basename)
     get_filename_component(_basename "${_input_file}" NAME_WE)
 
-    set(${_output_var} "${CMAKE_CURRENT_BINARY_DIR}/${_basename}.${_language_extension}" PARENT_SCOPE)
+    if(IS_ABSOLUTE ${_input_file})
+      file(RELATIVE_PATH _input_relative ${CMAKE_CURRENT_SOURCE_DIR} ${_input_file})
+    else()
+      set(_input_relative ${_input_file})
+    endif()
+
+    get_filename_component(_output_relative_dir "${_input_relative}" DIRECTORY)
+    string(REPLACE "." "_" _output_relative_dir "${_output_relative_dir}")
+    if(_output_relative_dir)
+      set(_output_relative_dir "${_output_relative_dir}/")
+    endif()
+
+    set(${_output_var} "${CMAKE_CURRENT_BINARY_DIR}/${_output_relative_dir}${_basename}.${_language_extension}" PARENT_SCOPE)
   endfunction()
 
   set(generated_files)

tests/packages/multiple_packages/CMakeLists.txt

@@ -0,0 +1,47 @@
+cmake_minimum_required(VERSION 3.15...3.29)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES C)
+
+find_package(
+  Python
+  COMPONENTS Interpreter Development.Module
+  REQUIRED)
+find_package(Cython MODULE REQUIRED VERSION 3.0)
+include(UseCython)
+
+#-----------------------------------------------------------------------------
+# package1.module
+cython_compile_pyx(package1/module.pyx
+  LANGUAGE C
+  OUTPUT_VARIABLE module_c
+)
+
+python_add_library(module1 MODULE "${module_c}" WITH_SOABI)
+
+install(TARGETS module1 DESTINATION "package1")
+
+#-----------------------------------------------------------------------------
+# package1.package2.module
+cython_compile_pyx(package1/package2/module.pyx
+  LANGUAGE C
+  OUTPUT_VARIABLE module_c
+)
+
+python_add_library(module2 MODULE "${module_c}" WITH_SOABI)
+
+install(TARGETS module2 DESTINATION "package1/package2")
+
+#-----------------------------------------------------------------------------
+# package1.package3.module
+
+file(COPY package1/package2/module.pyx DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/..)
+
+cython_compile_pyx(${CMAKE_CURRENT_SOURCE_DIR}/../module.pyx
+  LANGUAGE C
+  CYTHON_ARGS
+    --module-name "package1.package3.module"
+  OUTPUT_VARIABLE module_c
+)
+
+python_add_library(module3 MODULE "${module_c}" WITH_SOABI)
+
+install(TARGETS module3 DESTINATION "package1/package3")

tests/packages/multiple_packages/package1/__init__.py

@@ -0,0 +1,4 @@
+# cython: language_level=3
+
+def square(float x):
+    return x * x

tests/packages/multiple_packages/package1/module.pyx

@@ -0,0 +1,4 @@
+# cython: language_level=3
+
+def square(float x):
+    return x * x

tests/packages/multiple_packages/package1/package2/__init__.py

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["scikit-build-core", "cython", "cython-cmake"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "example"
+version = "0.0.1"

tests/packages/multiple_packages/package1/package2/module.pyx

@@ -127,3 +127,34 @@ def test_directive_cxx(monkeypatch, tmp_path):
     build_files = {x.name for x in Path("build").iterdir()}
     assert "simple.cxx.dep" in build_files
     assert "simple.cxx" in build_files
+
+
+def test_multiple_packages(monkeypatch, tmp_path):
+    package_dir = tmp_path / "pkg5"
+    shutil.copytree(DIR / "packages/multiple_packages", package_dir)
+    monkeypatch.chdir(package_dir)
+    build_dir = tmp_path / "build"
+
+    wheel = build_wheel(
+        str(tmp_path), {"build-dir": str(build_dir), "wheel.license-files": []}
+    )
+
+    with zipfile.ZipFile(tmp_path / wheel) as f:
+        file_names = set(f.namelist())
+    assert len(file_names) == 6
+
+    build_files = {x.name for x in build_dir.iterdir()}
+    assert "module.c.dep" not in build_files
+    assert "module.c" not in build_files
+
+    package1_build_files = {x.name for x in (build_dir / "package1").iterdir()}
+    assert "module.c.dep" in package1_build_files
+    assert "module.c" in package1_build_files
+
+    package2_build_files = {x.name for x in (build_dir / "package1/package2").iterdir()}
+    assert "module.c.dep" in package2_build_files
+    assert "module.c" in package2_build_files
+
+    package3_build_files = {x.name for x in (build_dir / "__").iterdir()}
+    assert "module.c.dep" in package3_build_files
+    assert "module.c" in package3_build_files