Use better pattern for scikit-build extensions

CMakeLists.txt

@@ -61,14 +61,8 @@ if(NOT Python3_FOUND AND NOT Python2_FOUND)
 endif()
 
 if(Python3_FOUND)
-    function(Python_add_library)
-        Python3_add_library(${ARGV})
-    endfunction()
     set(PYVER PY3)
 else()
-    function(Python_add_library)
-        Python2_add_library(${ARGV})
-    endfunction()
     set(PYVER PY2)
 endif()
 

README.rst

@@ -47,10 +47,10 @@ The simplest approach is to install via
 
     .. code:: bash
 
-        mkvirtualenv --system-site-packages pylada
+        python -m venv pylada
         source pylada/bin/activate
         pip install git+https://github.com/pylada/pylada-light
-    
+
     This last approach is recommended since it keeps the pylada environment
     isolated from the rest of the system. Susbsequently, this environment can
     be accessed by running the second line.
@@ -62,19 +62,20 @@ Installation for development
 
     .. code:: bash
 
-        mkvirtualenv --system-site-packages pylada
+        python -m venv pylada
         source pylada/bin/activate
         git clone https://github.com/pylada/pylada-light
         cd pylada-light
-        pip install cython setuptools wheel scikit-build cmake ninja numpy
-        python setup.py develop
+        python -m pip install cython setuptools wheel scikit-build cmake ninja numpy
+        python -m pip install -e .[dev]
         python setup.py test
-    
+        ln -s src/pylada . # because https://github.com/scikit-build/scikit-build/issues/363
+
     The above creates a virtual environment and installs pylada inside it in
     development mode. This means that the virtual environment will know about
     the pylada flavor in development. It is possible to edit a file, do
-    :bash:`make`, launch python and debug. One just needs to active the virtual
-    environment once per session.
+    :bash:`make`, launch python and debug. One just needs to active the
+    virtual environment once per session.
 
-    When modifying files that are built (`.pyx`, `.cc`, `.h`), it is necessary to run `python
-    setup.py develop` again.
+    When modifying files that are built (`.pyx`, `.cc`, `.h`), it may be
+    necessary to run `python setup.py develop` again.

src/pylada/CMakeLists.txt

@@ -8,6 +8,7 @@ file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/_version.py"
 )
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/_version.py" DESTINATION ${PY_ROOT_DIR})
 
+include_directories("${PYTHON_INCLUDE_DIR}")
 add_subdirectory(crystal)
 add_subdirectory(decorations)
 add_subdirectory(ewald)

src/pylada/crystal/CMakeLists.txt

@@ -30,16 +30,18 @@ set(cython_sources
 foreach(filename ${cython_sources})
     get_filename_component(name "${filename}" NAME_WE)
     add_cython_target(cython_${name} ${filename} CXX ${PYVER}})
-    Python_add_library(${name} MODULE ${cython_${name}})
-    target_link_libraries(${name} PRIVATE Eigen3::Eigen)
+    add_library(${name} MODULE ${cython_${name}})
+    python_extension_module(${name})
+    target_link_libraries(${name} Eigen3::Eigen)
     target_include_directories(${name} PRIVATE "${PY_HEADER_DIR}" "${NumPy_INCLUDE_DIRS}")
     install(TARGETS ${name} LIBRARY DESTINATION ${PY_ROOT_DIR}/crystal)
 endforeach()
 
 add_cython_target(cython_cutilities cutilities.pyx CXX ${PYVER})
-Python_add_library(cutilities MODULE ${cython_cutilities} smith_normal_form.cc gruber.cc noopt.cc)
+add_library(cutilities MODULE ${cython_cutilities} smith_normal_form.cc gruber.cc noopt.cc)
+python_extension_module(cutilities)
 target_include_directories(cutilities PRIVATE "${PY_HEADER_DIR}" "${NumPy_INCLUDE_DIRS}")
-target_link_libraries(cutilities PRIVATE Eigen3::Eigen)
+target_link_libraries(cutilities Eigen3::Eigen)
 install(TARGETS cutilities LIBRARY DESTINATION ${PY_ROOT_DIR}/crystal)
 
 add_subdirectory(defects)

src/pylada/crystal/defects/CMakeLists.txt

@@ -24,7 +24,11 @@
 ###############################
 
 add_cython_target(defects_cython _defects.pyx CXX ${PYVER})
-Python_add_library(_defects MODULE ${defects_cython} third_order.cc)
-target_link_libraries(_defects PRIVATE Eigen3::Eigen)
-target_include_directories(_defects PRIVATE "${PY_HEADER_DIR}" "${NumPy_INCLUDE_DIRS}")
+add_library(_defects MODULE ${defects_cython} third_order.cc)
+python_extension_module(_defects)
+target_link_libraries(_defects Eigen3::Eigen)
+target_include_directories(
+    _defects PRIVATE
+    "${PY_HEADER_DIR}" "${NumPy_INCLUDE_DIRS}" "${PYTHON_INCLUDE_DIR}"
+)
 install(TARGETS _defects LIBRARY DESTINATION ${PY_ROOT_DIR}/crystal/defects)

src/pylada/decorations/CMakeLists.txt

@@ -21,6 +21,10 @@
 ###############################
 
 add_cython_target(decorations_cython _decorations.pyx CXX ${PYVER}})
-Python_add_library(_decorations MODULE ${decorations_cython})
-target_include_directories(_decorations PRIVATE "${PY_HEADER_DIR}" "${NumPy_INCLUDE_DIRS}")
+add_library(_decorations MODULE ${decorations_cython})
+python_extension_module(_decorations)
+target_include_directories(
+    _decorations PRIVATE
+    "${PY_HEADER_DIR}" "${NumPy_INCLUDE_DIRS}" "${PYTHON_INCLUDE_DIR}"
+)
 install(TARGETS _decorations LIBRARY DESTINATION ${PY_ROOT_DIR}/decorations)

src/pylada/ewald/CMakeLists.txt

@@ -20,7 +20,8 @@
 #  <http://www.gnu.org/licenses/>.
 ###############################
 add_cython_target(ewald_cython ewald.pyx CXX ${PYVER})
-Python_add_library(ewald MODULE
+add_library(ewald MODULE
     ${ewald_cython} ep_com.f90 erfc.cc ewaldf.f90 ewald.cc)
+python_extension_module(ewald)
 target_include_directories(ewald PRIVATE "${PY_HEADER_DIR}")
 install(TARGETS ewald LIBRARY DESTINATION ${PY_ROOT_DIR}/ewald)