Replace monkeypatch distutils with CMake setuptools Extensions

CMakeLists.txt

@@ -0,0 +1,31 @@
+cmake_minimum_required(VERSION 3.13)
+
+project(${TARGET_NAME})
+
+set(CMAKE_VERBOSE_MAKEFILE on)
+
+add_library(${TARGET_NAME} SHARED ${ALL_SRC})
+
+target_compile_options(${TARGET_NAME} PRIVATE ${ALL_COMP_ARGS})
+
+set_target_properties(${TARGET_NAME} PROPERTIES SUFFIX ${SHARED_SUFFIX})
+
+target_compile_features(${TARGET_NAME} PRIVATE cxx_std_17)
+
+set_target_properties(${TARGET_NAME} PROPERTIES PREFIX "")
+
+target_include_directories(${TARGET_NAME} PUBLIC ${ALL_INC_DIR})
+
+target_link_directories(${TARGET_NAME} PUBLIC ${ALL_LIB_DIR})
+
+
+if(APPLE)
+    set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -undefined dynamic_lookup")
+endif()
+
+target_link_libraries(${TARGET_NAME}
+    ${ALL_LIB}
+    ${ALL_EXT_LINK}
+)
+
+target_compile_definitions(${TARGET_NAME} PUBLIC ${ALL_DEF})

INSTALL

@@ -8,6 +8,7 @@ See also: http://pymolwiki.org/index.php/Linux_Install
 REQUIREMENTS
 
     - C++17 compiler (e.g. gcc 8+)
+    - CMake (3.13+)
     - Python 3.6+
     - Pmw (Python Megawidgets) (optional, for legacy GUI/plugins)
       https://github.com/schrodinger/pmw-patched

contrib/champ/champ_module.c

@@ -1053,7 +1053,7 @@ static PyMethodDef champ_methods[] = {
   {NULL,		                    NULL}     /* sentinel */        
 };
 
-PyObject * PyInit__champ(void)
+PyMODINIT_FUNC PyInit__champ(void)
 {
   static struct PyModuleDef moduledef = {
     PyModuleDef_HEAD_INIT,

layer4/Cmd.cpp

@@ -6531,7 +6531,7 @@ static PyMethodDef Cmd_methods[] = {
 extern "C" {
 #endif
 
-PyObject * PyInit__cmd(void)
+PyMODINIT_FUNC PyInit__cmd(void)
 {
   static struct PyModuleDef moduledef = {
     PyModuleDef_HEAD_INIT,

setup.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #
-# This script only applies if you are performing a Python Distutils-based
+# This script only applies if you are performing a Python setuptools-based
 # installation of PyMOL.
 #
 # It may assume that all of PyMOL's external dependencies are
@@ -9,12 +9,16 @@
 import argparse
 import glob
 import os
+import pathlib
 import re
 import sys
+import sysconfig
 import shutil
 
-from distutils.core import setup, Extension
-from distutils.util import change_root
+from setuptools import setup, Extension
+from setuptools.command.build_ext import build_ext
+from setuptools.command.build_py import build_py
+from setuptools.command.install import install
 
 import create_shadertext
 
@@ -33,7 +37,6 @@ class options:
     no_libxml = False
     no_glut = True
     use_msgpackc = 'guess'
-    help_distutils = False
     testing = False
     openvr = False
     use_openmp = 'no' if MAC else 'yes'
@@ -58,8 +61,6 @@ parser.add_argument('--use-vtkm', choices=('1.5', '1.6', '1.7', 'no'),
 parser.add_argument('--use-msgpackc', choices=('c++11', 'c', 'guess', 'no'),
                     help="c++11: use msgpack-c header-only library; c: link against "
                     "shared library; no: disable fast MMTF load support")
-parser.add_argument('--help-distutils', action="store_true",
-                    help="show help for distutils options and exit")
 parser.add_argument('--testing', action="store_true",
                     help="Build C-level tests")
 parser.add_argument('--openvr', dest='openvr', action='store_true')
@@ -68,10 +69,7 @@ parser.add_argument('--no-vmd-plugins', dest='vmd_plugins',
                     help='Disable VMD molfile plugins (libnetcdf dependency)')
 options, sys.argv[1:] = parser.parse_known_args(namespace=options)
 
-if options.help_distutils:
-    sys.argv.append("--help")
-
-if True:
+if False:
     import monkeypatch_distutils
     monkeypatch_distutils.set_parallel_jobs(options.jobs)
 
@@ -137,16 +135,104 @@ def guess_msgpackc():
     return 'no'
 
 
-# Important: import 'distutils.command' modules after monkeypatch_distutils
-from distutils.command.build_ext import build_ext
-from distutils.command.build_py import build_py
-from distutils.command.install import install
+class CMakeExtension(Extension):
+
+    def __init__(self,
+                 name,
+                 sources,
+                 include_dirs=[],
+                 libraries=[],
+                 library_dirs=[],
+                 define_macros=[],
+                 extra_link_args=[],
+                 extra_compile_args=[]):
+        # don't invoke the original build_ext for this special extension
+        super().__init__(name, sources=[])
+        self.sources = sources
+        self.include_dirs = include_dirs
+        self.libraries = libraries
+        self.library_dirs = library_dirs
+        self.define_macros = define_macros
+        self.extra_link_args = extra_link_args
+        self.extra_compile_args = extra_compile_args
+
 
 class build_ext_pymol(build_ext):
-    def initialize_options(self):
-        build_ext.initialize_options(self)
+    def initialize_options(self) -> None:
+        super().initialize_options()
         if DEBUG and not WIN:
-            self.debug = True
+            self.debug = False
+
+    def run(self):
+        for ext in self.extensions:
+            self.build_cmake(ext)
+
+    def build_cmake(self, ext):
+        cwd = pathlib.Path().absolute()
+
+        # these dirs will be created in build_py, so if you don't have
+        # any python sources to bundle, the dirs will be missing
+        name_split = ext.name.split('.')
+        target_name = name_split[-1]
+        build_temp = pathlib.Path(self.build_temp) / target_name
+        build_temp.mkdir(parents=True, exist_ok=True)
+        extdir = pathlib.Path(self.get_ext_fullpath(ext.name))
+        extdirabs = extdir.absolute()
+
+        extdir.parent.mkdir(parents=True, exist_ok=True)
+
+        def concat_paths(paths):
+            return ''.join(path.replace('\\', '/') + ";" for path in paths)
+
+        config = 'Debug' if DEBUG else 'Release'
+        lib_output_dir = str(extdir.parent.absolute())
+        all_files = ext.sources
+        all_src = concat_paths(all_files)
+        all_defs = ''.join(mac[0] + ";" for mac in ext.define_macros)
+        all_libs = ''.join(f"{lib};" for lib in ext.libraries)
+        all_ext_link = ' '.join(ext.extra_link_args)
+        all_comp_args = ''.join(f"{arg};" for arg in ext.extra_compile_args)
+        all_lib_dirs = concat_paths(ext.library_dirs)
+        all_inc_dirs = concat_paths(ext.include_dirs)
+
+        lib_mode = "RUNTIME" if WIN else "LIBRARY"
+
+        shared_suffix = sysconfig.get_config_var('EXT_SUFFIX')
+
+        cmake_args = [
+            f"-DTARGET_NAME={target_name}",
+            f"-DCMAKE_{lib_mode}_OUTPUT_DIRECTORY={lib_output_dir}",
+            f"-DCMAKE_BUILD_TYPE={config}",
+            f"-DALL_INC_DIR={all_inc_dirs}",
+            f"-DALL_SRC={all_src}",
+            f"-DALL_DEF={all_defs}",
+            f"-DALL_LIB_DIR={all_lib_dirs}",
+            f"-DALL_LIB={all_libs}",
+            f"-DALL_COMP_ARGS={all_comp_args}",
+            f"-DALL_EXT_LINK={all_ext_link}",
+            f"-DSHARED_SUFFIX={shared_suffix}"
+        ]
+
+        # example of build args
+        build_args = ['--config', config]
+        if not WIN:  # Win /MP flag on compilation level
+            cpu_count = os.cpu_count() or 1
+            build_args += [f'-j{cpu_count}']
+
+        os.chdir(str(build_temp))
+        self.spawn(['cmake', str(cwd)] + cmake_args)
+        if not self.dry_run:
+            self.spawn(['cmake', '--build', '.'] + build_args)
+
+        if WIN:
+            # Move up from VS release folder
+            cmake_lib_loc = pathlib.Path(lib_output_dir, "Release", f"{target_name}{shared_suffix}")
+            if cmake_lib_loc.exists():
+                shutil.move(cmake_lib_loc, extdirabs)
+
+        # Troubleshooting: if fail on line above then delete all possible
+        # temporary CMake files including "CMakeCache.txt" in top level dir.
+        os.chdir(str(cwd))
 
 
 class build_py_pymol(build_py):
@@ -175,10 +261,11 @@ class install_pymol(install):
             self.pymol_path = os.path.join(
                 self.install_libbase, 'pymol', 'pymol_path')
         elif self.root is not None:
-            self.pymol_path = change_root(self.root, self.pymol_path)
+            self.pymol_path = install_pymol.change_root(
+                self.root, self.pymol_path)
 
     def run(self):
-        install.run(self)
+        super().run()
         self.install_pymol_path()
 
         if not self.no_launcher:
@@ -304,7 +391,7 @@ ext_comp_args = [
     '-Wno-char-subscripts',
     # optimizations
     "-Og" if DEBUG else "-O3",
-] if not WIN else []
+] if not WIN else ["/MP"]
 ext_link_args = []
 ext_objects = []
 data_files = []
@@ -382,9 +469,9 @@ if MAC:
 
     if options.osx_frameworks:
         ext_link_args += [
-            "-framework", "OpenGL",
+            "-framework OpenGL",
         ] + (not options.no_glut) * [
-            "-framework", "GLUT",
+            "-framework GLUT",
         ]
         def_macros += [
             ("_PYMOL_OSX", None),
@@ -527,22 +614,37 @@ package_dir = dict((x, os.path.join(base, x))
                    for base in ['modules']
                    for x in get_packages(base))
 
-ext_modules += [
-    Extension("pymol._cmd",
-              get_sources(pymol_src_dirs),
-              include_dirs=inc_dirs,
-              libraries=libs,
-              library_dirs=lib_dirs,
-              define_macros=def_macros,
-              extra_link_args=ext_link_args,
-              extra_compile_args=ext_comp_args,
-              extra_objects=ext_objects,
-              ),
+# Python includes
+inc_dirs.append(sysconfig.get_paths()['include'])
+inc_dirs.append(sysconfig.get_paths()['platinclude'])
 
-    Extension("chempy.champ._champ",
-              get_sources(['contrib/champ']),
-              include_dirs=["contrib/champ"],
-              ),
+champ_inc_dirs = ['contrib/champ']
+champ_inc_dirs.append(sysconfig.get_paths()['include'])
+champ_inc_dirs.append(sysconfig.get_paths()['platinclude'])
+
+if WIN:
+    # pyconfig.py forces linking against pythonXY.lib on MSVC
+    py_lib = pathlib.Path(sysconfig.get_paths()['stdlib']).parent / 'libs'
+    lib_dirs.append(str(py_lib))
+
+ext_modules += [
+    CMakeExtension(
+        name="pymol._cmd",
+        sources=get_sources(pymol_src_dirs),
+        include_dirs=inc_dirs,
+        libraries=libs,
+        library_dirs=lib_dirs,
+        define_macros=def_macros,
+        extra_link_args=ext_link_args,
+        extra_compile_args=ext_comp_args,
+    ),
+
+    CMakeExtension(
+        name="chempy.champ._champ",
+        sources=get_sources(['contrib/champ']),
+        include_dirs=champ_inc_dirs,
+        library_dirs=lib_dirs,
+    ),
 ]
 
 distribution = setup(  # Distribution meta-data