Python setup.py with CMake

LICENSE

 LICENSE for pymolfile
 ---------------------
 
-All files of pymolfile except the files under vmd_molfile_plugins directory 
-which are licensed below with "LICENSE for VMD molfile_plugins" are 
-licensed under the following UIUC Open Source License:
-
+Exceptions for pymolfile LICENSE:
+---------------------------------
+- FindNetCDF.cmake is LICENSE with BSD-2 Clause (See section 'LICENSE for 
+  FindNetCDF.cmake file' in the file and below)
+- VMD molfile_plugins under molfile_plugins directory are licensed with 
+  UIUC Open Source Licence (See section 'LICENSE for VMD molfile_plugins' 
+  in this file)
+
+All files of pymolfile except the files listed above are licensed with
+UIUC Open Source License at section 'LICENSE for Pymolfile' in this file
+
+LICENSE for Pymolfile:
 -----------------------------------------------------------------------------
-
 University of Illinois Open Source License
 Copyright 2017 University of Warwick 
 All rights reserved.
@@ -41,12 +48,11 @@ THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
 OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
 OTHER DEALINGS WITH THE SOFTWARE.
+-----------------------------------------------------------------------------
 
 
-
-LICENSE for VMD molfile_plugins
--------------------------------
-
+LICENSE for VMD molfile_plugins:
+-----------------------------------------------------------------------------
 University of Illinois Open Source License
 Copyright 2006 Theoretical and Computational Biophysics Group, 
 All rights reserved.
@@ -81,5 +87,34 @@ THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
 OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
 OTHER DEALINGS WITH THE SOFTWARE.
+-----------------------------------------------------------------------------
+
+
+LICENSE for FindNetCDF.cmake file:
+-----------------------------------------------------------------------------
+Copyright Jed Brown
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+-----------------------------------------------------------------------------
 
 

pymolfile/molfile/molfile_plugins/compile/FindNetCDF.cmake

+# - Find NetCDF
+# Find the native NetCDF includes and library
+#
+#  NETCDF_INCLUDES    - where to find netcdf.h, etc
+#  NETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  NETCDF_FOUND       - True if NetCDF found including required interfaces (see below)
+#
+# Your package can require certain interfaces to be FOUND by setting these
+#
+#  NETCDF_CXX         - require the C++ interface and link the C++ library
+#  NETCDF_F77         - require the F77 interface and link the fortran library
+#  NETCDF_F90         - require the F90 interface and link the fortran library
+#
+# The following are not for general use and are included in
+# NETCDF_LIBRARIES if the corresponding option above is set.
+#
+#  NETCDF_LIBRARIES_C    - Just the C interface
+#  NETCDF_LIBRARIES_CXX  - C++ interface, if available
+#  NETCDF_LIBRARIES_F77  - Fortran 77 interface, if available
+#  NETCDF_LIBRARIES_F90  - Fortran 90 interface, if available
+#
+# Normal usage would be:
+#  set (NETCDF_F90 "YES")
+#  find_package (NetCDF REQUIRED)
+#  target_link_libraries (uses_f90_interface ${NETCDF_LIBRARIES})
+#  target_link_libraries (only_uses_c_interface ${NETCDF_LIBRARIES_C})
+
+# Taken from: https://github.com/jedbrown/cmake-modules/blob/master/FindNetCDF.cmake
+#
+# Below copyright author list is gathered using 
+#     "git shortlog -s FindNetCDF.cmake"
+# at Oct 24th, 2017
+#
+#Copyright Jed Brown
+#All rights reserved.
+#
+#Redistribution and use in source and binary forms, with or without modification,
+#are permitted provided that the following conditions are met:
+#
+#* Redistributions of source code must retain the above copyright notice, this
+#  list of conditions and the following disclaimer.
+#
+#* Redistributions in binary form must reproduce the above copyright notice, this
+#  list of conditions and the following disclaimer in the documentation and/or
+#  other materials provided with the distribution.
+#
+#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+#ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+#(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+#LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+#ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+
+if (NETCDF_INCLUDES AND NETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (NETCDF_FIND_QUIETLY TRUE)
+endif (NETCDF_INCLUDES AND NETCDF_LIBRARIES)
+
+find_path (NETCDF_INCLUDES netcdf.h
+  HINTS NETCDF_DIR ENV NETCDF_DIR)
+
+find_library (NETCDF_LIBRARIES_C       NAMES netcdf)
+mark_as_advanced(NETCDF_LIBRARIES_C)
+
+set (NetCDF_has_interfaces "YES") # will be set to NO if we're missing any interfaces
+set (NetCDF_libs "${NETCDF_LIBRARIES_C}")
+
+get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARIES_C}" PATH)
+
+macro (NetCDF_check_interface lang header libs)
+  if (NETCDF_${lang})
+    find_path (NETCDF_INCLUDES_${lang} NAMES ${header}
+      HINTS "${NETCDF_INCLUDES}" NO_DEFAULT_PATH)
+    find_library (NETCDF_LIBRARIES_${lang} NAMES ${libs}
+      HINTS "${NetCDF_lib_dirs}" NO_DEFAULT_PATH)
+    mark_as_advanced (NETCDF_INCLUDES_${lang} NETCDF_LIBRARIES_${lang})
+    if (NETCDF_INCLUDES_${lang} AND NETCDF_LIBRARIES_${lang})
+      list (INSERT NetCDF_libs 0 ${NETCDF_LIBRARIES_${lang}}) # prepend so that -lnetcdf is last
+    else (NETCDF_INCLUDES_${lang} AND NETCDF_LIBRARIES_${lang})
+      set (NetCDF_has_interfaces "NO")
+      message (STATUS "Failed to find NetCDF interface for ${lang}")
+    endif (NETCDF_INCLUDES_${lang} AND NETCDF_LIBRARIES_${lang})
+  endif (NETCDF_${lang})
+endmacro (NetCDF_check_interface)
+
+NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
+NetCDF_check_interface (F77 netcdf.inc  netcdff)
+NetCDF_check_interface (F90 netcdf.mod  netcdff)
+
+set (NETCDF_LIBRARIES "${NetCDF_libs}" CACHE STRING "All NetCDF libraries required for interface level")
+
+# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (NetCDF DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDES NetCDF_has_interfaces)
+
+mark_as_advanced (NETCDF_LIBRARIES NETCDF_INCLUDES)

setup.py

@@ -14,6 +14,62 @@ except:
     from Cython.Build import cythonize
     from Cython.Distutils import build_ext
 
+# from http://www.benjack.io/2017/06/12/python-cpp-tests.html
+class CMakeExtension(Extension):
+    def __init__(self, name, sourcedir=''):
+        Extension.__init__(self, name, sources=[])
+        self.sourcedir = os.path.abspath(sourcedir)
+
+class CMakeBuild(build_ext):
+    def run(self):
+        try:
+            out = subprocess.check_output(['cmake', '--version'])
+        except OSError:
+            raise RuntimeError(
+                "CMake must be installed to build the following extensions: " +
+                ", ".join(e.name for e in self.extensions))
+
+        if platform.system() == "Windows":
+            cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)',
+                                         out.decode()).group(1))
+            if cmake_version < '3.1.0':
+                raise RuntimeError("CMake >= 3.1.0 is required on Windows")
+
+        for ext in self.extensions:
+            self.build_extension(ext)
+
+    def build_extension(self, ext):
+        extdir = os.path.abspath(
+            os.path.dirname(self.get_ext_fullpath(ext.name)))
+        cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
+                      '-DPYTHON_EXECUTABLE=' + sys.executable]
+
+        cfg = 'Debug' if self.debug else 'Release'
+        build_args = ['--config', cfg]
+
+        if platform.system() == "Windows":
+            cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(
+                cfg.upper(),
+                extdir)]
+            if sys.maxsize > 2**32:
+                cmake_args += ['-A', 'x64']
+            build_args += ['--', '/m']
+        else:
+            cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
+            build_args += ['--', '-j2']
+
+        env = os.environ.copy()
+        env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(
+            env.get('CXXFLAGS', ''),
+            self.distribution.get_version())
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args,
+                              cwd=self.build_temp, env=env)
+        subprocess.check_call(['cmake', '--build', '.'] + build_args,
+                              cwd=self.build_temp)
+        print()  # Add an empty line for cleaner output
+
 def get_ext_filename_without_platform_suffix(filename):
     name, ext = os.path.splitext(filename)
     ext_suffix = sysconfig.get_config_var('EXT_SUFFIX')
@@ -41,8 +97,8 @@ CLASSIFIERS = [
     "Intended Audience :: Developers",
     "License :: OSI Approved :: University of Illinois Open Source License (UIUC)",
     "Programming Language :: C",
+    "Programming Language :: C++",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 2",
     "Programming Language :: Python :: 3",
     "Topic :: Scientific/Engineering :: Physics",
     "Topic :: Scientific/Engineering :: Chemistry",
@@ -157,7 +213,7 @@ if __name__ == '__main__':
     #    command_extension={'build_ext': BuildExtWithoutPlatformSuffix}
     #else:
     #    command_extension={}
-    command_extension={}
+    command_extension=dict(build_ext=CMakeBuild)
 
     setup(
         name = "pymolfile",
@@ -172,7 +228,7 @@ if __name__ == '__main__':
         packages = find_packages(),
         cmdclass= command_extension,
         ext_modules = [
-            #libmolfile_plugin_compile(cmake_libmolfile_plugin_compile),
+            CMakeExtension('molfile', sourcedir='pymolfile/molfile/'),
             libpymolfile_module,
         ],
         py_modules=["pymolfile"],