Initial attenpt to add cmake setup

pymolfile/CMakeLists.txt → pymolfile/molfile/CMakeLists.txt

 cmake_minimum_required(VERSION 2.8.12)
 
+if(NOT DEFINED CMAKE_MACOSX_RPATH)
+    set(CMAKE_MACOSX_RPATH 0)
+endif()
+
 project(molfile)
 
 # Set source directory
 set(SOURCE_DIR "molfile")
 
 # Tell CMake that headers are also in SOURCE_DIR
-include_directories(${SOURCE_DIR}, "./vmd_molfile_plugin/molfile_plugin/include", "./vmd_molfile_plugin/molfile_plugin/lib")
+include_directories(${SOURCE_DIR} "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/include" "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/lib")
 
-set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx", "${SOURCE_DIR}/pymolfile.c")
+set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx" "${SOURCE_DIR}/pymolfile.c" "${SOURCE_DIR}/lib/libmolfile_plugin.a")
 

pymolfile/molfile/vmd_molfile_plugins/CMakeLists.txt

+
+find_package (EXPAT)
+find_package (NetCDF)
+
+# Set source directory
+set(SOURCE_DIR "molfile")
+
+# Tell CMake that headers are also in SOURCE_DIR
+include_directories(${SOURCE_DIR} "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/include" "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/lib")
+
+set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx" "${SOURCE_DIR}/pymolfile.c" "${SOURCE_DIR}/lib/libmolfile_plugin.a")
+

setup.py

 #!/usr/bin/env python
 
 import sys
-from setuptools import setup, Extension, find_packages
+try:
+    from setuptools.command.build_ext import build_ext
+    from setuptools import setup, Extension, Command, find_packages
+except:
+    from distutils.command.build_ext import build_ext
+    from distutils import setup, Extension, Command, find_packages
 
 
 VERSION = "0.0.1"
@@ -91,6 +96,37 @@ largefile_macros = [
 ]
 
 if __name__ == '__main__':
+    libpymolfile_module = Extension(
+            'pymolfile/molfile/_libpymolfile', 
+            sources=[
+                'pymolfile/molfile/libpymolfile.i' , 
+                'pymolfile/molfile/pymolfile.c'
+                ],
+            swig_opts=['-py3 -c++ -python'],
+            library_dirs=[
+                '/usr/lib', 
+                'lib/'
+                ],
+            libraries=['libmolfile_plugin.a'],
+            include_dirs = [
+                get_numpy_include, 
+                '/usr/include',
+                'pymolfile/molfile',
+                'pymolfile/molfile/lib/'
+                'pymolfile/molfile/include/',
+                'pymolfile/molfile/include/molfile_plugin/include',
+                'pymolfile/molfile/lib/molfile_plugin/lib',
+                'pymolfile/molfile/include/plugin_src/include',
+                'pymolfile/molfile/include/netcdf/include',
+                'pymolfile/molfile/include/expat/include',
+                'pymolfile/molfile/include/tng/include',
+                ],
+            extra_compile_args = [
+                '-DNDEBUG', '-DUNIX', '-D__UNIX',  '-m64', 
+                '-fPIC', '-O2', '-w', '-fmessage-length=0'
+                ]
+            )
+
     setup(
         name = "pymolfile",
         author = "Berk Onat",
@@ -103,34 +139,36 @@ if __name__ == '__main__':
         zip_safe = False,
         packages = find_packages(),
         ext_modules = [
-            LibpymolfileExtension(cmake_compile
-                ),
-            NumpyExtension(
-                "pymolfile/molfile._libpymolfile",
-                sources = [
-                    "pymolfile/molfile/libpymolfile_wrap.cxx",
-                    "pymolfile/molfile/pymolfile.c",
-                    "pymolfile/molfile/lib/libmolfile_plugin.a",
-                ],
-                include_dirs = [ 
-                    get_numpy_include, 
-                    "pymolfile/molfile/include/",
-                    "pymolfile/molfile/include/molfile_plugin/include",
-                    "pymolfile/molfile/lib/molfile_plugin/lib",
-                    "pymolfile/molfile/include/plugin_src/include",
-                    "pymolfile/molfile/include/netcdf/include",
-                    "pymolfile/molfile/include/expat/include",
-                    "pymolfile/molfile/include/tng/include",
-                    ],
-                define_macros = largefile_macros
-            ),
+            #libmolfile_plugin_compile(cmake_libmolfile_plugin_compile),
+            libpymolfile_module,
+#            NumpyExtension(
+#                "pymolfile/molfile/_libpymolfile",
+#                "pymolfile"
+#                sources = [
+#                    "pymolfile/molfile/libpymolfile_wrap.cxx",
+#                    "pymolfile/molfile/pymolfile.c",
+#                    "pymolfile/molfile/lib/libmolfile_plugin.a",
+#                ],
+#                include_dirs = [ 
+#                    get_numpy_include, 
+#                    "pymolfile/molfile/include/",
+#                    "pymolfile/molfile/include/molfile_plugin/include",
+#                    "pymolfile/molfile/lib/molfile_plugin/lib",
+#                    "pymolfile/molfile/include/plugin_src/include",
+#                    "pymolfile/molfile/include/netcdf/include",
+#                    "pymolfile/molfile/include/expat/include",
+#                    "pymolfile/molfile/include/tng/include",
+#                    ],
+#                define_macros = largefile_macros
+#            ),
         ],
+        py_modules=["pymolfile"],
         requires = [ "numpy" ],
         setup_requires = [ "numpy" ],
         install_requires = [ "numpy" ],
         extras_require = {
-            "netcdf": [ "netCDF Library" ],
-            "tng_io": [ "TNG Library" ],
-            "expat": [ "Expat XML Library" ]
+          #?do we need this?  "netcdf": [ "netCDF Library" ],
+          #?and this?  "tng_io": [ "TNG Library" ],
+          #?and this?  "expat": [ "Expat XML Library" ]
         }
     )

test.py

@@ -24,10 +24,14 @@ path="./test/"
 #sfname = path + "betaGal.mrc"
 #sfname = path + "adrenalin.mol2"
 #sfname = path + "adrenalin.sdf"
-#sfname = path + "1CRN.cif"
 #sfname = path + "esp.dx"
 #sfname = path + "md_ascii_trj.gro"
 sfname = path + "md_ascii_trj.pdb"
+#sfname = path + "3pqr.pqr"
+#cfname = path + "3pqr_validation.xml"
+#sfname = path + "3pqr-pot.dxbin"
+#sfname = path + "3pqr.cns"
+#sfname = path + "1cnr.ply"
 
 print("Reading file...")
 moltopo = pym.OpenMolfile(sfname, silent=True)