First compiling version with setup.py without libmolfile_plugins.a

pymolfile/molfile/compile.sh

@@ -10,7 +10,7 @@ g++-7 -fPIC -Wall -Wextra -shared -g -Wunused-function -Wunused-parameter  \
     -I./include/netcdf/include \
     -I./include/expat/include \
     -I./include/tng/include \
-    libpymolfile_wrap.cxx pymolfile.c -o _libpymolfile.so  -L. \
+    libpymolfile_wrap.cxx pymolfile.cxx -o _libpymolfile.so  -L. \
     -L./lib/molfile_plugin/lib \
     -L./lib/netcdf/lib \
     -L./lib/expat/lib \

pymolfile/molfile/pymolfile.h

@@ -52,10 +52,6 @@ struct MolObject {
 };
 */
 
-static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj);
-static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*data)(PyObject *));
-void del_molfile_plugin_list(PyObject* molcapsule);
-void del_molfile_file_handle(PyObject* molcapsule);
 
 #if PY_VERSION_HEX >= 0x03000000
 #define PyInt_AsSsize_t PyLong_AsSsize_t
@@ -69,6 +65,11 @@ void del_molfile_file_handle(PyObject* molcapsule);
 #define PyString_Type PyBytes_Type
 #define PyInt_Type PyLong_Type
 
+void del_molfile_plugin_list(PyObject* molcapsule);
+void del_molfile_file_handle(PyObject* molcapsule);
+
+static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj);
+
 static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
 {
     void *ret = PyCapsule_GetPointer(obj, "plugin_handle");
@@ -78,6 +79,7 @@ static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
     return ret;
 }
 
+static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(PyObject *));
 static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(PyObject *))
 {
     PyObject *ret = PyCapsule_New(ptr, "plugin_handle", destr);
@@ -90,11 +92,18 @@ static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(PyObject
 #else
 #define PyBytes_FromString PyString_FromString
 
+void del_molfile_plugin_list(void* molcapsule);
+void del_molfile_file_handle(void* molcapsule);
+
+static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj);
+
 static void * PyMolfileCapsule_AsVoidPtr(PyObject *obj)
 {
     return PyCObject_AsVoidPtr(obj);
 }
 
+static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(void *));
+
 static PyObject * PyMolfileCapsule_FromVoidPtr(void *ptr, void (*destr)(void *))
 {
     return PyCObject_FromVoidPtr(ptr, destr);

setup.py

 #!/usr/bin/env python
 
+import os
+import sysconfig
 import sys
 try:
     from setuptools.command.build_ext import build_ext
     from setuptools import setup, Extension, Command, find_packages
+    from Cython.Build import cythonize
+    from Cython.Distutils import build_ext
 except:
     from distutils.command.build_ext import build_ext
     from distutils import setup, Extension, Command, find_packages
+    from Cython.Build import cythonize
+    from Cython.Distutils import build_ext
 
+def get_ext_filename_without_platform_suffix(filename):
+    name, ext = os.path.splitext(filename)
+    ext_suffix = sysconfig.get_config_var('EXT_SUFFIX')
+
+    if ext_suffix == ext:
+        return filename
+
+    ext_suffix = ext_suffix.replace(ext, '')
+    idx = name.find(ext_suffix)
+
+    if idx == -1:
+        return filename
+    else:
+        return name[:idx] + ext
+
+class BuildExtWithoutPlatformSuffix(build_ext):
+    def get_ext_filename(self, ext_name):
+        filename = super().get_ext_filename(ext_name)
+        return get_ext_filename_without_platform_suffix(filename)
 
 VERSION = "0.0.1"
 CLASSIFIERS = [
@@ -96,36 +121,46 @@ largefile_macros = [
 ]
 
 if __name__ == '__main__':
+
     libpymolfile_module = Extension(
             'pymolfile/molfile/_libpymolfile', 
             sources=[
                 'pymolfile/molfile/libpymolfile.i' , 
-                'pymolfile/molfile/pymolfile.c'
+                'pymolfile/molfile/pymolfile.cxx'
                 ],
-            swig_opts=['-py3 -c++ -python'],
+            swig_opts=['-py3', '-Wall', '-c++'],
             library_dirs=[
-                '/usr/lib', 
-                'lib/'
+                'pymolfile/molfile/lib/',
+                'pymolfile/molfile/lib/tng/lib/'
                 ],
-            libraries=['libmolfile_plugin.a'],
+            libraries=['netcdf','tng_io','expat'],
             include_dirs = [
-                get_numpy_include, 
-                '/usr/include',
+                get_numpy_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/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'
-                ]
+                '-fPIC', '-shared', '-O2', '-w'
+                #'-DNDEBUG', '-DUNIX', '-D__UNIX',  '-m64', 
+                #'-fPIC', '-O2', '-w', '-fmessage-length=0'
+                ],
+            extra_link_args = [
+                'pymolfile/molfile/lib/molfile_plugin/lib/libmolfile_plugin.a'
+                ],
+            define_macros = largefile_macros
             )
+    #if sys.version_info > (3,):
+    #    command_extension={'build_ext': BuildExtWithoutPlatformSuffix}
+    #else:
+    #    command_extension={}
+    command_extension={}
 
     setup(
         name = "pymolfile",
@@ -138,29 +173,10 @@ if __name__ == '__main__':
         url = "https://gitlab.mpcdf.mpg.de/berko/pymolfile",
         zip_safe = False,
         packages = find_packages(),
+        cmdclass= command_extension,
         ext_modules = [
             #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" ],