pymolfile installer updated

pymolfile/molfile/libpymolfile.py

+# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 3.0.12
+#
+# Do not make changes to this file unless you know what you are doing--modify
+# the SWIG interface file instead.
+
+"""
+
+:Author:  Berk Onat <b.onat@warwick.ac.uk>
+:Year:    2017
+:Licence: UIUC LICENSE
+
+
+
+"""
+
+
+from sys import version_info as _swig_python_version_info
+if _swig_python_version_info >= (2, 7, 0):
+    def swig_import_helper():
+        import importlib
+        pkg = __name__.rpartition('.')[0]
+        mname = '.'.join((pkg, '_libpymolfile')).lstrip('.')
+        try:
+            return importlib.import_module(mname)
+        except ImportError:
+            return importlib.import_module('_libpymolfile')
+    _libpymolfile = swig_import_helper()
+    del swig_import_helper
+elif _swig_python_version_info >= (2, 6, 0):
+    def swig_import_helper():
+        from os.path import dirname
+        import imp
+        fp = None
+        try:
+            fp, pathname, description = imp.find_module('_libpymolfile', [dirname(__file__)])
+        except ImportError:
+            import _libpymolfile
+            return _libpymolfile
+        try:
+            _mod = imp.load_module('_libpymolfile', fp, pathname, description)
+        finally:
+            if fp is not None:
+                fp.close()
+        return _mod
+    _libpymolfile = swig_import_helper()
+    del swig_import_helper
+else:
+    import _libpymolfile
+del _swig_python_version_info
+
+try:
+    _swig_property = property
+except NameError:
+    pass  # Python < 2.2 doesn't have 'property'.
+
+try:
+    import builtins as __builtin__
+except ImportError:
+    import __builtin__
+
+def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
+    if (name == "thisown"):
+        return self.this.own(value)
+    if (name == "this"):
+        if type(value).__name__ == 'SwigPyObject':
+            self.__dict__[name] = value
+            return
+    method = class_type.__swig_setmethods__.get(name, None)
+    if method:
+        return method(self, value)
+    if (not static):
+        if _newclass:
+            object.__setattr__(self, name, value)
+        else:
+            self.__dict__[name] = value
+    else:
+        raise AttributeError("You cannot add attributes to %s" % self)
+
+
+def _swig_setattr(self, class_type, name, value):
+    return _swig_setattr_nondynamic(self, class_type, name, value, 0)
+
+
+def _swig_getattr(self, class_type, name):
+    if (name == "thisown"):
+        return self.this.own()
+    method = class_type.__swig_getmethods__.get(name, None)
+    if method:
+        return method(self)
+    raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
+
+
+def _swig_repr(self):
+    try:
+        strthis = "proxy of " + self.this.__repr__()
+    except __builtin__.Exception:
+        strthis = ""
+    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
+
+try:
+    _object = object
+    _newclass = 1
+except __builtin__.Exception:
+    class _object:
+        pass
+    _newclass = 0
+
+
+def molfile_plugin_list(maxsize: 'int') -> "PyObject *":
+    """molfile_plugin_list(maxsize) -> PyObject *"""
+    return _libpymolfile.molfile_plugin_list(maxsize)
+
+def molfile_init() -> "int":
+    """molfile_init() -> int"""
+    return _libpymolfile.molfile_init()
+
+def molfile_finish() -> "int":
+    """molfile_finish() -> int"""
+    return _libpymolfile.molfile_finish()
+
+def get_plugin(molcapsule: 'PyObject *', plug_no: 'int') -> "PyObject *":
+    """get_plugin(molcapsule, plug_no) -> PyObject *"""
+    return _libpymolfile.get_plugin(molcapsule, plug_no)
+
+def molfile_plugin_info(molcapsule: 'PyObject *', plugin_no: 'int') -> "PyObject *":
+    """molfile_plugin_info(molcapsule, plugin_no) -> PyObject *"""
+    return _libpymolfile.molfile_plugin_info(molcapsule, plugin_no)
+
+def open_file_read(molcapsule: 'PyObject *', fname: 'char *', ftype: 'char *', natoms: 'int') -> "PyObject *":
+    """open_file_read(molcapsule, fname, ftype, natoms) -> PyObject *"""
+    return _libpymolfile.open_file_read(molcapsule, fname, ftype, natoms)
+
+def close_file_read(molpack: 'PyObject *') -> "PyObject *":
+    """close_file_read(molpack) -> PyObject *"""
+    return _libpymolfile.close_file_read(molpack)
+
+def read_fill_structure(molpack: 'PyObject *', prototype: 'PyObject *') -> "PyObject *":
+    """read_fill_structure(molpack, prototype) -> PyObject *"""
+    return _libpymolfile.read_fill_structure(molpack, prototype)
+
+def read_fill_bonds(molpack: 'PyObject *') -> "PyObject *":
+    """read_fill_bonds(molpack) -> PyObject *"""
+    return _libpymolfile.read_fill_bonds(molpack)
+
+def read_fill_angles(molpack: 'PyObject *') -> "PyObject *":
+    """read_fill_angles(molpack) -> PyObject *"""
+    return _libpymolfile.read_fill_angles(molpack)
+
+def read_fill_next_timestep(molpack: 'PyObject *') -> "PyObject *":
+    """read_fill_next_timestep(molpack) -> PyObject *"""
+    return _libpymolfile.read_fill_next_timestep(molpack)
+
+def are_plugins_same(molpack_a: 'PyObject *', molpack_b: 'PyObject *') -> "PyObject *":
+    """are_plugins_same(molpack_a, molpack_b) -> PyObject *"""
+    return _libpymolfile.are_plugins_same(molpack_a, molpack_b)
+
+def are_filehandles_same(molpack_a: 'PyObject *', molpack_b: 'PyObject *') -> "PyObject *":
+    """are_filehandles_same(molpack_a, molpack_b) -> PyObject *"""
+    return _libpymolfile.are_filehandles_same(molpack_a, molpack_b)
+# This file is compatible with both classic and new-style classes.
+
+

setup.py

@@ -10,39 +10,21 @@ import subprocess
 from distutils.version import LooseVersion
 
 try:
-    from setuptools.command.build_ext import build_ext
-    #from setuptools.command.build_ext import build_ext as _build_ext
-    from setuptools import Distribution, setup, Extension, Command, find_packages
+    from setuptools import setup, Extension, Command, find_packages
     from setuptools.command.install import install
-    #from Cython.Build import cythonize
-    #from Cython.Distutils import build_ext as _build_ext
+    from Cython.Build import cythonize
+    from Cython.Distutils import build_ext
 except:
-    from distutils.command.build_ext import build_ext
-    #from distutils.command.build_ext import build_ext as _build_ext
-    from distutils import Distribution, setup, Extension, Command, find_packages
+    from distutils import setup, Extension, Command, find_packages
     from distutils.command.install import install
-    #from Cython.Build import cythonize
-    #from Cython.Distutils import build_ext as _build_ext
+    from Cython.Build import cythonize
+    from Cython.Distutils import build_ext
     
 try:
     from setuptools.command.build_clib import build_clib as _build_clib
 except:
     from distutils.command.build_clib import build_clib as _build_clib
 
-#def use_system():
-#    install_type = os.environ.get("SODIUM_INSTALL")
-#    
-#    if install_type == "system":
-#        # If we are forcing system installs, don't compile the bundled one
-#        return True
-#    else:
-#        # By default we just use the bundled copy
-#        return False
-
-#class Distribution(Distribution):
-#    def has_c_libraries(self):
-#        return not use_system()
-
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=''):
         Extension.__init__(self, name, sources=[])
@@ -88,21 +70,6 @@ class build_clib(_build_clib):
 
         print()  # Add an empty line for cleaner output
 
-#def build_ext(_build_ext):
-#    def run(self):
-#        buildflag = True
-#        if buildflag:
-#        #if self.distribution.has_c_libraries():
-#            build_clib = self.get_finalized_command("build_clib")
-#            self.include_dirs.append(
-#                    os.path.join(build_clib.build_clib, "include"),
-#                    )
-#            self.library_dirs.insert(0,
-#                    os.path.join(build_clib.build_clib, "lib"),
-#                    )
-#        for ext in self.extensions:
-#            return _build_ext.run(ext)
-
 def get_ext_filename_without_platform_suffix(filename):
     name, ext = os.path.splitext(filename)
     ext_suffix = sysconfig.get_config_var('EXT_SUFFIX')
@@ -132,7 +99,6 @@ CLASSIFIERS = [
     "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",
@@ -203,32 +169,23 @@ def get_numpy_include():
     return numpy_include
 
 # from SimpleTraj setup.py (https://github.com/arose/simpletraj)
-# Needed for large-file seeking under 32bit systems (migth need for indexing and access).
-largefile_macros = [
-    ( "_LARGEFILE_SOURCE", None ),
-    ( "_LARGEFILE64_SOURCE", None ),
-    ( "_FILE_OFFSET_BITS","64" )
-]
 
 if __name__ == '__main__':
 
     libpymolfile_module = Extension(
-            'pymolfile/molfile/libpymolfile', 
+            'pymolfile/molfile/_libpymolfile', 
             sources=[
                 'pymolfile/molfile/libpymolfile.i' , 
                 'pymolfile/molfile/pymolfile.cxx',
-                #'build/molfile_plugins/compile/lib/',
-                #'build/external/tng/lib/',
                 ],
             swig_opts=['-py3', '-Wall', '-c++'],
             library_dirs=[
                 'build/external/tng/lib',
                 'build/molfile_plugins/compile/lib/'
                 ],
-            libraries=['netcdf','tng_io','expat'],
+            libraries=['netcdf','expat','tcl'],
             include_dirs = [
                 get_numpy_include(),
-                #get_cmake_includes(),
                 'pymolfile/molfile',
                 'pymolfile/molfile/molfile_plugins/include',
                 'pymolfile/molfile/molfile_plugins/molfile_plugin/include',
@@ -236,20 +193,13 @@ if __name__ == '__main__':
                 'build/external/tng/include',
                 ],
             extra_compile_args = [
-                '-fPIC', '-shared', '-O2', '-w'
-                #'-DNDEBUG', '-DUNIX', '-D__UNIX',  '-m64', 
-                #'-fPIC', '-O2', '-w', '-fmessage-length=0'
+                '-fPIC', '-shared', '-O0', '-g', '-w' 
                 ],
             extra_link_args = [
-                'build/molfile_plugins/compile/lib/libmolfile_plugin.a'
+                'build/molfile_plugins/compile/lib/libmolfile_plugin.a',
+                'build/external/tng/lib/libtng_io.a',
                 ],
-            #define_macros = largefile_macros
             )
-    #if sys.version_info > (3,):
-    #    command_extension={'build_ext': BuildExtWithoutPlatformSuffix}
-    #else:
-    command_extension={}
-    #command_extension=dict(build_ext=CMakeBuild)
 
     setup(
         name = "pymolfile",
@@ -262,19 +212,15 @@ if __name__ == '__main__':
         url = "https://gitlab.mpcdf.mpg.de/berko/pymolfile",
         zip_safe = False,
         packages = find_packages(),
-        #library_dirs=[
-        #    'build/external/tng/lib'
-        #],
         libraries = [('molfile_plugin', { 'sources' : ['build/molfile_plugins/compile/lib/libmolfile_plugin.a']})],
         cmdclass= {
             'build_clib' : build_clib,
-            'build_ext'  : BuildExtWithoutPlatformSuffix,
+            'build_ext'  : build_ext,
         },
-        #distclass=Distribution,
         ext_modules = [
-            #CMakeExtension('molfile', sourcedir='pymolfile/molfile/'),
             libpymolfile_module,
         ],
+        package_data={'pymolfile': ['LICENSE', 'pymolfile/molfile/libpymolfile.py']},
         py_modules=["pymolfile"],
         requires = [ "numpy" ],
         setup_requires = [ "numpy" ],