From e7b14982a97dd026f4eb28c7ab286553556e2854 Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Mon, 30 Oct 2017 11:44:49 +0000
Subject: [PATCH] Correction to setup.py
---
setup.py | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 61 insertions(+), 5 deletions(-)
diff --git a/setup.py b/setup.py
index 559217e..95f46b1 100644
--- a/setup.py
+++ b/setup.py
@@ -11,18 +11,38 @@ from distutils.version import LooseVersion
try:
from setuptools.command.build_ext import build_ext
- from setuptools import setup, Extension, Command, find_packages
+ #from setuptools.command.build_ext import build_ext as _build_ext
+ from setuptools import Distribution, 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
except:
from distutils.command.build_ext import build_ext
- from distutils import setup, Extension, Command, find_packages
+ #from distutils.command.build_ext import build_ext as _build_ext
+ from distutils import Distribution, 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
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=[])
@@ -68,6 +88,20 @@ 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)
@@ -168,6 +202,14 @@ def get_numpy_include():
numpy_include = np.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(
@@ -175,9 +217,8 @@ if __name__ == '__main__':
sources=[
'pymolfile/molfile/libpymolfile.i' ,
'pymolfile/molfile/pymolfile.cxx',
- 'build/molfile_plugins/compile/lib/libmolfile_plugin.a',
- 'build/molfile_plugins/compile/lib/libmolfile_plugin.h',
- 'build/external/tng/lib',
+ #'build/molfile_plugins/compile/lib/',
+ #'build/external/tng/lib/',
],
swig_opts=['-py3', '-Wall', '-c++'],
library_dirs=[
@@ -187,6 +228,7 @@ if __name__ == '__main__':
libraries=['netcdf','tng_io','expat'],
include_dirs = [
get_numpy_include(),
+ #get_cmake_includes(),
'pymolfile/molfile',
'pymolfile/molfile/molfile_plugins/include',
'pymolfile/molfile/molfile_plugins/molfile_plugin/include',
@@ -195,11 +237,19 @@ if __name__ == '__main__':
],
extra_compile_args = [
'-fPIC', '-shared', '-O2', '-w'
+ #'-DNDEBUG', '-DUNIX', '-D__UNIX', '-m64',
+ #'-fPIC', '-O2', '-w', '-fmessage-length=0'
],
extra_link_args = [
'build/molfile_plugins/compile/lib/libmolfile_plugin.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",
@@ -212,11 +262,17 @@ 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,
},
+ #distclass=Distribution,
ext_modules = [
+ #CMakeExtension('molfile', sourcedir='pymolfile/molfile/'),
libpymolfile_module,
],
py_modules=["pymolfile"],
--
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