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pymolfile
Commit 4a835052 authored by Berk Onat's avatar Berk Onat
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Python installer with setup.py is provided

parent 282efaa4
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Showing with 48 additions and 78 deletions
pymolfile/molfile/CMakeLists.txt
View file @ 4a835052
......@@ -5,8 +5,7 @@ project(molfile)
add_subdirectory(external)
add_subdirectory(molfile_plugins/compile)
#set_source_files_properties( tng/include/tng/tng_io.h PROPERTIES GENERATED TRUE )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_BINARY_DIR}/molfile_plugins/compile/")
add_dependencies( molfile_plugins_comp tngio_comp )
#add_dependencies( molfile_plugins_comp TNGBuilder )
pymolfile/molfile/external/CMakeLists.txt
View file @ 4a835052
......@@ -14,21 +14,13 @@ message("GIT_EXECUTABLE='${GIT_EXECUTABLE}'")
ExternalProject_Add(tng
PREFIX ${TNG_PREFIX}
GIT_REPOSITORY https://github.com/gromacs/tng.git
GIT_TAG v1.7.6
INSTALL_DIR ${TNG_INSTALL_DIR}
CMAKE_ARGS ${TNG_CMAKE_ARGS}
)
#set(LIB_TNGIO_FILES
# "${TNG_INSTALL_DIR}/include/tng/tng_io.h")
#
#if (APPLE)
# set(LIB_TNGIO_FILES ${LIB_TNGIO_FILES} "${TNG_INSTALL_DIR}/lib/libtng_io.dylib")
#else()
# set(LIB_TNGIO_FILES ${LIB_TNGIO_FILES} "${TNG_INSTALL_DIR}/lib/libtng_io.so")
#endif()
#
add_custom_target(tngio_comp ALL
DEPENDS ${TNG_INSTALL_DIR}
DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/tng
)
pymolfile/molfile/molfile_plugins/compile/CMakeLists.txt
View file @ 4a835052
......@@ -2,10 +2,11 @@ cmake_minimum_required(VERSION 2.8.12)
project(molfileplugins)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_BINARY_DIR})
find_package(EXPAT)
find_package(TCL)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/molfile_plugins/compile/cmake/Modules/")
find_package(NetCDF)
find_package(NETCDF)
if (EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.dylib"
OR EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.so"
......@@ -33,8 +34,8 @@ if(TARGET_ARCH MATCHES "^.*64.*$")
endif()
set(LIB_MOLFILE_FILES
"${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib/libmolfile_plugins.a"
"${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib/libmolfile_plugins.h")
"${CMAKE_CURRENT_BINARY_DIR}/lib/libmolfile_plugins.a"
"${CMAKE_CURRENT_BINARY_DIR}/lib/libmolfile_plugins.h")
if(UNIX AND NOT APPLE)
set(LINUX TRUE)
......@@ -124,6 +125,8 @@ if(UNIX)
add_custom_command(
OUTPUT ${LIB_MOLFILE_FILES}
COMMAND make dynlibs staticlibs bins \"ARCH = ${TARGET_ARCH}\" \"COPTO = ${TARGET_COPT} \" \"LOPTO = ${TARGET_LOPT} \" \"CC = ${CMAKE_C_COMPILER} \" \"CXX = ${CMAKE_CXX_COMPILER} \" \"DEF = ${TARGET_DEF}\" \"CCFLAGS = ${TARGET_CFLAGS} \" \"CXXFLAGS = ${TARGET_CXXFLG} \" \"AR = ${TARGET_AR}\" \"NM = ${TARGET_NM}\" \"RANLIB = ${TARGET_RANLIB}\" \"LIBTOOL = ${TARGET_LIBTOOL} \" ${TARGET_MOL_LIBS}
COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib ${CMAKE_CURRENT_BINARY_DIR}/lib
COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib
COMMENT "Compiling libmolfile_plugin.a"
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/molfile_plugins/molfile_plugin"
)
......@@ -151,6 +154,8 @@ if(WINCOMP)
add_custom_command(
OUTPUT ${LIB_MOLFILE_FILES}
COMMAND ${MYMAKE} dynlibs win32staticlibs "\" ARCH = ${TARGET_ARCH} \"" "\" COPTO = /Fo \"" "\" LOPTO = /OUT: \"" "\" ${TARGET_MOL_SETTINGS} \"" "\" DEF = ${TARGET_DEF} \"" "\" AR = ${TARGET_AR} \"" "\" NM = ${TARGET_NM} \"" "\" RANLIB = ${TARGET_RANLIB} \"" "\" SHLDFLAGS = ${TARGET_SHLDFLAGS} \"" "\"${TARGET_MOL_LIBS}\""
COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib ${CMAKE_CURRENT_BINARY_DIR}/molfile_plugins/compile/lib
COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib
COMMENT "Compiling libmolfile_plugin.a"
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}/molfile_plugins/molfile_plugin"
)
......@@ -160,10 +165,5 @@ add_custom_target(molfile_plugins_comp ALL
DEPENDS ${LIB_MOLFILE_FILES}
)
#add_library(molfile_plugins INTERFACE)
#target_include_directories(molfile_plugins INTERFACE "${CMAKE_CURRENT_BINARY_DIR}/lib/")
#target_link_libraries(molfile_plugins INTERFACE ${MOLFILE_LIBRARIES})
setup.py
View file @ 4a835052
......@@ -6,46 +6,38 @@ import sys
import sysconfig
import platform
import subprocess
from distutils.version import LooseVersion
try:
from distutils.version import LooseVersion
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
from setuptools.command.install import install
except:
from distutils.version import LooseVersion
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
from distutils.command.install import install
try:
from setuptools.command.build_clib import build_clib as _build_clib
except:
from distutils.command.build_clib import build_clib as _build_clib
# 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):
class build_clib(_build_clib):
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)
buildflag = True
if buildflag:
ext = CMakeExtension('molfile', sourcedir='pymolfile/molfile/'),
self.my_build_extension(ext)
def build_extension(self, ext):
def my_build_extension(self, ext):
extdir = os.path.abspath(
os.path.dirname(self.get_ext_fullpath(ext.name)))
os.path.dirname('pymolfile/molfile'))
cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
'-DPYTHON_EXECUTABLE=' + sys.executable]
......@@ -69,12 +61,14 @@ class CMakeBuild(build_ext):
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', '../pymolfile/molfile'] + cmake_args,
cwd=self.build_temp + '/../', env=env)
subprocess.check_call(['cmake', '--build', '.'] + build_args,
cwd=self.build_temp)
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')
......@@ -104,6 +98,7 @@ 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",
......@@ -173,52 +168,38 @@ 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(
'pymolfile/molfile/_libpymolfile',
sources=[
'pymolfile/molfile/libpymolfile.i' ,
'pymolfile/molfile/pymolfile.cxx'
'pymolfile/molfile/pymolfile.cxx',
'build/molfile_plugins/compile/lib/libmolfile_plugin.a',
'build/molfile_plugins/compile/lib/libmolfile_plugin.h',
'build/external/tng/lib',
],
swig_opts=['-py3', '-Wall', '-c++'],
library_dirs=[
'pymolfile/molfile/external/tng/lib/',
'pymolfile/molfile/molfile_plugins/compile/lib/'
'build/external/tng/lib',
'build/molfile_plugins/compile/lib/'
],
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',
'pymolfile/molfile/molfile_plugins/compile/lib/',
'pymolfile/molfile/external/tng/include',
'build/molfile_plugins/compile/lib/',
'build/external/tng/include',
],
extra_compile_args = [
'-fPIC', '-shared', '-O2', '-w'
#'-DNDEBUG', '-DUNIX', '-D__UNIX', '-m64',
#'-fPIC', '-O2', '-w', '-fmessage-length=0'
],
extra_link_args = [
'pymolfile/molfile/molfile_plugins/compile/lib/libmolfile_plugin.a'
'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",
......@@ -231,18 +212,16 @@ if __name__ == '__main__':
url = "https://gitlab.mpcdf.mpg.de/berko/pymolfile",
zip_safe = False,
packages = find_packages(),
cmdclass= command_extension,
cmdclass= {
'build_clib' : build_clib,
'build_ext' : BuildExtWithoutPlatformSuffix,
},
ext_modules = [
CMakeExtension('molfile', sourcedir='pymolfile/molfile/'),
libpymolfile_module,
],
py_modules=["pymolfile"],
requires = [ "numpy" ],
setup_requires = [ "numpy" ],
install_requires = [ "numpy" ],
extras_require = {
#?do we need this? "netcdf": [ "netCDF Library" ],
#?and this? "tng_io": [ "TNG Library" ],
#?and this? "expat": [ "Expat XML Library" ]
}
extras_require = {}
)
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