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#!/usr/bin/env python
#
# This script only applies if you are performing a Python Distutils-based
# installation of PyMOL.
#
# It may assume that all of PyMOL's external dependencies are
# pre-installed into the system.
from distutils.core import setup, Extension
from distutils.util import change_root
from distutils.errors import *
from distutils.command.install import install
from distutils.command.build import build
from glob import glob
import shutil
import sys, os, re
import distutils.ccompiler
import multiprocessing.pool
def CCompiler_compile(self, sources, output_dir=None, macros=None,
include_dirs=None, debug=0, extra_preargs=None, extra_postargs=None,
depends=None):
'''
Enable parallel and incremental build.
To do a clean build, please remove the "build" directory.
'''
macros, objects, extra_postargs, pp_opts, build = self._setup_compile(
output_dir, macros, include_dirs, sources, depends, extra_postargs)
cc_args = self._get_cc_args(pp_opts, debug, extra_preargs)
def _single_compile(obj):
try:
src, ext = build[obj]
except KeyError:
return
try:
if not self.force and \
os.path.getmtime(obj) > \
os.path.getmtime(src):
return
except OSError:
pass
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
pmap(_single_compile, objects)
return objects
# handle extra arguments
class options:
osx_frameworks = False
try:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--osx-frameworks', action="store_true")
options, sys.argv[1:] = parser.parse_known_args(namespace=options)
except ImportError:
print "argparse not available"
jobs = int(os.getenv('JOBS', 0))
pmap = map if jobs == 1 else multiprocessing.pool.ThreadPool(jobs or None).map
distutils.ccompiler.CCompiler.compile = CCompiler_compile
def posix_find_lib(names, lib_dirs):
# http://stackoverflow.com/questions/1376184/determine-if-c-library-is-installed-on-unix
from subprocess import Popen, PIPE
args = ["gcc", "-o", os.devnull, "-x", "c", "-"] + ["-L" + d for d in lib_dirs]
for name in names:
p = Popen(args + ["-l" + name], stdin=PIPE, stdout=PIPE, stderr=PIPE)
p.communicate("int main(){}")
if p.wait() == 0:
return name
raise IOError('could not find any of ' + str(names))
class install_pymol(install):
pymol_path = None
bundled_pmw = False
user_options = install.user_options + [
('pymol-path=', None, 'PYMOL_PATH'),
('bundled-pmw', None, 'install bundled Pmw module'),
]
def finalize_options(self):
install.finalize_options(self)
if self.pymol_path is None:
self.pymol_path = os.path.join(self.install_libbase, 'pymol')
elif self.root is not None:
self.pymol_path = change_root(self.root, self.pymol_path)
def run(self):
install.run(self)
self.install_pymol_path()
self.make_launch_script()
if self.bundled_pmw:
os.system("tar -C %s -zxvf modules/pmg_tk/pmw.tgz" % self.install_libbase)
def unchroot(self, name):
if self.root is not None and name.startswith(self.root):
return name[len(self.root):]
return name
def copy_tree_nosvn(self, src, dst):
ignore = lambda src, names: set(['.svn']).intersection(names)
if os.path.exists(dst):
shutil.rmtree(dst)
print 'copying', src, '->', dst
shutil.copytree(src, dst, ignore=ignore)
def copy(self, src, dst):
copy = self.copy_tree_nosvn if os.path.isdir(src) else self.copy_file
copy(src, dst)
def install_pymol_path(self):
self.mkpath(self.pymol_path)
def make_launch_script(self):
if sys.platform.startswith('win'):
launch_script = 'pymol.bat'
else:
launch_script = 'pymol'
python_exe = os.path.abspath(sys.executable)
pymol_file = self.unchroot(os.path.join(self.install_libbase, 'pymol', '__init__.py'))
pymol_path = self.unchroot(self.pymol_path)
with open(launch_script, 'w') as out:
if sys.platform.startswith('win'):
out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
out.write('"%s" "%s"' % (python_exe, pymol_file))
out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
else:
out.write('#!/bin/bash' + os.linesep)
if sys.platform.startswith('darwin'):
out.write('[ "$DISPLAY" == "" ] && export DISPLAY=":0.0"' + os.linesep)
out.write('export PYMOL_PATH="%s"' % pymol_path + os.linesep)
out.write('"%s" "%s" "$@"' % (python_exe, pymol_file) + os.linesep)
os.chmod(launch_script, 0755)
self.mkpath(self.install_scripts)
self.copy(launch_script, self.install_scripts)
#============================================================================
# should be something like (build_base + "/generated"), but that's only
# known to build and install instances
generated_dir = os.path.join(os.environ.get("PYMOL_BLD", "build"), "generated")
import create_shadertext
create_shadertext.create_all(generated_dir)
pymol_src_dirs = [
"ov/src",
"layer0",
"layer1",
"layer2",
"layer3",
"layer4",
"layer5",
"modules/cealign/src",
"modules/cealign/src/tnt",
generated_dir,
]
def_macros = [
("_PYMOL_LIBPNG", None),
("_PYMOL_INLINE", None),
("_PYMOL_OPENGL_SHADERS", None),
("_PYMOL_CGO_DRAWARRAYS", None),
("_PYMOL_CGO_DRAWBUFFERS", None),
("_PYMOL_GL_CALLLISTS", None),
]
libs = []
pyogl_libs = []
lib_dirs = []
ext_comp_args = []
ext_link_args = []
if True:
# VMD plugin support
pymol_src_dirs += [
'contrib/uiuc/plugins/include',
'contrib/uiuc/plugins/molfile_plugin/src',
]
def_macros += [
("_PYMOL_VMD_PLUGINS", None),
]
inc_dirs = list(pymol_src_dirs)
#============================================================================
if sys.platform=='win32':
# NOTE: this branch not tested in years and may not work...
inc_dirs += [
"win32/include"]
libs=["opengl32","glu32","glut32","libpng","zlib"]
pyogl_libs = ["opengl32","glu32","glut32"]
lib_dirs=["win32/lib"]
def_macros += [
("WIN32",None),
("_PYMOL_LIBPNG",None),
]
ext_link_args=['/NODEFAULTLIB:"LIBC"']
#============================================================================
elif sys.platform=='cygwin':
# NOTE: this branch not tested in years and may not work...
libs=["glut32","opengl32","glu32","png"]
pyogl_libs = ["glut32","opengl32","glu32"]
lib_dirs=["/usr/lib/w32api"]
def_macros += [
("CYGWIN",None),
("_PYMOL_LIBPNG",None)]
#============================================================================
else: # unix style (linux, mac, ...)
def_macros += [
("_PYMOL_FREETYPE",None),
("NO_MMLIBS",None),
("_CGO_DRAWARRAYS",None),
("OPENGL_ES_2",None),
]
try:
import numpy
inc_dirs += [
numpy.get_include(),
]
def_macros += [
("_PYMOL_NUMPY", None),
]
except ImportError:
print "numpy not available"
libs += ["png", "freetype"]
try:
prefix_path = os.environ['PREFIX_PATH'].split(os.pathsep)
except KeyError:
prefix_path = ["/usr", "/usr/X11", "/opt/local", "/sw"]
for prefix in prefix_path:
inc_dirs += filter(os.path.isdir, [prefix + s for s in ["/include", "/include/freetype2"]])
lib_dirs += filter(os.path.isdir, [prefix + s for s in ["/lib64", "/lib"]])
if sys.platform == 'darwin' and options.osx_frameworks:
ext_link_args += [
"-framework", "OpenGL",
"-framework", "GLUT",
]
else:
glut = posix_find_lib(['glut', 'freeglut'], lib_dirs)
pyogl_libs += ["GL", "GLU", glut]
libs += ["GLEW"]
libs += pyogl_libs
ext_comp_args += ["-ffast-math", "-funroll-loops", "-O3", "-fcommon"]
def get_pymol_version():
return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]
def get_sources(subdirs, suffixes=('.c', '.cpp')):
return [f for d in subdirs for s in suffixes for f in glob(d + '/*' + s)]
def get_packages(base, parent='', r=None):
from os.path import join, exists
if r is None:
r = []
if parent:
r.append(parent)
for name in os.listdir(join(base, parent)):
if '.' not in name and exists(join(base, parent, name, '__init__.py')):
get_packages(base, join(parent, name), r)
return r
package_dir = dict((x, os.path.join(base, x))
for base in ['modules']
for x in get_packages(base))
ext_modules = [
Extension("pymol._cmd",
get_sources(pymol_src_dirs),
include_dirs = inc_dirs,
libraries = libs,
library_dirs = lib_dirs,
define_macros = def_macros,
extra_link_args = ext_link_args,
extra_compile_args = ext_comp_args,
),
Extension("chempy.champ._champ",
get_sources(['contrib/champ']),
include_dirs=["contrib/champ"],
),
]
distribution = setup ( # Distribution meta-data
cmdclass = {'install': install_pymol},
name = "pymol",
version = get_pymol_version(),
author = "Schrodinger",
url = "http://pymol.org",
contact = "pymol-users@lists.sourceforge.net",
description = ("PyMOL is a Python-enhanced molecular graphics tool. "
"It excels at 3D visualization of proteins, small molecules, density, "
"surfaces, and trajectories. It also includes molecular editing, "
"ray tracing, and movies. Open Source PyMOL is free to everyone!"),
package_dir = package_dir,
packages = list(package_dir),
ext_modules = ext_modules,
)
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