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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 glob import glob
import shutil
import sys, os, re
# non-empty DEBUG variable turns off optimization and adds -g flag
DEBUG = bool(os.getenv('DEBUG', ''))
WIN = sys.platform.startswith('win')
MAC = sys.platform.startswith('darwin')
# handle extra arguments
class options:
osx_frameworks = True
jobs = int(os.getenv('JOBS', 0))
no_libxml = False
no_glut = True
use_msgpackc = 'guess'
help_distutils = False
testing = False
openvr = False
use_openmp = 'no' if MAC else 'yes'
use_vtkm = 'no'
vmd_plugins = True
try:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--glut', dest='no_glut', action="store_false",
help="link with GLUT (legacy GUI)")
parser.add_argument('--no-osx-frameworks', dest='osx_frameworks',
help="on MacOS use XQuartz instead of native frameworks",
action="store_false")
parser.add_argument('--jobs', '-j', type=int, help="for parallel builds "
"(defaults to number of processors)")
parser.add_argument('--no-libxml', action="store_true",
help="skip libxml2 dependency, disables COLLADA export")
parser.add_argument('--use-openmp', choices=('yes', 'no'),
help="Use OpenMP")
parser.add_argument('--use-vtkm', choices=('1.5.x', 'master', 'no'),
help="Use VTK-m for isosurface generation")
parser.add_argument('--use-msgpackc', choices=('c++11', 'c', 'guess', 'no'),
help="c++11: use msgpack-c header-only library; c: link against "
"shared library; no: disable fast MMTF load support")
parser.add_argument('--help-distutils', action="store_true",
help="show help for distutils options and exit")
parser.add_argument('--testing', action="store_true",
help="Build C-level tests")
parser.add_argument('--openvr', dest='openvr', action='store_true')
parser.add_argument('--no-vmd-plugins', dest='vmd_plugins',
action='store_false',
help='Disable VMD molfile plugins (libnetcdf dependency)')
options, sys.argv[1:] = parser.parse_known_args(namespace=options)
except ImportError:
print("argparse not available")
if options.help_distutils:
sys.argv.append("--help")
if True:
import monkeypatch_distutils
monkeypatch_distutils.set_parallel_jobs(options.jobs)
def forms_uic(build_lib='modules'):
'''
Convert Qt UI files in "modules/pmg_qt/forms" to Python files in place
'''
def get_prefix_path():
'''
Return a list of paths which will be searched for "include",
"include/freetype2", "lib", "lib64" etc.
'''
try:
return os.environ['PREFIX_PATH'].split(os.pathsep)
except KeyError:
pass
if sys.platform.startswith("freebsd"):
return ["/usr/local"]
X11 = ['/usr/X11'] * (not options.osx_frameworks)
if sys.platform == 'darwin':
for prefix in ['/sw', '/opt/local', '/usr/local']:
if sys.base_prefix.startswith(prefix):
return [prefix] + X11
if is_conda_env():
if sys.platform.startswith('win'):
return [os.path.join(sys.prefix, 'Library')]
return [sys.prefix] + X11
return ['/usr'] + X11
def is_conda_env():
return (
'conda' in sys.prefix or
'conda' in sys.version or
'Continuum' in sys.version or
sys.prefix == os.getenv('CONDA_PREFIX'))
def guess_msgpackc():
for prefix in prefix_path:
f = os.path.join(prefix, 'include', 'msgpack', 'version_master.h')
try:
m = re.search(r'MSGPACK_VERSION_MAJOR\s+(\d+)', open(f).read())
except EnvironmentError:
continue
if m is not None:
major = int(m.group(1))
if major > 1:
return 'c++11'
return 'no'
# Important: import 'distutils.command' modules after monkeypatch_distutils
from distutils.command.build_ext import build_ext
from distutils.command.build_py import build_py
from distutils.command.install import install
class build_ext_pymol(build_ext):
def initialize_options(self):
build_ext.initialize_options(self)
if DEBUG and not WIN:
self.debug = True
class build_py_pymol(build_py):
def run(self):
build_py.run(self)
forms_uic(self.build_lib)
class install_pymol(install):
pymol_path = None
bundled_pmw = False
no_launcher = False
user_options = install.user_options + [
('pymol-path=', None, 'PYMOL_PATH'),
('bundled-pmw', None, 'install bundled Pmw module'),
('no-launcher', None, 'skip installation of the pymol launcher'),
]
def finalize_options(self):
install.finalize_options(self)
self.pymol_path_is_default = self.pymol_path is None
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()
if not self.no_launcher:
self.make_launch_script()
if self.bundled_pmw:
raise Exception('--bundled-pmw has been removed, please install Pmw from '
'https://github.com/schrodinger/pmw-patched')
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([
]).intersection(names)
if os.path.exists(dst):
shutil.rmtree(dst)
print('copying %s -> %s' % (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)
if options.openvr:
self.copy('contrib/vr/README.md',
os.path.join(self.pymol_path, 'README-VR.txt'))
def make_launch_script(self):
if sys.platform.startswith('win'):
launch_script = 'pymol.bat'
else:
launch_script = 'pymol'
self.mkpath(self.install_scripts)
launch_script = os.path.join(self.install_scripts, launch_script)
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'):
# paths relative to launcher, if possible
try:
python_exe = '%~dp0\\' + os.path.relpath(python_exe, self.install_scripts)
except ValueError:
pass
try:
pymol_file = '%~dp0\\' + os.path.relpath(pymol_file, self.install_scripts)
except ValueError:
pymol_file = os.path.abspath(pymol_file)
if not self.pymol_path_is_default:
out.write(f'set PYMOL_PATH={pymol_path}' + os.linesep)
out.write('"%s" "%s"' % (python_exe, pymol_file))
out.write(' %*' + os.linesep)
else:
out.write('#!/bin/sh' + os.linesep)
if not self.pymol_path_is_default:
out.write(f'export PYMOL_PATH="{pymol_path}"' + os.linesep)
out.write('exec "%s" "%s" "$@"' % (python_exe, pymol_file) + os.linesep)
os.chmod(launch_script, 0o755)
#============================================================================
# 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)
# can be changed with environment variable PREFIX_PATH
prefix_path = get_prefix_path()
inc_dirs = [
"include",
]
pymol_src_dirs = [
"ov/src",
"layer0",
"layer1",
"layer2",
"layer3",
"layer4",
"layer5",
generated_dir,
]
def_macros = [
("_PYMOL_LIBPNG", None),
("_PYMOL_FREETYPE", None),
]
if DEBUG and not WIN:
def_macros += [
# bounds checking in STL containers
("_GLIBCXX_ASSERTIONS", None),
]
libs = ["png", "freetype"]
lib_dirs = []
ext_comp_args = [
"-Werror=return-type",
"-Wunused-variable",
"-Wno-switch",
"-Wno-narrowing",
# legacy stuff
'-Wno-char-subscripts',
# optimizations
"-Og" if DEBUG else "-O3",
] if not WIN else []
ext_link_args = []
ext_objects = []
data_files = []
ext_modules = []
if options.use_openmp == 'yes':
def_macros += [
("PYMOL_OPENMP", None),
]
if MAC:
ext_comp_args += ["-Xpreprocessor", "-fopenmp"]
libs += ["omp"]
elif WIN:
ext_comp_args += ["/openmp"]
else:
ext_comp_args += ["-fopenmp"]
ext_link_args += ["-fopenmp"]
if options.vmd_plugins:
# VMD plugin support
inc_dirs += [
'contrib/uiuc/plugins/include',
]
pymol_src_dirs += [
'contrib/uiuc/plugins/molfile_plugin/src',
]
def_macros += [
("_PYMOL_VMD_PLUGINS", None),
]
if not options.no_libxml:
# COLLADA support
def_macros += [
("_HAVE_LIBXML", None)
]
libs += ["xml2"]
if options.use_msgpackc == 'guess':
options.use_msgpackc = guess_msgpackc()
if options.use_msgpackc == 'no':
def_macros += [("_PYMOL_NO_MSGPACKC", None)]
else:
if options.use_msgpackc == 'c++11':
def_macros += [("MMTF_MSGPACK_USE_CPP11", None)]
else:
libs += ['msgpackc']
pymol_src_dirs += ["contrib/mmtf-c"]
if options.no_glut:
def_macros += [
("_PYMOL_NO_MAIN", None),
]
if options.testing:
pymol_src_dirs += ["layerCTest"]
def_macros += [("_PYMOL_CTEST", None)]
if options.openvr:
def_macros += [("_PYMOL_OPENVR", None)]
pymol_src_dirs += [
"contrib/vr",
]
inc_dirs += pymol_src_dirs
#============================================================================
if MAC:
libs += ["GLEW"]
if options.osx_frameworks:
ext_link_args += [
"-framework", "OpenGL",
] + (not options.no_glut) * [
"-framework", "GLUT",
]
def_macros += [
("_PYMOL_OSX", None),
]
else:
libs += [
"GL",
] + (not options.no_glut) * [
"glut",
]
if WIN:
# clear
libs = []
def_macros += [
("WIN32", None),
]
libs += [
"Advapi32", # Registry (RegCloseKey etc.)
"Ws2_32", # htonl
]
if True:
libs += [
"glew32",
"freetype",
"libpng",
] + (not options.no_glut) * [
"freeglut",
] + (not options.no_libxml) * [
"libxml2",
]
if DEBUG:
ext_comp_args += ['/Z7']
ext_link_args += ['/DEBUG']
libs += [
"opengl32",
]
if not (MAC or WIN):
libs += [
"GL",
"GLEW",
] + (not options.no_glut) * [
"glut",
]
if options.use_vtkm != "no":
for prefix in prefix_path:
vtkm_inc_dir = os.path.join(prefix, "include", "vtkm-1.5")
if os.path.exists(vtkm_inc_dir):
break
else:
raise LookupError('VTK-m headers not found.'
f' PREFIX_PATH={":".join(prefix_path)}')
def_macros += [
("_PYMOL_VTKM", None),
]
inc_dirs += [
vtkm_inc_dir,
vtkm_inc_dir + "/vtkm/thirdparty/diy/vtkmdiy/include",
vtkm_inc_dir + "/vtkm/thirdparty/lcl/vtkmlcl",
] + (options.use_vtkm != "master") * [
vtkm_inc_dir + "/vtkm/thirdparty/diy",
vtkm_inc_dir + "/vtkm/thirdparty/taotuple",
]
libs += [
"vtkm_cont-1.5",
"vtkm_filter_contour-1.5"
if options.use_vtkm == "master" else "vtkm_filter-1.5",
]
if options.vmd_plugins:
libs += [
"netcdf",
]
if options.openvr:
libs += [
"openvr_api",
]
if True:
try:
import numpy
inc_dirs += [
numpy.get_include(),
]
def_macros += [
("_PYMOL_NUMPY", None),
]
except ImportError:
print("numpy not available")
if True:
for prefix in prefix_path:
for dirs, suffixes in [
[inc_dirs, [("include",), ("include", "freetype2"), ("include", "libxml2"), ("include", "openvr")]],
[lib_dirs, [("lib64",), ("lib",)]],
]:
dirs.extend(filter(os.path.isdir, [os.path.join(prefix, *s) for s in suffixes]))
if True:
# optimization currently causes a clang segfault on OS X 10.9 when
# compiling layer2/RepCylBond.cpp
if sys.platform == 'darwin':
ext_comp_args += ["-fno-strict-aliasing"]
def get_pymol_version():
return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]
def get_sources(subdirs, suffixes=('.c', '.cpp')):
return sorted([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,
extra_objects = ext_objects,
),
Extension("chempy.champ._champ",
get_sources(['contrib/champ']),
include_dirs=["contrib/champ"],
),
]
distribution = setup ( # Distribution meta-data
cmdclass = {
'build_ext': build_ext_pymol,
'build_py': build_py_pymol,
'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),
package_data = {'pmg_qt': ['forms/*.ui']},
ext_modules = ext_modules,
data_files = data_files,
)
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