#!/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, )