import os
import subprocess
import shutil
import sys
import glob
def _lib_name(component):
return 'libost_%s.dylib' % component
def _deps_for_lib(lib, pool, recursive=True):
if lib in pool:
return
otool=subprocess.Popen(['otool', '-L', lib], stdout=subprocess.PIPE)
output=otool.communicate()[0]
lines=output.split('\n')[1:]
for line in lines:
d=line.split(' ')[0].strip()
if len(d)>0:
if d==lib:
continue
if d not in pool:
if d.startswith('/System') or d.startswith('/usr/lib'):
continue
if recursive:
_deps_for_lib(d, pool)
pool.add(d)
return
def collect_deps(stage_dir, components, binaries, site_packages,
site_packages_dir):
"""
Collect the dependencies for the given components and returns a list of
frameworks/libraries that the component depends on.
"""
pool=set()
for component in components:
lib_name=os.path.abspath(os.path.join(stage_dir, 'lib',
_lib_name(component)))
if not os.path.exists(lib_name):
print 'WARNING:', lib_name, 'does not exist'
if lib_name not in pool:
_deps_for_lib(lib_name, pool)
pool.add(lib_name)
for bin in binaries:
bin_name=os.path.abspath(os.path.join(stage_dir, 'bin',
bin))
if not os.path.exists(bin_name):
print 'WARNING:', bin_name, 'does not exist'
continue
if bin_name not in pool:
_deps_for_lib(bin_name, pool)
for site_package in site_packages:
full_path=get_python_module_path(site_package)
print full_path
if not os.path.exists(full_path):
print 'WARNING:', site_package, 'does not exists'
continue
if os.path.isdir(full_path):
for so_file in glob.glob(os.path.join(full_path, '*.so')):
_deps_for_lib(so_file, pool)
return pool
BINARIES=['gosty', 'chemdict_tool']
COMPONENTS=['mol', 'geom', 'conop', 'gfx', 'gui', 'seq_alg', 'seq',
'img', 'img_alg', 'info', 'io', 'db', 'base']
SCRIPTS=['dng', 'ost']
CHANGE_ID_RPATH='install_name_tool -id @rpath/%s %s'
CHANGE_ID='install_name_tool -id @executable_path/%s %s'
CHANGE_LOAD_CMD_RPATH='install_name_tool -change %s @rpath/%s %s'
CHANGE_LOAD_CMD='install_name_tool -change %s @executable_path/%s %s'
ADD_RPATH='install_name_tool -add_rpath %s %s 2> /dev/null'
SITE_PACKAGES=['sip.so', 'sipconfig.py', 'sipdistutils.py', 'PyQt4']
REMOVE_HEADERS='rm -rf `find %s/lib -type d -name Headers`'
REMOVE_CURRENT='rm -rf `find %s/lib -type d -name Current`'
# collect libs of non-standard libraries/frameworks we depend on
def copy_binaries(stage_dir, outdir, binary_names, scripts, use_rpath,
append_bin=True):
exe_path=os.path.abspath(os.path.join(outdir, 'bin'))
for binary_name in binary_names:
if append_bin:
bin_name=os.path.join(stage_dir, 'bin', binary_name)
else:
bin_name=os.path.join(stage_dir, binary_name)
if not os.path.exists(bin_name):
print 'WARNING:', binary_name, 'does not exist'
continue
dst_name=os.path.join(outdir, 'bin', os.path.basename(bin_name))
shutil.copy(bin_name, dst_name)
update_load_commands(dst_name, True, use_rpath, exe_path)
os.system(ADD_RPATH % ('../lib', dst_name))
for script in scripts:
shutil.copy(os.path.join(stage_dir, 'bin', script),
os.path.join(outdir,'bin', script))
def split_framework_components(abs_path):
"""
Splits the path pointing to a dynamic library within a framework
'/System/Frameworks/A.framework/Versions/4/A' =>
['/System/Frameworks/A.framework', 'Versions/4/A']
"""
parts=abs_path.split('/')
for i, s in enumerate(parts):
if s.endswith('.framework'):
lead=os.path.join('/', *parts[:i+1])
trail=os.path.join(*parts[i+1:])
return lead, trail
def change_id(id, lib, use_rpath):
os.chmod(lib, 0666)
if use_rpath:
os.system(CHANGE_ID_RPATH % (id,lib))
else:
os.system(CHANGE_ID % (id,lib))
os.chmod(lib, 0444)
def update_load_commands(lib, exe, use_rpath, exe_path):
direct_deps=set()
_deps_for_lib(lib, direct_deps, recursive=False)
os.chmod(lib, 0666)
for direct_dep in direct_deps:
if direct_dep.endswith('.dylib'):
if use_rpath:
new_name=os.path.basename(direct_dep)
os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
else:
new_name=os.path.join('../lib', os.path.basename(direct_dep))
os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
else:
assert direct_dep.find('.framework/')>=0
if use_rpath:
framework_path, rel_path=split_framework_components(direct_dep)
framework_name=os.path.basename(framework_path)
new_name=os.path.join(framework_name, rel_path)
os.system(CHANGE_LOAD_CMD_RPATH % (direct_dep, new_name, lib))
else:
framework_path, rel_path=split_framework_components(direct_dep)
framework_name=os.path.basename(framework_path)
new_name=os.path.join('../lib', framework_name, rel_path)
os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
if use_rpath:
os.system(ADD_RPATH % ('.', lib))
if exe:
os.chmod(lib, 0555)
else:
os.chmod(lib, 0444)
def copy_deps(dependencies, outdir, use_rpath):
exe_path=os.path.join(outdir, 'bin')
for dep in dependencies:
if dep.endswith('.dylib'):
dst_name=os.path.join(outdir, 'lib', os.path.basename(dep))
if not os.path.exists(dep):
continue
shutil.copy(dep, dst_name)
if use_rpath:
change_id(os.path.basename(dep), dst_name, use_rpath)
else:
change_id('../lib/%s' % os.path.basename(dep), dst_name, use_rpath)
update_load_commands(dst_name, False, use_rpath, exe_path)
else:
assert dep.find('.framework/')>=0
framework_path, rel_path=split_framework_components(dep)
framework_name=os.path.basename(framework_path)
dst_name=os.path.join(outdir, 'lib', framework_name)
shutil.copytree(framework_path, dst_name)
if use_rpath:
change_id(os.path.join(dst_name, rel_path),
os.path.join(dst_name, rel_path), use_rpath)
else:
change_id(os.path.join('../lib', framework_name, rel_path),
os.path.join(dst_name, rel_path), use_rpath)
os.unlink(os.path.join(dst_name, os.path.splitext(framework_name)[0]))
update_load_commands(os.path.join(dst_name, rel_path), False,
use_rpath, exe_path)
def update_pymod_shared_objects(args, path, files):
lib_path, use_rpath=args
exe_path=os.path.abspath(os.path.join(lib_path, '../bin'))
for f in files:
if not os.path.exists(os.path.join(path, f)):
continue
base, ext=os.path.splitext(f)
if ext=='.so':
path_to_lib_path=os.path.relpath(lib_path, path)
abs_name=os.path.join(path, f)
os.system(ADD_RPATH % (path_to_lib_path, abs_name))
update_load_commands(abs_name, False, use_rpath, exe_path)
elif ext in ('.pyc', '.pyo'):
os.unlink(os.path.join(path, f))
def get_site_package_dir():
"""
Get site-package directory of this python installation. This assumes
that ost was linked against the same version of Python
"""
for p in sys.path:
pattern='/site-packages'
index=p.find(pattern)
if index>=0:
return p[:index+len(pattern)]
raise RuntimeError("Couldn't determine site-packages location")
def get_python_module_path(module):
for path in sys.path:
full_path=os.path.join(path, module)
if os.path.exists(full_path):
return full_path
return None
def get_python_home():
"""
Derive Python home by looking at the location of the os module
"""
return os.path.dirname(sys.modules['os'].__file__)
def check_install_name_tool_capabilities():
"""
Find out whether install_name_tool supports the add_rpath option.
"""
inst_name_tool=subprocess.Popen('install_name_tool', shell=True,
stderr=subprocess.PIPE)
output=inst_name_tool.communicate()[1]
return output.find('-add_rpath')!=-1
def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
macports_workaround=False):
site_packages=get_site_package_dir()
# figure out if install_name_tool supports the -add_rpath option.
use_rpath=True
if not check_install_name_tool_capabilities():
print "install_name_tool doesn't support the -add_rpath option."
print "I will fallback to the more arcane @executable_path"
use_rpath=False
elif force_no_rpath:
print "I will use the arcane @executable_path"
use_rpath=False
if os.path.exists(outdir):
shutil.rmtree(outdir)
os.system('mkdir -p "%s"' % outdir)
os.system('mkdir -p "%s/lib"' % outdir)
os.system('mkdir -p "%s/bin"' % outdir)
print 'copying shared datafiles'
shutil.copytree(os.path.join(stage_dir, 'share'),
os.path.join(outdir, 'share'))
print 'collecting dependencies'
deps=collect_deps(stage_dir, COMPONENTS, BINARIES, SITE_PACKAGES,
site_packages)
print 'copying dependencies'
copy_deps(deps, outdir, use_rpath)
print 'copying binaries'
copy_binaries(stage_dir, outdir, BINARIES, SCRIPTS, use_rpath)
print 'copying pymod'
shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'),
os.path.join(outdir, 'lib/openstructure'))
copied_py_framework=False
non_std_python=False
if os.path.exists(os.path.join(outdir, 'lib/Python.framework')):
framework_path=os.path.join(outdir, 'lib/Python.framework')
nonstd_python=True
copied_py_framework=True
if len(glob.glob(os.path.join(outdir, 'lib', 'libpython*')))>0:
non_std_python=True
if non_std_python:
print 'looks like we are using a non-standard python.'
python_home=get_python_home()
if not copied_py_framework:
print 'also copying python modules from %s' % python_home
modules_dst=os.path.join(outdir, 'lib', os.path.basename(python_home))
shutil.copytree(python_home, modules_dst)
if os.path.exists(os.path.join(modules_dst, 'site-packages')):
shutil.rmtree(os.path.join(modules_dst, 'site-packages'))
copy_binaries(os.path.join(python_home, '../..'), outdir,
['python'], [], use_rpath)
python_bin=os.path.abspath(os.path.join(python_home, '../../bin/python'))
else:
# For MacPorts it's even more involved. Python is not executed directly
# but rather uses a wrapper executable that calls the actual python exe.
# We have to include that one into the bundle.
if macports_workaround:
path_to_app='../../Resources/Python.app/Contents/MacOS/'
exe_path=os.path.join(python_home, path_to_app)
copy_binaries(exe_path, outdir, ['python'], [],
use_rpath, append_bin=False)
python_bin=os.path.join('/opt/local/bin/python')
else:
copy_binaries(os.path.join(python_home, '../..'), outdir,
['python'], [], use_rpath)
python_bin=os.path.abspath(os.path.join(python_home, '../../bin/python'))
# remove all versions but the one we are using
version_string=sys.version[0:3]
prefix, postfix=split_framework_components(python_home)
site_packages_dir=os.path.join(outdir, 'lib', 'Python.framework',
postfix, 'site-packages')
if os.path.exists(site_packages_dir):
shutil.rmtree(site_packages_dir)
for directory in glob.glob(os.path.join(framework_path, 'Versions/*')):
if os.path.basename(directory)!=version_string:
shutil.rmtree(directory)
# replace the python executable
ost_script=os.path.join(outdir, 'bin', 'ost')
os.chmod(ost_script, 0666)
script=''.join(open(ost_script, 'r').readlines())
script=script.replace(python_bin, '$BIN_DIR/python')
open(ost_script, 'w').write(script)
os.chmod(ost_script, 0555)
elif use_rpath==False:
print 'BIG FAT WARNING: Creating bundle with @executable_path and default'
print 'Python might not work. Test carefully before deploying.'
if no_includes:
os.system(REMOVE_HEADERS % outdir)
os.system(REMOVE_CURRENT % outdir)
print 'copying site-packages'
for sp in SITE_PACKAGES:
src=get_python_module_path(sp)
if os.path.isdir(src):
shutil.copytree(src, os.path.join(outdir, 'lib/openstructure', sp))
else:
shutil.copy(src, os.path.join(outdir, 'lib/openstructure', sp))
print 'updating link commands of python shared objects'
os.path.walk(os.path.join(outdir, 'lib'),
update_pymod_shared_objects,
(os.path.join(outdir, 'lib'), use_rpath))