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Commit 8de50567 authored by marco's avatar marco
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updated bundle creation on mac 

We are now capable of installing OpenStructure without admin rights on Mac

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2378 5a81b35b-ba03-0410-adc8-b2c5c5119f08
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deployment/macos/Installer.pmdoc/01dng-contents.xml deleted 100644 → 0
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<pkg-contents spec="1.12"><f n="DNG.app" o="marco" g="staff" p="16893" pt="/Users/marco/Projects/ost/deployment/macos/DNG.app" m="true" t="file"><f n="Contents" o="marco" g="staff" p="16893"><f n="Info.plist" o="marco" g="staff" p="33204"><mod>mode</mod></f><f n="MacOS" o="marco" g="staff" p="16893"><f n="dng" o="marco" g="staff" p="33277"><mod>mode</mod></f><mod>mode</mod></f><f n="PkgInfo" o="marco" g="staff" p="33204"><mod>mode</mod></f><mod>mode</mod></f><mod>mode</mod></f></pkg-contents>
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<pkgref spec="1.12" uuid="4C7C03C1-13A5-49A8-8A66-B35160BCA334"><config><identifier>org.openstructure.DNG.pkg</identifier><version>1</version><description></description><post-install type="none"/><requireAuthorization/><installFrom relative="true" mod="true" includeRoot="true">DNG.app</installFrom><installTo mod="true">/Applications/OpenStructure</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>requireAuthorization</mod><mod>relocatable</mod><mod>installTo.path</mod><mod>installFrom.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>01dng-contents.xml</file-list><component id="org.openstructure.OpenStructure" path="/Users/marco/Projects/ost/deployment/macos/DNG.app" version="" isRelocatable="true"><locator-info><token title="pkmk-token-10"><search-rule><combo identifier="org.openstructure.OpenStructure" default-path="/Applications/DNG.app"/></search-rule></token></locator-info></component><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
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<pkgref spec="1.12" uuid="16CBBEAE-26C1-4732-A0CB-BBC43AB06B0B"><config><identifier>org.openstructure.OST.pkg</identifier><version>1</version><description></description><post-install type="none"/><requireAuthorization/><installFrom>/usr/openstructure</installFrom><installTo mod="true">/usr/openstructure</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"></packageStore><mod>parent</mod><mod>installTo.path</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>02openstructure-contents.xml</file-list><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
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<pkgref spec="1.12" uuid="C2FAE439-87F5-415C-91EE-0436CC2E4D66"><config><identifier>org.openstructure.Examples.pkg</identifier><version>1.0</version><description/><post-install type="none"/><requireAuthorization/><installFrom relative="true" mod="true">../../examples</installFrom><installTo mod="true">/Library/OpenStructure/examples</installTo><flags><followSymbolicLinks/></flags><packageStore type="internal"/><mod>installTo.path</mod><mod>installFrom.isRelativeType</mod><mod>installFrom.path</mod><mod>parent</mod><mod>installTo</mod><mod>identifier</mod></config><contents><file-list>03examples-contents.xml</file-list><filter>/CVS$</filter><filter>/\.svn$</filter><filter>/\.cvsignore$</filter><filter>/\.cvspass$</filter><filter>/\.DS_Store$</filter></contents></pkgref>
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deployment/macos/OpenStructure.pmdoc/index.xml 0 → 100644
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<pkmkdoc spec="1.12"><properties><title>OpenStructure</title><build>/Users/marco/Documents/OpenStructure.pkg</build><organization>org.openstructure</organization><userSees ui="easy"/><min-target os="3"/><domain system="true" user="true"/></properties><distribution><versions min-spec="1.000000"/><scripts></scripts></distribution><contents><choice title="DNG" id="choice6" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.DNG.pkg"/></choice><choice title="OpenStructure" id="choice7" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.OpenStructure.pkg"/></choice><choice title="examples" id="choice8" starts_selected="true" starts_enabled="true" starts_hidden="false"><pkgref id="org.openstructure.Examples.pkg"/></choice></contents><resources bg-scale="none" bg-align="topleft"><locale lang="en"/></resources><requirements><requirement id="sosv" operator="ge" value="'10.6.0'"><message-title>Snow Leopard Required</message-title><message>OpenStructure requires Snow Leopard in order to run</message></requirement></requirements><flags/><item type="file">01dng.xml</item><item type="file">02standalone.xml</item><item type="file">03examples.xml</item><mod>properties.title</mod><mod>properties.customizeOption</mod><mod>properties.userDomain</mod><mod>properties.anywhereDomain</mod><mod>properties.systemDomain</mod></pkmkdoc>
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deployment/macos/bundle.py 0 → 100644
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INFO_PLIST="""<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN"
"http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>CFBundleDevelopmentRegion</key>
<string>English</string>
<key>CFBundleExecutable</key>
<string>dng</string>
<key>CFBundleHelpBookFolder</key>
<string>OpenStructure Manual</string>
<key>CFBundleHelpBookName</key>
<string>_BUNDLE_ Help</string>
<key>CFBundleIconFile</key>
<string>icon.icns</string>
<key>CFBundleIdentifier</key>
<string>org.openstructure.OpenStructure</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleVersion</key>
<string></string>
<key>NSMainNibFile</key>
<string>MainMenu</string>
<key>NSPrincipalClass</key>
<string>NSApplication</string>
</dict>
</plist>"""
import os
from shutil import copy
import stat
def _WritePkgInfo(bundle):
pkg_info=open(os.path.join(bundle+'.app', 'Contents/PkgInfo'), 'w+')
pkg_info.write('APPL????')
pkg_info.close()
def _WriteInfoPList(bundle):
info_plist=open(os.path.join(bundle+'.app', 'Contents/Info.plist'), 'w+')
info_plist.write(INFO_PLIST)
info_plist.close()
def _WriteScript(bundle):
script="""#!/bin/sh
if [ -e $HOME/Library/OpenStructure/bin/dng ]; then
$HOME/Library/OpenStructure/bin/dng
else
/Library/OpenStructure/bin/dng
fi
"""
bin_path=os.path.join('%s.app' % bundle, 'Contents/MacOS/dng')
bin=open(bin_path, 'w+')
bin.write(script)
bin.close()
os.system('chmod a+x %s' % bin_path)
def _CreateBundleSkeleton(bundle):
bin_path=os.path.join('%s.app' % bundle, 'Contents/MacOS')
if not os.path.exists(bin_path):
os.makedirs(bin_path)
_WritePkgInfo(bundle)
_WriteInfoPList(bundle)
_WriteScript(bundle)
res_dir='%s.app/Contents/Resources' % bundle
if not os.path.exists(res_dir):
os.makedirs(res_dir)
copy('../../graphics/icon.icns', res_dir)
def create_bundle(bundle_name):
_CreateBundleSkeleton(bundle_name)
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deployment/macos/deploy.py 0 → 100644
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import bundle
import deps
bundle.create_bundle('DNG')
deps.make_standalone('../../stage', 'standalone', True)
deployment/macos/deps.py 0 → 100644
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import os
import subprocess
import shutil
import sys
def _LibName(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):
"""
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',
_LibName(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)
return pool
BINARIES=['gosty', 'chemdict_tool']
COMPONENTS=['mol', 'geom', 'conop', 'gfx', 'gui', 'seq_alg', 'seq',
'img', 'img_alg', 'qa', 'info', 'io', 'db', 'base']
SCRIPTS=['dng', 'ost']
CHANGE_ID='install_name_tool -id @rpath/%s %s'
CHANGE_LOAD_CMD='install_name_tool -change %s @rpath/%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):
for binary_name in binary_names:
bin_name=os.path.abspath(os.path.join(stage_dir, 'bin', 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)
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 update_load_commands(lib):
direct_deps=set()
_deps_for_lib(lib, direct_deps, recursive=False)
for direct_dep in direct_deps:
if direct_dep.endswith('.dylib'):
new_name=os.path.basename(direct_dep)
os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
else:
assert direct_dep.find('.framework/')>=0
framework_path, rel_path=split_framework_components(direct_dep)
framework_name=os.path.basename(framework_path)
dst_name=os.path.join(framework_name, rel_path)
new_name=os.path.join(framework_name, rel_path)
os.system(CHANGE_LOAD_CMD % (direct_dep, new_name, lib))
os.system(ADD_RPATH % ('.', lib))
def copy_deps(dependencies, outdir):
for dep in dependencies:
if dep.endswith('.dylib'):
dst_name=os.path.join(outdir, 'lib', os.path.basename(dep))
shutil.copy(dep, dst_name)
os.system(CHANGE_ID % (os.path.basename(dep), dst_name))
update_load_commands(dst_name)
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)
os.system(CHANGE_ID % (os.path.join(dst_name, rel_path),
os.path.join(dst_name, rel_path)))
update_load_commands(os.path.join(dst_name, rel_path))
def update_pymod_shared_objects(lib_path, path, files):
for f in files:
if os.path.splitext(f)[1] == '.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)
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 make_standalone(stage_dir, outdir, no_includes):
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)
print 'copying dependencies'
copy_deps(deps, outdir)
print 'copying binaries'
copy_binaries(stage_dir, outdir, BINARIES, SCRIPTS)
print 'copying pymod'
shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'),
os.path.join(outdir, 'lib/openstructure'))
if no_includes:
os.system(REMOVE_HEADERS % outdir)
os.system(REMOVE_CURRENT % outdir)
site_packages=get_site_package_dir()
print 'copying site-packages'
for sp in SITE_PACKAGES:
src=os.path.join(site_packages, 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', 'openstructure'),
update_pymod_shared_objects,
os.path.join(outdir, 'lib'))
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