diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 06457ad71f30651589b40be1b94fe7a710b243e4..ce0ee563ee198da60dede12cc4dcedb6e77dbbe3 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -215,7 +215,7 @@ macro(module)
RUNTIME_OUTPUT_DIRECTORY ${LIB_STAGE_PATH})
if (APPLE)
set_target_properties(${_LIB_NAME} PROPERTIES
- LINK_FLAGS "-Wl,-rpath,@@loader_path"
+ LINK_FLAGS "-Wl,-rpath,@loader_path"
INSTALL_NAME_DIR "@rpath")
endif()
if (WIN32)
@@ -350,7 +350,7 @@ macro(executable_libexec)
"${LIBEXEC_STAGE_PATH}")
if (APPLE AND NOT _ARG_NO_RPATH AND NOT _ARG_STATIC)
set_target_properties(${_ARG_NAME} PROPERTIES
- LINK_FLAGS "-Wl,-rpath,@loader_path/../lib")
+ LINK_FLAGS "-Wl,-rpath,@loader_path/../../lib")
endif()
if (_ARG_LINK)
target_link_libraries(${_ARG_NAME} ${_ARG_LINK})
diff --git a/deployment/macos/deploy.py b/deployment/macos/deploy.py
index dea9207ab211bf8b210ff1cf0b62748140a04def..51246c532816acdcbfc12c197191dee7d22375a8 100644
--- a/deployment/macos/deploy.py
+++ b/deployment/macos/deploy.py
@@ -20,8 +20,7 @@ bundle.create_bundle('DNG', opts.bundle)
if opts.bundle:
shutil.copytree('../../examples', 'DNG.app/Contents/examples')
os.system('rm `find DNG.app/Contents/examples/ -name "*.pyc"` 2> /dev/null')
- os.system('rm -rf DNG.app/Contents/examples/demos/harmony')
- os.system('rm -rf DNG.app/Contents/examples/demos/dokk')
+ os.system('rm -rf DNG.app/Contents/examples/code_fragments/')
if opts.dmg:
os.system('rm -rf openstructure.dmg')
os.system('hdiutil create -srcFolder DNG.app openstructure.dmg')
\ No newline at end of file
diff --git a/deployment/macos/deps.py b/deployment/macos/deps.py
index 627d73ef764773d2bc904f2fdc422a7737bf208b..e8bcc797802aae6898a7edf5220c108fdee5fac9 100644
--- a/deployment/macos/deps.py
+++ b/deployment/macos/deps.py
@@ -26,8 +26,8 @@ def _deps_for_lib(lib, pool, recursive=True):
pool.add(d)
return
-def collect_deps(stage_dir, components, binaries, site_packages,
- site_packages_dir):
+def collect_deps(stage_dir, components, binaries, libexec_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.
@@ -49,6 +49,14 @@ def collect_deps(stage_dir, components, binaries, site_packages,
continue
if bin_name not in pool:
_deps_for_lib(bin_name, pool)
+ for bin in libexec_binaries:
+ bin_name=os.path.abspath(os.path.join(stage_dir, 'libexec/openstructure',
+ 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
@@ -60,12 +68,15 @@ def collect_deps(stage_dir, components, binaries, site_packages,
_deps_for_lib(so_file, pool)
return pool
-BINARIES=['gosty', 'chemdict_tool']
+BINARIES=['chemdict_tool', 'tmalign', 'tmscore']
+LIBEXEC_BINARIES=['gosty']
COMPONENTS=['mol', 'geom', 'conop', 'gfx', 'gui', 'seq_alg', 'seq',
'img', 'img_alg', 'info', 'io', 'db', 'base']
SCRIPTS=['dng', 'ost']
+LIBEXEC_SCRIPTS=['ost_config']
+
CHANGE_ID_RPATH='install_name_tool -id @rpath/%s %s'
-CHANGE_ID='install_name_tool -id @executable_path/%s %s'
+CHANGE_ID='install_name_tool -id @rpath/%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'
@@ -74,25 +85,24 @@ 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,
+def copy_binaries(stage_dir, outdir, binary_names, scripts, bin_dir,
append_bin=True):
- exe_path=os.path.abspath(os.path.join(outdir, 'bin'))
+ exe_path=os.path.abspath(os.path.join(outdir, bin_dir))
for binary_name in binary_names:
if append_bin:
- bin_name=os.path.join(stage_dir, 'bin', binary_name)
+ bin_name=os.path.join(stage_dir, bin_dir, 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))
+ dst_name=os.path.join(outdir, bin_dir, 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))
+ update_load_commands(dst_name, True, exe_path)
for script in scripts:
- shutil.copy(os.path.join(stage_dir, 'bin', script),
- os.path.join(outdir,'bin', script))
+ shutil.copy(os.path.join(stage_dir, bin_dir, script),
+ os.path.join(outdir,bin_dir, script))
def split_framework_components(abs_path):
"""
@@ -108,46 +118,31 @@ def split_framework_components(abs_path):
trail=os.path.join(*parts[i+1:])
return lead, trail
-def change_id(id, lib, use_rpath):
+def change_id(id, lib):
os.chmod(lib, 0666)
- if use_rpath:
- os.system(CHANGE_ID_RPATH % (id,lib))
- else:
- os.system(CHANGE_ID % (id,lib))
+ os.system(CHANGE_ID_RPATH % (id,lib))
os.chmod(lib, 0444)
-def update_load_commands(lib, exe, use_rpath, exe_path):
+def update_load_commands(lib, exe, 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))
+ new_name=os.path.basename(direct_dep)
+ os.system(CHANGE_LOAD_CMD_RPATH % (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))
+ 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))
if exe:
os.chmod(lib, 0555)
else:
os.chmod(lib, 0444)
-def copy_deps(dependencies, outdir, use_rpath):
+def copy_deps(dependencies, outdir):
exe_path=os.path.join(outdir, 'bin')
for dep in dependencies:
if dep.endswith('.dylib'):
@@ -155,29 +150,21 @@ def copy_deps(dependencies, outdir, use_rpath):
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)
+ change_id(os.path.basename(dep), dst_name)
+ update_load_commands(dst_name, False, 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)
+ change_id(os.path.join(dst_name, rel_path),
+ os.path.join(dst_name, rel_path))
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)
+ exe_path)
-def update_pymod_shared_objects(args, path, files):
- lib_path, use_rpath=args
+def update_pymod_shared_objects(lib_path, path, files):
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)):
@@ -187,7 +174,7 @@ def update_pymod_shared_objects(args, path, files):
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)
+ update_load_commands(abs_name, False, exe_path)
elif ext in ('.pyc', '.pyo'):
os.unlink(os.path.join(path, f))
@@ -217,43 +204,30 @@ def get_python_home():
"""
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)
+ os.system('mkdir -p "%s/libexec/openstructure"' % 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,
+ deps=collect_deps(stage_dir, COMPONENTS, BINARIES, LIBEXEC_BINARIES,
+ SITE_PACKAGES,
site_packages)
print 'copying dependencies'
- copy_deps(deps, outdir, use_rpath)
+ copy_deps(deps, outdir)
print 'copying binaries'
- copy_binaries(stage_dir, outdir, BINARIES, SCRIPTS, use_rpath)
+ copy_binaries(stage_dir, outdir, BINARIES, SCRIPTS, 'bin')
+ print 'copying libexec binaries'
+ copy_binaries(stage_dir, outdir, LIBEXEC_BINARIES, LIBEXEC_SCRIPTS,
+ 'libexec/openstructure')
print 'copying pymod'
shutil.copytree(os.path.join(stage_dir, 'lib/openstructure'),
os.path.join(outdir, 'lib/openstructure'))
@@ -275,7 +249,7 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
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')
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
@@ -285,11 +259,11 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
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)
+ 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'], [])
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]
@@ -302,15 +276,12 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
if os.path.basename(directory)!=version_string:
shutil.rmtree(directory)
# replace the python executable
- ost_script=os.path.join(outdir, 'bin', 'ost')
+ ost_script=os.path.join(outdir, 'libexec', 'openstructure', 'ost_config')
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)
@@ -325,4 +296,4 @@ def make_standalone(stage_dir, outdir, no_includes, force_no_rpath=False,
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))
+ os.path.join(outdir, 'lib'))
diff --git a/modules/bindings/src/CMakeLists.txt b/modules/bindings/src/CMakeLists.txt
index 3c178c5f3b7d0158a90e8e1f14d1b21242ec18e4..7dd88cfe58b24ccc734a14eb65b022c3ad718b60 100644
--- a/modules/bindings/src/CMakeLists.txt
+++ b/modules/bindings/src/CMakeLists.txt
@@ -1,5 +1,5 @@
if (COMPILE_TMTOOLS)
enable_language(Fortran)
- executable(NAME tmalign SOURCES tmalign.f NO_RPATH)
- executable(NAME tmscore SOURCES tmscore.f NO_RPATH)
+ executable(NAME tmalign SOURCES tmalign.f)
+ executable(NAME tmscore SOURCES tmscore.f)
endif()
\ No newline at end of file