[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-36-g4ca1579
Radostan Riedel
raybuntu at googlemail.com
Mon Jul 23 18:52:52 UTC 2012
The following commit has been merged in the master branch:
commit 4ca1579906ae7f62be8aeb70757360e5cd627a66
Author: Radostan Riedel <raybuntu at googlemail.com>
Date: Mon Jul 23 19:02:03 2012 +0200
Rearrange Patches and remove rpath option and fix unnecessary linking for py-ext
diff --git a/debian/patches/0005-upstream-fix-for-declaration-errors-in-gcc4.7.patch b/debian/patches/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
similarity index 100%
rename from debian/patches/0005-upstream-fix-for-declaration-errors-in-gcc4.7.patch
rename to debian/patches/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
diff --git a/debian/patches/0006-fix-for-gcc4.7-compilation-error.patch b/debian/patches/0005-fix-for-gcc4.7-compilation-error.patch
similarity index 100%
rename from debian/patches/0006-fix-for-gcc4.7-compilation-error.patch
rename to debian/patches/0005-fix-for-gcc4.7-compilation-error.patch
diff --git a/debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch b/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
similarity index 88%
rename from debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch
rename to debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
index ca83b63..ec2152d 100644
--- a/debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch
+++ b/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
@@ -1,5 +1,5 @@
From: Radostan Riedel <raybuntu at googlemail.com>
-Date: Thu, 19 Jul 2012 14:38:29 +0200
+Date: Mon, 23 Jul 2012 18:28:04 +0200
Subject: options for system libs installtarget and prefix
---
@@ -10,8 +10,8 @@ Subject: options for system libs installtarget and prefix
cctbx_sources/gltbx/SConscript | 2 +-
cctbx_sources/iotbx/mtz/SConscript | 3 +-
cctbx_sources/iotbx/pdb/SConscript | 2 +-
- cctbx_sources/libtbx/SConscript | 82 ++++++++++++++++++-
- cctbx_sources/libtbx/env_config.py | 28 +++++++
+ cctbx_sources/libtbx/SConscript | 79 +++++++++++++++++-
+ cctbx_sources/libtbx/env_config.py | 21 +++++
cctbx_sources/mmtbx/den/SConscript | 2 +-
cctbx_sources/mmtbx/geometry_restraints/SConscript | 2 +-
cctbx_sources/mmtbx/secondary_structure/SConscript | 2 +-
@@ -21,10 +21,10 @@ Subject: options for system libs installtarget and prefix
.../smtbx/refinement/boost_python/SConscript | 4 +-
.../refinement/constraints/boost_python/SConscript | 4 +-
cctbx_sources/spotfinder/SConscript | 2 +-
- 18 files changed, 191 insertions(+), 66 deletions(-)
+ 18 files changed, 181 insertions(+), 66 deletions(-)
diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
-index 0d95318..5417e1b 100644
+index 866b1c1..ed21fb4 100644
--- a/cctbx_sources/boost_adaptbx/SConscript
+++ b/cctbx_sources/boost_adaptbx/SConscript
@@ -9,7 +9,13 @@ import sys, os
@@ -32,7 +32,7 @@ index 0d95318..5417e1b 100644
Import("env_base", "env_etc")
env_etc.boost_dist = libtbx.env.dist_path("boost")
-env_etc.boost_include = env_etc.boost_dist
-+if not env_etc.check_syslib('boost_python', extra_libs='python%s'%env_etc.py_dot_str)\
++if not env_etc.check_syslib('boost_python', extra_libs=env_etc.py_lib)\
+ or not env_etc.check_syslib('boost_thread'):
+ env_etc.boost_include = env_etc.boost_dist
+else:
@@ -62,10 +62,10 @@ index 0d95318..5417e1b 100644
SHLIBPREFIX="",
- LIBS=["boost_python"] + env_etc.libs_python + env_etc.libm)
+ LIBS=[env_etc.boost_python] + env_etc.libs_python + env_etc.libm)
- if (libtbx.env.build_options.libtoolize):
- # Need to unset libtool since it does not support linking python-ext
- env_etc.unset_libtool(env_no_includes_boost_python_ext, env_etc.rpath)
-@@ -238,10 +245,11 @@ object/function_doc_signature.cpp
+ env_no_includes_boost_python_ext.Append(
+ LIBPATH=env_etc.libpath_python)
+ env_no_includes_boost_python_ext.Append(
+@@ -235,10 +242,11 @@ object/function_doc_signature.cpp
bpl_dll_sources = [os.path.join(prefix, path) for path in bpl_dll_sources]
#
env.Repository(os.path.dirname(env_etc.boost_dist))
@@ -73,7 +73,7 @@ index 0d95318..5417e1b 100644
- env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
- else:
- env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources)
-+ if not env_etc.check_syslib('boost_python', extra_libs='python%s'%env_etc.py_dot_str):
++ if not env_etc.check_syslib('boost_python', extra_libs=env_etc.py_lib):
+ if (env_etc.static_bpl):
+ env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
+ else:
@@ -260,7 +260,7 @@ index 6af2664..9b89fe1 100644
env.SharedLibrary(
target="#lib/iotbx_pdb_ext",
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index ba00dd3..ee7b1de 100644
+index debf569..a1580f7 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -4,7 +4,7 @@ from libtbx import easy_run
@@ -272,17 +272,9 @@ index ba00dd3..ee7b1de 100644
op = os.path
if (hasattr(Environment, "Clone")):
-@@ -1083,6 +1083,7 @@ def unset_libtool(env, rpath):
- )
- env_etc.unset_libtool = unset_libtool
-
-+env_etc.rpath = ''
- if (libtbx.env.build_options.libtoolize):
- env_etc.shlibsuffix = ".la"
- env_base.Append(LIBSUFFIXES=[env_etc.shlibsuffix])
-@@ -1093,4 +1094,83 @@ if (libtbx.env.build_options.libtoolize):
- env_etc.shlinkflags.remove('-shared')
- env_etc.set_libtool(env_base, env_etc.rpath)
+@@ -1018,4 +1018,81 @@ def enable_cuda_if_possible():
+ enable_openmp_if_possible()
+ enable_cuda_if_possible()
+env_etc.use_system_libs = False
+def check_syslib(lib, extra_libs=None):
@@ -300,17 +292,14 @@ index ba00dd3..ee7b1de 100644
+ return True
+env_etc.check_syslib = check_syslib
+
-+env_etc.py_vers = libtbx.env_config.python_version()
-+env_etc.py_major = env_etc.py_vers[0]
-+env_etc.py_minor = env_etc.py_vers[1]
-+env_etc.py_dot_str = '%s.%s'%(env_etc.py_major, env_etc.py_minor)
-+env_etc.py_str = '-py%s%s'%(env_etc.py_major, env_etc.py_minor)
++env_etc.py_str = '-py%s%s'%(sys.version[0], sys.version[2])
++env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
+
+if (libtbx.env.build_options.use_system_libs):
+ env_etc.use_system_libs = True
+
+if env_etc.check_syslib('boost_python%s'%env_etc.py_str,
-+ extra_libs='python%s'%env_etc.py_dot_str):
++ extra_libs=env_etc.py_lib):
+ env_etc.boost_python = 'boost_python%s'%env_etc.py_str
+ env_etc.scitbx_boost_python = 'scitbx_boost_python%s'%env_etc.py_str
+else:
@@ -323,6 +312,7 @@ index ba00dd3..ee7b1de 100644
+env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
+env_etc.libpath = os.path.join(env_etc.install_path, 'lib')
+env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
++env_etc.rpath = os.path.join(env_etc.prefix, 'lib')
+
+def create_install_targets():
+ cwd = os.getcwd()
@@ -365,63 +355,43 @@ index ba00dd3..ee7b1de 100644
+
Export("env_base", "env_etc")
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index 2285c9d..281bb42 100644
+index c3e1c7d..5efad84 100644
--- a/cctbx_sources/libtbx/env_config.py
+++ b/cctbx_sources/libtbx/env_config.py
-@@ -161,6 +161,9 @@ def python_include_path(must_exist=True):
- % include_path)
- return include_path
-
-+def python_version(must_exist=True):
-+ return sys.version_info
-+
- def ld_library_path_var_name():
- if (os.name == "nt"):
- return "PATH"
-@@ -703,6 +706,9 @@ Wait for the command to finish, then try again.""" % vars())
+@@ -701,6 +701,9 @@ Wait for the command to finish, then try again.""" % vars())
+ precompile_headers=command_line.options.precompile_headers,
+ static_libraries=command_line.options.static_libraries,
static_exe=command_line.options.static_exe,
- libtoolize=command_line.options.libtoolize,
- rpath=command_line.options.rpath,
+ use_system_libs=command_line.options.use_system_libs,
+ install_prefix=command_line.options.install_prefix,
+ install_destdir=command_line.options.install_destdir,
scan_boost=command_line.options.scan_boost,
write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
boost_python_no_py_signatures
-@@ -1762,6 +1768,9 @@ class build_options:
+@@ -1759,6 +1762,9 @@ class build_options:
+ warning_level,
static_libraries,
static_exe,
- libtoolize,
+ use_system_libs,
+ install_prefix,
+ install_destdir,
- rpath,
scan_boost,
write_full_flex_fwd_h=default_write_full_flex_fwd_h,
-@@ -1833,6 +1842,9 @@ class build_options:
+ build_boost_python_extensions=default_build_boost_python_extensions,
+@@ -1822,6 +1828,9 @@ class build_options:
+ print >> f, "Boost threads enabled:", self.enable_boost_threads
print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
print >> f, "Enable CUDA:", self.enable_cuda
- print >> f, "Libtoolize:", self.libtoolize
+ print >> f, "Use System Libraries:", self.use_system_libs
+ print >> f, "Install Prefix:", self.install_prefix
+ print >> f, "Install Destdir:", self.install_destdir
print >> f, "Use opt_resources if available:", self.opt_resources
print >> f, "Use environment flags:", self.use_environment_flags
if( self.use_environment_flags ):
-@@ -1955,12 +1967,28 @@ class pre_process_args:
+@@ -1940,6 +1949,18 @@ class pre_process_args:
action="store_true",
default=False,
- help="build all shared libraries with libtool. Optionally set --rpath")
-+ parser.option(None, "--use_system_libs",
-+ action="store_true",
-+ default=False,
-+ help="Use system Libraries to build.")
- parser.option(None, "--rpath",
- type="string",
- action="store",
- default="/usr/lib",
- help="sets the rpath libtool (implies --libtoolize). Default: /usr/lib",
- metavar="DIRECTORY")
+ help="link all executables statically (implies --static_libraries)")
+ parser.option(None, "--install_destdir",
+ type="string",
+ action="store",
diff --git a/debian/patches/0004-adding-shlib-versioning.patch b/debian/patches/0007-adding-shlib-versioning.patch
similarity index 66%
rename from debian/patches/0004-adding-shlib-versioning.patch
rename to debian/patches/0007-adding-shlib-versioning.patch
index 14fa237..827c284 100644
--- a/debian/patches/0004-adding-shlib-versioning.patch
+++ b/debian/patches/0007-adding-shlib-versioning.patch
@@ -1,36 +1,36 @@
From: Radostan Riedel <raybuntu at googlemail.com>
-Date: Sun, 8 Jul 2012 18:15:24 +0200
+Date: Mon, 23 Jul 2012 18:33:07 +0200
Subject: adding-shlib-versioning
---
cctbx_sources/boost_adaptbx/SConscript | 3 ++
- cctbx_sources/libtbx/SConscript | 75 ++++++++++++++++++++++++++++++++
- cctbx_sources/libtbx/env_config.py | 21 +++++++++
- 3 files changed, 99 insertions(+)
+ cctbx_sources/libtbx/SConscript | 74 ++++++++++++++++++++++++++++++++
+ cctbx_sources/libtbx/env_config.py | 7 +++
+ 3 files changed, 84 insertions(+)
diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
-index 866b1c1..0d95318 100644
+index ed21fb4..17f0e89 100644
--- a/cctbx_sources/boost_adaptbx/SConscript
+++ b/cctbx_sources/boost_adaptbx/SConscript
-@@ -51,6 +51,9 @@ if (not env_etc.no_boost_python):
+@@ -58,6 +58,9 @@ if (not env_etc.no_boost_python):
SHLINKFLAGS=env_etc.shlinkflags_bpl,
SHLIBPREFIX="",
- LIBS=["boost_python"] + env_etc.libs_python + env_etc.libm)
+ LIBS=[env_etc.boost_python] + env_etc.libs_python + env_etc.libm)
+ if (libtbx.env.build_options.libtoolize):
+ # Need to unset libtool since it does not support linking python-ext
-+ env_etc.unset_libtool(env_no_includes_boost_python_ext, env_etc.rpath)
++ env_etc.unset_libtool(env_no_includes_boost_python_ext)
env_no_includes_boost_python_ext.Append(
LIBPATH=env_etc.libpath_python)
env_no_includes_boost_python_ext.Append(
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index debf569..ba00dd3 100644
+index a1580f7..0ee8b6f 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
-@@ -1018,4 +1018,79 @@ def enable_cuda_if_possible():
- enable_openmp_if_possible()
- enable_cuda_if_possible()
+@@ -1056,6 +1056,80 @@ env_etc.libpath = os.path.join(env_etc.install_path, 'lib')
+ env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
+ env_etc.rpath = os.path.join(env_etc.prefix, 'lib')
-+def set_libtool(env, rpath):
++def set_libtool(env):
+ # Versioning can be provided by appending "-version-info 3:12:1" to SHLINKFLAGS
+ # Please see:
+ # http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
@@ -38,7 +38,7 @@ index debf569..ba00dd3 100644
+ env_etc.shobjsuffix_save = env['SHOBJSUFFIX']
+ env_etc.SharedLibBuilder_save = env['BUILDERS']['SharedLibrary']
+ env.Replace(
-+ SHLINKFLAGS='-rpath ' + rpath,
++ SHLINKFLAGS='-rpath ' + env_etc.rpath,
+ SHOBJSUFFIX='.lo',
+ SHLIBSUFFIX='.la',
+ )
@@ -49,7 +49,7 @@ index debf569..ba00dd3 100644
+ ShCAction = SCons.Action.Action(LIBTOOLCCOM + "$SHCCCOM", "$SHCCCOMSTR")
+ ShCXXAction = SCons.Action.Action(LIBTOOLCXXCOM + "$SHCXXCOM", "$SHCXXCOMSTR")
+ ShLinkAction = SCons.Action.Action(LIBTOOLLINK + "$SHLINKCOM", "$SHLINKCOMSTR")
-+ libtool_install = 'libtool --mode=install install -D ${TARGET.abspath} %s%s/${TARGET.file}'%(abs(libtbx.env.lib_path), rpath)
++ libtool_install = 'libtool --mode=install install -D ${TARGET.abspath} %s%s/${TARGET.file}'%(abs(libtbx.env.lib_path), env_etc.rpath)
+
+ action_list = [ SCons.Defaults.SharedCheck,
+ ShLinkAction,
@@ -83,12 +83,12 @@ index debf569..ba00dd3 100644
+ lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
+ if not os.path.exists(lib_dir):
+ os.makedirs(lib_dir)
-+ libtool_install_path = '#lib' + rpath
++ libtool_install_path = '#lib' + env_etc.rpath
+ env.Append(LIBPATH=libtool_install_path)
+ env['BUILDERS']['SharedLibrary'] = LibtoolBuilder
+env_etc.set_libtool = set_libtool
+
-+def unset_libtool(env, rpath):
++def unset_libtool(env):
+ env['BUILDERS']['SharedLibrary'] = env_etc.SharedLibBuilder_save
+ env.Replace(
+ SHOBJSUFFIX=env_etc.shobjsuffix_save,
@@ -98,71 +98,51 @@ index debf569..ba00dd3 100644
+if (libtbx.env.build_options.libtoolize):
+ env_etc.shlibsuffix = ".la"
+ env_base.Append(LIBSUFFIXES=[env_etc.shlibsuffix])
-+ env_etc.rpath = libtbx.env.build_options.rpath
+ rpath_link = ['-rpath', env_etc.rpath]
+ env_etc.shlinkflags.extend(rpath_link)
+ if '-shared' in env_etc.shlinkflags:
+ env_etc.shlinkflags.remove('-shared')
-+ env_etc.set_libtool(env_base, env_etc.rpath)
++ env_etc.set_libtool(env_base)
+
- Export("env_base", "env_etc")
+ def create_install_targets():
+ cwd = os.getcwd()
+ rp = libtbx.env.repository_paths
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index c3e1c7d..2285c9d 100644
+index 5efad84..e1cc775 100644
--- a/cctbx_sources/libtbx/env_config.py
+++ b/cctbx_sources/libtbx/env_config.py
-@@ -701,6 +701,8 @@ Wait for the command to finish, then try again.""" % vars())
- precompile_headers=command_line.options.precompile_headers,
- static_libraries=command_line.options.static_libraries,
- static_exe=command_line.options.static_exe,
+@@ -704,6 +704,7 @@ Wait for the command to finish, then try again.""" % vars())
+ use_system_libs=command_line.options.use_system_libs,
+ install_prefix=command_line.options.install_prefix,
+ install_destdir=command_line.options.install_destdir,
+ libtoolize=command_line.options.libtoolize,
-+ rpath=command_line.options.rpath,
scan_boost=command_line.options.scan_boost,
write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
boost_python_no_py_signatures
-@@ -1759,6 +1761,8 @@ class build_options:
- warning_level,
- static_libraries,
- static_exe,
+@@ -1765,6 +1766,7 @@ class build_options:
+ use_system_libs,
+ install_prefix,
+ install_destdir,
+ libtoolize,
-+ rpath,
scan_boost,
write_full_flex_fwd_h=default_write_full_flex_fwd_h,
build_boost_python_extensions=default_build_boost_python_extensions,
-@@ -1784,6 +1788,12 @@ class build_options:
- if (self.static_exe):
- self.static_libraries = True
- if (self.msvc_arch_flag == "None"): self.msvc_arch_flag = None
-+ if self.rpath != '/usr/lib':
-+ if (not op.isabs(self.rpath)):
-+ raise RuntimeError("Not an absolute path name:"
-+ " --rpath %s" % show_string(self.rpath))
-+ else:
-+ self.libtoolize = True
-
- def get_flags_from_environment(self):
- if (self.use_environment_flags ):
-@@ -1822,6 +1832,7 @@ class build_options:
+@@ -1828,6 +1830,7 @@ class build_options:
print >> f, "Boost threads enabled:", self.enable_boost_threads
print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
print >> f, "Enable CUDA:", self.enable_cuda
+ print >> f, "Libtoolize:", self.libtoolize
- print >> f, "Use opt_resources if available:", self.opt_resources
- print >> f, "Use environment flags:", self.use_environment_flags
- if( self.use_environment_flags ):
-@@ -1940,6 +1951,16 @@ class pre_process_args:
- action="store_true",
- default=False,
- help="link all executables statically (implies --static_libraries)")
+ print >> f, "Use System Libraries:", self.use_system_libs
+ print >> f, "Install Prefix:", self.install_prefix
+ print >> f, "Install Destdir:", self.install_destdir
+@@ -1961,6 +1964,10 @@ class pre_process_args:
+ default="/usr/local",
+ help="sets the prefix for the install targets. Default: /usr/local",
+ metavar="DIRECTORY")
+ parser.option(None, "--libtoolize",
+ action="store_true",
+ default=False,
-+ help="build all shared libraries with libtool. Optionally set --rpath")
-+ parser.option(None, "--rpath",
-+ type="string",
-+ action="store",
-+ default="/usr/lib",
-+ help="sets the rpath libtool (implies --libtoolize). Default: /usr/lib",
-+ metavar="DIRECTORY")
++ help="build all shared libraries with libtool.")
parser.option(None, "--scan_boost",
action="store_true",
default=False,
diff --git a/debian/patches/0008-add-with_pycbf-option.patch b/debian/patches/0008-add-with_pycbf-option.patch
index 95e3f3b..daf976b 100644
--- a/debian/patches/0008-add-with_pycbf-option.patch
+++ b/debian/patches/0008-add-with_pycbf-option.patch
@@ -1,12 +1,12 @@
From: Radostan Riedel <raybuntu at googlemail.com>
-Date: Thu, 19 Jul 2012 11:27:37 +0200
+Date: Mon, 23 Jul 2012 18:34:58 +0200
Subject: add with_pycbf option
---
cctbx_sources/cbflib_adaptbx/SConscript | 9 +++++----
cctbx_sources/libtbx/SConscript | 1 +
- cctbx_sources/libtbx/env_config.py | 6 ++++++
- 3 files changed, 12 insertions(+), 4 deletions(-)
+ cctbx_sources/libtbx/env_config.py | 10 ++++++++++
+ 3 files changed, 16 insertions(+), 4 deletions(-)
diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
index 4ac6717..14deee3 100644
@@ -29,10 +29,10 @@ index 4ac6717..14deee3 100644
Export("env_cbflib_boost_python_ext")
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index ee7b1de..26f2808 100644
+index 0ee8b6f..5419e3c 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
-@@ -1127,6 +1127,7 @@ else:
+@@ -1048,6 +1048,7 @@ else:
env_etc.boost_python = 'boost_python'
env_etc.scitbx_boost_python = 'scitbx_boost_python'
@@ -41,34 +41,38 @@ index ee7b1de..26f2808 100644
env_etc.destdir = libtbx.env.build_options.install_destdir
env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index 281bb42..bd4b612 100644
+index e1cc775..7c0cbc4 100644
--- a/cctbx_sources/libtbx/env_config.py
+++ b/cctbx_sources/libtbx/env_config.py
-@@ -707,6 +707,7 @@ Wait for the command to finish, then try again.""" % vars())
- libtoolize=command_line.options.libtoolize,
- rpath=command_line.options.rpath,
+@@ -702,6 +702,7 @@ Wait for the command to finish, then try again.""" % vars())
+ static_libraries=command_line.options.static_libraries,
+ static_exe=command_line.options.static_exe,
use_system_libs=command_line.options.use_system_libs,
+ with_pycbf=command_line.options.with_pycbf,
install_prefix=command_line.options.install_prefix,
install_destdir=command_line.options.install_destdir,
- scan_boost=command_line.options.scan_boost,
-@@ -1769,6 +1770,7 @@ class build_options:
+ libtoolize=command_line.options.libtoolize,
+@@ -1764,6 +1765,7 @@ class build_options:
+ static_libraries,
static_exe,
- libtoolize,
use_system_libs,
+ with_pycbf,
install_prefix,
install_destdir,
- rpath,
-@@ -1971,6 +1973,10 @@ class pre_process_args:
+ libtoolize,
+@@ -1952,6 +1954,14 @@ class pre_process_args:
action="store_true",
default=False,
- help="Use system Libraries to build.")
+ help="link all executables statically (implies --static_libraries)")
++ parser.option(None, "--use_system_libs",
++ action="store_true",
++ default=False,
++ help="Use system Libraries to build.")
+ parser.option(None, "--with_pycbf",
+ action="store_true",
+ default=False,
+ help="Build pycbf extension.")
- parser.option(None, "--rpath",
+ parser.option(None, "--install_destdir",
type="string",
action="store",
--
diff --git a/debian/patches/0010-adding-setup_py.patch b/debian/patches/0010-adding-setup_py.patch
index ae1c18b..fb27334 100644
--- a/debian/patches/0010-adding-setup_py.patch
+++ b/debian/patches/0010-adding-setup_py.patch
@@ -5,8 +5,8 @@ Subject: adding-setup_py
---
cctbx_sources/stdlib.py | 4 ++
sconsutils.py | 155 +++++++++++++++++++++++++++++++++++++++++++++++
- setup.py | 123 +++++++++++++++++++++++++++++++++++++
- 3 files changed, 282 insertions(+)
+ setup.py | 122 +++++++++++++++++++++++++++++++++++++
+ 3 files changed, 281 insertions(+)
create mode 100755 cctbx_sources/stdlib.py
create mode 100644 sconsutils.py
create mode 100755 setup.py
@@ -23,7 +23,7 @@ index 0000000..759f689
+random = stdlib_import("random")
diff --git a/sconsutils.py b/sconsutils.py
new file mode 100644
-index 0000000..d568ba7
+index 0000000..07d393d
--- /dev/null
+++ b/sconsutils.py
@@ -0,0 +1,155 @@
@@ -90,7 +90,7 @@ index 0000000..d568ba7
+ module_dist_paths = {}
+ for key, value in env.module_dist_paths.items():
+ head, module = os.path.split(abs(value))
-+ module_dist_paths[key] = relocatable_path(build_path,
++ module_dist_paths[key] = relocatable_path(build_path,
+ os.path.join(rel_path, module))
+ env.module_dist_paths = module_dist_paths
+ for module in env.module_list:
@@ -184,10 +184,10 @@ index 0000000..d568ba7
+ return out, list(outext)
diff --git a/setup.py b/setup.py
new file mode 100755
-index 0000000..0f0b48a
+index 0000000..c260365
--- /dev/null
+++ b/setup.py
-@@ -0,0 +1,123 @@
+@@ -0,0 +1,122 @@
+from distutils.core import setup, Extension
+import sys, os, shutil
+
@@ -223,7 +223,6 @@ index 0000000..0f0b48a
+# trailing slash is important
+init_dir = opj(BUILDDIR, SRCDIR, 'libtbx/')
+build_opts = [ '--libtoolize',
-+ '--rpath', '/usr/lib',
+ '--use_system_libs',
+ '--install_prefix', PREFIX,
+ ]
diff --git a/debian/patches/0011-fix-missing-python-lib-during-linking.patch b/debian/patches/0011-fix-missing-python-lib-during-linking.patch
index 2d78645..1c1a9ed 100644
--- a/debian/patches/0011-fix-missing-python-lib-during-linking.patch
+++ b/debian/patches/0011-fix-missing-python-lib-during-linking.patch
@@ -3,20 +3,45 @@ Date: Thu, 19 Jul 2012 23:26:30 +0200
Subject: fix missing python lib during linking
---
- cctbx_sources/libtbx/SConscript | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
+ cctbx_sources/libtbx/SConscript | 3 ++-
+ cctbx_sources/scitbx/boost_python/SConscript | 2 +-
+ 2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index 26f2808..90a4d95 100644
+index 5419e3c..ad08c18 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
-@@ -56,7 +56,7 @@ def set_python_include_and_libs(env_etc):
+@@ -54,9 +54,11 @@ def set_python_include_and_libs(env_etc):
+ env_etc.python_include = libtbx.env_config.python_include_path()
+ if (sys.platform == "win32"):
env_etc.libs_python = ["python" + sys.version[0] + sys.version[2]]
++ env_etc.py_lib = 'python%s%s'%(sys.version[0], sys.version[2])
env_etc.libpath_python = [sys.prefix + r"\libs"]
else:
-- env_etc.libs_python = []
-+ env_etc.libs_python = ["python%s.%s"%(sys.version[0], sys.version[2])]
+ env_etc.libs_python = []
++ env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
env_etc.libpath_python = []
if (env_etc.compiler.startswith("darwin_")):
env_etc.python_framework = "/".join(
+@@ -1035,7 +1037,6 @@ def check_syslib(lib, extra_libs=None):
+ env_etc.check_syslib = check_syslib
+
+ env_etc.py_str = '-py%s%s'%(sys.version[0], sys.version[2])
+-env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
+
+ if (libtbx.env.build_options.use_system_libs):
+ env_etc.use_system_libs = True
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index 1f396e5..b906eb3 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -7,7 +7,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(LIBPATH=env_etc.libpath_python)
+-env.Append(LIBS=[env_etc.boost_python] + env_etc.libs_python)
++env.Append(LIBS=[env_etc.boost_python] + [env_etc.py_lib,] + env_etc.libs_python)
+ env_etc.include_registry.append(
+ env=env,
+ paths=env_etc.scitbx_common_includes + [env_etc.python_include])
--
diff --git a/debian/patches/series b/debian/patches/series
index 0b85700..1d9286c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,10 +1,10 @@
0001-remove-hardcoded-libtbx_build-env.patch
0002-fix-opengl-header-missing-gltbx.patch
0003-correct-paths-in-dispatcher-creation.patch
-0004-adding-shlib-versioning.patch
-0005-upstream-fix-for-declaration-errors-in-gcc4.7.patch
-0006-fix-for-gcc4.7-compilation-error.patch
-0007-options-for-system-libs-installtarget-and-prefix.patch
+0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
+0005-fix-for-gcc4.7-compilation-error.patch
+0006-options-for-system-libs-installtarget-and-prefix.patch
+0007-adding-shlib-versioning.patch
0008-add-with_pycbf-option.patch
0009-build-libann-statically.patch
0010-adding-setup_py.patch
--
Packaging for cctbx
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