[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-74-gadfeb7f
Radostan Riedel
raybuntu at googlemail.com
Tue Aug 7 19:19:27 UTC 2012
The following commit has been merged in the master branch:
commit adfeb7f68748723efab57fabeb3224a9ca56b624
Author: Radostan Riedel <raybuntu at googlemail.com>
Date: Tue Aug 7 18:35:08 2012 +0200
Rework some patches. Split some patches up.
diff --git a/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch b/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
index c996e90..dcce118 100644
--- a/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
+++ b/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
@@ -6,22 +6,16 @@ Subject: options for system libs installtarget and prefix
cctbx_sources/boost_adaptbx/SConscript | 26 +-
cctbx_sources/cbflib_adaptbx/SConscript | 89 +++---
.../detectors/boost_python/SConscript | 4 +-
- .../detectors/boost_python/cbf_binary_adaptor.h | 4 +-
- .../detectors/boost_python/general_cbf_write.h | 4 +-
- .../cbflib_adaptbx/detectors/cbf_adaptor.h | 4 +-
- .../detectors/cbf_byte_offset_optimized.cpp | 6 +-
- .../cbflib_adaptbx/detectors/tst_memory.cpp | 4 +-
cctbx_sources/ccp4io_adaptbx/SConscript | 284 ++++++++++----------
- cctbx_sources/ccp4io_adaptbx/ext.cpp | 2 +-
cctbx_sources/cctbx/SConscript | 2 +-
- cctbx_sources/clipper_adaptbx/SConscript | 86 +++---
- cctbx_sources/clipper_adaptbx/clipper/SConscript | 2 +-
+ cctbx_sources/clipper_adaptbx/SConscript | 94 ++++---
+ cctbx_sources/clipper_adaptbx/clipper/SConscript | 10 +-
cctbx_sources/gltbx/SConscript | 20 +-
cctbx_sources/iotbx/cif/boost_python/SConscript | 13 +-
cctbx_sources/iotbx/mtz/SConscript | 3 +-
cctbx_sources/iotbx/pdb/SConscript | 2 +-
cctbx_sources/libtbx/SConscript | 80 +++++-
- cctbx_sources/libtbx/env_config.py | 30 +++
+ cctbx_sources/libtbx/env_config.py | 34 +++
cctbx_sources/mmtbx/den/SConscript | 2 +-
cctbx_sources/mmtbx/geometry_restraints/SConscript | 2 +-
cctbx_sources/mmtbx/secondary_structure/SConscript | 2 +-
@@ -31,7 +25,7 @@ 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 +-
- 28 files changed, 422 insertions(+), 267 deletions(-)
+ 22 files changed, 425 insertions(+), 260 deletions(-)
diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
index 866b1c1..ed21fb4 100644
@@ -225,80 +219,6 @@ index 2027439..8e987cc 100644
env.SharedLibrary(
target="#lib/cbflib_ext",
source=["cbflib_ext.cpp",])
-diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
-index 66677bd..516b319 100644
---- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
-+++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
-@@ -3,8 +3,8 @@
- #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
- #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
- #include <cbflib_adaptbx/detectors/buffer_based_service.h>
--#include <include/cbf_binary.h>
--#include <include/cbf_compress.h>
-+#include <cbf/cbf_binary.h>
-+#include <cbf/cbf_compress.h>
-
- namespace iotbx {
- namespace detectors {
-diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
-index c6c1afb..f45b4d1 100644
---- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
-+++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
-@@ -1,8 +1,8 @@
- #ifndef GENERAL_CBF_WRITE_H
- #define GENERAL_CBF_WRITE_H
- #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
--#include "cbf_binary.h"
--#include "cbf_compress.h"
-+#include "cbf/cbf_binary.h"
-+#include "cbf/cbf_compress.h"
-
- namespace iotbx {
- namespace detectors {
-diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
-index b5cc407..3787c7b 100644
---- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
-+++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
-@@ -8,8 +8,8 @@
- #include <exception>
- #include <scitbx/array_family/flex_types.h>
- #include <scitbx/array_family/versa_matrix.h>
--#include <include/cbf.h>
--#include <include/cbf_simple.h>
-+#include <cbf/cbf.h>
-+#include <cbf/cbf_simple.h>
- #include <cbflib_adaptbx/detectors/basic.h>
-
- #undef cbf_failnez
-diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
-index 2edbfb5..526556f 100644
---- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
-+++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
-@@ -244,9 +244,9 @@ extern "C" {
- #include <limits.h>
- #include <ctype.h>
-
--#include "cbf.h"
--#include "cbf_file.h"
--#include "cbf_byte_offset.h"
-+#include "cbf/cbf.h"
-+#include "cbf/cbf_file.h"
-+#include "cbf/cbf_byte_offset.h"
- #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
-
- /* Changes made in the byte-offset algorithm
-diff --git a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
-index 5f5d9b1..d121530 100644
---- a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
-+++ b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
-@@ -1,5 +1,5 @@
--#include <include/cbf.h>
--#include <include/cbf_simple.h>
-+#include <cbf/cbf.h>
-+#include <cbf/cbf_simple.h>
- #include <cstdio>
- #include <string>
- #include <exception>
diff --git a/cctbx_sources/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript
index f55cc92..01600d6 100644
--- a/cctbx_sources/ccp4io_adaptbx/SConscript
@@ -615,17 +535,6 @@ index f55cc92..01600d6 100644
+ ]
)
env_ext.SharedLibrary( target = "#lib/ccp4io_adaptbx_ext", source = sources )
-diff --git a/cctbx_sources/ccp4io_adaptbx/ext.cpp b/cctbx_sources/ccp4io_adaptbx/ext.cpp
-index ce21568..e507515 100644
---- a/cctbx_sources/ccp4io_adaptbx/ext.cpp
-+++ b/cctbx_sources/ccp4io_adaptbx/ext.cpp
-@@ -1,5 +1,5 @@
- #include <boost/python.hpp>
--#include <mmdb_manager.h>
-+#include <mmdb/mmdb_manager.h>
- #include <ssm_align.h>
-
- namespace ccp4io_adaptbx { namespace boost_python {
diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
index af767ae..6ce770c 100644
--- a/cctbx_sources/cctbx/SConscript
@@ -640,10 +549,10 @@ index af767ae..6ce770c 100644
env=env_cctbx_boost_python_ext,
paths=env_etc.cctbx_common_includes + [env_etc.python_include])
diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
-index 9cce49e..21c81c4 100644
+index 9cce49e..c39047f 100644
--- a/cctbx_sources/clipper_adaptbx/SConscript
+++ b/cctbx_sources/clipper_adaptbx/SConscript
-@@ -3,54 +3,61 @@ Import("env_base", "env_etc")
+@@ -3,54 +3,63 @@ Import("env_base", "env_etc")
env_etc.clipper_dist = libtbx.env.dist_path("clipper")
env_etc.clipper_include = env_etc.clipper_dist
@@ -655,13 +564,9 @@ index 9cce49e..21c81c4 100644
SHLINKFLAGS=env_etc.shlinkflags,
LIBS=env_etc.libm)
-env.Prepend(CPPPATH=[env_etc.clipper_include])
-+if not env_etc.check_syslib('clipper-core'):
-+ env.Prepend(CPPPATH=[env_etc.clipper_include])
-+else:
-+ env.Prepend(CPPPATH=[env_etc.clipper_sysinclude])
-
- if (env_etc.static_libraries): builder = env.StaticLibrary
- else: builder = env.SharedLibrary
+-
+-if (env_etc.static_libraries): builder = env.StaticLibrary
+-else: builder = env.SharedLibrary
-builder(target='#lib/clipper',
- source = ["../clipper/clipper/core/"+file_name for file_name in """
- atomsf.cpp
@@ -699,52 +604,61 @@ index 9cce49e..21c81c4 100644
-""".split()])
-# fftmap_sparse.cpp
-# fftmap.cpp
-+if not env_etc.check_syslib('clipper-core'):
-+ builder(target='#lib/clipper-core',
-+ source = ["../clipper/clipper/core/"+file_name for file_name in """
-+ atomsf.cpp
-+ cell.cpp
-+ clipper_memory.cpp
-+ clipper_message.cpp
-+ clipper_stats.cpp
-+ clipper_types.cpp
-+ clipper_util.cpp
-+ container.cpp
-+ container_hkl.cpp
-+ container_map.cpp
-+ container_types.cpp
-+ coords.cpp
-+ derivs.cpp
-+ hkl_compute.cpp
-+ hkl_data.cpp
-+ hkl_datatypes.cpp
-+ hkl_info.cpp
-+ hkl_lookup.cpp
-+ hkl_operators.cpp
-+ map_interp.cpp
-+ map_utils.cpp
-+ nxmap.cpp
-+ nxmap_operator.cpp
-+ ramachandran.cpp
-+ resol_basisfn.cpp
-+ resol_fn.cpp
-+ resol_targetfn.cpp
-+ rotation.cpp
-+ spacegroup.cpp
-+ spacegroup_data.cpp
-+ symop.cpp
-+ xmap.cpp
-+ """.split()])
-+ # fftmap_sparse.cpp
-+ # fftmap.cpp
++if env_etc.check_syslib('clipper-core') and \
++ env_etc.check_syslib('clipper-contrib'):
++ env.Prepend(CPPPATH=[env_etc.clipper_sysinclude])
++ env_etc.clipper_libs=['clipper-core', 'clipper-contrib']
++ env_etc.has_clipper_contrib = True
++else:
++ env.Prepend(CPPPATH=[env_etc.clipper_include])
++ env_etc.clipper_libs=['clipper',]
++ if (env_etc.static_libraries): builder = env.StaticLibrary
++ else: builder = env.SharedLibrary
++ builder(target='#lib/'+env_etc.clipper_libs[0],
++ source = ["../clipper/clipper/core/"+file_name for file_name in """
++ atomsf.cpp
++ cell.cpp
++ clipper_memory.cpp
++ clipper_message.cpp
++ clipper_stats.cpp
++ clipper_types.cpp
++ clipper_util.cpp
++ container.cpp
++ container_hkl.cpp
++ container_map.cpp
++ container_types.cpp
++ coords.cpp
++ derivs.cpp
++ hkl_compute.cpp
++ hkl_data.cpp
++ hkl_datatypes.cpp
++ hkl_info.cpp
++ hkl_lookup.cpp
++ hkl_operators.cpp
++ map_interp.cpp
++ map_utils.cpp
++ nxmap.cpp
++ nxmap_operator.cpp
++ ramachandran.cpp
++ resol_basisfn.cpp
++ resol_fn.cpp
++ resol_targetfn.cpp
++ rotation.cpp
++ spacegroup.cpp
++ spacegroup_data.cpp
++ symop.cpp
++ xmap.cpp
++ """.split()])
++ # fftmap_sparse.cpp
++ # fftmap.cpp
env_exe = env.Clone()
-env_exe.Prepend(LIBS=["clipper"])
-+env_exe.Prepend(LIBS=["clipper-core"])
++env_exe.Prepend(LIBS=[env_etc.clipper_libs[0]])
exe = env_exe.Program(
target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
-@@ -77,6 +84,7 @@ if (hasattr(env_etc, "cctbx_include")):
+@@ -77,6 +86,7 @@ if (hasattr(env_etc, "cctbx_include")):
env=env_clipper_boost_python_ext,
paths=[
env_etc.clipper_include,
@@ -753,17 +667,28 @@ index 9cce49e..21c81c4 100644
env_etc.cctbx_include,
env_etc.scitbx_include,
diff --git a/cctbx_sources/clipper_adaptbx/clipper/SConscript b/cctbx_sources/clipper_adaptbx/clipper/SConscript
-index 9f79f83..37280af 100644
+index 9f79f83..1911eb1 100644
--- a/cctbx_sources/clipper_adaptbx/clipper/SConscript
+++ b/cctbx_sources/clipper_adaptbx/clipper/SConscript
-@@ -1,6 +1,6 @@
- Import("env_clipper_boost_python_ext")
+@@ -1,6 +1,10 @@
+-Import("env_clipper_boost_python_ext")
++Import("env_clipper_boost_python_ext", "env_etc")
env = env_clipper_boost_python_ext.Clone()
-env.Prepend(LIBS=["clipper", "cctbx"])
-+env.Prepend(LIBS=["clipper-core", "cctbx"])
++env.Prepend(LIBS=env_etc.clipper_libs+["cctbx"])
++if (env_etc.has_clipper_contrib):
++ clipper_contrib_files = []
++else:
++ clipper_contrib_files = ["../../clipper/clipper/contrib/sfweight.cpp",]
env.SharedLibrary(
target="#lib/clipper_ext",
source=[
+@@ -8,4 +12,4 @@ env.SharedLibrary(
+ "hendrickson_lattman_bpl.cpp",
+ "sigmaa_bpl.cpp",
+ "../../clipper/clipper/contrib/sfweight.cpp",
+- "../../clipper/clipper/cctbx/clipper_cctbx.cpp"])
++ "../../clipper/clipper/cctbx/clipper_cctbx.cpp"]+clipper_contrib_files)
diff --git a/cctbx_sources/gltbx/SConscript b/cctbx_sources/gltbx/SConscript
index 4b2213d..04e0654 100644
--- a/cctbx_sources/gltbx/SConscript
@@ -959,7 +884,7 @@ index debf569..a74442f 100644
+
Export("env_base", "env_etc")
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index c3e1c7d..3284148 100644
+index c3e1c7d..0885527 100644
--- a/cctbx_sources/libtbx/env_config.py
+++ b/cctbx_sources/libtbx/env_config.py
@@ -701,6 +701,10 @@ Wait for the command to finish, then try again.""" % vars())
@@ -995,10 +920,14 @@ index c3e1c7d..3284148 100644
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 +1952,24 @@ class pre_process_args:
+@@ -1940,6 +1952,28 @@ class pre_process_args:
action="store_true",
default=False,
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, "--install_destdir",
+ type="string",
+ action="store",
diff --git a/debian/patches/0007-adding-shlib-versioning.patch b/debian/patches/0007-adding-shlib-versioning.patch
index 82b67b3..772061e 100644
--- a/debian/patches/0007-adding-shlib-versioning.patch
+++ b/debian/patches/0007-adding-shlib-versioning.patch
@@ -168,7 +168,7 @@ index a74442f..de7abea 100644
env_base.Install(dest, Glob('%s/*'%(exe_dev)))
env_base.Alias("install-bin", dest)
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index 3284148..bd96147 100644
+index 0885527..3d9133e 100644
--- a/cctbx_sources/libtbx/env_config.py
+++ b/cctbx_sources/libtbx/env_config.py
@@ -705,6 +705,7 @@ Wait for the command to finish, then try again.""" % vars())
@@ -195,7 +195,7 @@ index 3284148..bd96147 100644
print >> f, "Use System Libraries:", self.use_system_libs
print >> f, "Install Prefix:", self.install_prefix
print >> f, "Libdir:", self.libdir
-@@ -1970,6 +1973,10 @@ class pre_process_args:
+@@ -1974,6 +1977,10 @@ class pre_process_args:
default="/usr/local",
help="sets the prefix for the install targets. Default: /usr/local",
metavar="DIRECTORY")
diff --git a/debian/patches/0008-Fix-to-skip-pycbf-build.patch b/debian/patches/0008-Fix-to-skip-pycbf-build.patch
new file mode 100644
index 0000000..7aa3a39
--- /dev/null
+++ b/debian/patches/0008-Fix-to-skip-pycbf-build.patch
@@ -0,0 +1,52 @@
+From: Radostan Riedel <raybuntu at googlemail.com>
+Date: Tue, 7 Aug 2012 18:08:30 +0200
+Subject: Fix to skip pycbf build
+
+---
+ cctbx_sources/cbflib_adaptbx/SConscript | 8 ++++----
+ cctbx_sources/cbflib_adaptbx/libtbx_refresh.py | 16 ++++++++--------
+ 2 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
+index 334cfc2..42ab9c3 100644
+--- a/cctbx_sources/cbflib_adaptbx/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/SConscript
+@@ -90,10 +90,10 @@ if (not env_etc.no_boost_python):
+ env=env_cbflib_boost_python_ext,
+ paths=env_etc.cbflib_common_includes + [env_etc.python_include])
+
+- env_cbflib_boost_python_ext.SharedLibrary(
+- target='#lib/_pycbf',
+- source=[prefix+"/pycbf/pycbf_wrap.c"],
+- LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
++ #env_cbflib_boost_python_ext.SharedLibrary(
++ # target='#lib/_pycbf',
++ # source=[prefix+"/pycbf/pycbf_wrap.c"],
++ # LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
+
+ Export("env_cbflib_boost_python_ext")
+
+diff --git a/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py b/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
+index 51b3e42..dd1b8e9 100644
+--- a/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
++++ b/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
+@@ -1,11 +1,11 @@
+ from libtbx.str_utils import show_string
+ import os
+ op = os.path
+-pycbf_py = self.env.under_dist(module_name="cbflib", path="pycbf/pycbf.py")
+-if (not op.isfile(pycbf_py)):
+- raise RuntimeError("Missing file: %s" % show_string(pycbf_py))
+-target_dir = self.env.under_build(path="lib")
+-if (not op.isdir(target_dir)):
+- os.makedirs(target_dir)
+-print " Copying to lib: %s" % show_string(pycbf_py)
+-open(op.join(target_dir, "pycbf.py"), "w").write(open(pycbf_py).read())
++#pycbf_py = self.env.under_dist(module_name="cbflib", path="pycbf/pycbf.py")
++#if (not op.isfile(pycbf_py)):
++# raise RuntimeError("Missing file: %s" % show_string(pycbf_py))
++#target_dir = self.env.under_build(path="lib")
++#if (not op.isdir(target_dir)):
++# os.makedirs(target_dir)
++#print " Copying to lib: %s" % show_string(pycbf_py)
++#open(op.join(target_dir, "pycbf.py"), "w").write(open(pycbf_py).read())
diff --git a/debian/patches/0008-add-with_pycbf-option.patch b/debian/patches/0008-add-with_pycbf-option.patch
deleted file mode 100644
index af2dc58..0000000
--- a/debian/patches/0008-add-with_pycbf-option.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-From: Radostan Riedel <raybuntu at googlemail.com>
-Date: Sat, 4 Aug 2012 14:55:29 +0200
-Subject: add with_pycbf option
-
----
- cctbx_sources/cbflib_adaptbx/SConscript | 9 +++++----
- cctbx_sources/libtbx/SConscript | 1 +
- 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 334cfc2..04f227a 100644
---- a/cctbx_sources/cbflib_adaptbx/SConscript
-+++ b/cctbx_sources/cbflib_adaptbx/SConscript
-@@ -90,10 +90,11 @@ if (not env_etc.no_boost_python):
- env=env_cbflib_boost_python_ext,
- paths=env_etc.cbflib_common_includes + [env_etc.python_include])
-
-- env_cbflib_boost_python_ext.SharedLibrary(
-- target='#lib/_pycbf',
-- source=[prefix+"/pycbf/pycbf_wrap.c"],
-- LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
-+ if env_etc.with_pycbf:
-+ env_cbflib_boost_python_ext.SharedLibrary(
-+ target='#lib/_pycbf',
-+ source=[prefix+"/pycbf/pycbf_wrap.c"],
-+ LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
-
- Export("env_cbflib_boost_python_ext")
-
-diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index de7abea..221082b 100644
---- a/cctbx_sources/libtbx/SConscript
-+++ b/cctbx_sources/libtbx/SConscript
-@@ -1048,6 +1048,7 @@ else:
- env_etc.boost_python = 'boost_python'
- env_etc.scitbx_boost_python = 'scitbx_boost_python'
-
-+env_etc.with_pycbf = libtbx.env.build_options.with_pycbf
- env_etc.prefix = libtbx.env.build_options.install_prefix
- env_etc.destdir = libtbx.env.build_options.install_destdir
- env_etc.libdir = libtbx.env.build_options.libdir
-diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index bd96147..76367bc 100644
---- a/cctbx_sources/libtbx/env_config.py
-+++ b/cctbx_sources/libtbx/env_config.py
-@@ -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,
- libdir=command_line.options.libdir,
- install_destdir=command_line.options.install_destdir,
-@@ -1765,6 +1766,7 @@ class build_options:
- static_libraries,
- static_exe,
- use_system_libs,
-+ with_pycbf,
- install_prefix,
- libdir,
- install_destdir,
-@@ -1955,6 +1957,14 @@ class pre_process_args:
- action="store_true",
- default=False,
- 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, "--install_destdir",
- type="string",
- action="store",
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 6a331cb..57aeca7 100644
--- a/debian/patches/0011-fix-missing-python-lib-during-linking.patch
+++ b/debian/patches/0011-fix-missing-python-lib-during-linking.patch
@@ -8,7 +8,7 @@ Subject: fix missing python lib during linking
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index 221082b..fdb757b 100644
+index de7abea..a10d535 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -54,9 +54,11 @@ def set_python_include_and_libs(env_etc):
diff --git a/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch b/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
index 6b859e2..3573ca4 100644
--- a/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
+++ b/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
@@ -8,7 +8,7 @@ Subject: fix to support LDFLAGS in use_enviroment_flags
2 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index fdb757b..830e0ad 100644
+index a10d535..000f942 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -777,11 +777,15 @@ else:
@@ -37,7 +37,7 @@ index fdb757b..830e0ad 100644
env_base_sync_with_env_etc()
if (static_exe):
-@@ -1066,8 +1073,10 @@ def set_libtool(env):
+@@ -1065,8 +1072,10 @@ def set_libtool(env):
# for reference. Otherwise it will be set to 0:0:0
env_etc.shobjsuffix_save = env['SHOBJSUFFIX']
env_etc.SharedLibBuilder_save = env['BUILDERS']['SharedLibrary']
@@ -50,10 +50,10 @@ index fdb757b..830e0ad 100644
SHLIBSUFFIX='.la',
)
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index 76367bc..c5dbb80 100644
+index 3d9133e..d8fb063 100644
--- a/cctbx_sources/libtbx/env_config.py
+++ b/cctbx_sources/libtbx/env_config.py
-@@ -1805,6 +1805,7 @@ class build_options:
+@@ -1803,6 +1803,7 @@ class build_options:
self.env_cxxflags = ""
self.env_cflags = ""
self.env_cppflags = ""
@@ -61,7 +61,7 @@ index 76367bc..c5dbb80 100644
flg = os.environ.get("CXXFLAGS")
if flg is not None:
self.env_cxxflags = flg
-@@ -1814,6 +1815,9 @@ class build_options:
+@@ -1812,6 +1813,9 @@ class build_options:
flg = os.environ.get("CPPFLAGS")
if flg is not None:
self.env_cppflags = flg
@@ -71,7 +71,7 @@ index 76367bc..c5dbb80 100644
def report(self, f=None):
if (f is None): f = sys.stdout
-@@ -1845,6 +1849,7 @@ class build_options:
+@@ -1843,6 +1847,7 @@ class build_options:
print >>f, " CXXFLAGS = ", self.env_cxxflags
print >>f, " CFLAGS = ", self.env_cflags
print >>f, " CPPFLAGS = ", self.env_cppflags
@@ -79,7 +79,7 @@ index 76367bc..c5dbb80 100644
class include_registry:
-@@ -2006,7 +2011,7 @@ class pre_process_args:
+@@ -2000,7 +2005,7 @@ class pre_process_args:
action="store_true",
default=False,
help="add compiler flags from environment variables: CXXFLAGS, CFLAGS,"
diff --git a/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch b/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
index 4f979e5..89ad477 100644
--- a/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
+++ b/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
@@ -7,7 +7,7 @@ Subject: Fix to append CPPFLAGS to CXXFLAGS.
1 file changed, 2 insertions(+)
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index 830e0ad..6925fbc 100644
+index 000f942..4149672 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -798,6 +798,8 @@ else:
diff --git a/debian/patches/0017-autogenerate-pkgconfig-files.patch b/debian/patches/0017-autogenerate-pkgconfig-files.patch
index 986ce2a..dceb53b 100644
--- a/debian/patches/0017-autogenerate-pkgconfig-files.patch
+++ b/debian/patches/0017-autogenerate-pkgconfig-files.patch
@@ -103,10 +103,10 @@ index 9b89fe1..8a83058 100644
env = env.Clone()
env_etc.include_registry.append(env=env, paths=[env_etc.fable_include])
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index 6925fbc..d953e6a 100644
+index 4149672..9857372 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
-@@ -1066,8 +1066,34 @@ env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
+@@ -1065,8 +1065,34 @@ env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
@@ -141,7 +141,7 @@ index 6925fbc..d953e6a 100644
def set_libtool(env):
# Versioning can be provided by appending "-version-info 3:12:1" to SHLINKFLAGS
# Please see:
-@@ -1193,6 +1219,11 @@ def create_install_targets():
+@@ -1192,6 +1218,11 @@ def create_install_targets():
src = os.path.join(src_dir, root, filename)
env_base.Install(dest, src)
env_base.Alias("install-header", dest)
@@ -153,7 +153,7 @@ index 6925fbc..d953e6a 100644
if src_dir == lib_dir:
break
-@@ -1200,7 +1231,11 @@ def create_install_targets():
+@@ -1199,7 +1230,11 @@ def create_install_targets():
dest = env_etc.binpath
env_base.Install(dest, Glob('%s/*'%(exe_dev)))
env_base.Alias("install-bin", dest)
diff --git a/debian/patches/0018-Fix-to-use-systems-include-path.patch b/debian/patches/0018-Fix-to-use-systems-include-path.patch
new file mode 100644
index 0000000..58b6afb
--- /dev/null
+++ b/debian/patches/0018-Fix-to-use-systems-include-path.patch
@@ -0,0 +1,128 @@
+From: Radostan Riedel <raybuntu at googlemail.com>
+Date: Tue, 7 Aug 2012 18:15:43 +0200
+Subject: Fix to use systems include path
+
+---
+ .../detectors/boost_python/cbf_binary_adaptor.h | 4 ++--
+ .../detectors/boost_python/general_cbf_write.h | 4 ++--
+ .../cbflib_adaptbx/detectors/cbf_adaptor.h | 4 ++--
+ .../detectors/cbf_byte_offset_optimized.cpp | 6 +++---
+ .../cbflib_adaptbx/detectors/tst_memory.cpp | 4 ++--
+ cctbx_sources/ccp4io_adaptbx/ext.cpp | 2 +-
+ cctbx_sources/iotbx/mtz/ext.cpp | 2 +-
+ cctbx_sources/iotbx/mtz/object.h | 6 +++---
+ 8 files changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
+index 66677bd..516b319 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
+@@ -3,8 +3,8 @@
+ #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
+ #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
+ #include <cbflib_adaptbx/detectors/buffer_based_service.h>
+-#include <include/cbf_binary.h>
+-#include <include/cbf_compress.h>
++#include <cbf/cbf_binary.h>
++#include <cbf/cbf_compress.h>
+
+ namespace iotbx {
+ namespace detectors {
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
+index c6c1afb..f45b4d1 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
+@@ -1,8 +1,8 @@
+ #ifndef GENERAL_CBF_WRITE_H
+ #define GENERAL_CBF_WRITE_H
+ #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
+-#include "cbf_binary.h"
+-#include "cbf_compress.h"
++#include "cbf/cbf_binary.h"
++#include "cbf/cbf_compress.h"
+
+ namespace iotbx {
+ namespace detectors {
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
+index b5cc407..3787c7b 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
+@@ -8,8 +8,8 @@
+ #include <exception>
+ #include <scitbx/array_family/flex_types.h>
+ #include <scitbx/array_family/versa_matrix.h>
+-#include <include/cbf.h>
+-#include <include/cbf_simple.h>
++#include <cbf/cbf.h>
++#include <cbf/cbf_simple.h>
+ #include <cbflib_adaptbx/detectors/basic.h>
+
+ #undef cbf_failnez
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
+index 2edbfb5..526556f 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
+@@ -244,9 +244,9 @@ extern "C" {
+ #include <limits.h>
+ #include <ctype.h>
+
+-#include "cbf.h"
+-#include "cbf_file.h"
+-#include "cbf_byte_offset.h"
++#include "cbf/cbf.h"
++#include "cbf/cbf_file.h"
++#include "cbf/cbf_byte_offset.h"
+ #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
+
+ /* Changes made in the byte-offset algorithm
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
+index 5f5d9b1..d121530 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
++++ b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
+@@ -1,5 +1,5 @@
+-#include <include/cbf.h>
+-#include <include/cbf_simple.h>
++#include <cbf/cbf.h>
++#include <cbf/cbf_simple.h>
+ #include <cstdio>
+ #include <string>
+ #include <exception>
+diff --git a/cctbx_sources/ccp4io_adaptbx/ext.cpp b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+index ce21568..e507515 100644
+--- a/cctbx_sources/ccp4io_adaptbx/ext.cpp
++++ b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python.hpp>
+-#include <mmdb_manager.h>
++#include <mmdb/mmdb_manager.h>
+ #include <ssm_align.h>
+
+ namespace ccp4io_adaptbx { namespace boost_python {
+diff --git a/cctbx_sources/iotbx/mtz/ext.cpp b/cctbx_sources/iotbx/mtz/ext.cpp
+index b1a0db7..6aa416a 100644
+--- a/cctbx_sources/iotbx/mtz/ext.cpp
++++ b/cctbx_sources/iotbx/mtz/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python/module.hpp>
+-#include <ccp4_errno.h>
++#include <gpp4/ccp4/ccp4_errno.h>
+
+ namespace iotbx { namespace mtz { namespace boost_python {
+
+diff --git a/cctbx_sources/iotbx/mtz/object.h b/cctbx_sources/iotbx/mtz/object.h
+index da35fcf..b593534 100644
+--- a/cctbx_sources/iotbx/mtz/object.h
++++ b/cctbx_sources/iotbx/mtz/object.h
+@@ -6,9 +6,9 @@
+ # include <math.h>
+ #endif
+
+-#include <cmtzlib.h>
+-#include <ccp4_array.h>
+-#include <ccp4_errno.h>
++#include <gpp4/ccp4/cmtzlib.h>
++#include <gpp4/ccp4/ccp4_array.h>
++#include <gpp4/ccp4/ccp4_errno.h>
+ #include <cctbx/sgtbx/space_group.h>
+ #include <cctbx/hendrickson_lattman.h>
+ #include <boost/shared_ptr.hpp>
diff --git a/debian/patches/0019-Fix-to-skip-build-of-clipper-examples.patch b/debian/patches/0019-Fix-to-skip-build-of-clipper-examples.patch
new file mode 100644
index 0000000..ffd4ebb
--- /dev/null
+++ b/debian/patches/0019-Fix-to-skip-build-of-clipper-examples.patch
@@ -0,0 +1,52 @@
+From: Radostan Riedel <raybuntu at googlemail.com>
+Date: Tue, 7 Aug 2012 18:19:02 +0200
+Subject: Fix to skip build of clipper examples
+
+---
+ cctbx_sources/clipper_adaptbx/SConscript | 33 +++++++++++++++---------------
+ 1 file changed, 17 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
+index c39047f..b0699ad 100644
+--- a/cctbx_sources/clipper_adaptbx/SConscript
++++ b/cctbx_sources/clipper_adaptbx/SConscript
+@@ -61,22 +61,23 @@ else:
+ env_exe = env.Clone()
+ env_exe.Prepend(LIBS=[env_etc.clipper_libs[0]])
+
+-exe = env_exe.Program(
+- target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
+- +env["PROGSUFFIX"],
+- source = ["../clipper/examples/symtest.cpp",
+- ])
+-libtbx.env.write_dispatcher_in_bin(
+- source_file=exe[0].get_abspath(),
+- target_file="clipper.symtest")
+-exe = env_exe.Program(
+- target='#exe_dev/'+env["PROGPREFIX"]+'clipper.sanity_check'
+- +env["PROGSUFFIX"],
+- source = ["sanity_check.cpp",
+- ])
+-libtbx.env.write_dispatcher_in_bin(
+- source_file=exe[0].get_abspath(),
+- target_file="clipper.sanity_check")
++# Skip building clipper examples in Debian
++#exe = env_exe.Program(
++# target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
++# +env["PROGSUFFIX"],
++# source = ["../clipper/examples/symtest.cpp",
++# ])
++#libtbx.env.write_dispatcher_in_bin(
++# source_file=exe[0].get_abspath(),
++# target_file="clipper.symtest")
++#exe = env_exe.Program(
++# target='#exe_dev/'+env["PROGPREFIX"]+'clipper.sanity_check'
++# +env["PROGSUFFIX"],
++# source = ["sanity_check.cpp",
++# ])
++#libtbx.env.write_dispatcher_in_bin(
++# source_file=exe[0].get_abspath(),
++# target_file="clipper.sanity_check")
+
+ if (hasattr(env_etc, "cctbx_include")):
+ if (not env_etc.no_boost_python):
diff --git a/debian/patches/series b/debian/patches/series
index f2751ad..49c088b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,7 +5,7 @@
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
+0008-Fix-to-skip-pycbf-build.patch
0009-build-libann-statically.patch
0010-adding-setup_py.patch
0011-fix-missing-python-lib-during-linking.patch
@@ -15,3 +15,5 @@
0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch
0016-adapt-test_utils-in-libtbx-for-setup_py-test.patch
0017-autogenerate-pkgconfig-files.patch
+0018-Fix-to-use-systems-include-path.patch
+0019-Fix-to-skip-build-of-clipper-examples.patch
--
Packaging for cctbx
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