[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-65-ga56fa3f
Radostan Riedel
raybuntu at googlemail.com
Sat Aug 4 19:27:23 UTC 2012
The following commit has been merged in the master branch:
commit 84b0280e2af5740a3cb2b399052ead284023979a
Author: Radostan Riedel <raybuntu at googlemail.com>
Date: Sat Aug 4 15:22:18 2012 +0200
Fix to use systems libcbf
diff --git a/debian/copyright b/debian/copyright
index 01d477d..df447bc 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -76,6 +76,18 @@ License: LGPL-3
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser Public License for more details.
+Files: cctbx_sources/cbflib/examples/*
+Author: Paul Ellis
+ Herbert J. Bernstein <yaya at bernstein-plus-sons.com>
+Copyright: Copyright © 2006-2012 Herbert J. Bernstein
+License: GPL or LGPL
+ YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL.
+ ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF THE LGPL.
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in '/usr/share/common-licenses/GPL' and the
+ complete text of the GNU Lesser General Public License in
+ '/usr/share/common-licenses/LGPL'.
+
Files: cctbx_sources/gui_resources/icons/crystal_project/*
Author: Everaldo Coelho <contact at everaldo.com>
Copyright: Copyright © Everaldo Coelho <contact at everaldo.com>
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 6c058d7..67ff303 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
@@ -4,6 +4,13 @@ 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 +-
@@ -24,7 +31,7 @@ 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 +-
- 21 files changed, 348 insertions(+), 216 deletions(-)
+ 28 files changed, 412 insertions(+), 267 deletions(-)
diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
index 866b1c1..ed21fb4 100644
@@ -84,8 +91,216 @@ index 866b1c1..ed21fb4 100644
if (bool(int(ARGUMENTS.get("boost_python_tests", "0")))):
warn_if_unexpected_md5_hexdigest(
path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"),
+diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
+index 4ac6717..334cfc2 100644
+--- a/cctbx_sources/cbflib_adaptbx/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/SConscript
+@@ -3,9 +3,14 @@ import os
+ Import("env_base","env_etc")
+
+ env_etc.cbflib_dist = libtbx.env.dist_path("cbflib")
+-env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
+- env_etc.norm_join(env_etc.cbflib_dist,"include"),
+- ]
++if not env_etc.check_syslib('cbf'):
++ env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
++ env_etc.norm_join(env_etc.cbflib_dist,"include"),
++ ]
++else:
++ env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
++ "",
++ ]
+ env_etc.cbflib_adaptbx_dist = libtbx.env.dist_path("cbflib_adaptbx")
+
+ env_etc.cbflib_common_includes = [
+@@ -34,39 +39,47 @@ cbflib_092_forward = []
+ if os.path.isfile( os.path.join(env_etc.cbflib_dist,"src","cbf_ws.c") ):
+ cbflib_092_forward.append("src/cbf_ws.c")
+
+-env.StaticLibrary(target='#lib/cbf',
+- source = [prefix+"/"+s for s in [
+- "examples/img.c",
+- "src/cbf.c",
+- "src/cbf_alloc.c",
+- "src/cbf_ascii.c",
+- "src/cbf_binary.c",
+- "src/cbf_byte_offset.c",
+- "src/cbf_canonical.c",
+- "src/cbf_codes.c",
+- "src/cbf_compress.c",
+- "src/cbf_context.c",
+- "src/cbf_file.c",
+- "src/cbf_lex.c",
+- "src/cbf_packed.c",
+- "src/cbf_predictor.c",
+- "src/cbf_read_binary.c",
+- "src/cbf_read_mime.c",
+- "src/cbf_simple.c",
+- "src/cbf_string.c",
+- "src/cbf_stx.c",
+- "src/cbf_tree.c",
+- "src/cbf_uncompressed.c",
+- "src/cbf_write.c",
+- "src/cbf_write_binary.c",
+- "src/md5c.c",
+- ] + cbflib_092_forward ] + [
+- "detectors/mar_adaptor.cpp",
+- "detectors/cbf_adaptor.cpp",
+- "detectors/cbf_byte_offset_optimized.cpp",
+- "detectors/buffer_based_service.cpp",
+- ],
+- CPPPATH=env_etc.cbflib_common_includes )
++cbflib_src = ["src/cbf.c",
++ "src/cbf_alloc.c",
++ "src/cbf_ascii.c",
++ "src/cbf_binary.c",
++ "src/cbf_byte_offset.c",
++ "src/cbf_canonical.c",
++ "src/cbf_codes.c",
++ "src/cbf_compress.c",
++ "src/cbf_context.c",
++ "src/cbf_file.c",
++ "src/cbf_lex.c",
++ "src/cbf_packed.c",
++ "src/cbf_predictor.c",
++ "src/cbf_read_binary.c",
++ "src/cbf_read_mime.c",
++ "src/cbf_simple.c",
++ "src/cbf_string.c",
++ "src/cbf_stx.c",
++ "src/cbf_tree.c",
++ "src/cbf_uncompressed.c",
++ "src/cbf_write.c",
++ "src/cbf_write_binary.c",
++ "src/md5c.c",
++ ]
++adaptor_src = ["detectors/mar_adaptor.cpp",
++ "detectors/cbf_adaptor.cpp",
++ "detectors/cbf_byte_offset_optimized.cpp",
++ "detectors/buffer_based_service.cpp",
++ ]
++if not env_etc.check_syslib('cbf'):
++ env.StaticLibrary(target='#lib/cbf',
++ source = [prefix+"/"+s for s in [
++ "examples/img.c"] + cbflib_src + cbflib_092_forward] + adaptor_src,
++ CPPPATH=env_etc.cbflib_common_includes )
++ env_etc.cbf_lib = ['cbf',]
++else:
++ env.StaticLibrary(target='#lib/cbf_adaptor',
++ source = [prefix+"/"+s for s in [
++ "examples/img.c"]] + adaptor_src,
++ CPPPATH=env_etc.cbflib_common_includes )
++ env_etc.cbf_lib = ['cbf','cbf_adaptor']
+
+ if (not env_etc.no_boost_python):
+ Import("env_no_includes_boost_python_ext")
+@@ -80,7 +93,7 @@ if (not env_etc.no_boost_python):
+ env_cbflib_boost_python_ext.SharedLibrary(
+ target='#lib/_pycbf',
+ source=[prefix+"/pycbf/pycbf_wrap.c"],
+- LIBS=["cbf"]+env_etc.libs_python+env_etc.libm)
++ LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
+
+ Export("env_cbflib_boost_python_ext")
+
+@@ -89,7 +102,7 @@ if (not env_etc.no_boost_python):
+ env_standalone = env.Clone(
+ LIBS = [env_etc.libm,],CPPPATH=env_etc.cbflib_common_includes
+ )
+-env_standalone.Prepend(LIBS=["cbf",])
++env_standalone.Prepend(LIBS=env_etc.cbf_lib)
+
+ for source in ["detectors/tst_memory",]:
+ target = "cbflib."+os.path.basename(source)
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
+index 2027439..8e987cc 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
+@@ -1,6 +1,6 @@
+-Import("env_cbflib_boost_python_ext")
++Import("env_cbflib_boost_python_ext", "env_etc")
+ env = env_cbflib_boost_python_ext.Clone()
+-env.Prepend(LIBS=["cbf",])
++env.Prepend(LIBS=env_etc.cbf_lib)
+ 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..300c54f 100644
+index f55cc92..01600d6 100644
--- a/cctbx_sources/ccp4io_adaptbx/SConscript
+++ b/cctbx_sources/ccp4io_adaptbx/SConscript
@@ -36,118 +36,152 @@ else:
@@ -150,7 +365,7 @@ index f55cc92..300c54f 100644
- "static int reported_syminfo = 0",
- "static int reported_syminfo = 1"))
-source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
-+if not env_etc.check_syslib('gpp4', extra_libs=env_etc.py_lib)\
++if not env_etc.check_syslib('gpp4')\
+ or not env_etc.check_syslib('mmdb'):
+ build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
+ if (not op.isdir(build_ccp4io_adaptbx)):
diff --git a/debian/patches/0008-add-with_pycbf-option.patch b/debian/patches/0008-add-with_pycbf-option.patch
index f6469f0..a8c411b 100644
--- a/debian/patches/0008-add-with_pycbf-option.patch
+++ b/debian/patches/0008-add-with_pycbf-option.patch
@@ -1,5 +1,5 @@
From: Radostan Riedel <raybuntu at googlemail.com>
-Date: Mon, 23 Jul 2012 18:34:58 +0200
+Date: Sat, 4 Aug 2012 14:55:29 +0200
Subject: add with_pycbf option
---
@@ -9,22 +9,22 @@ Subject: add with_pycbf option
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
+index 334cfc2..04f227a 100644
--- a/cctbx_sources/cbflib_adaptbx/SConscript
+++ b/cctbx_sources/cbflib_adaptbx/SConscript
-@@ -77,10 +77,11 @@ if (not env_etc.no_boost_python):
+@@ -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=["cbf"]+env_etc.libs_python+env_etc.libm)
+- 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=["cbf"]+env_etc.libs_python+env_etc.libm)
++ LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
Export("env_cbflib_boost_python_ext")
diff --git a/debian/repack.local b/debian/repack.local
index ffc093b..b6e04ec 100755
--- a/debian/repack.local
+++ b/debian/repack.local
@@ -3,6 +3,7 @@ shopt -s extglob
rm rf cctbx_sources/boost/*
rm rf cctbx_sources/clipper/!(clipper)
rm rf cctbx_sources/ccp4io/lib/!(ssm)
+rm rf cctbx_sources/cbflib/!(examples)
rm rf cctbx_sources/clipper/clipper/!(cctbx)
rm rf cctbx_sources/scons/*
rm rf cctbx_sources/ucif/antlr3
--
Packaging for cctbx
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