[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-35-g3caabac
Radostan Riedel
raybuntu at googlemail.com
Mon Jul 23 12:22:56 UTC 2012
The following commit has been merged in the master branch:
commit 3caabacabc1adf958611f6e3345c1f583b9e7b8e
Author: Radostan Riedel <raybuntu at googlemail.com>
Date: Mon Jul 23 14:00:06 2012 +0200
Few bugfixes in setup.py and DESTDIR support.
diff --git a/debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch b/debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch
index d9f8979..ca83b63 100644
--- a/debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch
+++ b/debian/patches/0007-options-for-system-libs-installtarget-and-prefix.patch
@@ -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 | 80 +++++++++++++++++-
- cctbx_sources/libtbx/env_config.py | 19 +++++
+ cctbx_sources/libtbx/SConscript | 82 ++++++++++++++++++-
+ cctbx_sources/libtbx/env_config.py | 28 +++++++
cctbx_sources/mmtbx/den/SConscript | 2 +-
cctbx_sources/mmtbx/geometry_restraints/SConscript | 2 +-
cctbx_sources/mmtbx/secondary_structure/SConscript | 2 +-
@@ -21,7 +21,7 @@ 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 +-
- 18 files changed, 180 insertions(+), 66 deletions(-)
+ 18 files changed, 191 insertions(+), 66 deletions(-)
diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
index 0d95318..5417e1b 100644
@@ -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..109b0d8 100644
+index ba00dd3..ee7b1de 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -4,7 +4,7 @@ from libtbx import easy_run
@@ -280,7 +280,7 @@ index ba00dd3..109b0d8 100644
if (libtbx.env.build_options.libtoolize):
env_etc.shlibsuffix = ".la"
env_base.Append(LIBSUFFIXES=[env_etc.shlibsuffix])
-@@ -1093,4 +1094,81 @@ if (libtbx.env.build_options.libtoolize):
+@@ -1093,4 +1094,83 @@ if (libtbx.env.build_options.libtoolize):
env_etc.shlinkflags.remove('-shared')
env_etc.set_libtool(env_base, env_etc.rpath)
@@ -318,9 +318,11 @@ index ba00dd3..109b0d8 100644
+ env_etc.scitbx_boost_python = 'scitbx_boost_python'
+
+env_etc.prefix = libtbx.env.build_options.install_prefix
-+env_etc.binpath = os.path.join(env_etc.prefix, 'bin')
-+env_etc.libpath = os.path.join(env_etc.prefix, 'lib')
-+env_etc.inclpath = os.path.join(env_etc.prefix, 'include')
++env_etc.destdir = libtbx.env.build_options.install_destdir
++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.join(env_etc.install_path, 'lib')
++env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
+
+def create_install_targets():
+ cwd = os.getcwd()
@@ -363,7 +365,7 @@ index ba00dd3..109b0d8 100644
+
Export("env_base", "env_etc")
diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index 2285c9d..b6bab84 100644
+index 2285c9d..281bb42 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):
@@ -376,34 +378,37 @@ index 2285c9d..b6bab84 100644
def ld_library_path_var_name():
if (os.name == "nt"):
return "PATH"
-@@ -703,6 +706,8 @@ Wait for the command to finish, then try again.""" % vars())
+@@ -703,6 +706,9 @@ Wait for the command to finish, then try again.""" % vars())
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 +1767,8 @@ class build_options:
+@@ -1762,6 +1768,9 @@ class build_options:
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 +1840,8 @@ class build_options:
+@@ -1833,6 +1842,9 @@ class build_options:
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 +1964,22 @@ class pre_process_args:
+@@ -1955,12 +1967,28 @@ class pre_process_args:
action="store_true",
default=False,
help="build all shared libraries with libtool. Optionally set --rpath")
@@ -417,6 +422,12 @@ index 2285c9d..b6bab84 100644
default="/usr/lib",
help="sets the rpath libtool (implies --libtoolize). Default: /usr/lib",
metavar="DIRECTORY")
++ parser.option(None, "--install_destdir",
++ type="string",
++ action="store",
++ default="",
++ help="sets the destdir for the install targets.",
++ metavar="DIRECTORY")
+ parser.option(None, "--install_prefix",
+ type="string",
+ action="store",
diff --git a/debian/patches/0008-add-with_pycbf-option.patch b/debian/patches/0008-add-with_pycbf-option.patch
index 2f31cdc..95e3f3b 100644
--- a/debian/patches/0008-add-with_pycbf-option.patch
+++ b/debian/patches/0008-add-with_pycbf-option.patch
@@ -29,7 +29,7 @@ index 4ac6717..14deee3 100644
Export("env_cbflib_boost_python_ext")
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index 109b0d8..c899fbc 100644
+index ee7b1de..26f2808 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -1127,6 +1127,7 @@ else:
@@ -38,10 +38,10 @@ index 109b0d8..c899fbc 100644
+env_etc.with_pycbf = libtbx.env.build_options.with_pycbf
env_etc.prefix = libtbx.env.build_options.install_prefix
- env_etc.binpath = os.path.join(env_etc.prefix, 'bin')
- env_etc.libpath = os.path.join(env_etc.prefix, 'lib')
+ 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 b6bab84..687c00d 100644
+index 281bb42..bd4b612 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())
@@ -50,17 +50,17 @@ index b6bab84..687c00d 100644
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,
- write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
-@@ -1768,6 +1769,7 @@ class build_options:
+@@ -1769,6 +1770,7 @@ class build_options:
static_exe,
libtoolize,
use_system_libs,
+ with_pycbf,
install_prefix,
+ install_destdir,
rpath,
- scan_boost,
-@@ -1968,6 +1970,10 @@ class pre_process_args:
+@@ -1971,6 +1973,10 @@ class pre_process_args:
action="store_true",
default=False,
help="Use system Libraries to build.")
diff --git a/debian/patches/0010-adding-setup_py.patch b/debian/patches/0010-adding-setup_py.patch
index 8774c20..ae1c18b 100644
--- a/debian/patches/0010-adding-setup_py.patch
+++ b/debian/patches/0010-adding-setup_py.patch
@@ -4,9 +4,9 @@ Subject: adding-setup_py
---
cctbx_sources/stdlib.py | 4 ++
- sconsutils.py | 154 +++++++++++++++++++++++++++++++++++++++++++++++
- setup.py | 122 +++++++++++++++++++++++++++++++++++++
- 3 files changed, 280 insertions(+)
+ sconsutils.py | 155 +++++++++++++++++++++++++++++++++++++++++++++++
+ setup.py | 123 +++++++++++++++++++++++++++++++++++++
+ 3 files changed, 282 insertions(+)
create mode 100755 cctbx_sources/stdlib.py
create mode 100644 sconsutils.py
create mode 100755 setup.py
@@ -23,13 +23,13 @@ index 0000000..759f689
+random = stdlib_import("random")
diff --git a/sconsutils.py b/sconsutils.py
new file mode 100644
-index 0000000..93b1542
+index 0000000..d568ba7
--- /dev/null
+++ b/sconsutils.py
-@@ -0,0 +1,154 @@
+@@ -0,0 +1,155 @@
+from distutils.sysconfig import get_python_lib
+from distutils.command.build_ext import build_ext as _build_ext
-+from distutils.command.install import install as _install
++from distutils.command.install_lib import install_lib as _install_lib
+from distutils.cmd import Command as _Command
+import sys, os
+import SCons.Script
@@ -59,15 +59,16 @@ index 0000000..93b1542
+ os.environ['PYTHONPATH'] = ':'.join(sys.path)
+ self.spawn(argv)
+ os.chdir(cwd)
-+class install(_install, Command):
++class install_lib(_install_lib, Command):
+ def run(self):
-+ if self.root != None:
-+ ip = '--install_prefix'
++ super(install_lib, self).run()
++ install_root = self.get_finalized_command('install').root
++ if install_root != None:
++ ip = '--install_destdir'
+ if ip not in configure_list:
-+ configure_list.extend([ip, self.root + PREFIX])
++ configure_list.extend([ip, install_root])
+ self.run_scons(scons_installargv)
+ self.modify_libtbx_env()
-+ super(install, self).run()
+
+ def modify_libtbx_env(self):
+ """ Modify libtbx_env pickle object to set the correct paths. """
@@ -95,7 +96,7 @@ index 0000000..93b1542
+ for module in env.module_list:
+ paths = []
+ for path in module.dist_paths:
-+ if path != None:
++ if path != None:
+ head, tail = os.path.split(abs(path))
+ rp = relocatable_path(build_path, os.path.join(rel_path, tail))
+ paths.append(rp)
@@ -183,10 +184,10 @@ index 0000000..93b1542
+ return out, list(outext)
diff --git a/setup.py b/setup.py
new file mode 100755
-index 0000000..addf444
+index 0000000..0f0b48a
--- /dev/null
+++ b/setup.py
-@@ -0,0 +1,122 @@
+@@ -0,0 +1,123 @@
+from distutils.core import setup, Extension
+import sys, os, shutil
+
@@ -203,6 +204,7 @@ index 0000000..addf444
+boost = 'boost_adaptbx/boost'
+libtbx_pypath = 'libtbx/pythonpath'
+scons_path = '/usr/lib/scons/'
++PREFIX = '/usr'
+PATHLIST= [ SRCDIR,
+ opj(SRCDIR, libtbx_pypath),
+ opj(SRCDIR, clipper),
@@ -214,8 +216,7 @@ index 0000000..addf444
+ sys.path.append(p)
+
+import sconsutils
-+from sconsutils import build_ext, find_packages_and_extensions, install
-+
++from sconsutils import build_ext, find_packages_and_extensions, install_lib
+
+# Configure settings
+# We need this directory to get env_config.cold_start to run!
@@ -224,6 +225,7 @@ index 0000000..addf444
+build_opts = [ '--libtoolize',
+ '--rpath', '/usr/lib',
+ '--use_system_libs',
++ '--install_prefix', PREFIX,
+ ]
+conf_modules = [ 'annlib_adaptbx',
+ 'boost_adaptbx',
@@ -253,7 +255,7 @@ index 0000000..addf444
+sconsutils.configure_list.extend(build_opts)
+sconsutils.configure_list.extend(conf_modules)
+sconsutils.BUILDDIR = BUILDDIR
-+sconsutils.PREFIX = '/usr/'
++sconsutils.PREFIX = PREFIX
+
+# Build settings
+sconsutils.scons_buildargv = [sys.executable, '/usr/bin/scons']
@@ -264,7 +266,7 @@ index 0000000..addf444
+# Setup settings
+
+NAME = 'cctbx'
-+VERSION = '0.1'
++VERSION = '2012.05.08.2305'
+DESCRIPTION = 'cctbx'
+AUTHOR = 'cctbx'
+AUTHOR_EMAIL = 'cctbx at cci.lbl.gov'
@@ -305,7 +307,7 @@ index 0000000..addf444
+ package_dir = PACKDIR,
+ ext_modules = EXT_MODULES,
+ cmdclass = {'build_ext': build_ext,
-+ 'install': install},
++ 'install_lib': install_lib},
+ py_modules = MODS,
+ data_files = [('/usr/share/cctbx/%s'%(py_str), [libtbx_env])],
+ )
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 2f0b54f..2d78645 100644
--- a/debian/patches/0011-fix-missing-python-lib-during-linking.patch
+++ b/debian/patches/0011-fix-missing-python-lib-during-linking.patch
@@ -7,7 +7,7 @@ Subject: fix missing python lib during linking
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index c899fbc..ef57294 100644
+index 26f2808..90a4d95 100644
--- a/cctbx_sources/libtbx/SConscript
+++ b/cctbx_sources/libtbx/SConscript
@@ -56,7 +56,7 @@ def set_python_include_and_libs(env_etc):
--
Packaging for cctbx
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