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[simuPOP-devel] SF.net SVN: simupop:[4991] trunk
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From: <bpe...@us...> - 2015-08-31 15:19:41
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Revision: 4991
http://sourceforge.net/p/simupop/code/4991
Author: bpeng2000
Date: 2015-08-31 15:19:38 +0000 (Mon, 31 Aug 2015)
Log Message:
-----------
Remove SContruct because it is no longer used
Added Paths:
-----------
trunk/test/sample_64_ba_v3.pop
Removed Paths:
-------------
trunk/SConstruct
Deleted: trunk/SConstruct
===================================================================
--- trunk/SConstruct 2015-08-31 04:46:59 UTC (rev 4990)
+++ trunk/SConstruct 2015-08-31 15:19:38 UTC (rev 4991)
@@ -1,320 +0,0 @@
-#
-# $File: SConstruct $
-# $LastChangedDate: 2009-02-24 15:50:38 -0600 (Tue, 24 Feb 2009) $
-# $Rev: 2491 $
-#
-# This file is part of simuPOP, a forward-time population genetics
-# simulation environment. Please visit http://simupop.sourceforge.net
-# for details.
-#
-# Copyright (C) 2004 - 2009 Bo Peng (bp...@md...)
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# A scons based build system for simuPOP. It is better for development
-# usage because it is a real multi-thread, dependency-based build system
-# that can build part of the simuPOP modules..
-#
-# Usage:
-# scons [scons-options] [options] [targets]
-# where:
-# scons-options:
-# standard scons options like -j (number of threads)
-#
-# options:
-# prefix=/path/to/prefix:
-# prefix of installation, equivalent to the --prefix option of python setup.py
-# include-dirs=/path/to/include:/path/to/includes2
-# extra include directories, usually to boost library. The path separator is ; under windows.
-# library-dirs=/path/to/lib:/path/to/lib2
-# extra library directories, usually to boost library. The path separator is ; under windows.
-#
-# targets: one of more of
-# std op la laop ba baop mu muop: individual module
-# all = all modules
-# default to all modules
-# install: install specified targets
-# std_exe op_exe ....: individual executable for debugging purposes.
-# executable: std_exe, op_exe etc
-#
-#
-import os, sys
-import distutils.sysconfig
-
-# load all the module information from setup.py
-from setup import *
-# do not update version for this development version to avoid rebuild
-SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
-print 'Using swig version %d.%d.%d' % tuple(swig_version())
-# get information from python distutils
-vars = distutils.sysconfig.get_config_vars('CC', 'CXX', 'OPT', 'BASECFLAGS',
- 'CCSHARED', 'LDSHARED', 'SO', 'LIBDEST', 'INCLUDEPY')
-for i in range(len(vars)):
- if vars[i] is None:
- vars[i] = ""
-(cc, cxx, opt, basicflags, ccshared, ldshared, so_ext, lib_dest, python_inc_dir) = vars
-# C++ does not need this option, remove it to avoid annoying warning messages.
-opt = opt.replace('-Wstrict-prototypes', '').replace('-Wall', '')
-
-# get compiler and hack options
-from distutils.ccompiler import new_compiler
-comp = new_compiler()
-if comp.__dict__.has_key('initialized'):
- comp.initialize()
-if not comp.__dict__.has_key('ldflags_shared'):
- comp.ldflags_shared = ''
-if not comp.__dict__.has_key('compile_options'):
- comp.compile_options = []
-
-opts = Variables()
-opts.AddVariables(
- PathVariable('prefix', 'Where to install. see "python setup.py install --prefix"', None),
- PathVariable('include-dirs', 'Extra include directories, see "python setup.py build_ext --help"', None),
- PathVariable('library-dirs', 'Extra library directories, see "python setup.py build_ext --help"', None),
-)
-
-# common environment
-env = Environment(
- options=opts,
- # pass all environment variables because MSVC needs INCLUDE and LIB
- # but they may not exist on other platforms
- ENV=os.environ,
- tools=['default', 'swig'])
-
-# try to use the compiler used to build python
-if cc != '':
- env['CC'] = cc
-if cxx != '':
- env['CXX'] = cxx
-if ldshared != '':
- env['SHLINK'] = ldshared
-
-if env.has_key('prefix') and env['prefix'] is not None:
- pylib_dir = distutils.sysconfig.get_python_lib(plat_specific=1, prefix=env['prefix'])
- dest_dir = os.path.join(pylib_dir, 'simuPOP')
- prefix = env['prefix']
- print "Installing to", dest_dir
-else:
- pylib_dir = distutils.sysconfig.get_python_lib(plat_specific=1, prefix=None)
- dest_dir = os.path.join(pylib_dir, 'simuPOP')
- prefix = sys.prefix
-
-if os.name == 'nt':
- wrapper_flags = []
- extra_path = [os.path.join(sys.exec_prefix, 'libs'), 'win32']
- # treat warning as error. This is only set for development builds (scons)
- # because setup.py builds might be built by imcompatible version of compilers
- extra_flags = ['/Zi', '/WX']
-else:
- wrapper_flags = ['-Wno-unused-parameter', '-Wno-missing-field-initializers']
- extra_path = [os.path.join(os.path.split(lib_dest)[:-1])]
- # during development, output symbols (for profiling and debugging)
- # treat warning as error... (although an unused parameter warning from boost has to be allowed)
- extra_flags = ['-g', '-Wno-unused-parameter', '-Wno-char-subscripts', '-Wno-unused-variable',
- '-Wno-unused-function']
- #
- # GNU gcc:
- #
- # -Wconversion will produce a lot of warnings about type conversion. It is
- # useful but I cannot always turn it on because many warnings from boost will
- # overwhelm the output, and stop compiling if '-Werror' is defined. Because
- # MSVC does a reasonable job in detecting conversion problems and we have /WX
- # turned on for MSVC, we can turn on this option (and disable Werror) from
- # time to time to pick out warnings not detected by MSVC.
- #
- # Intel C++:
- #
- # -Wcheck and -Weffc++ give more warnings about coding style etc. They
- # also should not be turned on by default.
- #
- # -vec-report2 reports loops that are automatically vectorized, and remarks
- # for loops that cannot be vectorized.
- #
- #if USE_ICC:
- # extra_flags.extend(['-Wcheck', '-Weffc++', '-vec-report2'])
- #else:
- # extra_flags.append('-Wconversion')
- #
-
-def convert_def(defines):
- new_list = []
- for d in defines:
- if d[1] is not None:
- new_list.append(d)
- else:
- new_list.append(d[0])
- return new_list
-#
-# Building library gsl
-#
-gsl_env = env.Clone()
-gsl_env.VariantDir('build/gsl', '.')
-gsl_env['SWIGOUTDIR'] = 'build/gsl/src'
-gsl_env['SWIGFLAGS'] = SWIG_CC_FLAGS
-gsl = gsl_env.SharedLibrary(
- target = 'build/gsl/_gsl%s' % so_ext,
- source = ['build/gsl/' + x for x in GSL_FILES] + ['build/gsl/src/gsl.i'],
- SHLIBPREFIX = "",
- SHLIBSUFFIX = so_ext,
- SHLINKFLAGS = comp.ldflags_shared,
- LIBPATH = extra_path,
- # build for config.h
- CPPPATH = ['.', 'gsl', 'gsl/cdf', 'gsl/specfunc', 'build', python_inc_dir],
- CCFLAGS = comp.compile_options,
- CPPFLAGS = ' '.join([basicflags, ccshared, opt])
-)
-Alias('gsl', gsl)
-Alias('all', gsl)
-Alias('install', gsl_env.InstallAs(os.path.join(dest_dir, '_gsl%s' % so_ext), gsl[0]))
-Alias('install', gsl_env.InstallAs(os.path.join(dest_dir, 'gsl.py'), 'build/gsl/src/gsl.py'))
-#
-#
-# Building a library for common files
-#
-# Note that we suppress warnings when building these external source files
-# using -wd options
-std_common_env = env.Clone()
-std_common_env.VariantDir('build/std_common', '.')
-std_common_lib = std_common_env.StaticLibrary(
- target = 'build/std_common/common',
- source = ['build/std_common/' + x for x in LIB_FILES],
- CCFLAGS = ModuInfo('std', SIMUPOP_VER, SIMUPOP_REV)['extra_compile_args'] +\
- comp.compile_options + (['-wd1125', '-wd2259'] if USE_ICC else []),
- CPPPATH = ['.', 'gsl', 'build', ModuInfo('std', SIMUPOP_VER, SIMUPOP_REV)['include_dirs']],
- CPPDEFINES = convert_def(ModuInfo('std', SIMUPOP_VER, SIMUPOP_REV)['define_macros']),
- CPPFLAGS = ccshared + ' ' + opt,
-)
-op_common_env = env.Clone()
-op_common_env.VariantDir('build/op_common', '.')
-op_common_lib = op_common_env.StaticLibrary(
- target = 'build/op_common/common',
- source = ['build/op_common/' + x for x in LIB_FILES],
- CCFLAGS = ModuInfo('op', SIMUPOP_VER, SIMUPOP_REV)['extra_compile_args'] + \
- comp.compile_options + (['-wd1125'] if USE_ICC else []),
- CPPPATH = ['.', 'gsl', 'build', ModuInfo('op', SIMUPOP_VER, SIMUPOP_REV)['include_dirs']],
- CPPDEFINES = convert_def(ModuInfo('op', SIMUPOP_VER, SIMUPOP_REV)['define_macros']),
- CPPFLAGS = ccshared + ' ' + opt,
-)
-Alias('common', (std_common_lib, op_common_lib))
-
-#
-# Building modules
-#
-targets = []
-exe_targets = []
-all_modu = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop', 'lin', 'linop']
-all_exe = [x + '_exe' for x in all_modu]
-for key in all_modu:
- if key in BUILD_TARGETS:
- targets.append(key)
-for key in all_exe:
- if key in BUILD_TARGETS:
- exe_targets.append(key)
-
-if targets == [] and 'gsl' not in BUILD_TARGETS and len(exe_targets) == 0:
- targets = all_modu
-if 'all' in BUILD_TARGETS:
- targets = all_modu
-
-for mod in targets:
- mod_env = env.Clone()
- mod_env.VariantDir('build/' + mod, '.')
- mod_env['SWIGFLAGS'] = SWIG_CPP_FLAGS + ' -Isrc' # -Isrc for %include interface files under src
- mod_env['SWIGOUTDIR'] = 'build/%s/src' % mod
- info = ModuInfo(mod, SIMUPOP_VER, SIMUPOP_REV)
- mod_env.Command('build/%s/src/swigpyrun.h' % mod, None, ['swig %s $TARGET' % SWIG_RUNTIME_FLAGS])
- if 'op' in mod:
- common_lib = op_common_lib
- else:
- common_lib = std_common_lib
- mod_wrapper = mod_env.StaticLibrary(
- target = 'build/%s/src/_simuPOP_wrap_%s' % (mod, mod),
- source = ['build/%s/src/simuPOP_%s.i' % (mod, mod)],
- SHLIBPREFIX = "",
- SHLIBSUFFIX = so_ext,
- SHLINKFLAGS = comp.ldflags_shared,
- LIBPATH = info['library_dirs'] + extra_path,
- CPPPATH = [python_inc_dir, '.', 'src', 'build'] + info['include_dirs'],
- CPPDEFINES = convert_def(info['define_macros']),
- # No extra-flags because it can have -Werror and we cannot guarantee that there is
- # no warning coming out of the wrapper code.
- CCFLAGS = opt.split() + info['extra_compile_args'] + comp.compile_options + wrapper_flags,
- CPPFLAGS = ' '.join([basicflags, ccshared])
- )
- mod_lib = mod_env.SharedLibrary(
- target = 'build/%s/_simuPOP_%s' % (mod, mod),
- source = ['build/%s/src/%s' % (mod, x) for x in SOURCE_FILES],
- LIBS = info['libraries'] + [mod_wrapper, common_lib],
- SHLIBPREFIX = "",
- SHLIBSUFFIX = so_ext,
- SHLINKFLAGS = comp.ldflags_shared,
- LIBPATH = info['library_dirs'] + extra_path,
- CPPPATH = [python_inc_dir, '.', 'src', 'build'] + info['include_dirs'],
- CPPDEFINES = convert_def(info['define_macros']),
- CCFLAGS = info['extra_compile_args'] + comp.compile_options + extra_flags,
- CPPFLAGS = ' '.join([basicflags, ccshared, opt])
- )
- env.Depends('build/%s/src/swigpyrun.h' % mod, 'build/%s/src/utility.cpp' % mod)
- Alias(mod, mod_lib)
- Alias('all', mod_lib)
- pyInstall = env.InstallAs(os.path.join(dest_dir, 'simuPOP_%s.py' % mod),
- 'build/%s/src/simuPOP_%s.py' % (mod, mod))
- libInstall = env.InstallAs(os.path.join(dest_dir, '_simuPOP_%s%s' % (mod, so_ext)),
- mod_lib[0])
- mod_env.Depends(pyInstall, libInstall)
- Alias('install', libInstall)
- Alias('install', pyInstall)
-
-# module executable, for testing purposes.
-if os.name == 'nt':
- pylibs = ['python%d%d' % (sys.version_info[0], sys.version_info[1])]
-else:
- pylibs = ['python%d.%d' % (sys.version_info[0], sys.version_info[1]), 'util']
-
-for mod in exe_targets:
- mod_name = mod.split('_')[0]
- exe_env = env.Clone()
- exe_env.VariantDir('build/' + mod, '.')
- exe_env['SWIGFLAGS'] = SWIG_CPP_FLAGS + ' -Isrc' # -Isrc for %include interface files under src
- exe_env['SWIGOUTDIR'] = 'build/%s/src' % mod
- info = ModuInfo(mod_name, SIMUPOP_VER, SIMUPOP_REV)
- if 'op' in mod:
- common_lib = op_common_lib
- else:
- common_lib = std_common_lib
- mod_executable = exe_env.Program(
- target = 'build/simuPOP_%s' % mod,
- source = ['build/%s/src/%s' % (mod, x) for x in SOURCE_FILES],
- LIBS = info['libraries'] + [common_lib] + pylibs,
- LIBPATH = info['library_dirs'] + extra_path,
- CPPPATH = [python_inc_dir, '.', 'src', 'build'] + info['include_dirs'],
- CPPDEFINES = convert_def(info['define_macros'] + [('STANDALONE_EXECUTABLE', None)]),
- CCFLAGS = info['extra_compile_args'] + comp.compile_options + extra_flags,
- CPPFLAGS = ' '.join([basicflags, ccshared, opt])
- )
- Alias(mod, mod_executable)
- Alias('debug', mod_executable)
-
-
-env.Install(pylib_dir, 'simuOpt.py')
-Alias('install', pylib_dir)
-for pyfile in ['__init__.py', 'utils.py', 'plotter.py', 'sampling.py', 'sandbox.py', 'demography.py']:
- env.Install(dest_dir, 'src/%s' % pyfile)
- Alias('install', dest_dir)
-
-for datafile in PACKAGE_DATA:
- env.Install(dest_dir, 'src/%s' % datafile)
- Alias('install', dest_dir)
-
-Default('install')
Added: trunk/test/sample_64_ba_v3.pop
===================================================================
(Binary files differ)
Index: trunk/test/sample_64_ba_v3.pop
===================================================================
--- trunk/test/sample_64_ba_v3.pop 2015-08-31 04:46:59 UTC (rev 4990)
+++ trunk/test/sample_64_ba_v3.pop 2015-08-31 15:19:38 UTC (rev 4991)
Property changes on: trunk/test/sample_64_ba_v3.pop
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Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
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