8000 Merge branch 'feature/cyma57' into develop · PythonOptimizers/HSL.py@790488f · GitHub
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syarrasyarra
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Merge branch 'feature/cyma57' into develop
2 parents f6efb32 + 54ed2d0 commit 790488f

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‎.gitignore

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site.cfg
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.DS_Store
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# Byte-compiled / optimized / DLL files
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# C extensions
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*.so
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# Generated files
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*.pyx
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*.pxd
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*.c
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__pycache__/
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*.py[cod]
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*$py.class

‎DESCRIPTION.rst

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‎README.md

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python setup.py install.
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## Compilation of cython files
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cython -I ~/work/VirtualEnvs/nlpy_new/programs/cysparse/ _cyma57.pyx
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## Note
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weird behaviour of Cython, cannot cythonize some .pyx files using setup.py but works when invoking cython from command line ...
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So I modified setup.py to create c file using command line "cython"
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## TODO
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- [ ] make it work with CySparse

‎config/setup.cpy

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#!/usr/bin/env python
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# The file setup.py is automatically generated
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# Generate it with
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# python generate_code
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import pysparse
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from distutils.core import setup
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from setuptools import find_packages
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from distutils.extension import Extension
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from Cython.Distutils import build_ext
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from numpy.distutils.misc_util import Configuration
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from numpy.distutils.system_info import get_info
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from numpy.distutils.core import setup
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from Cython.Build import cythonize
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import numpy as np
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import ConfigParser
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import os
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import copy
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from codecs import open
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from os import path
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from subprocess import call
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# HELPERS
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#--------
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def prepare_Cython_extensions_as_C_extensions(extensions):
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"""
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Modify the list of sources to transform `Cython` extensions into `C` extensions.
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Args:
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extensions: A list of (`Cython`) `distutils` extensions.
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Warning:
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The extensions are changed in place. This function is not compatible with `C++` code.
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Note:
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Only `Cython` source files are modified into their `C` equivalent source files. Other file types are unchanged.
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"""
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for extension in extensions:
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c_sources = list()
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for source_path in extension.sources:
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path, source = os.path.split(source_path)
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filename, ext = os.path.splitext(source)
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if ext == '.pyx':
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c_sources.append(os.path.join(path, filename + '.c'))
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elif ext in ['.pxd', '.pxi']:
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pass
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else:
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# copy source as is
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c_sources.append(source_path)
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# modify extension in place
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extension.sources = c_sources
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def files_exist(file_list):
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for fname in file_list:
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if os.path.isfile(fname) == False:
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return False
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return True
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f2py_options = []
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hsl_config = ConfigParser.SafeConfigParser()
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hsl_config.read('site.cfg')
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version = {}
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with open(os.path.join('hsl', 'version.py')) as fp:
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exec(fp.read(), version)
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# later on we use: version['version']
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numpy_include = np.get_include()
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pysparse_inc = pysparse.get_include()
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# Use Cython?
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use_cython = hsl_config.getboolean('CODE_GENERATION', 'use_cython')
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if use_cython:
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try:
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from Cython.Distutils import build_ext
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from Cython.Build import cythonize
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except ImportError:
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raise ImportError("Check '%s': Cython is not properly installed." % hsl_config_file)
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# DEFAULT
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default_include_dir = hsl_config.get('DEFAULT', 'include_dirs').split(os.pathsep)
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default_library_dir = hsl_config.get('DEFAULT', 'library_dirs').split(os.pathsep)
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# Debug mode
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use_debug_symbols = hsl_config.getboolean('CODE_GENERATION', 'use_debug_symbols')
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# find user defined directories
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hsl_rootdir = hsl_config.get('HSL', 'hsl_rootdir')
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if hsl_rootdir == '':
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raise ValueError("Please provide HSL source directory!")
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metis_dir = hsl_config.get('METIS', 'metis_dir')
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metis_lib = hsl_config.get('METIS', 'metis_lib')
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# OPTIONAL
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build_cysparse_ext = False
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if hsl_config.has_section('CYSPARSE'):
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build_cysparse_ext = True
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cysparse_rootdir = hsl_config.get('CYSPARSE', 'cysparse_rootdir').split(os.pathsep)
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if cysparse_rootdir == '':
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raise ValueError("You must specify where CySparse source code is" +
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"located. Use `cysparse_rootdir` to specify its path.")
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config = Configuration('hsl', '', '')
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config.set_options(ignore_setup_xxx_py=True,
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assume_default_configuration=True,
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delegate_options_to_subpackages=True,
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quiet=True)
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# Set config.version
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config.get_version(os.path.join('hsl', 'version.py'))
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config.add_include_dirs([np.get_include(), pysparse.get_include()])
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config.add_include_dirs('include')
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# Get info from site.cfg
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blas_info = get_info('blas_opt', 0)
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if not blas_info:
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print 'No blas info found'
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lapack_info = get_info('lapack_opt', 0)
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if not lapack_info:
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print 'No lapack info found'
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########################################################################################################################
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# EXTENSIONS
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########################################################################################################################
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include_dirs = [numpy_include, 'include', '.']
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## Extensions using Fortran codes
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# Relevant files for building MA27 extension.
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ma27_src = ['fd05ad.f', 'ma27ad.f']
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libma27_src = ['ma27fact.f']
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pyma27_src = ['ma27_lib.c', 'hsl_alloc.c', '_pyma27.c']
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# Build PyMA27
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ma27_sources = [os.path.join(hsl_rootdir, name) for name in ma27_src]
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ma27_sources += [os.path.join('hsl', 'solvers', 'src', name) for name in libma27_src]
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pyma27_sources = [os.path.join('hsl', 'solvers', 'src', name) for name in pyma27_src]
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if files_exist(ma27_sources):
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config.add_library(name='hsl_ma27',
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sources=ma27_sources,
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include_dirs=[hsl_rootdir, os.path.join('hsl', 'solvers', 'src')],)
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config.add_extension(name='solvers._pyma27',
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sources=pyma27_sources,
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depends=[],
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libraries=['hsl_ma27'],
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include_dirs=['include', os.path.join('hsl', 'solvers', 'src')],)
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# Build PyMA57
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ma57_src = ['ddeps.f', 'ma57d.f']
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ma57_sources = [os.path.join(hsl_rootdir, 'ma57d', name) for name in ma57_src]
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if files_exist(ma57_sources):
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config.add_library(
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name='hsl_ma57',
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sources=ma57_sources,
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libraries=[metis_lib],
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library_dirs=[metis_dir],
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include_dirs=[hsl_rootdir, os.path.join('hsl', 'solvers', 'src')],)
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mc29_sources = [os.path.join(hsl_rootdir, 'mc29d', 'mc29d.f'),
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os.path.join('hsl', 'scaling', 'src', 'mc29.pyf')]
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config.add_extension(
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name='scaling._mc29',
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sources=mc29_sources,
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include_dirs=[os.path.join('hsl', 'scaling', 'src')],
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extra_link_args=[])
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mc21_sources = [os.path.join(hsl_rootdir, 'mc21d', 'mc21d.f'),
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os.path.join('hsl', 'ordering', 'src', 'mc21.pyf')]
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config.add_extension(
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name='ordering._mc21',
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sources=mc21_sources,
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include_dirs=[os.path.join('hsl', 'ordering', 'src')],
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extra_link_args=[])
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mc60_sources = [os.path.join(hsl_rootdir, 'mc60d', 'mc60d.f'),
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os.path.join('hsl', 'ordering', 'src', 'mc60.pyf')]
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config.add_extension(
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name='ordering._mc60',
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sources=mc60_sources,
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include_dirs=[os.path.join('hsl', 'ordering', 'src')],
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extra_link_args=[])
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## Extensions using Cython
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hsl_ext = []
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ext_params = {}
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ext_params['include_dirs'] = include_dirs
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if not use_debug_symbols:
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ext_params['extra_compile_args'] = ["-O2", '-std=c99', '-Wno-unused-function']
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ext_params['extra_link_args'] = []
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else:
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ext_params['extra_compile_args'] = ["-g", '-std=c99', '-Wno-unused-function']
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ext_params['extra_link_args'] = ["-g"]
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context_ext_params = copy.deepcopy(ext_params)
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{% for index_type in index_list %}
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{% for element_type in type_list %}
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cyma57_src_@index_type@_@element_type@ = ['ma57_lib.c',
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'hsl_alloc.c',
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'_cyma57_base_@index_type@_@element_type@.c']
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cyma57_sources_@index_type@_@element_type@ = [os.path.join('hsl', 'solvers', 'src', name) for name in cyma57_src_@index_type@_@element_type@]
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base_ext_params_@index_type@_@element_type@ = copy.deepcopy(ext_params)
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base_ext_params_@index_type@_@element_type@['library_dirs'] = [metis_dir]
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base_ext_params_@index_type@_@element_type@['libraries'] = D96B [metis_lib, 'hsl_ma57']
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retval = os.getcwd()
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os.chdir('hsl/solvers/src')
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call(['cython', '_cyma57_base_@index_type@_@element_type@.pyx'])
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os.chdir(retval)
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config.add_extension(
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name='solvers.src._cyma57_base_@index_type@_@element_type@',
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sources=cyma57_sources_@index_type@_@element_type@,
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**base_ext_params_@index_type@_@element_type@)
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retval = os.getcwd()
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os.chdir('hsl/solvers/src')
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call(['cython', '_cyma57_numpy_@index_type@_@element_type@.pyx'])
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os.chdir(retval)
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numpy_ext_params_@index_type@_@element_type@ = copy.deepcopy(ext_params)
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config.add_extension(name="solvers.src._cyma57_numpy_@index_type@_@element_type@",
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sources=['hsl/solvers/src/_cyma57_numpy_@index_type@_@element_type@.c'],
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**numpy_ext_params_@index_type@_@element_type@)
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{% endfor %}
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{% endfor %}
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if build_cysparse_ext:
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{% for index_type in index_list %}
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{% for element_type in type_list %}
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retval = os.getcwd()
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os.chdir('hsl/solvers/src')
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call(['cython', '-I', cysparse_rootdir[0], '_cyma57_cysparse_@index_type@_@element_type@.pyx'])
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os.chdir(retval)
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cysparse_ext_params_@index_type@_@element_type@ = copy.deepcopy(ext_params)
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cysparse_ext_params_@index_type@_@element_type@['include_dirs'].extend(cysparse_rootdir)
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config.add_extension(name="solvers.src._cyma57_cysparse_@index_type@_@element_type@",
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sources=['hsl/solvers/src/_cyma57_cysparse_@index_type@_@element_type@.c'],
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**cysparse_ext_params_@index_type@_@element_type@)
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{% endfor %}
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{% endfor %}
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packages_list = ['hsl', 'hsl.ordering', 'hsl.scaling', 'hsl.solvers',
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'hsl.solvers.src']
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# PACKAGE PREPARATION FOR EXCLUSIVE C EXTENSIONS
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########################################################################################################################
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# We only use the C files **without** Cython. In fact, Cython doesn't need to be installed.
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cythonize(hsl_ext)
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prepare_Cython_extensions_as_C_extensions(hsl_ext)
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for ext in hsl_ext:
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print ext.name
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print ext.sources
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print ext.libraries
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print ext.include_dirs
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config.add_extension(name=ext.name[4:],
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sources=ext.sources,
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depends=ext.depends,
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library_dirs=ext.library_dirs,
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libraries=ext.libraries,
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include_dirs=ext.include_dirs,)
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CLASSIFIERS = """\
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Development Status :: 4 - Beta
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Intended Audience :: Science/Research
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Intended Audience :: Developers
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License :: OSI Approved
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Programming Language :: Python
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Programming Language :: Cython
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Topic :: Software Development
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Topic :: Scientific/Engineering
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Operating System :: POSIX
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Operating System :: Unix
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Operating System :: MacOS :: MacOS X
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Natural Language :: English
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"""
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here = path.abspath(path.dirname(__file__))
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# Get the long description from the relevant file
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with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
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long_description = f.read()
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config.make_config_py()
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setup(packages=packages_list, zip_safe=False, **config.todict())

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