Merge remote-tracking branch 'upstream/master'

Author: woldman

Diff for: .gitignore

@@ -3,3 +3,5 @@
 *.so
 *.pyd
 build
+dist
+MANIFEST

Diff for: MANIFEST.in

@@ -0,0 +1,5 @@
+include MANIFEST.in
+include sode/cfiles/build.sh
+recursive-include sode *.pxd *.c *.h
+include addpath.sh
+include addpath.bat

Diff for: scripts/.gitignore

@@ -0,0 +1 @@
+sode-cexamples*

Diff for: scripts/sode

@@ -1,5 +1,7 @@
-#!/bin/sh
+#!/usr/bin/env python
 # copyright Oscar Benjamin 2011
 #
 # run sode as a python script.
-python -m sode.weiners $@
+import sys
+from sode.weiners import main
+main(sys.argv[1:])

Diff for: scripts/sode-cyexamples

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+#
+# executable front end to the sode.examples.cyexamples module
+import sys
+from sode.examples.cyexamples import main
+main(sys.argv[1:])

Diff for: scripts/sode-cyexamples.bat

@@ -0,0 +1,10 @@
+@echo off
+REM copyright Oscar Benjamin 2011
+REM
+REM run sode as a python script.
+REM
+REM Because of:
+REM STDIN/STDOUT Redirection May Not Work If Started from a File Association
+REM http://support.microsoft.com/kb/321788
+REM http://bugs.python.org/issue1012692
+python -m sode.examples.cyexamples %*

Diff for: scripts/sode-pyexamples

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+#
+# executable front end to the sode.examples.pyexamples module
+import sys
+from sode.examples.pyexamples import main
+main(sys.argv[1:])

Diff for: scripts/sode-pyexamples.bat

@@ -0,0 +1,10 @@
+@echo off
+REM copyright Oscar Benjamin 2011
+REM
+REM run sode as a python script.
+REM
+REM Because of:
+REM STDIN/STDOUT Redirection May Not Work If Started from a File Association
+REM http://support.microsoft.com/kb/321788
+REM http://bugs.python.org/issue1012692
+python -m sode.examples.pyexamples %*

Diff for: sode/examples/time.sh renamed to scripts/sode-time

@@ -28,24 +28,24 @@ for sys in\
         echo ----------- Example $sys -----------
         echo
         echo ----- In Pure python $t2 secs
-        time ./pyexamples.py solve --system-type=$sys --t1=$t1 --t2=$t2\
+        time sode-pyexamples solve --system-type=$sys --t1=$t1 --t2=$t2\
                                    --dtmax=$dtmax --dtout=$dtout > .tmppy
         echo
         echo ----- In Cython      $t2 secs
-        time ./cyexamples.py solve --system-type=$sys --t1=$t1 --t2=$t2\
+        time sode-cyexamples solve --system-type=$sys --t1=$t1 --t2=$t2\
                                    --dtmax=$dtmax --dtout=$dtout > .tmpcy
         echo
         echo ----- In Pure c      $t2 secs
-        time ./cexamples.exe $sys $t1 $t2 $dtmax $dtout > .tmpc
+        time sode-cexamples $sys $t1 $t2 $dtmax $dtout > .tmpc
         echo
 
         echo
         echo ----- In Cython      $t2l secs
-        time ./cyexamples.py solve --system-type=$sys --t1=$t1 --t2=$t2l\
+        time sode-cyexamples solve --system-type=$sys --t1=$t1 --t2=$t2l\
                                    --dtmax=$dtmax --dtout=$dtout > .tmpcy
         echo
         echo ----- In Pure c      $t2l secs
-        time ./cexamples.exe $sys $t1 $t2l $dtmax $dtout > .tmpc
+        time sode-cexamples $sys $t1 $t2l $dtmax $dtout > .tmpc
         echo
 
 done

Diff for: setup.py

@@ -1,42 +1,204 @@
 #!/usr/bin/env python
 #
-# Copyright Oscar Benjamin 2011 under new BSD license
+# Copyright Oscar Benjamin 2011 under GPLv3+
 
 import os, os.path, sys
 from distutils.core import setup
 from distutils.extension import Extension
+from distutils.command.build_ext import build_ext
+from distutils.cygwinccompiler import Mingw32CCompiler # ming32 fix
 
-from Cython.Distutils import build_ext
 import numpy
 
-import sode
+
+# Use Cython to generate the c-files if available
+#
+# The source distribution includes the generated c-files so someone can build
+# it without needing cython (although they still need a c-compiler).
+#
+# Ensuring that the c-files are distributed in the source distribution means
+# adding the c-files to MANIFEST.in and ensuring that the cython generated
+# c-files are up to date by remembering to do:
+#
+#    $ python setup.py build_ext --inplace
+#    $ python setup.py sdist
+#
+# See here:
+# http://stackoverflow.com/questions/4505747/how-should-i-structure-a-python-package-that-contains-cython-code
+try:
+    from Cython.Distutils import build_ext
+except ImportError:
+    use_cython = False
+else:
+    use_cython = True
 
 
+# These data structures are conditional on
+# 1) Whether cython is installed (ext_modules, cmdclass)
+# 2) Whether running on Windows (scripts/*.bat)
+cmdclass = {}
+ext_modules = []
+scripts = []
+
+
+# :::::::::::::::::::::::::::::
+#   Extension modules
+# :::::::::::::::::::::::::::::
+
+# Need to add the .pyx name if compiling fully with cython or the .c name when
+# compiling from sdist without cython.
+def add_cython_ext_module(modname, cname, cnames=[], **kwargs):
+    # Use cython to cythonise the .pyx files if possible
+    if use_cython:
+        cname = os.path.splitext(cname)[0] + '.pyx'
+    ext_modules.append(Extension(modname, [cname] + cnames, **kwargs))
+
+
+# Need to link with libm and librt on posix but not on Windows.
 if not 'win' in sys.platform:
-    libraries_cysode = ['m', 'rt']
-    libraries_examples = ['m']
+    libs_cysode = ['m', 'rt']
+    libs_cyexamples = ['m']
+    libs_cexamples = ['m', 'rt']
 else:
-    libraries_cysode = libraries_examples = []
-
-
-ext_modules = [
-    Extension(
-        'sode.cysode',
-        [os.path.join('sode', 'cysode.pyx'),
-         os.path.join('sode', 'cfiles', 'randnorm.c')],
-        include_dirs=[numpy.get_include(), '.'],
-        libraries=libraries_cysode
-    ),
-    Extension(
-        'sode.examples.cyfiles.examples',
-        [os.path.join('sode', 'examples', 'cyfiles', 'examples.pyx')],
-        include_dirs=[numpy.get_include()],
-        libraries = libraries_examples
-    )
-]
+    libs_cysode = []
+    libs_cyexamples = []
+    libs_cexamples = []
+
+
+# This extension module is a core part of sode
+add_cython_ext_module('sode.cysode',
+    os.path.join('sode', 'cysode.c'),
+    [os.path.join('sode', 'cfiles', 'randnorm.c')],
+    include_dirs = [numpy.get_include(), '.'],
+    libraries = libs_cysode,
+)
+
+
+# This extension module is for the examples
+add_cython_ext_module('sode.examples.cyexamples.examples',
+    os.path.join('sode', 'examples', 'cyexamples', 'examples.c'),
+    include_dirs = [numpy.get_include(), '.'],
+    libraries = libs_cyexamples,
+)
+
+
+# ::::::::::::::::::::::::::::::::
+#   Scripts
+# ::::::::::::::::::::::::::::::::
+
+# Executable entry points in scripts
+scripts = ['sode', 'sode-pyexamples', 'sode-cyexamples']
+scripts_dir = 'scripts'
+
+
+# These .bat files are needed so that Windows users can run the scripts
+# without the .py extension. Giving the scripts .py extensions can cause
+# problems with stdin/stdout redirection on Windows
+# http://support.microsoft.com/default.aspx?kbid=321788
+if 'win' in sys.platform:
+    scripts.extend([sname + '.bat' for sname in scripts])
+
+scripts.append('sode-time')
+
+scripts = [os.path.join(scripts_dir, sname) for sname in scripts]
 
+
+# ::::::::::::::::::::::::::::::::
+#   Standalone c program
+# ::::::::::::::::::::::::::::::::
+
+# monkey patch build_ext to also build a standalone c program
+# http://mail.python.org/pipermail/distutils-sig/2009-September/013216.html
+class MonkeyPatch_build_ext(build_ext):
+    def run(self):
+        global scripts
+        build_ext.run(self)
+        exe_name = build_examples_cprog(self.compiler)
+        scripts.append(exe_name)
+
+cmdclass['build_ext'] = MonkeyPatch_build_ext
+
+
+# We also need to build the examples c-program
+def build_examples_cprog(compiler):
+    if isinstance(compiler, Mingw32CCompiler):
+        mingw32_compiler_fix(compiler)
+
+    cfiles = ['main.c', 'examples.c', 'randnorm.c', 'solvers.c']
+    cfiles = [os.path.join('sode', 'cfiles', p) for p in cfiles]
+    exe_name = os.path.join(scripts_dir, 'sode-cexamples')
+
+    compiler.link_executable(cfiles, exe_name, libraries=libs_cexamples)
+
+    # compiler.exe_extension is None on posix, string on Windows
+    if compiler.exe_extension is not None:
+        exe_name += compiler.exe_extension
+
+    return exe_name
+
+
+# msvcr90 needs manifest etc. See:
+# http://developer.berlios.de/devlog/akruis/2012/06/10/msvcr90dll-and-mingw/
+# Since this is a standalone program we can just link against the old version
+# of msvcr.
+def mingw32_compiler_fix(compiler):
+    for n, dllname in enumerate(compiler.dll_libraries):
+        if dllname.startswith('msvcr'):
+            compiler.dll_libraries[n] = min(dllname, 'msvcr71')
+            return
+
+
+# :::::::::::::::::::::::::::::::
+#   Bring it all together
+# :::::::::::::::::::::::::::::::
+
+# Use the README.rst file as the front-page on PyPI
+#with open('README.rst') as README:
+#    LONG_DESCRIPTION = README.read()
+
+
+# Standard distutils setup
 setup(
+    # First the metadata
     name = 'sode',
-    cmdclass = {'build_ext': build_ext},
+    version = '0.0.3',
+    author = 'Oscar Benjamin',
+    author_email = '[email protected]',
+    url = 'https://github.com/oscarbenjamin/sode',
+    description = ('Python/Cython lib for solving ' +
+                   'Stochastic Ordinary Differential Equations'),
+    # long_description = open('README.rst').read()
+    platforms = ['linux2', 'win32', 'darwin'], # tested on these
+    license = 'GPLv3+',
+
+    classifiers = [
+        'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
+
+        'Intended Audience :: Science/Research',
+
+        'Topic :: Scientific/Engineering :: Mathematics',
+        'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Chemistry',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+
+        'Operating System :: POSIX :: Linux',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: MacOS :: MacOS X',
+
+        'Programming Language :: Cython',
+        'Programming Language :: Python :: Implementation :: CPython',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+    ],
+
+    # Dependency information
+    provides = ['sode'],
+    requires = ['numpy (>=1.4)', 'cython (>=0.15)'],
+
+    # Now the content
+    cmdclass = cmdclass,
     ext_modules = ext_modules,
+    packages = ['sode', 'sode.examples', 'sode.examples.pyexamples',
+                                         'sode.examples.cyexamples'],
+    scripts = scripts
 )

Diff for: sode/cfiles/build.sh

@@ -8,10 +8,9 @@
 
 from sode.script import MultiScript
 
-from cyfiles.examples import (Weiner, Weiner2, LinearAdditive2D,
-                              LinearMultiplicative,
-                              SinusoidalMultiplicative,
-                              TangentMultiplicative)
+from sode.examples.cyexamples.examples import (
+    Weiner, Weiner2, LinearAdditive2D, LinearMultiplicative,
+    SinusoidalMultiplicative, TangentMultiplicative)
 
 sysdict = {
     None:'weiner',

Diff for: sode/examples/.gitignore

@@ -2,18 +2,18 @@
 #
 # Copyright, Oscar Benjamin 2011
 #
-# This script brings together the example pure python SODE systems from the 
+# This script brings together the example pure python SODE systems from the
 # pyfiles package for comparison with the faster cython and pure-c
 # implementations.
 
 from sode.script import MultiScript
 
-from pyfiles.weiner import Weiner
-from pyfiles.weiner2 import Weiner2
-from pyfiles.lin2d import LinearAdditive2D
-from pyfiles.linmult import LinearMultiplicative
-from pyfiles.sinmult import SinusoidalMultiplicative
-from pyfiles.tanmult import TangentMultiplicative
+from sode.examples.pyexamples.weiner import Weiner
+from sode.examples.pyexamples.weiner2 import Weiner2
+from sode.examples.pyexamples.lin2d import LinearAdditive2D
+from sode.examples.pyexamples.linmult import LinearMultiplicative
+from sode.examples.pyexamples.sinmult import SinusoidalMultiplicative
+from sode.examples.pyexamples.tanmult import TangentMultiplicative
 
 
 sysdict = {