Switch to the new version of the setup.py script inspirated by orgasm

.pydevproject

@@ -5,5 +5,5 @@
 <path>/OBITools-1.0/textwrangler</path>
 </pydev_pathproperty>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python-2.7</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python2.7</pydev_property>
 </pydev_project>

MANIFEST.in

 include setup.py
+recursive-include distutils.ext *.py *.c
 recursive-include src *.pyx *.pxd *.c *.h
 recursive-include doc/sphinx/source *.txt *.rst *.py
 include doc/sphinx/make.bat
 include doc/sphinx/Makefile
+include README.txt
+include requirements.txt
+

distutils.ext/obidistutils/command/__init__.py

+
+def build_ext(*args,**kargs):
+    '''
+    Wrapper over the build_ext class to postpone the import of cython
+    '''
+    from build_ext import build_ext as _build_ext
+    return _build_ext(*args,**kargs)

distutils.ext/obidistutils/command/build.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+from distutils.command.build import build as ori_build
+
+
+class build(ori_build):
+    
+    def has_ctools(self):
+        return self.distribution.has_ctools()
+
+    def has_files(self):
+        return self.distribution.has_files()
+
+    def has_executables(self):
+        return self.distribution.has_executables()
+    
+    def has_ext_modules(self):
+        return self.distribution.has_ext_modules()
+    
+    def has_littlebigman(self):
+        return True
+    
+    sub_commands = [('littlebigman', has_littlebigman),
+                    ('build_ctools', has_ctools),
+                    ('build_files', has_files),
+                    ('build_cexe', has_executables),
+                    ('build_ext', has_ext_modules)] \
+                   + ori_build.sub_commands
+    

distutils.ext/obidistutils/command/build_cexe.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+import os
+from obidistutils.command.build_ctools import build_ctools
+from distutils.sysconfig import customize_compiler
+from distutils.errors import DistutilsSetupError
+from distutils import log
+
+
+class build_cexe(build_ctools):
+
+    description = "build C/C++ executable distributed with Python extensions"
+
+
+    def initialize_options(self):
+        build_ctools.initialize_options(self)
+        self.built_files = None
+
+
+    def finalize_options(self):
+        # This might be confusing: both build-cexe and build-temp default
+        # to build-temp as defined by the "build" command.  This is because
+        # I think that C libraries are really just temporary build
+        # by-products, at least from the point of view of building Python
+        # extensions -- but I want to keep my options open.
+
+        build_cexe_dir = self.build_cexe
+        build_ctools.finalize_options(self)
+
+        if build_cexe_dir is None:
+            self.build_cexe=None
+            
+        self.set_undefined_options('build',
+                                   ('build_scripts',  'build_cexe'))
+
+        self.set_undefined_options('build_files',
+                                   ('files',  'built_files'))
+                   
+        self.executables = self.distribution.executables
+
+        if self.executables:
+            self.check_executable_list(self.executables)
+                            
+
+        # XXX same as for build_ext -- what about 'self.define' and
+        # 'self.undef' ?
+
+    def substitute_sources(self,exe_name,sources):
+        """
+        Substitutes source file name starting by an @ by the actual
+        name of the built file (see --> build_files)
+        """
+        sources = list(sources)
+        for i in xrange(len(sources)):
+            print exe_name,sources[i],
+            if sources[i][0]=='@':
+                try:
+                    filename = self.built_files[sources[i][1:]]
+                except KeyError:
+                    raise DistutilsSetupError, \
+                        ('The %s filename declared in the source '
+                         'files of the program %s have not been '
+                         'built by the installation process') % (sources[i],
+                                                                 exe_name)
+                sources[i]=filename
+                print "changed to ",filename
+            else:
+                print " ok"
+
+        return sources
+    

distutils.ext/obidistutils/command/build_ctools.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+import os
+
+
+from obidistutils.command.build_exe import build_exe
+from distutils.sysconfig import customize_compiler
+from distutils.errors import DistutilsSetupError
+from distutils import log
+
+class build_ctools(build_exe):
+    description = "build C/C++ executable not distributed with Python extensions"
+
+    def initialize_options(self):
+        build_exe.initialize_options(self)
+        
+        # List of built tools
+        self.ctools = None
+        self.littlebigman = None
+
+
+    def finalize_options(self):
+        # This might be confusing: both build-cexe and build-temp default
+        # to build-temp as defined by the "build" command.  This is because
+        # I think that C libraries are really just temporary build
+        # by-products, at least from the point of view of building Python
+        # extensions -- but I want to keep my options open.
+            
+        build_exe.finalize_options(self)
+        
+        
+        self.set_undefined_options('build',
+                                    ('build_temp', 'build_cexe'))
+
+        self.set_undefined_options('littlebigman',
+                                   ('littlebigman',  'littlebigman'))
+                   
+        self.executables = self.distribution.ctools
+        self.check_executable_list(self.executables)
+        
+        if self.littlebigman =='-DLITTLE_END':
+            if self.define is None:
+                self.define=[('LITTLE_END',None)]
+            else:
+                self.define.append('LITTLE_END',None)
+
+        self.ctools = set()
+
+    def run(self):
+        
+        build_exe.run(self)
+        for e,p in self.executables:
+            self.ctools.add(e)
+            
+
+

distutils.ext/obidistutils/command/build_exe.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+import os
+
+from distutils.core import Command
+from distutils.sysconfig import customize_compiler
+from distutils.errors import DistutilsSetupError
+from distutils import log
+from distutils.ccompiler import show_compilers
+
+import subprocess
+
+class build_exe(Command):
+    
+    description = "build an executable -- Abstract command "
+
+    user_options = [
+        ('build-cexe', 'x',
+         "directory to build C/C++ libraries to"),
+        ('build-temp', 't',
+         "directory to put temporary build by-products"),
+        ('debug', 'g',
+         "compile with debugging information"),
+        ('force', 'f',
+         "forcibly build everything (ignore file timestamps)"),
+        ('compiler=', 'c',
+         "specify the compiler type"),
+        ]
+
+    boolean_options = ['debug', 'force']
+
+    help_options = [
+        ('help-compiler', None,
+         "list available compilers", show_compilers),
+        ]
+
+    def initialize_options(self):
+        self.build_cexe = None
+        self.build_temp = None
+
+        # List of executables to build
+        self.executables = None
+
+        # Compilation options for all libraries
+        self.include_dirs = None
+        self.define = None
+        self.undef = None
+        self.extra_compile_args = None
+        self.debug = None
+        self.force = 0
+        self.compiler = None
+        self.sse = None
+        self.built_files=None
+
+    def finalize_options(self):
+        # This might be confusing: both build-cexe and build-temp default
+        # to build-temp as defined by the "build" command.  This is because
+        # I think that C libraries are really just temporary build
+        # by-products, at least from the point of view of building Python
+        # extensions -- but I want to keep my options open.
+        self.set_undefined_options('build',
+                                   ('build_temp', 'build_temp'),
+                                   ('compiler', 'compiler'),
+                                   ('debug', 'debug'),
+                                   ('force', 'force'))
+
+        if self.include_dirs is None:
+            self.include_dirs = self.distribution.include_dirs or []
+            
+        if isinstance(self.include_dirs, str):
+            self.include_dirs = self.include_dirs.split(os.pathsep)
+
+        self.sse = self.distribution.sse
+        
+        if self.sse is not None:
+            if self.extra_compile_args is None:
+                self.extra_compile_args=['-m%s' % self.sse]
+            else:
+                self.extra_compile_args.append('-m%s' % self.sse)
+
+        # XXX same as for build_ext -- what about 'self.define' and
+        # 'self.undef' ?
+
+    def run(self):
+
+        if not self.executables:
+            return
+
+        self.mkpath(self.build_cexe)
+
+        # Yech -- this is cut 'n pasted from build_ext.py!
+        from distutils.ccompiler import new_compiler
+        self.compiler = new_compiler(compiler=self.compiler,
+                                     dry_run=self.dry_run,
+                                     force=self.force)
+        customize_compiler(self.compiler)
+
+        if self.include_dirs is not None:
+            self.compiler.set_include_dirs(self.include_dirs)
+        if self.define is not None:
+            # 'define' option is a list of (name,value) tuples
+            for (name,value) in self.define:
+                self.compiler.define_macro(name, value)
+
+        if self.undef is not None:
+            for macro in self.undef:
+                self.compiler.undefine_macro(macro)
+                
+        self.build_executables(self.executables)
+
+
+    def check_executable_list(self, executables):
+        """Ensure that the list of executables is valid.
+
+        `executable` is presumably provided as a command option 'executables'.
+        This method checks that it is a list of 2-tuples, where the tuples
+        are (executable_name, build_info_dict).
+
+        Raise DistutilsSetupError if the structure is invalid anywhere;
+        just returns otherwise.
+        """
+        if not isinstance(executables, list):
+            raise DistutilsSetupError, \
+                  "'executables' option must be a list of tuples"
+
+        for exe in executables:
+            if not isinstance(exe, tuple) and len(exe) != 2:
+                raise DistutilsSetupError, \
+                      "each element of 'executables' must a 2-tuple"
+
+            name, build_info = exe
+
+            if not isinstance(name, str):
+                raise DistutilsSetupError, \
+                      "first element of each tuple in 'executables' " + \
+                      "must be a string (the executables name)"
+            if '/' in name or (os.sep != '/' and os.sep in name):
+                raise DistutilsSetupError, \
+                      ("bad executable name '%s': " +
+                       "may not contain directory separators") % \
+                      exe[0]
+
+            if not isinstance(build_info, dict):
+                raise DistutilsSetupError, \
+                      "second element of each tuple in 'executables' " + \
+                      "must be a dictionary (build info)"
+
+    def get_executable_names(self):
+        # Assume the executables list is valid -- 'check_executable_list()' is
+        # called from 'finalize_options()', so it should be!
+        if not self.executables:
+            return None
+
+        exe_names = []
+        for (exe_name, build_info) in self.executables:
+            exe_names.append(exe_name)
+        return exe_names
+
+
+    def get_source_files(self):
+        self.check_executable_list(self.executables)
+        filenames = []
+        for (exe_name, build_info) in self.executables:
+            sources = build_info.get('sources')
+            if sources is None or not isinstance(sources, (list, tuple)):
+                raise DistutilsSetupError, \
+                      ("in 'executables' option (library '%s'), "
+                       "'sources' must be present and must be "
+                       "a list of source filenames") % exe_name
+
+            filenames.extend(sources)
+        return filenames
+    
+    def substitute_sources(self,exe_name,sources):
+        return list(sources)
+
+    def build_executables(self, executables):
+        for (exe_name, build_info) in executables:
+            sources = build_info.get('sources')
+            if sources is None or not isinstance(sources, (list, tuple)):
+                raise DistutilsSetupError, \
+                      ("in 'executables' option (library '%s'), " +
+                       "'sources' must be present and must be " +
+                       "a list of source filenames") % exe_name
+            sources = self.substitute_sources(exe_name,sources)
+
+            log.info("building '%s' program", exe_name)
+
+            # First, compile the source code to object files in the library
+            # directory.  (This should probably change to putting object
+            # files in a temporary build directory.)
+            macros = build_info.get('macros')
+            include_dirs = build_info.get('include_dirs')
+            extra_args = self.extra_compile_args or []
+            
+            objects = self.compiler.compile(sources,
+                                            output_dir=self.build_temp,
+                                            macros=macros,
+                                            include_dirs=include_dirs,
+                                            extra_postargs=extra_args,
+                                            debug=self.debug)
+
+            # Now "link" the object files together into a static library.
+            # (On Unix at least, this isn't really linking -- it just
+            # builds an archive.  Whatever.)
+            self.compiler.link_executable(objects, exe_name,
+                                            output_dir=self.build_cexe,
+                                            debug=self.debug)
+

distutils.ext/obidistutils/command/build_ext.py

+'''
+Created on 13 fevr. 2014
+
+@author: coissac
+'''
+
+from Cython.Distutils import build_ext  as ori_build_ext  # @UnresolvedImport
+from distutils.errors import DistutilsSetupError
+import os
+
+
+class build_ext(ori_build_ext):
+    def modifyDocScripts(self):
+        print >>open("doc/sphinx/build_dir.txt","w"),self.build_lib
+        
+    def initialize_options(self):
+        ori_build_ext.initialize_options(self)  
+        self.littlebigman = None
+        self.built_files = None
+
+    
+    def finalize_options(self):
+        ori_build_ext.finalize_options(self)
+
+        self.set_undefined_options('littlebigman',
+                                   ('littlebigman',  'littlebigman'))
+        
+        self.set_undefined_options('build_files',
+                                   ('files',  'built_files'))
+
+        self.cython_c_in_temp = 1
+                   
+        if self.littlebigman =='-DLITTLE_END':
+            if self.define is None:
+                self.define=[('LITTLE_END',None)]
+            else:
+                self.define.append('LITTLE_END',None)
+        
+    def substitute_sources(self,exe_name,sources):
+        """
+        Substitutes source file name starting by an @ by the actual
+        name of the built file (see --> build_files)
+        """
+        sources = list(sources)
+        for i in xrange(len(sources)):
+            print exe_name,sources[i],
+            if sources[i][0]=='@':
+                try:
+                    filename = self.built_files[sources[i][1:]]
+                except KeyError:
+                    tmpfilename = os.path.join(self.build_temp,sources[i][1:])
+                    if os.path.isfile       (tmpfilename):
+                        filename = tmpfilename
+                    else:
+                        raise DistutilsSetupError, \
+                            ('The %s filename declared in the source '
+                             'files of the program %s have not been '
+                             'built by the installation process') % (sources[i],
+                                                                     exe_name)
+                sources[i]=filename
+                print "changed to ",filename
+            else:
+                print " ok"
+
+        return sources
+
+    def build_extensions(self):
+        # First, sanity-check the 'extensions' list
+        
+        for ext in self.extensions:
+            ext.sources = self.substitute_sources(ext.name,ext.sources)
+            
+        self.check_extensions_list(self.extensions)
+
+        for ext in self.extensions:
+            print "#####>",ext.sources
+            ext.sources = self.cython_sources(ext.sources, ext)
+            self.build_extension(ext)
+
+        
+    def run(self):
+        self.modifyDocScripts()
+        ori_build_ext.run(self)
+        
+        
+        
+
+
+        
\ No newline at end of file

distutils.ext/obidistutils/command/build_files.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+import os.path
+
+from distutils.core import Command
+from distutils.util import convert_path
+from distutils import log, sysconfig
+from distutils.dep_util import newer
+from distutils import log
+
+
+
+class build_files(Command):
+            
+    def initialize_options(self):
+        self.files=None
+        self.ctools=None
+        self.build_temp=None
+        self.build_cexe=None
+
+    def finalize_options(self):
+        
+        self.set_undefined_options('build_ctools',
+                                   ('ctools',  'ctools'),
+                                   ('build_temp','build_temp'),
+                                   ('build_cexe','build_cexe'),
+                                   )
+        
+        self.files = {}
+        
+    def run(self):
+        
+        for dest,prog,command in self.distribution.files:
+            destfile = os.path.join(self.build_temp,dest)
+            if prog in self.ctools:
+                progfile = os.path.join(self.build_cexe,prog)
+            else:
+                progfile = prog 
+                
+            log.info("Building file : %s" % dest)
+            
+            commandline = command % {'prog' : progfile,
+                                     'dest' : destfile}
+
+            log.info("    --> %s" % commandline)
+            
+            os.system(commandline)
+            self.files[dest]=destfile
+            
+            log.info("Done.\n")
+            
+            
+            
+        

distutils.ext/obidistutils/command/build_filters.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+from obidistutils.command.build_scripts import build_scripts
+
+class build_filters(build_scripts):
+    pass
+

distutils.ext/obidistutils/command/build_scripts.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+import os.path
+
+from distutils.command.build_scripts import build_scripts as ori_build_scripts,\
+    first_line_re
+from distutils.util import convert_path
+from distutils import log, sysconfig
+from distutils.dep_util import newer
+from stat import ST_MODE
+
+
+
+class build_scripts(ori_build_scripts):
+            
+    def copy_scripts (self):
+        """Copy each script listed in 'self.scripts'; if it's marked as a
+        Python script in the Unix way (first line matches 'first_line_re',
+        ie. starts with "\#!" and contains "python"), then adjust the first
+        line to refer to the current Python interpreter as we copy.
+        """        
+        self.mkpath(self.build_dir)
+        rawbuild_dir = os.path.join(os.path.dirname(self.build_dir),'raw_scripts')
+        self.mkpath(rawbuild_dir)
+        
+        outfiles = []
+        for script in self.scripts:
+            adjust = 0
+            script = convert_path(script)
+            outfile = os.path.join(self.build_dir, os.path.splitext(os.path.basename(script))[0])
+            rawoutfile = os.path.join(rawbuild_dir, os.path.basename(script))
+            outfiles.append(outfile)
+
+            if not self.force and not newer(script, outfile):
+                log.debug("not copying %s (up-to-date)", script)
+                continue
+
+            # Always open the file but ignore failures in dry-run mode --
+            # that way, we'll get accurate feedback if we can read the
+            # script.
+            try:
+                f = open(script, "r")
+            except IOError:
+                if not self.dry_run:
+                    raise
+                f = None
+            else:
+                first_line = f.readline()
+                if not first_line:
+                    self.warn("%s is an empty file (skipping)" % script)
+                    continue
+
+                match = first_line_re.match(first_line)
+                if match:
+                    adjust = 1
+                    post_interp = match.group(1) or ''
+            
+            log.info("Store the raw script %s -> %s", script,rawoutfile)        
+            self.copy_file(script, rawoutfile)
+
+
+            if adjust:
+                log.info("copying and adjusting %s -> %s", script,
+                         self.build_dir)
+                if not self.dry_run:
+                    outf = open(outfile, "w")
+                    if not sysconfig.python_build:
+                        outf.write("#!%s%s\n" %
+                                   (self.executable,
+                                    post_interp))
+                    else:
+                        outf.write("#!%s%s\n" %
+                                   (os.path.join(
+                            sysconfig.get_config_var("BINDIR"),
+                           "python%s%s" % (sysconfig.get_config_var("VERSION"),
+                                           sysconfig.get_config_var("EXE"))),
+                                    post_interp))
+                    outf.writelines(f.readlines())
+                    outf.close()
+                if f:
+                    f.close()
+            else:
+                if f:
+                    f.close()
+                self.copy_file(script, outfile)
+
+        if os.name == 'posix':
+            for F in outfiles:
+                if self.dry_run:
+                    log.info("changing mode of %s", F)
+                else:
+                    oldmode = os.stat(F)[ST_MODE] & 07777
+                    newmode = (oldmode | 0555) & 07777
+                    if newmode != oldmode:
+                        log.info("changing mode of %s from %o to %o",
+                                 F, oldmode, newmode)
+                        os.chmod(F, newmode)
+

distutils.ext/obidistutils/command/install.py

+'''
+Created on 6 oct. 2014
+
+@author: coissac
+'''
+
+from distutils.command.install import install as install_ori
+
+class install(install_ori):