BUG count obiuniq with merged

.project

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>OBITools-1.1</name>
+	<name>OBITools</name>
 	<comment></comment>
 	<projects>
 	</projects>

.pydevproject

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?eclipse-pydev version="1.0"?><pydev_project>
 <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
-<path>/obitools/src</path>
+<path>/OBITools-1.0/src</path>
 <path>/${PROJECT_DIR_NAME}/distutils.ext</path>
 </pydev_pathproperty>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>

MANIFEST.in

@@ -1,8 +1,7 @@
 include setup.py
-recursive-include distutils.ext *.py *.c *.pem
+recursive-include distutils.ext *.py *.c
 recursive-include src *.pyx *.pxd *.c *.h *.cfiles
 recursive-include doc/sphinx/source *.txt *.rst *.py
-recursive-include doc/sphinx/sphinxext *.py
 include doc/sphinx/make.bat
 include doc/sphinx/Makefile
 include README.txt

distutils.ext/obidistutils/command/build.py

@@ -7,7 +7,6 @@ Created on 20 oct. 2012
 from distutils.command.build import build as ori_build
 from obidistutils.serenity.checksystem import is_mac_system
 
-from distutils import log
 
 class build(ori_build):
     
@@ -28,20 +27,11 @@ class build(ori_build):
     
     def has_pidname(self):
         return is_mac_system()
-
-    def has_doc(self):
-        return True
-    
     
     sub_commands = [('littlebigman', has_littlebigman),
                     ('pidname',has_pidname),
                     ('build_ctools', has_ctools),
                     ('build_files', has_files),
                     ('build_cexe', has_executables)] \
-                   + ori_build.sub_commands + \
-                   [('build_sphinx',has_doc)]
-                   
-    def run(self):
-        log.info('\n\nRunning obidistutils build process\n\n')
-        ori_build.run(self)
+                   + ori_build.sub_commands
     

distutils.ext/obidistutils/command/build_cexe.py

@@ -4,8 +4,11 @@ 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):

distutils.ext/obidistutils/command/build_ext.py

@@ -4,35 +4,26 @@ Created on 13 fevr. 2014
 @author: coissac
 '''
 
-from distutils import log
-import sys
-from obidistutils.serenity import is_serenity
-
-import os
-from obidistutils.serenity.checkpackage import install_requirements
-from obidistutils.serenity.rerun import rerun_with_anothe_python
-
 try:
     from Cython.Distutils import build_ext  as ori_build_ext  # @UnresolvedImport
 except ImportError:
-    if not is_serenity() and install_requirements():
-        log.info("Restarting installation with all dependencies ok")
-        rerun_with_anothe_python(os.path.realpath(sys.executable))
-    
+    from distutils.command.build_ext import build_ext as ori_build_ext 
 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)  # @UndefinedVariable
+        ori_build_ext.initialize_options(self)  
         self.littlebigman = None
         self.built_files = None
 
     
     def finalize_options(self):
-        ori_build_ext.finalize_options(self)  # @UndefinedVariable
+        ori_build_ext.finalize_options(self)
 
         self.set_undefined_options('littlebigman',
                                    ('littlebigman',  'littlebigman'))
@@ -92,21 +83,8 @@ class build_ext(ori_build_ext):
         
     def run(self):
         self.modifyDocScripts()
-        ori_build_ext.run(self)  # @UndefinedVariable
+        ori_build_ext.run(self)
         
-
-    
-#     from obidistutils.serenity.getcython import get_a_cython_module
-#     import imp
-#     import os.path 
-#     
-#     log.info("No cython installed, try to install a temporary cython")
-#     cython = get_a_cython_module()
-#     sys.path.insert(0,os.path.dirname(os.path.dirname(cython.__file__)))
-#     f, filename, description=imp.find_module('Distutils',[os.path.dirname(cython.__file__)])
-#     submodule = imp.load_module('Cython.Distutils', f, filename, description)
-#     ori_build_ext = submodule.build_ext
-#     
         
         
 

distutils.ext/obidistutils/command/build_sphinx.py

@@ -1,38 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-
-from distutils import log
-from obidistutils.serenity.checkpackage import install_requirements
-from obidistutils.serenity.rerun import rerun_with_anothe_python
-from obidistutils.serenity import is_serenity
-import os
-import sys
-
-try:
-    from sphinx.setup_command import BuildDoc as ori_build_sphinx
-except ImportError:
-    if not is_serenity() and install_requirements():
-        log.info("Restarting installation with all dependencies ok")
-        rerun_with_anothe_python(os.path.realpath(sys.executable))
-    
-class build_sphinx(ori_build_sphinx):
-    '''
-    Build Sphinx documentation in html, epub and man formats 
-    '''
-
-    description = __doc__
-
-    def run(self):
-        self.builder='html'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='epub'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='man'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-    

distutils.ext/obidistutils/command/install.py

@@ -4,22 +4,11 @@ Created on 6 oct. 2014
 @author: coissac
 '''
 
-try:
-    from setuptools.command.install import install as install_ori
-    has_setuptools=True
-except ImportError:
-    from distutils.command.install import install as install_ori
-    has_setuptools=False
-
-from distutils import log
+from distutils.command.install import install as install_ori
 
 class install(install_ori):
     
     def __init__(self,dist):
         install_ori.__init__(self, dist)
         self.sub_commands.insert(0, ('build',lambda self: True))
-        self.sub_commands.append(('install_sphinx',lambda self: self.distribution.serenity))
-
-    def run(self):
-        log.info('\n\nRunning obidistutils install process\n\n')
-        install_ori.run(self)
+        

distutils.ext/obidistutils/command/install_scripts.py

@@ -3,13 +3,8 @@ Created on 20 oct. 2012
 
 @author: coissac
 '''
-try:
-    from setuptools.command.install_scripts import install_scripts as ori_install_scripts
-    has_setuptools = True
-except ImportError:
-    from distutils.command.install_scripts import install_scripts as ori_install_scripts
-    has_setuptools = False
 
+from distutils.command.install_scripts import install_scripts as ori_install_scripts
 import os.path
 from distutils import log
 
@@ -18,8 +13,7 @@ class install_scripts(ori_install_scripts):
     def initialize_options(self):
         ori_install_scripts.initialize_options(self)
         self.deprecated_scripts = None
-        self.public_dir = None
-                        
+        
     def revove_dot_py(self):
         for filename in self.get_outputs():
             pyfile = "%s.py" % filename
@@ -34,23 +28,8 @@ class install_scripts(ori_install_scripts):
                 except:
                     log.info('Unix command %s is not present in build dir' % command)
                     
-    def install_public_link(self):
-        self.mkpath(self.public_dir)
-        for file in self.get_outputs():
-            if self.dry_run:
-                log.info("changing mode of %s", file)
-            else:
-                log.info("exporting file %s -> %s", file,os.path.join(self.public_dir,
-                                        os.path.split(file)[1]
-                                        ))
-                dest = os.path.join(self.public_dir,
-                                    os.path.split(file)[1]
-                                   )
-                if os.path.exists(dest):
-                    os.unlink(dest)
-                os.symlink(file,dest)
-                    
-    def remove_deprecated_script(self):        
+    def remove_deprecated_script(self):
+        
         if self.deprecated_scripts is not None:
             for f in self.deprecated_scripts:
                 try:
@@ -67,13 +46,8 @@ class install_scripts(ori_install_scripts):
 
 
     def run(self):
-
         self.remove_deprecated_script()
         ori_install_scripts.run(self)
-        if self.distribution.serenity:
-            self.public_dir=os.path.join(self.install_dir,"../export/bin")
-            self.public_dir=os.path.abspath(self.public_dir)
-            self.install_public_link()
         self.revove_dot_py()
 
 

distutils.ext/obidistutils/command/install_sphinx.py

@@ -1,46 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-from distutils.core import Command
-import os.path
-import glob
-
-class install_sphinx(Command):
-    '''
-    Install the sphinx documentation
-    '''
-    
-    description = "Install the sphinx documentation in serenity mode"
-
-    boolean_options = ['force', 'skip-build']
-
-
-    def initialize_options (self):
-        self.install_doc = None
-        self.build_dir = None
-
-    def finalize_options (self):
-        self.set_undefined_options('build_sphinx', ('build_dir', 'build_dir'))
-        self.set_undefined_options('install',
-                                   ('install_scripts', 'install_doc'))
-
-    def run (self):
-        if self.distribution.serenity:
-            self.install_doc = os.path.join(self.install_doc,"../export/share")
-            self.install_doc=os.path.abspath(self.install_doc)
-            self.mkpath(self.install_doc)
-            self.mkpath(os.path.join(self.install_doc,'html'))
-            outfiles = self.copy_tree(os.path.join(self.build_dir,'html'), 
-                                      os.path.join(self.install_doc,'html'))
-                
-            self.mkpath(os.path.join(self.install_doc,'man','man1'))
-            outfiles = self.copy_tree(os.path.join(self.build_dir,'man'), 
-                                      os.path.join(self.install_doc,'man','man1'))
-
-            for epub in glob.glob(os.path.join(self.build_dir,'epub/*.epub')):
-                self.copy_file(os.path.join(epub), 
-                               os.path.join(self.install_doc,os.path.split(epub)[1]))
-            
-        

distutils.ext/obidistutils/command/pidname.py

@@ -8,7 +8,7 @@ import os
 
 from obidistutils.command.build_exe import build_exe
 from obidistutils.serenity.checksystem import is_mac_system
-from distutils import log
+
 
 class pidname(build_exe):
     
@@ -44,9 +44,7 @@ class pidname(build_exe):
 
     def run(self):
         if is_mac_system():
-            log.info("Building pidname...")
             build_exe.run(self)
-            log.info("Done")
             self.pidname=True
         else:
             self.pidname=False

distutils.ext/obidistutils/command/sdist.py

@@ -1,46 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-
-import os.path
-
-try:
-    from setuptools.command.sdist import sdist as orig_sdist
-except ImportError:
-    from distutils.command.sdist import sdist as orig_sdist
-    
-from distutils import dir_util
-
-class sdist(orig_sdist):
-
-    def make_distribution(self):
-        """Create the source distribution(s).  First, we create the release
-        tree with 'make_release_tree()'; then, we create all required
-        archive files (according to 'self.formats') from the release tree.
-        Finally, we clean up by blowing away the release tree (unless
-        'self.keep_temp' is true).  The list of archive files created is
-        stored so it can be retrieved later by 'get_archive_files()'.
-        """
-        # Don't warn about missing meta-data here -- should be (and is!)
-        # done elsewhere.
-        base_dir = self.distribution.get_fullname()
-        base_name = os.path.join(self.dist_dir,base_dir)
-
-        self.make_release_tree(os.path.join('tmp',base_dir), self.filelist.files)
-        archive_files = []              # remember names of files we create
-        # tar archive must be created last to avoid overwrite and remove
-        if 'tar' in self.formats:
-            self.formats.append(self.formats.pop(self.formats.index('tar')))
-
-        for fmt in self.formats:
-            file = self.make_archive(base_name, fmt, root_dir='tmp',base_dir=base_dir,
-                                     owner=self.owner, group=self.group)
-            archive_files.append(file)
-            self.distribution.dist_files.append(('sdist', '', file))
-
-        self.archive_files = archive_files
-
-        if not self.keep_temp:
-            dir_util.remove_tree(os.path.join('tmp',base_dir), dry_run=self.dry_run)

distutils.ext/obidistutils/core.py

@@ -8,12 +8,10 @@ from os import path
 import os.path
 import glob
 import sys
-from obidistutils.command.sdist import sdist
 
 
 try:
     from setuptools import setup as ori_setup
-    from setuptools.command.egg_info import egg_info
     has_setuptools = True
 except ImportError:
     from distutils.core import setup as ori_setup
@@ -21,16 +19,15 @@ except ImportError:
 
 from distutils.extension import Extension
 
+
 from obidistutils.command.build import build
 from obidistutils.command.littlebigman import littlebigman
 from obidistutils.command.build_cexe import build_cexe
-from obidistutils.command.build_sphinx import build_sphinx
 from obidistutils.command import build_ext
 from obidistutils.command.build_ctools import build_ctools
 from obidistutils.command.build_files import build_files
 from obidistutils.command.build_scripts import build_scripts
 from obidistutils.command.install_scripts import install_scripts
-from obidistutils.command.install_sphinx import install_sphinx
 from obidistutils.command.install import install
 from obidistutils.command.pidname import pidname
 
@@ -125,15 +122,8 @@ COMMANDS = {'build':build,
             'build_cexe':build_cexe, 
             'build_ext': build_ext,
             'build_scripts':build_scripts, 
-            'build_sphinx':build_sphinx, 
             'install_scripts':install_scripts,
-            'install_sphinx':install_sphinx,
-            'install':install,
-            'sdist':sdist}
-
-if has_setuptools:
-    COMMANDS['egg_info']=egg_info
-    
+            'install':install}
 
 CTOOLS =[]
 CEXES  =[]
@@ -143,11 +133,11 @@ def setup(**attrs):
     
     if has_setuptools:
         try:
-             
+            
             requirements = open('requirements.txt').readlines()
             requirements = [x.strip() for x in requirements]
             requirements = [x for x in requirements if x[0]!='-']
-         
+        
             if 'install_requires' not in attrs:
                 attrs['install_requires']=requirements
             else:
@@ -155,7 +145,6 @@ def setup(**attrs):
         except IOError:
             pass
 
-
     if 'distclass' not in attrs:
         attrs['distclass']=Distribution
 
@@ -188,9 +177,6 @@ def setup(**attrs):
         
     if 'sse' not in attrs:
         attrs['sse']=None
-        
-    if 'serenity' not in attrs:
-        attrs['serenity']=False
     
 
     EXTENTION=findCython(SRC)
@@ -201,7 +187,5 @@ def setup(**attrs):
     
     if 'ext_modules' not in attrs:
         attrs['ext_modules'] = EXTENTION
-        
-    print "$$$$$$$$$$$$$$$$$$$$$$$$$$$",COMMANDS
     
     ori_setup(**attrs)

distutils.ext/obidistutils/dist.py

@@ -4,10 +4,8 @@ Created on 20 oct. 2012
 @author: coissac
 '''
 
-try:
-    from setuptools.dist import Distribution as ori_Distribution
-except ImportError:
-    from distutils.dist import Distribution as ori_Distribution
+
+from distutils.dist import Distribution as ori_Distribution
 
 class Distribution(ori_Distribution):
     
@@ -19,7 +17,6 @@ class Distribution(ori_Distribution):
         self.deprecated_scripts = None
         self.zip_safe=False
         self.sse = None
-        self.serenity=attrs['serenity']
         
         ori_Distribution.__init__(self, attrs)
         
@@ -32,7 +29,6 @@ class Distribution(ori_Distribution):
                                                         "By default the name is PACKAGE-VERSION"
                                      ))
         
-        
     def has_executables(self):
         return self.executables is not None and self.executables
         

distutils.ext/obidistutils/serenity/__init__.py

@@ -42,7 +42,7 @@ from obidistutils.serenity.util import save_argv
                         
 from obidistutils.serenity.snake import snake
 
-from obidistutils.serenity.globals import PIP_MINVERSION, local_serenity
+from obidistutils.serenity.globals import PIP_MINVERSION
                             
     
 def serenity_snake(envname,package,version,minversion=PIP_MINVERSION):
@@ -63,9 +63,7 @@ def serenity_snake(envname,package,version,minversion=PIP_MINVERSION):
         
     log.info("%s will be installed with python : %s" % (package,virtualpython))
         
-    if install_requirements():    
-        log.info("Restarting installation with all dependencies ok")
-        rerun_with_anothe_python(virtualpython)
+    install_requirements()
     
     log.set_threshold(old)
     
@@ -73,9 +71,6 @@ def serenity_assert(version,minversion=PIP_MINVERSION):
     check_requirements()
 
 
-def is_serenity():
-    from obidistutils.serenity.globals import local_serenity
-    return local_serenity and local_serenity[0]
 
 def serenity_mode(package,version):
     
@@ -105,13 +100,12 @@ def serenity_mode(package,version):
     sys.argv = [sys.argv[0]] + unknown
     
     if args.serenity:
-        local_serenity.append(True)
         serenity_snake(args.virtual,package,version)
     else:
-        local_serenity.append(False)       
+        pass
+        # serenity_assert(package,version)
+        
     
     log.set_threshold(old)
     
-    return args.serenity
-    
     

distutils.ext/obidistutils/serenity/checkpackage.py

@@ -80,7 +80,7 @@ def install_requirements(skip_virtualenv=True,pip=None):
     if pip is None:
         pip = get_a_pip_module()
     
-    install_something=False
+ 
     try:
         requirements = open('requirements.txt').readlines()
         requirements = [x.strip() for x in requirements]
@@ -93,12 +93,9 @@ def install_requirements(skip_virtualenv=True,pip=None):
                 if not ok:
                     log.info("  Installing requirement : %s" % x)
                     pip_install_package(x,pip=pip)
-                    install_something=True
                 
     except IOError:
         pass
-    
-    return install_something
  
 
 def check_requirements(skip_virtualenv=True,pip=None):

distutils.ext/obidistutils/serenity/checkpip.py

@@ -56,13 +56,41 @@ def get_a_pip_module(minversion=PIP_MINVERSION):
     tmpdir = get_serenity_dir()
     
     if not local_pip:    
+#        if not is_pip_installed(minversion):
+#             try:
+#                 if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
+#                     os.environ['https_proxy']=os.environ['http_proxy']
+#                 pipinstallscript = urllib2.urlopen('https://bootstrap.pypa.io/get-pip.py')
+#             except:
+#                 raise DistutilsError,"Pip (>=%s) is not install on your system and I cannot install it" % PIP_MINVERSION
+#             
+#             script = pipinstallscript.read()
+#             getpip_py = os.path.join(tmpdir, "get-pip.py")
+#             with open(getpip_py, "wb") as fp:
+#                 log.info("Downloading temporary pip...")
+#                 fp.write(script)
+#                 log.info("   done.")
+#                 
+#             getpip = imp.load_source("getpip",getpip_py)
+#             ZIPFILE=getpip.ZIPFILE
+#     
+#             pip_zip = os.path.join(tmpdir, "pip.zip")
+#             with open(pip_zip, "wb") as fp:
+#                 log.info("Installing temporary pip...")
+#                 fp.write(base64.decodestring(ZIPFILE))
+#                 log.info("   done.")
+#                 
+#             # Add the zipfile to sys.path so that we can import it
+#             sys.path.insert(0,pip_zip)
+#             zi = zipimport.zipimporter(pip_zip)
+#             pip = zi.load_module("pip") 
+#            pip = importlib.import_module('obidistutils.serenity.pip')
+#        else:
         serenity = importlib.import_module('obidistutils.serenity')
         sys.path.insert(0, os.path.dirname(serenity.__file__))
         pip = importlib.import_module('pip')
 
         local_pip.append(pip)
-    else:
-        pip = local_pip[-1]
     
     # Prepare the CERT certificat for https download
             

distutils.ext/obidistutils/serenity/checksystem.py

@@ -5,12 +5,10 @@ Created on 2 oct. 2014
 '''
 
 from distutils import util
-from distutils import log
 
 def is_mac_system():
     platform = util.get_platform().split('-')[0]
-    if platform=='macosx':
-        log.info('You are running on a Mac platform')
+    
     return platform=='macosx'
 
 def is_windows_system():

distutils.ext/obidistutils/serenity/getcython.py

@@ -1,72 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import imp
-import importlib
-
-from distutils.errors import DistutilsError
-from distutils.version import StrictVersion  
-from distutils import log       
-
-from obidistutils.serenity.globals import local_cython  # @UnusedImport
-
-from obidistutils.serenity.checkpip import get_a_pip_module
-
-from obidistutils.serenity.checkpackage import get_package_requirement
-from obidistutils.serenity.checkpackage import parse_package_requirement
-from obidistutils.serenity.checkpackage import is_installed
-from obidistutils.serenity.checkpackage import pip_install_package
-
-from obidistutils.serenity.util import get_serenity_dir
-
-
-def get_a_cython_module(pip=None):
-    
-    global local_cython
-
-    if not local_cython:
-        if pip is None:
-            pip = get_a_pip_module()
-         
-        
-        cython_req = get_package_requirement('Cython',pip)
-        if cython_req is None:
-            cython_req='Cython'
-        
-        requirement_project,requirement_relation,minversion = parse_package_requirement(cython_req)  # @UnusedVariable
-        
-        
-        
-        if cython_req is None or not is_installed(cython_req, pip):
-            tmpdir = get_serenity_dir()
-            
-            ok = pip_install_package(cython_req,directory=tmpdir,pip=pip)
-            
-            log.debug('temp install dir : %s' % tmpdir)
-                
-            if ok!=0:
-                raise DistutilsError, "I cannot install a cython package"
-    
-            f, filename, description = imp.find_module('Cython', [tmpdir])
-            
-            cythonmodule = imp.load_module('Cython', f, filename, description)
-            
-            if minversion is not None:
-                assert StrictVersion(cythonmodule.__version__) >= minversion, \
-                       "Unable to find suitable version of cython get %s instead of %s" % (cythonmodule.__version__,
-                                                                                        minversion)
-    
-        else:
-            cythonmodule = importlib.import_module('Cython') 
-            
-        local_cython.append(cythonmodule)
-           
-    return local_cython[0]
-
-        
-
-    
-    

distutils.ext/obidistutils/serenity/globals.py

@@ -11,5 +11,3 @@ saved_args=[]
 tmpdir=[]
 local_pip=[]
 local_virtualenv=[]
-local_cython=[]
-local_serenity=[]

distutils.ext/obidistutils/serenity/pip/__init__.py

@@ -106,7 +106,7 @@ def create_main_parser():
 
     parser = ConfigOptionParser(**parser_kw)
     parser.disable_interspersed_args()
-    
+
     pip_pkg_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
     parser.version = 'pip %s from %s (python %s)' % (
         __version__,  pip_pkg_dir, sys.version[:3])