switch to the new version 1.2.7

bug on windows cygwin

.project

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

@@ -1,7 +1,8 @@
 include setup.py
-recursive-include distutils.ext *.py *.c
+recursive-include distutils.ext *.py *.c *.pem
 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

@@ -7,6 +7,7 @@ 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):
     
@@ -28,10 +29,19 @@ 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
+                   + ori_build.sub_commands + \
+                   [('build_sphinx',has_doc)]
+                   
+    def run(self):
+        log.info('\n\nRunning obidistutils build process\n\n')
+        ori_build.run(self)
     

distutils.ext/obidistutils/command/build_cexe.py

@@ -4,11 +4,8 @@ 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

@@ -4,26 +4,35 @@ 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:
-    from distutils.command.build_ext import build_ext as ori_build_ext 
-from distutils.errors import DistutilsSetupError
-import os
+    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.errors import DistutilsSetupError
 
 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)  
+        ori_build_ext.initialize_options(self)  # @UndefinedVariable
         self.littlebigman = None
         self.built_files = None
 
     
     def finalize_options(self):
-        ori_build_ext.finalize_options(self)
+        ori_build_ext.finalize_options(self)  # @UndefinedVariable
 
         self.set_undefined_options('littlebigman',
                                    ('littlebigman',  'littlebigman'))
@@ -83,10 +92,23 @@ class build_ext(ori_build_ext):
         
     def run(self):
         self.modifyDocScripts()
-        ori_build_ext.run(self)
+        ori_build_ext.run(self)  # @UndefinedVariable
         
 
     
+#     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

@@ -0,0 +1,38 @@
+'''
+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

@@ -4,11 +4,22 @@ Created on 6 oct. 2014
 @author: coissac
 '''
 
-from distutils.command.install import install as install_ori
+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
 
 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

@@ -3,8 +3,13 @@ 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
 
@@ -13,6 +18,7 @@ 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():
@@ -28,8 +34,23 @@ class install_scripts(ori_install_scripts):
                 except:
                     log.info('Unix command %s is not present in build dir' % command)
                     
-    def remove_deprecated_script(self):
+    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):        
         if self.deprecated_scripts is not None:
             for f in self.deprecated_scripts:
                 try:
@@ -46,8 +67,13 @@ 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

@@ -0,0 +1,46 @@
+'''
+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):
     
@@ -44,7 +44,9 @@ 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

@@ -0,0 +1,46 @@
+'''
+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

@@ -8,10 +8,12 @@ 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
@@ -19,15 +21,16 @@ 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
 
@@ -122,8 +125,15 @@ COMMANDS = {'build':build,
             'build_cexe':build_cexe, 
             'build_ext': build_ext,
             'build_scripts':build_scripts, 
+            'build_sphinx':build_sphinx, 
             'install_scripts':install_scripts,
-            'install':install}
+            'install_sphinx':install_sphinx,
+            'install':install,
+            'sdist':sdist}
+
+if has_setuptools:
+    COMMANDS['egg_info']=egg_info
+    
 
 CTOOLS =[]
 CEXES  =[]
@@ -145,6 +155,7 @@ def setup(**attrs):
         except IOError:
             pass
 
+
     if 'distclass' not in attrs:
         attrs['distclass']=Distribution
 
@@ -178,6 +189,9 @@ def setup(**attrs):
     if 'sse' not in attrs:
         attrs['sse']=None
         
+    if 'serenity' not in attrs:
+        attrs['serenity']=False
+    
 
     EXTENTION=findCython(SRC)
     CEXTENTION=findC(SRC)

distutils.ext/obidistutils/dist.py

@@ -4,8 +4,10 @@ Created on 20 oct. 2012
 @author: coissac
 '''
 
-
-from distutils.dist import Distribution as ori_Distribution
+try:
+    from setuptools.dist import Distribution as ori_Distribution
+except ImportError:
+    from distutils.dist import Distribution as ori_Distribution
 
 class Distribution(ori_Distribution):
     
@@ -17,6 +19,7 @@ class Distribution(ori_Distribution):
         self.deprecated_scripts = None
         self.zip_safe=False
         self.sse = None
+        self.serenity=attrs['serenity']
         
         ori_Distribution.__init__(self, attrs)
         
@@ -29,6 +32,7 @@ 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
+from obidistutils.serenity.globals import PIP_MINVERSION, local_serenity
                             
     
 def serenity_snake(envname,package,version,minversion=PIP_MINVERSION):
@@ -63,7 +63,9 @@ def serenity_snake(envname,package,version,minversion=PIP_MINVERSION):
         
     log.info("%s will be installed with python : %s" % (package,virtualpython))
         
-    install_requirements()
+    if install_requirements():    
+        log.info("Restarting installation with all dependencies ok")
+        rerun_with_anothe_python(virtualpython)
     
     log.set_threshold(old)
     
@@ -71,6 +73,9 @@ 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):
     
@@ -100,12 +105,13 @@ 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:
-        pass
-        # serenity_assert(package,version)
-        
+        local_serenity.append(False)       
     
     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]
@@ -93,10 +93,13 @@ 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

@@ -56,41 +56,13 @@ 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

@@ -5,10 +5,12 @@ 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

@@ -0,0 +1,72 @@
+'''
+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

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