Actualiser README.md

better check of format

.gitignore

@@ -0,0 +1,24 @@
+/OBITools-1.1.19/
+/OBITools-1.1.20/
+/OBITools-1.1.21/
+/OBITools-1.1.22/
+/OBITools-1.2.0/
+/obitools.test/
+/build/
+/dist/
+/OBITools-1.2.2/
+/OBITools-1.2.3/
+/OBITools-1.2.4/
+/OBITools-1.2.5/
+/OBITools-1.2.6/
+/OBITools-1.2.7/
+/OBITools-1.2.8/
+/OBITools-1.2.9/
+/OBITools-1.2.10/
+/.DS_Store
+/OBITools-1.2.11/
+/OBITools-1.2.12/
+/obitools.test.old/
+/coucou
+/toto.fasta
+/OBITools-1.2.13/

.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-1.1/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>

Dockerfile

@@ -0,0 +1,102 @@
+FROM python:2.7.17-alpine AS builder
+
+RUN apk add --no-cache \
+    bash flex build-base curl openssl-dev bzip2-dev readline-dev sqlite-dev zlib-dev xz-dev tk-dev libffi-dev make ncurses-dev git
+
+RUN pip install Cython==0.29
+
+RUN mkdir -p /app
+WORKDIR /app
+COPY src .
+
+RUN gcc -o littlebigman littlebigman.c
+RUN python setup.py build_ext --inplace
+RUN python setup.py install
+RUN ./install.sh
+
+WORKDIR /app
+RUN git clone https://forge.metabarcoding.org/obitools/ecopcr.git
+WORKDIR /app/ecopcr/src
+RUN make clean && make \
+    && cp ecoPCR ecofind ecogrep /usr/local/bin
+
+WORKDIR /app
+RUN git clone https://forge.metabarcoding.org/obitools/ecoprimers.git
+WORKDIR /app/ecoprimers/src
+RUN make clean && make \
+    && cp ecoPrimers /usr/local/bin \
+    && cp ../tools/ecoPCRFormat.py /usr/local/bin/ecoPCRFormat \
+    && chmod +x /usr/local/bin/ecoPCRFormat
+
+WORKDIR /app
+RUN git clone --recurse-submodules https://forge.metabarcoding.org/obitools/sumatra.git
+WORKDIR /app/sumatra
+RUN make clean && make \
+    && cp sumatra /usr/local/bin 
+
+WORKDIR /app
+RUN git clone --recurse-submodules https://forge.metabarcoding.org/obitools/sumaclust.git
+WORKDIR /app/sumaclust
+RUN make clean && make \
+    && cp sumaclust /usr/local/bin 
+
+RUN find /usr/local/bin /usr/local/python2/bin /usr/local/python2/lib -type f -exec file {} \; | \
+    grep -E 'ELF (32-bit|64-bit) (executable|shared object)' | \
+    cut -d: -f1 | \
+    xargs -r strip --strip-unneeded || true
+
+RUN pip install "virtualenv<20" && \
+    virtualenv --system-site-packages /obitools-doc 
+    
+ENV PATH="/obitools-doc/bin:${PATH}"
+RUN pip install "sphinx==1.8.5"
+
+COPY doc /obitools-doc/doc
+
+RUN echo "/doc" > /obitools-doc/doc/sphinx/build_dir.txt
+
+ENV PYTHONPATH="/app"
+
+WORKDIR /obitools-doc/doc/sphinx
+RUN make html
+RUN cp /app/docserver.sh /usr/local/bin/docserver
+RUN chmod +x /usr/local/bin/docserver
+
+
+#--- Image finale minimaliste ---
+FROM python:2.7.17-alpine
+LABEL org.opencontainers.image.title="OBITools2 (legacy)"
+LABEL org.opencontainers.image.description="Legacy OBITools2 environment for compatibility with older pipelines and benchmarks. Includes OBITools2, ecoPCR, ecoPrimers, sumatra, and sumaclust. Python 2-based software stack. Full documentation embedded in the image."
+LABEL org.opencontainers.image.version="latest"
+LABEL org.opencontainers.image.authors="Eric Coissac <eric.coissac@metabarcoding.org>"
+LABEL org.opencontainers.image.url="https://registry.metabarcoding.org/image/obitools%2Fobitools2"
+LABEL org.opencontainers.image.documentation="https://metabarcoding.org/en/obitools/obitools2"
+LABEL org.opencontainers.image.source="https://forge.metabarcoding.org/obitools/obitools"
+
+# Dépendances runtime seulement (exemple)
+RUN apk add --no-cache \
+    openssl \
+    zlib \
+    libgomp
+
+# Copier Python compilé et libs depuis le builder
+COPY --from=builder /usr/local/lib/python2.7/site-packages /usr/local/lib/python2.7/site-packages
+COPY --from=builder /usr/local/bin /usr/local/bin
+COPY --from=builder /obitools-doc/doc/sphinx/build/html /doc
+
+RUN rm -rf /usr/local/share /usr/local/include /usr/local/lib/pkgconfig /usr/local/lib/python2.7/test && \
+    find /usr/local/bin /usr/local/python2/bin /usr/local/python2/lib -type f -exec file {} \; | \
+    grep -E 'ELF (32-bit|64-bit) (executable|shared object)' | \
+    cut -d: -f1 | \
+    xargs -r strip --strip-unneeded || true
+
+RUN mkdir -p /data 
+
+ENV LD_LIBRARY_PATH=/usr/local/lib
+ENV PATH="/usr/local/bin:${PATH}"
+
+VOLUME ["/data"]
+
+WORKDIR /data
+
+CMD ["ash"]

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

README.md

@@ -0,0 +1,11 @@
+# Legacy OBITools status
+
+Legacy OBITools is 20 years old. It was developed using Python 2, a language that is no longer supported. Therefore, maintaining this code is impossible. It has now been superseded by OBITools4, the latest version in the OBITools lineage.
+
+In order to enable users to continue using Legacy OBITools, a Docker image has been created and made available on the [metabarcoding.org registry](https://registry.metabarcoding.org). While we discourage using this old version for new projects, being able to run it can still be useful for reproducibility purposes.
+
+You can find more information about using this Docker image on the [relevant page](https://metabarcoding.org/en/obitools/obitools2) of the [new metabarcoding website](https://metabarcoding.org).
+
+All the best,
+
+Eric Coissac

distutils.ext/.gitignore

@@ -0,0 +1,2 @@
+*.pyc
+/.DS_Store

distutils.ext/obidistutils/.gitignore

@@ -0,0 +1 @@
+/*.pyc

distutils.ext/obidistutils/command/.gitignore

@@ -0,0 +1 @@
+/*.pyc

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):
     
@@ -27,11 +28,20 @@ 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 
+    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
-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)  
+        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'))
@@ -83,8 +92,21 @@ 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 +1,41 @@
+'''
+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
+    
+    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)
+
+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))
+        
+    
+    

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
 
@@ -13,7 +18,8 @@ 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
@@ -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  =[]
@@ -133,11 +143,11 @@ 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:
@@ -145,6 +155,7 @@ def setup(**attrs):
         except IOError:
             pass
 
+
     if 'distclass' not in attrs:
         attrs['distclass']=Distribution
 
@@ -177,6 +188,9 @@ def setup(**attrs):
         
     if 'sse' not in attrs:
         attrs['sse']=None
+        
+    if 'serenity' not in attrs:
+        attrs['serenity']=False
     
 
     EXTENTION=findCython(SRC)
@@ -187,5 +201,5 @@ def setup(**attrs):
     
     if 'ext_modules' not in attrs:
         attrs['ext_modules'] = EXTENTION
-    
+            
     ori_setup(**attrs)

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/.gitignore

@@ -0,0 +1 @@
+/*.pyc

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]
@@ -93,9 +93,12 @@ 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=[]

distutils.ext/obidistutils/serenity/pip/.gitignore

@@ -0,0 +1 @@
+/*.pyc

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])

distutils.ext/obidistutils/serenity/pip/_vendor/.gitignore

@@ -0,0 +1 @@
+/*.pyc

distutils.ext/obidistutils/serenity/rerun.py

@@ -16,7 +16,7 @@ from obidistutils.serenity.checkpython import is_good_python27, \
                                               lookfor_good_python27
 
 
-def rerun_with_anothe_python(path):
+def rerun_with_anothe_python(path, fork=False):
         
     if saved_args:
         args = saved_args
@@ -32,8 +32,13 @@ def rerun_with_anothe_python(path):
     sys.stderr.flush()
     sys.stdout.flush()
     
-
-    os.execv(path,list(args))
+    if fork:
+        log.info('Forking a new install process')
+        os.system(' '.join(list(args)))
+        log.info('External process ended')
+        sys.exit(0)
+    else:
+        os.execv(path,list(args))
 
 def enforce_good_python():
     if is_good_python27():

distutils.ext/obidistutils/serenity/virtual.py

@@ -18,7 +18,8 @@ from obidistutils.serenity.globals import PIP_MINVERSION, \
 
 from obidistutils.serenity.checkpip import get_a_pip_module
 
-from obidistutils.serenity.checkpackage import get_package_requirement
+from obidistutils.serenity.checkpackage import get_package_requirement,\
+    install_requirements
 from obidistutils.serenity.checkpackage import parse_package_requirement
 from obidistutils.serenity.checkpackage import is_installed
 from obidistutils.serenity.checkpackage import pip_install_package
@@ -61,7 +62,7 @@ def get_a_virtualenv_module(pip=None):
             
             if minversion is not None:
                 assert StrictVersion(vitualenvmodule.__version__) >= minversion, \
-                       "Unable to find suitable version of pip get %s instead of %s" % (vitualenvmodule.__version__,
+                       "Unable to find suitable version of virtualenv get %s instead of %s" % (vitualenvmodule.__version__,
                                                                                         minversion)
     
         else:
@@ -112,7 +113,7 @@ def serenity_virtualenv(envname,package,version,minversion=PIP_MINVERSION,pip=No
                  
     else:
         ok = False
-        
+                
         
     #
     # Creates a new virtualenv

doc/sphinx/Makefile

@@ -56,6 +56,11 @@ json:
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished."
+
 htmlhelp:
 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
 	@echo

doc/sphinx/source/conf.py

@@ -12,6 +12,7 @@
 # serve to show the default.
 
 import sys, os
+import glob
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -37,7 +38,7 @@ import obitools.version
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 
               'sphinx.ext.coverage', 'sphinx.ext.viewcode',
               'sphinx.ext.graphviz', 'sphinx.ext.inheritance_diagram',
-              'sphinx.ext.pngmath',
+              'sphinx.ext.imgmath',
 #              'matplotlib.sphinxext.mathmpl',
 #              'matplotlib.sphinxext.only_directives',
 #              'matplotlib.sphinxext.plot_directive',
@@ -61,7 +62,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'OBITools'
-copyright = u'2009 - 2013, OBITool Development Team'
+copyright = u'2009 - 2015, OBITool Development Team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -244,3 +245,18 @@ PygmentsBridge.latex_formatter = CustomLatexFormatter
 epub_publisher=u"metabarcoding.org"
 epub_author=u"OBITools Development Team"
 
+#--options for the man format -------------------------------
+
+
+man_pages = [] 
+
+for f in glob.glob('scripts/*.rst'): 
+    man_pages.append(( 
+        f[:-4],                    # source file (no extension) 
+        os.path.split(f[:-4])[1],  # output file (under output dir) 
+        'description of %s' % os.path.split(f[:-4])[1],   # description 
+        'The OBITools Development Team - LECA',               # author 
+        1,                         # section 
+    )) 
+
+

doc/sphinx/source/conversions.rst

@@ -5,5 +5,7 @@ File format conversions
    :maxdepth: 2
    
    scripts/obiconvert
+   scripts/obipr2
+   scripts/obisilva
    scripts/obitaxonomy
    scripts/obitab

doc/sphinx/source/filtering.rst

@@ -3,12 +3,12 @@ Sequence sampling and filtering
 
 .. toctree::
    :maxdepth: 2
-   
+
+   scripts/obiextract
    scripts/obigrep
    scripts/obihead
    scripts/obisample
    scripts/obiselect
    scripts/obisplit
+   scripts/obisubset
    scripts/obitail
-   
-   

doc/sphinx/source/optionsSet/inputformat.txt

@@ -3,6 +3,24 @@ Options to specify input format
 
 .. program:: obitools
 
+
+Restrict the analysis to a sub-part of the input file
+.....................................................
+
+.. cmdoption::  --skip <N>
+
+      The N first sequence records of the file are discarded from the analysis and 
+      not reported to the output file
+      
+
+.. cmdoption::  --only <N>
+
+      Only the N next sequence records of the file are analyzed. The following sequences
+      in the file are neither analyzed, neither reported to the output file.
+      This option can be used conjointly with the `--skip` option.
+      
+
+
 Sequence annotated format
 .........................
 

doc/sphinx/source/scripts/ecotag.rst

@@ -1,55 +1,79 @@
 .. automodule:: ecotag
-   
+
    :py:mod:`ecotag` specific options
    ---------------------------------
 
-   .. cmdoption::  -R <FILENAME>, --ref-database=<FILENAME>   
-   
+   .. cmdoption::  -R <FILENAME>, --ref-database=<FILENAME>
+
         <FILENAME> is the fasta file containing the reference sequences
 
    .. cmdoption::  -m FLOAT, --minimum-identity=FLOAT
-   
-        When sequence identity is less than FLOAT, the taxonomic 
-        assignment for the sequence record is not indicated in ``ecotag``'s 
-        output. FLOAT is included in a [0,1] interval.
-        (This option doesn't seem to work).
+
+        When the best match with the reference database present an identity
+        level below FLOAT, the taxonomic assignment for the sequence record
+        is not computed. The sequence record is nevertheless included in the
+        output file. FLOAT is included in a [0,1] interval.
+
+   .. cmdoption::    --minimum-circle=FLOAT
+
+        minimum identity considered for the assignment circle.
+        FLOAT is included in a [0,1] interval.
 
    .. cmdoption::  -x RANK, --explain=RANK
-   
+
    .. cmdoption::  -u, --uniq
-   
-        When this option is specified, the program first dereplicates the sequence 
-        records to work on unique sequences only. This option greatly improves 
+
+        When this option is specified, the program first dereplicates the sequence
+        records to work on unique sequences only. This option greatly improves
         the program's speed, especially for highly redundant datasets.
 
    .. cmdoption::  --sort=<KEY>
-   
+
         The output is sorted based on the values of the relevant attribute.
 
    .. cmdoption::  -r, --reverse
-   
+
         The output is sorted in reverse order (should be used with the --sort option).
-        (Works even if the --sort option is not set, but could not find on what 
+        (Works even if the --sort option is not set, but could not find on what
         the output is sorted).
 
    .. cmdoption::  -E FLOAT, --errors=FLOAT
-   
-        FLOAT is the fraction of reference sequences that will 
-        be ignored when looking for the most recent common ancestor. This 
-        option is useful when a non-negligible proportion of reference sequences 
-        is expected to be assigned to the wrong taxon, for example because of 
+
+        FLOAT is the fraction of reference sequences that will
+        be ignored when looking for the lowest common ancestor. This
+        option is useful when a non-negligible proportion of reference sequences
+        is expected to be assigned to the wrong taxon, for example because of
         taxonomic misidentification. FLOAT is included in a [0,1] interval.
 
+
+   .. cmdoption::  -M INTEGER, --min-matches=FLOAT
+
+        Define the minimum congruent assignation. If this minimum is reached and
+        the -E option is activated, the lowest common ancestor algorithm tolarated
+        that some sequences do not provide the same taxonomic annotation (see the
+        -E option).
+
+
+   .. cmdoption::  --cache-size=INTEGER
+
+        A cache for computed similarities is maintained by `ecotag`. the default
+        size for this cache is 1,000,000 of scores. This option allows to change
+        the cache size.
+
    .. include:: ../optionsSet/taxonomyDB.txt
-   
+
+   .. include:: ../optionsSet/inputformat.txt
+
+   .. include:: ../optionsSet/outputformat.txt
+
    .. include:: ../optionsSet/defaultoptions.txt
-   
+
    :py:mod:`ecotag` added sequence attributes
    ------------------------------------------
-   
+
       .. hlist::
            :columns: 3
-           
+
            - :doc:`best_identity <../attributes/best_identity>`
            - :doc:`best_match <../attributes/best_match>`
            - :doc:`family <../attributes/family>`
@@ -65,4 +89,3 @@
            - :doc:`species_list <../attributes/species_list>`
            - :doc:`species_name <../attributes/species_name>`
            - :doc:`taxid <../attributes/taxid>`
-      

doc/sphinx/source/scripts/obiextract.rst

@@ -0,0 +1,61 @@
+.. automodule:: obiextract
+   
+   :py:mod:`obiextract` specific options
+   -------------------------------------  
+
+   .. cmdoption::  -s <KEY>, --sample=<KEY>  
+   
+                   Attribute containing sample descriptions. By default the attribute
+                   name used for describing samples is set to ``merged_sample``.
+                   
+
+   .. cmdoption::  -e <SAMPLE_NAME>, --extract=<KEY>   
+   
+        Attribute indicating which <SAMPLE_NAME> have to be extracted. 
+        Several ``-p`` options can be added for specifying several samples.
+        If you want to extract a large number of samples, please refer to the ``-E``
+        option described below 
+ 
+        .. TIP:: The ``<KEY>`` can be simply the key of an attribute, or a *Python* expression
+                 similarly to the ``-p`` option of :py:mod:`obigrep`.
+
+    *Example:*
+    
+    		.. code-block:: bash
+    
+       			> obiextract -e sampleA -e sampleB allseqs.fasta > samplesAB.fasta
+     
+		This command extracts from the ``allseqs.fasta`` file data related to samples ``A`` and ``B``.
+   
+             
+   .. cmdoption::  -E <FILENAME>, --extract-list=<FILENAME>  
+   
+		Allows for indicating a file name where a list of sample is stored. The file must be a simple
+		text file with a sample name per line.
+
+   	*Example:*
+        
+    		.. code-block:: bash
+    
+       			> obiextract -E subset.txt allseqs.fasta > subset_samples.fasta
+    
+		This command extracts from the ``allseqs.fasta`` file data related to samples listed in the ``subset.txt`` file.
+
+
+   .. include:: ../optionsSet/inputformat.txt
+   
+   .. include:: ../optionsSet/outputformat.txt
+    
+   .. include:: ../optionsSet/defaultoptions.txt
+   
+   :py:mod:`obiextract` modified sequence attributes
+   -------------------------------------------------
+
+		- :doc:`count <../attributes/count>`
+
+   :py:mod:`obiextract` used sequence attribute
+   --------------------------------------------
+   
+		- :doc:`count <../attributes/count>`
+     
+   

doc/sphinx/source/scripts/obipr2.rst

@@ -0,0 +1,22 @@
+.. automodule:: obipr2
+   
+   :py:mod:`obipr2` specific options
+   -------------------------------------  
+
+   .. cmdoption::  --local=<DIRNAME> 
+   
+		Specify you have already downloaded a copy of the PR2 database located at the following URL
+		`<http://5.196.17.195/pr2/download/entire_database>`_
+		
+    *Example:*
+
+    		.. code-block:: bash
+    
+       			> obipr2 --local=PR2Dir
+       			
+       		This format **PR2** database pre-downloaded in the `PR2Dir` directory.
+		
+
+   .. include:: ../optionsSet/defaultoptions.txt
+   
+   

doc/sphinx/source/scripts/obisilva.rst

@@ -0,0 +1,71 @@
+.. automodule:: obisilva
+   
+   :py:mod:`obisilva` specific options
+   -------------------------------------  
+
+   .. cmdoption::  -s , --ssu  
+   
+        Specify that you are interested in the **SSU** database.
+                   
+    *Example:*
+
+    		.. code-block:: bash
+    
+       			> obisilva --ssu --parc
+
+		This download and format into an ecoPCR database the latest version of the **SSUParc** database of **Silva**.
+
+   .. cmdoption::  -l, --lsu   
+   
+        Specify that you are interested in the **LSU** database.
+
+    *Example:*
+    
+    		.. code-block:: bash
+    
+       			> obisilva --ssu --parc
+
+		This download and format into an ecoPCR database the latest version of the **LSUParc** database of **Silva**.
+   
+             
+   .. cmdoption::  -p , --parc  
+   
+		Specify that you are interested in the **Parc** (complete) version of the **Silva** database.
+
+
+   .. cmdoption::  -r , --ref  
+   
+		Specify that you are interested in the **Reference** (cleaned to keep only high quality sequences) 
+		version of the **Silva** database.
+
+   .. cmdoption::  -n , --nr  
+   
+		Specify that you are interested in the **Non redundant** version of the **Silva** database.
+		just a version of the to closely related sequence is kept in this version of the database
+		
+		.. warning::
+			Non redundant version of **Silva** exists only for the SSU sequences 
+			in its **Reference** and  **Truncated** version
+
+   .. cmdoption::  -t , --trunc 
+   
+		Specify that you are interested in the **Truncated** (limited to the rDNA element without flanked regions) 
+		version of the **Silva** database.
+
+   .. cmdoption::  --local=<DIRNAME> 
+   
+		Specify you have already downloaded a copy of the **Silva** database located at the following URL
+		`<http://www.arb-**Silva**.de/no_cache/download/archive/current/Exports/>`_
+		
+    *Example:*
+
+    		.. code-block:: bash
+    
+       			> obisilva --ssu --parc --local=**Silva**Dir
+       			
+       		This format the **SSUParc** version of the **Silva** database pre-downloaded in the `**Silva**Dir` directory.
+		
+
+   .. include:: ../optionsSet/defaultoptions.txt
+   
+   

doc/sphinx/source/scripts/obisubset.rst

@@ -0,0 +1,81 @@
+.. automodule:: obisubset
+ 
+
+   :py:mod:`obisubset` specific options
+   ------------------------------------
+
+   .. cmdoption::  -s <TAGNAME>,  --sample=<TAGNAME>,
+
+     The option ``-s`` allows to specify the tag containing sample descriptions,
+     the default value is set to *merged_sample*.
+
+     *Example:*
+
+         .. code-block:: bash
+
+             > obiuniq -m sample seq1.fasta > seq2.fasta
+             > obisubset -s merged_sample -n sample1 seq2.fasta > seq3.fasta
+
+         After the dereplication of the sequences using the
+         in the new attribute ``merged_sample``.
+
+   .. cmdoption::  -o <TAGNAME>,  --other-tag=<TAGNAME>,
+
+     Another tag to clean according to the sample subset
+
+     *Example:*
+
+          .. code-block:: bash
+
+              > obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta
+
+   .. cmdoption::  -l <FILENAME>,  --sample-list=<FILENAME>,
+
+     File containing the samples names (one sample id per line).
+
+     *Example:*
+
+          .. code-block:: bash
+
+              > obisubset -s merged_sample -o -l ids.txt seq2.fasta > seq3.fasta
+
+   .. cmdoption::  -p <REGEX>,  --sample-pattern=<REGEX>,
+
+     A regular expression pattern matching the sample ids to extract.
+
+     *Example:*
+
+         .. code-block:: bash
+
+             > obisubset -s merged_sample -o -p "negative_.*" seq2.fasta > seq3.fasta
+
+   .. cmdoption::  -n <SAMPLEIDS>,  --sample-name=<SAMPLEIDS>,
+
+     A sample id to extract
+
+     *Example:*
+
+          .. code-block:: bash
+
+              > obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta
+
+   .. include:: ../optionsSet/inputformat.txt
+
+   .. include:: ../optionsSet/outputformat.txt
+
+   .. include:: ../optionsSet/defaultoptions.txt
+
+   :py:mod:`obisubset` modifies sequence attributes
+   ------------------------------------------------
+
+      .. hlist::
+           :columns: 3
+
+           - :doc:`count <../attributes/count>`
+           - :doc:`merged_* <../attributes/merged_star>`
+
+   :py:mod:`obisubset` used sequence attribute
+   -------------------------------------------
+
+           - :doc:`count <../attributes/taxid>`
+           - :doc:`merged_* <../attributes/merged_star>`

doc/sphinx/source/welcome.rst

@@ -20,7 +20,7 @@ Ecology Resources*, submitted.
 :latex:`\vspace{\fill}`
     
 Installing the ``OBITools``
----------------------------
+===========================
 
 Availability of the ``OBITools``
 ................................
@@ -35,150 +35,10 @@ and all the sources can be downloaded from our subversion server
 Prerequisites
 .............
 
-To install the ``OBITools``, you need that these softwares are installed on your 
-system:
-
-* Python 2.7 (installed by default on most ``Unix`` systems, available from 
-  `the Python website <http://www.python.org/>`_)
-* ``gcc`` (installed by default on most ``Unix`` systems, available from the 
-  GNU sites dedicated to `GCC <https://www.gnu.org/software/gcc/>`_ and 
-  `GMake <https://www.gnu.org/software/make/>`_)
-  
-On a linux system 
-^^^^^^^^^^^^^^^^^
-
-You have to take care that the Python-dev packages are installed.
-
-On MacOSX
-^^^^^^^^^
-
-The C compiler and all the other compilation tools are included in the `XCode <https://itunes.apple.com/fr/app/xcode/id497799835?mt=12>`_
-application not installed by default. The Python included in the system is not
-suitable for running the ``OBITools``. You have to install a complete distribution
-of Python that you can download as a `MacOSX package from the Python website <https://www.python.org/downloads/>`_.
-  
-User level installation
-.......................
-
-There is two main ways for installing the ``OBITools``. The easiest one is to install them
-using the :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` script.
-
-Once downloaded, move the file :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` in the directory where you want to install
-the ``OBITools``. From a Unix terminal you must now run the command :
-
-  .. code-block:: bash
-
-      > python get-obitools.py
-      
-The script will create a new directory at the place you are running it in which all the
-``OBITools`` will be installed. No system privilege are required, and you system will not
-be altered in any way by the obitools installation.
-
-The newly created directory is named OBITools-VERSION where version is substituted by the
-latest version number available.
-
-Inside the newly created directory all the ``OBITools`` are installed. Close to this directory
-there is a shell script named ``obitools``. Running this script activate the ``OBITools``
-by reconfiguring your Unix environment. 
-
-  .. code-block:: bash
-
-	> ./obitools
-
-Once activated you can desactivate the ``OBITools`` byt typing the command ``exit``.
-
-  .. code-block:: bash
-
-	> exit
-	
-	OBITools are no more activated, Bye...
-	======================================
-	
-
-System level installation
-.........................
-
-As all the Python software deposited on `PyPI <https://pypi.python.org/pypi/obitools>`_, ``OBITools`` can be
-installed using the `pip` (`https://pypi.python.org/pypi/pip <https://pypi.python.org/pypi/pip>`_) command.
-We recommand to use `pip` over `easy_install` as python package manager. 
-If you have not ``pip`` installed on your computer, please visite the
-following page: `http://pip.readthedocs.org/en/latest/installing.html <http://pip.readthedocs.org/en/latest/installing.html>`_ . 
-
-Remember that Python 2.7, and a C compiler have to be installed before the ``OBITools``.
-
-To install ``OBITools`` you have first to install dependencies
- 
-  .. code-block:: bash
-  
-	> pip install -U virtualenv
-	
-	> pip install -U sphinx
-	
-	> pip install -U cython
-	
-You can now install ``OBITools`` themselves.
-
-  .. code-block:: bash
-  
-	> pip install -U obitools
-
-Perhaps that on your system, the system administrator privilege are required to realise
-these installations. If you are yourself administrator of your computer run the above commands
-with the ``sudo`` command in front.
-  
-  .. code-block:: bash
-  
-	> sudo pip install -U virtualenv
-	
-	> sudo pip install -U sphinx
-	
-	> sudo pip install -U cython
-	
-	> sudo pip install -U obitools
-
-Retrieving the sources of the OBITools
-......................................
-
-If you want to compile by yourself the ``OBITools``, you will need to install the same
-prerequisite:
-
-  .. code-block:: bash
-  
-	> pip install -U virtualenv
-	
-	> pip install -U sphinx
-	
-	> pip install -U cython
-	
-moreover you need to install any subversion client (a list of clients is available from `Wikipedia <http://en.wikipedia.org/wiki/Comparison_of_Subversion_clients>`_)
-
-Then you can download the 
-
-  .. code-block:: bash
-
-      > svn co http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools/branches/OBITools-1.00/ OBITools
-
-This command will create a new directory called ``OBITools``.
-
-Compiling and installing the ``OBITools``
-.........................................
-
-From the directory where you retrieved the sources, execute the following commands:
- 
-  .. code-block:: bash
-
-      > cd OBITools
-
-      > python setup.py build
-
-      > python setup.py install
-      
-Once installed, you can test your installation by running the commands of the 
-:doc:`tutorials <./tutorials>`.
 
 
 Introduction
-------------
+============
 
 DNA metabarcoding is an emerging approach for biodiversity studies (Taberlet et
 al. 2012). Originally mainly developed by microbiologists (e.g. Sogin et al.
@@ -303,7 +163,7 @@ plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655.
 
 
 Basic concepts of the ``OBITools``
-----------------------------------
+==================================
 
 Once installed, the ``OBITools`` enrich the Unix command line interface with a set
 of new commands dedicated to NGS data processing. Most of them have a name

doc/sphinx/sphinxext/.gitignore

@@ -0,0 +1 @@
+*.pyc

get_obitools/getpackage/pip/__init__.py

@@ -0,0 +1,277 @@
+#!/usr/bin/env python
+import os
+import optparse
+
+import sys
+import re
+
+from pip.exceptions import InstallationError, CommandError, PipError
+from pip.log import logger
+from pip.util import get_installed_distributions, get_prog
+from pip.vcs import git, mercurial, subversion, bazaar  # noqa
+from pip.baseparser import ConfigOptionParser, UpdatingDefaultsHelpFormatter
+from pip.commands import commands, get_summaries, get_similar_commands
+
+# This fixes a peculiarity when importing via __import__ - as we are
+# initialising the pip module, "from pip import cmdoptions" is recursive
+# and appears not to work properly in that situation.
+import pip.cmdoptions
+cmdoptions = pip.cmdoptions
+
+# The version as used in the setup.py and the docs conf.py
+__version__ = "1.5.6"
+
+
+def autocomplete():
+    """Command and option completion for the main option parser (and options)
+    and its subcommands (and options).
+
+    Enable by sourcing one of the completion shell scripts (bash or zsh).
+    """
+    # Don't complete if user hasn't sourced bash_completion file.
+    if 'PIP_AUTO_COMPLETE' not in os.environ:
+        return
+    cwords = os.environ['COMP_WORDS'].split()[1:]
+    cword = int(os.environ['COMP_CWORD'])
+    try:
+        current = cwords[cword - 1]
+    except IndexError:
+        current = ''
+
+    subcommands = [cmd for cmd, summary in get_summaries()]
+    options = []
+    # subcommand
+    try:
+        subcommand_name = [w for w in cwords if w in subcommands][0]
+    except IndexError:
+        subcommand_name = None
+
+    parser = create_main_parser()
+    # subcommand options
+    if subcommand_name:
+        # special case: 'help' subcommand has no options
+        if subcommand_name == 'help':
+            sys.exit(1)
+        # special case: list locally installed dists for uninstall command
+        if subcommand_name == 'uninstall' and not current.startswith('-'):
+            installed = []
+            lc = current.lower()
+            for dist in get_installed_distributions(local_only=True):
+                if dist.key.startswith(lc) and dist.key not in cwords[1:]:
+                    installed.append(dist.key)
+            # if there are no dists installed, fall back to option completion
+            if installed:
+                for dist in installed:
+                    print(dist)
+                sys.exit(1)
+
+        subcommand = commands[subcommand_name]()
+        options += [(opt.get_opt_string(), opt.nargs)
+                    for opt in subcommand.parser.option_list_all
+                    if opt.help != optparse.SUPPRESS_HELP]
+
+        # filter out previously specified options from available options
+        prev_opts = [x.split('=')[0] for x in cwords[1:cword - 1]]
+        options = [(x, v) for (x, v) in options if x not in prev_opts]
+        # filter options by current input
+        options = [(k, v) for k, v in options if k.startswith(current)]
+        for option in options:
+            opt_label = option[0]
+            # append '=' to options which require args
+            if option[1]:
+                opt_label += '='
+            print(opt_label)
+    else:
+        # show main parser options only when necessary
+        if current.startswith('-') or current.startswith('--'):
+            opts = [i.option_list for i in parser.option_groups]
+            opts.append(parser.option_list)
+            opts = (o for it in opts for o in it)
+
+            subcommands += [i.get_opt_string() for i in opts
+                            if i.help != optparse.SUPPRESS_HELP]
+
+        print(' '.join([x for x in subcommands if x.startswith(current)]))
+    sys.exit(1)
+
+
+def create_main_parser():
+    parser_kw = {
+        'usage': '\n%prog <command> [options]',
+        'add_help_option': False,
+        'formatter': UpdatingDefaultsHelpFormatter(),
+        'name': 'global',
+        'prog': get_prog(),
+    }
+
+    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])
+
+    # add the general options
+    gen_opts = cmdoptions.make_option_group(cmdoptions.general_group, parser)
+    parser.add_option_group(gen_opts)
+
+    parser.main = True # so the help formatter knows
+
+    # create command listing for description
+    command_summaries = get_summaries()
+    description = [''] + ['%-27s %s' % (i, j) for i, j in command_summaries]
+    parser.description = '\n'.join(description)
+
+    return parser
+
+
+def parseopts(args):
+    parser = create_main_parser()
+
+    # Note: parser calls disable_interspersed_args(), so the result of this call
+    # is to split the initial args into the general options before the
+    # subcommand and everything else.
+    # For example:
+    #  args: ['--timeout=5', 'install', '--user', 'INITools']
+    #  general_options: ['--timeout==5']
+    #  args_else: ['install', '--user', 'INITools']
+    general_options, args_else = parser.parse_args(args)
+
+    # --version
+    if general_options.version:
+        sys.stdout.write(parser.version)
+        sys.stdout.write(os.linesep)
+        sys.exit()
+
+    # pip || pip help -> print_help()
+    if not args_else or (args_else[0] == 'help' and len(args_else) == 1):
+        parser.print_help()
+        sys.exit()
+
+    # the subcommand name
+    cmd_name = args_else[0].lower()
+
+    #all the args without the subcommand
+    cmd_args = args[:]
+    cmd_args.remove(args_else[0].lower())
+
+    if cmd_name not in commands:
+        guess = get_similar_commands(cmd_name)
+
+        msg = ['unknown command "%s"' % cmd_name]
+        if guess:
+            msg.append('maybe you meant "%s"' % guess)
+
+        raise CommandError(' - '.join(msg))
+
+    return cmd_name, cmd_args
+
+
+def main(initial_args=None):
+    if initial_args is None:
+        initial_args = sys.argv[1:]
+
+    autocomplete()
+
+    try:
+        cmd_name, cmd_args = parseopts(initial_args)
+    except PipError:
+        e = sys.exc_info()[1]
+        sys.stderr.write("ERROR: %s" % e)
+        sys.stderr.write(os.linesep)
+        sys.exit(1)
+
+    command = commands[cmd_name]()
+    return command.main(cmd_args)
+
+
+def bootstrap():
+    """
+    Bootstrapping function to be called from install-pip.py script.
+    """
+    pkgs = ['pip']
+    try:
+        import setuptools
+    except ImportError:
+        pkgs.append('setuptools')
+    return main(['install', '--upgrade'] + pkgs + sys.argv[1:])
+
+############################################################
+## Writing freeze files
+
+
+class FrozenRequirement(object):
+
+    def __init__(self, name, req, editable, comments=()):
+        self.name = name
+        self.req = req
+        self.editable = editable
+        self.comments = comments
+
+    _rev_re = re.compile(r'-r(\d+)$')
+    _date_re = re.compile(r'-(20\d\d\d\d\d\d)$')
+
+    @classmethod
+    def from_dist(cls, dist, dependency_links, find_tags=False):
+        location = os.path.normcase(os.path.abspath(dist.location))
+        comments = []
+        from pip.vcs import vcs, get_src_requirement
+        if vcs.get_backend_name(location):
+            editable = True
+            try:
+                req = get_src_requirement(dist, location, find_tags)
+            except InstallationError:
+                ex = sys.exc_info()[1]
+                logger.warn("Error when trying to get requirement for VCS system %s, falling back to uneditable format" % ex)
+                req = None
+            if req is None:
+                logger.warn('Could not determine repository location of %s' % location)
+                comments.append('## !! Could not determine repository location')
+                req = dist.as_requirement()
+                editable = False
+        else:
+            editable = False
+            req = dist.as_requirement()
+            specs = req.specs
+            assert len(specs) == 1 and specs[0][0] == '=='
+            version = specs[0][1]
+            ver_match = cls._rev_re.search(version)
+            date_match = cls._date_re.search(version)
+            if ver_match or date_match:
+                svn_backend = vcs.get_backend('svn')
+                if svn_backend:
+                    svn_location = svn_backend(
+                        ).get_location(dist, dependency_links)
+                if not svn_location:
+                    logger.warn(
+                        'Warning: cannot find svn location for %s' % req)
+                    comments.append('## FIXME: could not find svn URL in dependency_links for this package:')
+                else:
+                    comments.append('# Installing as editable to satisfy requirement %s:' % req)
+                    if ver_match:
+                        rev = ver_match.group(1)
+                    else:
+                        rev = '{%s}' % date_match.group(1)
+                    editable = True
+                    req = '%s@%s#egg=%s' % (svn_location, rev, cls.egg_name(dist))
+        return cls(dist.project_name, req, editable, comments)
+
+    @staticmethod
+    def egg_name(dist):
+        name = dist.egg_name()
+        match = re.search(r'-py\d\.\d$', name)
+        if match:
+            name = name[:match.start()]
+        return name
+
+    def __str__(self):
+        req = self.req
+        if self.editable:
+            req = '-e %s' % req
+        return '\n'.join(list(self.comments) + [str(req)]) + '\n'
+
+
+if __name__ == '__main__':
+    exit = main()
+    if exit:
+        sys.exit(exit)

get_obitools/getpackage/pip/__main__.py

@@ -0,0 +1,7 @@
+import sys
+from .runner import run
+
+if __name__ == '__main__':
+    exit = run()
+    if exit:
+        sys.exit(exit)

get_obitools/getpackage/pip/_vendor/__init__.py

@@ -0,0 +1,8 @@
+"""
+pip._vendor is for vendoring dependencies of pip to prevent needing pip to
+depend on something external.
+
+Files inside of pip._vendor should be considered immutable and should only be
+updated to versions from upstream.
+"""
+from __future__ import absolute_import

get_obitools/getpackage/pip/_vendor/_markerlib/__init__.py

@@ -0,0 +1,16 @@
+try:
+    import ast
+    from pip._vendor._markerlib.markers import default_environment, compile, interpret
+except ImportError:
+    if 'ast' in globals():
+        raise
+    def default_environment():
+        return {}
+    def compile(marker):
+        def marker_fn(environment=None, override=None):
+            # 'empty markers are True' heuristic won't install extra deps.
+            return not marker.strip()
+        marker_fn.__doc__ = marker
+        return marker_fn
+    def interpret(marker, environment=None, override=None):
+        return compile(marker)()

get_obitools/getpackage/pip/_vendor/_markerlib/markers.py

@@ -0,0 +1,119 @@
+# -*- coding: utf-8 -*-
+"""Interpret PEP 345 environment markers.
+
+EXPR [in|==|!=|not in] EXPR [or|and] ...
+
+where EXPR belongs to any of those:
+
+    python_version = '%s.%s' % (sys.version_info[0], sys.version_info[1])
+    python_full_version = sys.version.split()[0]
+    os.name = os.name
+    sys.platform = sys.platform
+    platform.version = platform.version()
+    platform.machine = platform.machine()
+    platform.python_implementation = platform.python_implementation()
+    a free string, like '2.6', or 'win32'
+"""
+
+__all__ = ['default_environment', 'compile', 'interpret']
+
+import ast
+import os
+import platform
+import sys
+import weakref
+
+_builtin_compile = compile
+
+try:
+    from platform import python_implementation
+except ImportError:
+    if os.name == "java":
+        # Jython 2.5 has ast module, but not platform.python_implementation() function.
+        def python_implementation():
+            return "Jython"
+    else:
+        raise
+
+
+# restricted set of variables
+_VARS = {'sys.platform': sys.platform,
+         'python_version': '%s.%s' % sys.version_info[:2],
+         # FIXME parsing sys.platform is not reliable, but there is no other
+         # way to get e.g. 2.7.2+, and the PEP is defined with sys.version
+         'python_full_version': sys.version.split(' ', 1)[0],
+         'os.name': os.name,
+         'platform.version': platform.version(),
+         'platform.machine': platform.machine(),
+         'platform.python_implementation': python_implementation(),
+         'extra': None # wheel extension
+        }
+
+for var in list(_VARS.keys()):
+    if '.' in var:
+        _VARS[var.replace('.', '_')] = _VARS[var]
+
+def default_environment():
+    """Return copy of default PEP 385 globals dictionary."""
+    return dict(_VARS)
+
+class ASTWhitelist(ast.NodeTransformer):
+    def __init__(self, statement):
+        self.statement = statement # for error messages
+
+    ALLOWED = (ast.Compare, ast.BoolOp, ast.Attribute, ast.Name, ast.Load, ast.Str)
+    # Bool operations
+    ALLOWED += (ast.And, ast.Or)
+    # Comparison operations
+    ALLOWED += (ast.Eq, ast.Gt, ast.GtE, ast.In, ast.Is, ast.IsNot, ast.Lt, ast.LtE, ast.NotEq, ast.NotIn)
+
+    def visit(self, node):
+        """Ensure statement only contains allowed nodes."""
+        if not isinstance(node, self.ALLOWED):
+            raise SyntaxError('Not allowed in environment markers.\n%s\n%s' %
+                               (self.statement,
+                               (' ' * node.col_offset) + '^'))
+        return ast.NodeTransformer.visit(self, node)
+
+    def visit_Attribute(self, node):
+        """Flatten one level of attribute access."""
+        new_node = ast.Name("%s.%s" % (node.value.id, node.attr), node.ctx)
+        return ast.copy_location(new_node, node)
+
+def parse_marker(marker):
+    tree = ast.parse(marker, mode='eval')
+    new_tree = ASTWhitelist(marker).generic_visit(tree)
+    return new_tree
+
+def compile_marker(parsed_marker):
+    return _builtin_compile(parsed_marker, '<environment marker>', 'eval',
+                   dont_inherit=True)
+
+_cache = weakref.WeakValueDictionary()
+
+def compile(marker):
+    """Return compiled marker as a function accepting an environment dict."""
+    try:
+        return _cache[marker]
+    except KeyError:
+        pass
+    if not marker.strip():
+        def marker_fn(environment=None, override=None):
+            """"""
+            return True
+    else:
+        compiled_marker = compile_marker(parse_marker(marker))
+        def marker_fn(environment=None, override=None):
+            """override updates environment"""
+            if override is None:
+                override = {}
+            if environment is None:
+                environment = default_environment()
+            environment.update(override)
+            return eval(compiled_marker, environment)
+    marker_fn.__doc__ = marker
+    _cache[marker] = marker_fn
+    return _cache[marker]
+
+def interpret(marker, environment=None):
+    return compile(marker)(environment)

get_obitools/getpackage/pip/_vendor/colorama/__init__.py

@@ -0,0 +1,7 @@
+# Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
+from .initialise import init, deinit, reinit
+from .ansi import Fore, Back, Style
+from .ansitowin32 import AnsiToWin32
+
+__version__ = '0.3.1'
+

get_obitools/getpackage/pip/_vendor/colorama/ansi.py

@@ -0,0 +1,50 @@
+# Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
+'''
+This module generates ANSI character codes to printing colors to terminals.
+See: http://en.wikipedia.org/wiki/ANSI_escape_code
+'''
+
+CSI = '\033['
+
+def code_to_chars(code):
+    return CSI + str(code) + 'm'
+
+class AnsiCodes(object):
+    def __init__(self, codes):
+        for name in dir(codes):
+            if not name.startswith('_'):
+                value = getattr(codes, name)
+                setattr(self, name, code_to_chars(value))
+
+class AnsiFore:
+    BLACK   = 30
+    RED     = 31
+    GREEN   = 32
+    YELLOW  = 33
+    BLUE    = 34
+    MAGENTA = 35
+    CYAN    = 36
+    WHITE   = 37
+    RESET   = 39
+
+class AnsiBack:
+    BLACK   = 40
+    RED     = 41
+    GREEN   = 42
+    YELLOW  = 43
+    BLUE    = 44
+    MAGENTA = 45
+    CYAN    = 46
+    WHITE   = 47
+    RESET   = 49
+
+class AnsiStyle:
+    BRIGHT    = 1
+    DIM       = 2
+    NORMAL    = 22
+    RESET_ALL = 0
+
+Fore = AnsiCodes( AnsiFore )
+Back = AnsiCodes( AnsiBack )
+Style = AnsiCodes( AnsiStyle )
+

get_obitools/getpackage/pip/_vendor/colorama/ansitowin32.py

@@ -0,0 +1,190 @@
+# Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
+import re
+import sys
+
+from .ansi import AnsiFore, AnsiBack, AnsiStyle, Style
+from .winterm import WinTerm, WinColor, WinStyle
+from .win32 import windll
+
+
+winterm = None
+if windll is not None:
+    winterm = WinTerm()
+
+
+def is_a_tty(stream):
+    return hasattr(stream, 'isatty') and stream.isatty()
+
+
+class StreamWrapper(object):
+    '''
+    Wraps a stream (such as stdout), acting as a transparent proxy for all
+    attribute access apart from method 'write()', which is delegated to our
+    Converter instance.
+    '''
+    def __init__(self, wrapped, converter):
+        # double-underscore everything to prevent clashes with names of
+        # attributes on the wrapped stream object.
+        self.__wrapped = wrapped
+        self.__convertor = converter
+
+    def __getattr__(self, name):
+        return getattr(self.__wrapped, name)
+
+    def write(self, text):
+        self.__convertor.write(text)
+
+
+class AnsiToWin32(object):
+    '''
+    Implements a 'write()' method which, on Windows, will strip ANSI character
+    sequences from the text, and if outputting to a tty, will convert them into
+    win32 function calls.
+    '''
+    ANSI_RE = re.compile('\033\[((?:\d|;)*)([a-zA-Z])')
+
+    def __init__(self, wrapped, convert=None, strip=None, autoreset=False):
+        # The wrapped stream (normally sys.stdout or sys.stderr)
+        self.wrapped = wrapped
+
+        # should we reset colors to defaults after every .write()
+        self.autoreset = autoreset
+
+        # create the proxy wrapping our output stream
+        self.stream = StreamWrapper(wrapped, self)
+
+        on_windows = sys.platform.startswith('win')
+
+        # should we strip ANSI sequences from our output?
+        if strip is None:
+            strip = on_windows
+        self.strip = strip
+
+        # should we should convert ANSI sequences into win32 calls?
+        if convert is None:
+            convert = on_windows and is_a_tty(wrapped)
+        self.convert = convert
+
+        # dict of ansi codes to win32 functions and parameters
+        self.win32_calls = self.get_win32_calls()
+
+        # are we wrapping stderr?
+        self.on_stderr = self.wrapped is sys.stderr
+
+
+    def should_wrap(self):
+        '''
+        True if this class is actually needed. If false, then the output
+        stream will not be affected, nor will win32 calls be issued, so
+        wrapping stdout is not actually required. This will generally be
+        False on non-Windows platforms, unless optional functionality like
+        autoreset has been requested using kwargs to init()
+        '''
+        return self.convert or self.strip or self.autoreset
+
+
+    def get_win32_calls(self):
+        if self.convert and winterm:
+            return {
+                AnsiStyle.RESET_ALL: (winterm.reset_all, ),
+                AnsiStyle.BRIGHT: (winterm.style, WinStyle.BRIGHT),
+                AnsiStyle.DIM: (winterm.style, WinStyle.NORMAL),
+                AnsiStyle.NORMAL: (winterm.style, WinStyle.NORMAL),
+                AnsiFore.BLACK: (winterm.fore, WinColor.BLACK),
+                AnsiFore.RED: (winterm.fore, WinColor.RED),
+                AnsiFore.GREEN: (winterm.fore, WinColor.GREEN),
+                AnsiFore.YELLOW: (winterm.fore, WinColor.YELLOW),
+                AnsiFore.BLUE: (winterm.fore, WinColor.BLUE),
+                AnsiFore.MAGENTA: (winterm.fore, WinColor.MAGENTA),
+                AnsiFore.CYAN: (winterm.fore, WinColor.CYAN),
+                AnsiFore.WHITE: (winterm.fore, WinColor.GREY),
+                AnsiFore.RESET: (winterm.fore, ),
+                AnsiBack.BLACK: (winterm.back, WinColor.BLACK),
+                AnsiBack.RED: (winterm.back, WinColor.RED),
+                AnsiBack.GREEN: (winterm.back, WinColor.GREEN),
+                AnsiBack.YELLOW: (winterm.back, WinColor.YELLOW),
+                AnsiBack.BLUE: (winterm.back, WinColor.BLUE),
+                AnsiBack.MAGENTA: (winterm.back, WinColor.MAGENTA),
+                AnsiBack.CYAN: (winterm.back, WinColor.CYAN),
+                AnsiBack.WHITE: (winterm.back, WinColor.GREY),
+                AnsiBack.RESET: (winterm.back, ),
+            }
+
+
+    def write(self, text):
+        if self.strip or self.convert:
+            self.write_and_convert(text)
+        else:
+            self.wrapped.write(text)
+            self.wrapped.flush()
+        if self.autoreset:
+            self.reset_all()
+
+
+    def reset_all(self):
+        if self.convert:
+            self.call_win32('m', (0,))
+        elif not self.wrapped.closed and is_a_tty(self.wrapped):
+            self.wrapped.write(Style.RESET_ALL)
+
+
+    def write_and_convert(self, text):
+        '''
+        Write the given text to our wrapped stream, stripping any ANSI
+        sequences from the text, and optionally converting them into win32
+        calls.
+        '''
+        cursor = 0
+        for match in self.ANSI_RE.finditer(text):
+            start, end = match.span()
+            self.write_plain_text(text, cursor, start)
+            self.convert_ansi(*match.groups())
+            cursor = end
+        self.write_plain_text(text, cursor, len(text))
+
+
+    def write_plain_text(self, text, start, end):
+        if start < end:
+            self.wrapped.write(text[start:end])
+            self.wrapped.flush()
+
+
+    def convert_ansi(self, paramstring, command):
+        if self.convert:
+            params = self.extract_params(paramstring)
+            self.call_win32(command, params)
+
+
+    def extract_params(self, paramstring):
+        def split(paramstring):
+            for p in paramstring.split(';'):
+                if p != '':
+                    yield int(p)
+        return tuple(split(paramstring))
+
+
+    def call_win32(self, command, params):
+        if params == []:
+            params = [0]
+        if command == 'm':
+            for param in params:
+                if param in self.win32_calls:
+                    func_args = self.win32_calls[param]
+                    func = func_args[0]
+                    args = func_args[1:]
+                    kwargs = dict(on_stderr=self.on_stderr)
+                    func(*args, **kwargs)
+        elif command in ('H', 'f'): # set cursor position
+            func = winterm.set_cursor_position
+            func(params, on_stderr=self.on_stderr)
+        elif command in ('J'):
+            func = winterm.erase_data
+            func(params, on_stderr=self.on_stderr)
+        elif command == 'A':
+            if params == () or params == None:
+                num_rows = 1
+            else:
+                num_rows = params[0]
+            func = winterm.cursor_up
+            func(num_rows, on_stderr=self.on_stderr)
+

get_obitools/getpackage/pip/_vendor/colorama/initialise.py

@@ -0,0 +1,56 @@
+# Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
+import atexit
+import sys
+
+from .ansitowin32 import AnsiToWin32
+
+
+orig_stdout = sys.stdout
+orig_stderr = sys.stderr
+
+wrapped_stdout = sys.stdout
+wrapped_stderr = sys.stderr
+
+atexit_done = False
+
+
+def reset_all():
+    AnsiToWin32(orig_stdout).reset_all()
+
+
+def init(autoreset=False, convert=None, strip=None, wrap=True):
+
+    if not wrap and any([autoreset, convert, strip]):
+        raise ValueError('wrap=False conflicts with any other arg=True')
+
+    global wrapped_stdout, wrapped_stderr
+    sys.stdout = wrapped_stdout = \
+        wrap_stream(orig_stdout, convert, strip, autoreset, wrap)
+    sys.stderr = wrapped_stderr = \
+        wrap_stream(orig_stderr, convert, strip, autoreset, wrap)
+
+    global atexit_done
+    if not atexit_done:
+        atexit.register(reset_all)
+        atexit_done = True
+
+
+def deinit():
+    sys.stdout = orig_stdout
+    sys.stderr = orig_stderr
+
+
+def reinit():
+    sys.stdout = wrapped_stdout
+    sys.stderr = wrapped_stdout
+
+
+def wrap_stream(stream, convert, strip, autoreset, wrap):
+    if wrap:
+        wrapper = AnsiToWin32(stream,
+            convert=convert, strip=strip, autoreset=autoreset)
+        if wrapper.should_wrap():
+            stream = wrapper.stream
+    return stream
+
+

get_obitools/getpackage/pip/_vendor/colorama/win32.py

@@ -0,0 +1,137 @@
+# Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
+
+# from winbase.h
+STDOUT = -11
+STDERR = -12
+
+import ctypes
+from ctypes import LibraryLoader
+
+try:
+    windll = LibraryLoader(ctypes.WinDLL)
+    from ctypes import wintypes
+except (AttributeError, ImportError):
+    windll = None
+    SetConsoleTextAttribute = lambda *_: None
+else:
+    from ctypes import (
+        byref, Structure, c_char, c_short, c_uint32, c_ushort, POINTER
+    )
+
+    class CONSOLE_SCREEN_BUFFER_INFO(Structure):
+        """struct in wincon.h."""
+        _fields_ = [
+            ("dwSize", wintypes._COORD),
+            ("dwCursorPosition", wintypes._COORD),
+            ("wAttributes", wintypes.WORD),
+            ("srWindow", wintypes.SMALL_RECT),
+            ("dwMaximumWindowSize", wintypes._COORD),
+        ]
+        def __str__(self):
+            return '(%d,%d,%d,%d,%d,%d,%d,%d,%d,%d,%d)' % (
+                self.dwSize.Y, self.dwSize.X
+                , self.dwCursorPosition.Y, self.dwCursorPosition.X
+                , self.wAttributes
+                , self.srWindow.Top, self.srWindow.Left, self.srWindow.Bottom, self.srWindow.Right
+                , self.dwMaximumWindowSize.Y, self.dwMaximumWindowSize.X
+            )
+
+    _GetStdHandle = windll.kernel32.GetStdHandle
+    _GetStdHandle.argtypes = [
+        wintypes.DWORD,
+    ]
+    _GetStdHandle.restype = wintypes.HANDLE
+
+    _GetConsoleScreenBufferInfo = windll.kernel32.GetConsoleScreenBufferInfo
+    _GetConsoleScreenBufferInfo.argtypes = [
+        wintypes.HANDLE,
+        POINTER(CONSOLE_SCREEN_BUFFER_INFO),
+    ]
+    _GetConsoleScreenBufferInfo.restype = wintypes.BOOL
+
+    _SetConsoleTextAttribute = windll.kernel32.SetConsoleTextAttribute
+    _SetConsoleTextAttribute.argtypes = [
+        wintypes.HANDLE,
+        wintypes.WORD,
+    ]
+    _SetConsoleTextAttribute.restype = wintypes.BOOL
+
+    _SetConsoleCursorPosition = windll.kernel32.SetConsoleCursorPosition
+    _SetConsoleCursorPosition.argtypes = [
+        wintypes.HANDLE,
+        wintypes._COORD,
+    ]
+    _SetConsoleCursorPosition.restype = wintypes.BOOL
+
+    _FillConsoleOutputCharacterA = windll.kernel32.FillConsoleOutputCharacterA
+    _FillConsoleOutputCharacterA.argtypes = [
+        wintypes.HANDLE,
+        c_char,
+        wintypes.DWORD,
+        wintypes._COORD,
+        POINTER(wintypes.DWORD),
+    ]
+    _FillConsoleOutputCharacterA.restype = wintypes.BOOL
+
+    _FillConsoleOutputAttribute = windll.kernel32.FillConsoleOutputAttribute
+    _FillConsoleOutputAttribute.argtypes = [
+        wintypes.HANDLE,
+        wintypes.WORD,
+        wintypes.DWORD,
+        wintypes._COORD,
+        POINTER(wintypes.DWORD),
+    ]
+    _FillConsoleOutputAttribute.restype = wintypes.BOOL
+
+    handles = {
+        STDOUT: _GetStdHandle(STDOUT),
+        STDERR: _GetStdHandle(STDERR),
+    }
+
+    def GetConsoleScreenBufferInfo(stream_id=STDOUT):
+        handle = handles[stream_id]
+        csbi = CONSOLE_SCREEN_BUFFER_INFO()
+        success = _GetConsoleScreenBufferInfo(
+            handle, byref(csbi))
+        return csbi
+
+    def SetConsoleTextAttribute(stream_id, attrs):
+        handle = handles[stream_id]
+        return _SetConsoleTextAttribute(handle, attrs)
+
+    def SetConsoleCursorPosition(stream_id, position):
+        position = wintypes._COORD(*position)
+        # If the position is out of range, do nothing.
+        if position.Y <= 0 or position.X <= 0:
+            return
+        # Adjust for Windows' SetConsoleCursorPosition:
+        #    1. being 0-based, while ANSI is 1-based.
+        #    2. expecting (x,y), while ANSI uses (y,x).
+        adjusted_position = wintypes._COORD(position.Y - 1, position.X - 1)
+        # Adjust for viewport's scroll position
+        sr = GetConsoleScreenBufferInfo(STDOUT).srWindow
+        adjusted_position.Y += sr.Top
+        adjusted_position.X += sr.Left
+        # Resume normal processing
+        handle = handles[stream_id]
+        return _SetConsoleCursorPosition(handle, adjusted_position)
+
+    def FillConsoleOutputCharacter(stream_id, char, length, start):
+        handle = handles[stream_id]
+        char = c_char(char)
+        length = wintypes.DWORD(length)
+        num_written = wintypes.DWORD(0)
+        # Note that this is hard-coded for ANSI (vs wide) bytes.
+        success = _FillConsoleOutputCharacterA(
+            handle, char, length, start, byref(num_written))
+        return num_written.value
+
+    def FillConsoleOutputAttribute(stream_id, attr, length, start):
+        ''' FillConsoleOutputAttribute( hConsole, csbi.wAttributes, dwConSize, coordScreen, &cCharsWritten )'''
+        handle = handles[stream_id]
+        attribute = wintypes.WORD(attr)
+        length = wintypes.DWORD(length)
+        num_written = wintypes.DWORD(0)
+        # Note that this is hard-coded for ANSI (vs wide) bytes.
+        return _FillConsoleOutputAttribute(
+            handle, attribute, length, start, byref(num_written))

get_obitools/getpackage/pip/_vendor/colorama/winterm.py

@@ -0,0 +1,120 @@
+# Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
+from . import win32
+
+
+# from wincon.h
+class WinColor(object):
+    BLACK   = 0
+    BLUE    = 1
+    GREEN   = 2
+    CYAN    = 3
+    RED     = 4
+    MAGENTA = 5
+    YELLOW  = 6
+    GREY    = 7
+
+# from wincon.h
+class WinStyle(object):
+    NORMAL = 0x00 # dim text, dim background
+    BRIGHT = 0x08 # bright text, dim background
+
+
+class WinTerm(object):
+
+    def __init__(self):
+        self._default = win32.GetConsoleScreenBufferInfo(win32.STDOUT).wAttributes
+        self.set_attrs(self._default)
+        self._default_fore = self._fore
+        self._default_back = self._back
+        self._default_style = self._style
+
+    def get_attrs(self):
+        return self._fore + self._back * 16 + self._style
+
+    def set_attrs(self, value):
+        self._fore = value & 7
+        self._back = (value >> 4) & 7
+        self._style = value & WinStyle.BRIGHT
+
+    def reset_all(self, on_stderr=None):
+        self.set_attrs(self._default)
+        self.set_console(attrs=self._default)
+
+    def fore(self, fore=None, on_stderr=False):
+        if fore is None:
+            fore = self._default_fore
+        self._fore = fore
+        self.set_console(on_stderr=on_stderr)
+
+    def back(self, back=None, on_stderr=False):
+        if back is None:
+            back = self._default_back
+        self._back = back
+        self.set_console(on_stderr=on_stderr)
+
+    def style(self, style=None, on_stderr=False):
+        if style is None:
+            style = self._default_style
+        self._style = style
+        self.set_console(on_stderr=on_stderr)
+
+    def set_console(self, attrs=None, on_stderr=False):
+        if attrs is None:
+            attrs = self.get_attrs()
+        handle = win32.STDOUT
+        if on_stderr:
+            handle = win32.STDERR
+        win32.SetConsoleTextAttribute(handle, attrs)
+
+    def get_position(self, handle):
+        position = win32.GetConsoleScreenBufferInfo(handle).dwCursorPosition
+        # Because Windows coordinates are 0-based,
+        # and win32.SetConsoleCursorPosition expects 1-based.
+        position.X += 1
+        position.Y += 1
+        return position
+    
+    def set_cursor_position(self, position=None, on_stderr=False):
+        if position is None:
+            #I'm not currently tracking the position, so there is no default.
+            #position = self.get_position()
+            return
+        handle = win32.STDOUT
+        if on_stderr:
+            handle = win32.STDERR
+        win32.SetConsoleCursorPosition(handle, position)
+
+    def cursor_up(self, num_rows=0, on_stderr=False):
+        if num_rows == 0:
+            return
+        handle = win32.STDOUT
+        if on_stderr:
+            handle = win32.STDERR
+        position = self.get_position(handle)
+        adjusted_position = (position.Y - num_rows, position.X)
+        self.set_cursor_position(adjusted_position, on_stderr)
+
+    def erase_data(self, mode=0, on_stderr=False):
+        # 0 (or None) should clear from the cursor to the end of the screen.
+        # 1 should clear from the cursor to the beginning of the screen.
+        # 2 should clear the entire screen. (And maybe move cursor to (1,1)?)
+        #
+        # At the moment, I only support mode 2. From looking at the API, it
+        #    should be possible to calculate a different number of bytes to clear,
+        #    and to do so relative to the cursor position.
+        if mode[0] not in (2,):
+            return
+        handle = win32.STDOUT
+        if on_stderr:
+            handle = win32.STDERR
+        # here's where we'll home the cursor
+        coord_screen = win32.COORD(0,0)
+        csbi = win32.GetConsoleScreenBufferInfo(handle)
+        # get the number of character cells in the current buffer
+        dw_con_size = csbi.dwSize.X * csbi.dwSize.Y
+        # fill the entire screen with blanks
+        win32.FillConsoleOutputCharacter(handle, ' ', dw_con_size, coord_screen)
+        # now set the buffer's attributes accordingly
+        win32.FillConsoleOutputAttribute(handle, self.get_attrs(), dw_con_size, coord_screen );
+        # put the cursor at (0, 0)
+        win32.SetConsoleCursorPosition(handle, (coord_screen.X, coord_screen.Y))

get_obitools/getpackage/pip/_vendor/distlib/__init__.py

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012-2014 Vinay Sajip.
+# Licensed to the Python Software Foundation under a contributor agreement.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+import logging
+
+__version__ = '0.1.8'
+
+class DistlibException(Exception):
+    pass
+
+try:
+    from logging import NullHandler
+except ImportError: # pragma: no cover
+    class NullHandler(logging.Handler):
+        def handle(self, record): pass
+        def emit(self, record): pass
+        def createLock(self): self.lock = None
+
+logger = logging.getLogger(__name__)
+logger.addHandler(NullHandler())

get_obitools/getpackage/pip/_vendor/distlib/_backport/__init__.py

@@ -0,0 +1,6 @@
+"""Modules copied from Python 3 standard libraries, for internal use only.
+
+Individual classes and functions are found in d2._backport.misc.  Intended
+usage is to always import things missing from 3.1 from that module: the
+built-in/stdlib objects will be used if found.
+"""

get_obitools/getpackage/pip/_vendor/distlib/_backport/misc.py

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012 The Python Software Foundation.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+"""Backports for individual classes and functions."""
+
+import os
+import sys
+
+__all__ = ['cache_from_source', 'callable', 'fsencode']
+
+
+try:
+    from imp import cache_from_source
+except ImportError:
+    def cache_from_source(py_file, debug=__debug__):
+        ext = debug and 'c' or 'o'
+        return py_file + ext
+
+
+try:
+    callable = callable
+except NameError:
+    from collections import Callable
+
+    def callable(obj):
+        return isinstance(obj, Callable)
+
+
+try:
+    fsencode = os.fsencode
+except AttributeError:
+    def fsencode(filename):
+        if isinstance(filename, bytes):
+            return filename
+        elif isinstance(filename, str):
+            return filename.encode(sys.getfilesystemencoding())
+        else:
+            raise TypeError("expect bytes or str, not %s" %
+                            type(filename).__name__)

get_obitools/getpackage/pip/_vendor/distlib/_backport/shutil.py

@@ -0,0 +1,761 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012 The Python Software Foundation.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+"""Utility functions for copying and archiving files and directory trees.
+
+XXX The functions here don't copy the resource fork or other metadata on Mac.
+
+"""
+
+import os
+import sys
+import stat
+from os.path import abspath
+import fnmatch
+import collections
+import errno
+from . import tarfile
+
+try:
+    import bz2
+    _BZ2_SUPPORTED = True
+except ImportError:
+    _BZ2_SUPPORTED = False
+
+try:
+    from pwd import getpwnam
+except ImportError:
+    getpwnam = None
+
+try:
+    from grp import getgrnam
+except ImportError:
+    getgrnam = None
+
+__all__ = ["copyfileobj", "copyfile", "copymode", "copystat", "copy", "copy2",
+           "copytree", "move", "rmtree", "Error", "SpecialFileError",
+           "ExecError", "make_archive", "get_archive_formats",
+           "register_archive_format", "unregister_archive_format",
+           "get_unpack_formats", "register_unpack_format",
+           "unregister_unpack_format", "unpack_archive", "ignore_patterns"]
+
+class Error(EnvironmentError):
+    pass
+
+class SpecialFileError(EnvironmentError):
+    """Raised when trying to do a kind of operation (e.g. copying) which is
+    not supported on a special file (e.g. a named pipe)"""
+
+class ExecError(EnvironmentError):
+    """Raised when a command could not be executed"""
+
+class ReadError(EnvironmentError):
+    """Raised when an archive cannot be read"""
+
+class RegistryError(Exception):
+    """Raised when a registery operation with the archiving
+    and unpacking registeries fails"""
+
+
+try:
+    WindowsError
+except NameError:
+    WindowsError = None
+
+def copyfileobj(fsrc, fdst, length=16*1024):
+    """copy data from file-like object fsrc to file-like object fdst"""
+    while 1:
+        buf = fsrc.read(length)
+        if not buf:
+            break
+        fdst.write(buf)
+
+def _samefile(src, dst):
+    # Macintosh, Unix.
+    if hasattr(os.path, 'samefile'):
+        try:
+            return os.path.samefile(src, dst)
+        except OSError:
+            return False
+
+    # All other platforms: check for same pathname.
+    return (os.path.normcase(os.path.abspath(src)) ==
+            os.path.normcase(os.path.abspath(dst)))
+
+def copyfile(src, dst):
+    """Copy data from src to dst"""
+    if _samefile(src, dst):
+        raise Error("`%s` and `%s` are the same file" % (src, dst))
+
+    for fn in [src, dst]:
+        try:
+            st = os.stat(fn)
+        except OSError:
+            # File most likely does not exist
+            pass
+        else:
+            # XXX What about other special files? (sockets, devices...)
+            if stat.S_ISFIFO(st.st_mode):
+                raise SpecialFileError("`%s` is a named pipe" % fn)
+
+    with open(src, 'rb') as fsrc:
+        with open(dst, 'wb') as fdst:
+            copyfileobj(fsrc, fdst)
+
+def copymode(src, dst):
+    """Copy mode bits from src to dst"""
+    if hasattr(os, 'chmod'):
+        st = os.stat(src)
+        mode = stat.S_IMODE(st.st_mode)
+        os.chmod(dst, mode)
+
+def copystat(src, dst):
+    """Copy all stat info (mode bits, atime, mtime, flags) from src to dst"""
+    st = os.stat(src)
+    mode = stat.S_IMODE(st.st_mode)
+    if hasattr(os, 'utime'):
+        os.utime(dst, (st.st_atime, st.st_mtime))
+    if hasattr(os, 'chmod'):
+        os.chmod(dst, mode)
+    if hasattr(os, 'chflags') and hasattr(st, 'st_flags'):
+        try:
+            os.chflags(dst, st.st_flags)
+        except OSError as why:
+            if (not hasattr(errno, 'EOPNOTSUPP') or
+                why.errno != errno.EOPNOTSUPP):
+                raise
+
+def copy(src, dst):
+    """Copy data and mode bits ("cp src dst").
+
+    The destination may be a directory.
+
+    """
+    if os.path.isdir(dst):
+        dst = os.path.join(dst, os.path.basename(src))
+    copyfile(src, dst)
+    copymode(src, dst)
+
+def copy2(src, dst):
+    """Copy data and all stat info ("cp -p src dst").
+
+    The destination may be a directory.
+
+    """
+    if os.path.isdir(dst):
+        dst = os.path.join(dst, os.path.basename(src))
+    copyfile(src, dst)
+    copystat(src, dst)
+
+def ignore_patterns(*patterns):
+    """Function that can be used as copytree() ignore parameter.
+
+    Patterns is a sequence of glob-style patterns
+    that are used to exclude files"""
+    def _ignore_patterns(path, names):
+        ignored_names = []
+        for pattern in patterns:
+            ignored_names.extend(fnmatch.filter(names, pattern))
+        return set(ignored_names)
+    return _ignore_patterns
+
+def copytree(src, dst, symlinks=False, ignore=None, copy_function=copy2,
+             ignore_dangling_symlinks=False):
+    """Recursively copy a directory tree.
+
+    The destination directory must not already exist.
+    If exception(s) occur, an Error is raised with a list of reasons.
+
+    If the optional symlinks flag is true, symbolic links in the
+    source tree result in symbolic links in the destination tree; if
+    it is false, the contents of the files pointed to by symbolic
+    links are copied. If the file pointed by the symlink doesn't
+    exist, an exception will be added in the list of errors raised in
+    an Error exception at the end of the copy process.
+
+    You can set the optional ignore_dangling_symlinks flag to true if you
+    want to silence this exception. Notice that this has no effect on
+    platforms that don't support os.symlink.
+
+    The optional ignore argument is a callable. If given, it
+    is called with the `src` parameter, which is the directory
+    being visited by copytree(), and `names` which is the list of
+    `src` contents, as returned by os.listdir():
+
+        callable(src, names) -> ignored_names
+
+    Since copytree() is called recursively, the callable will be
+    called once for each directory that is copied. It returns a
+    list of names relative to the `src` directory that should
+    not be copied.
+
+    The optional copy_function argument is a callable that will be used
+    to copy each file. It will be called with the source path and the
+    destination path as arguments. By default, copy2() is used, but any
+    function that supports the same signature (like copy()) can be used.
+
+    """
+    names = os.listdir(src)
+    if ignore is not None:
+        ignored_names = ignore(src, names)
+    else:
+        ignored_names = set()
+
+    os.makedirs(dst)
+    errors = []
+    for name in names:
+        if name in ignored_names:
+            continue
+        srcname = os.path.join(src, name)
+        dstname = os.path.join(dst, name)
+        try:
+            if os.path.islink(srcname):
+                linkto = os.readlink(srcname)
+                if symlinks:
+                    os.symlink(linkto, dstname)
+                else:
+                    # ignore dangling symlink if the flag is on
+                    if not os.path.exists(linkto) and ignore_dangling_symlinks:
+                        continue
+                    # otherwise let the copy occurs. copy2 will raise an error
+                    copy_function(srcname, dstname)
+            elif os.path.isdir(srcname):
+                copytree(srcname, dstname, symlinks, ignore, copy_function)
+            else:
+                # Will raise a SpecialFileError for unsupported file types
+                copy_function(srcname, dstname)
+        # catch the Error from the recursive copytree so that we can
+        # continue with other files
+        except Error as err:
+            errors.extend(err.args[0])
+        except EnvironmentError as why:
+            errors.append((srcname, dstname, str(why)))
+    try:
+        copystat(src, dst)
+    except OSError as why:
+        if WindowsError is not None and isinstance(why, WindowsError):
+            # Copying file access times may fail on Windows
+            pass
+        else:
+            errors.extend((src, dst, str(why)))
+    if errors:
+        raise Error(errors)
+
+def rmtree(path, ignore_errors=False, onerror=None):
+    """Recursively delete a directory tree.
+
+    If ignore_errors is set, errors are ignored; otherwise, if onerror
+    is set, it is called to handle the error with arguments (func,
+    path, exc_info) where func is os.listdir, os.remove, or os.rmdir;
+    path is the argument to that function that caused it to fail; and
+    exc_info is a tuple returned by sys.exc_info().  If ignore_errors
+    is false and onerror is None, an exception is raised.
+
+    """
+    if ignore_errors:
+        def onerror(*args):
+            pass
+    elif onerror is None:
+        def onerror(*args):
+            raise
+    try:
+        if os.path.islink(path):
+            # symlinks to directories are forbidden, see bug #1669
+            raise OSError("Cannot call rmtree on a symbolic link")
+    except OSError:
+        onerror(os.path.islink, path, sys.exc_info())
+        # can't continue even if onerror hook returns
+        return
+    names = []
+    try:
+        names = os.listdir(path)
+    except os.error:
+        onerror(os.listdir, path, sys.exc_info())
+    for name in names:
+        fullname = os.path.join(path, name)
+        try:
+            mode = os.lstat(fullname).st_mode
+        except os.error:
+            mode = 0
+        if stat.S_ISDIR(mode):
+            rmtree(fullname, ignore_errors, onerror)
+        else:
+            try:
+                os.remove(fullname)
+            except os.error:
+                onerror(os.remove, fullname, sys.exc_info())
+    try:
+        os.rmdir(path)
+    except os.error:
+        onerror(os.rmdir, path, sys.exc_info())
+
+
+def _basename(path):
+    # A basename() variant which first strips the trailing slash, if present.
+    # Thus we always get the last component of the path, even for directories.
+    return os.path.basename(path.rstrip(os.path.sep))
+
+def move(src, dst):
+    """Recursively move a file or directory to another location. This is
+    similar to the Unix "mv" command.
+
+    If the destination is a directory or a symlink to a directory, the source
+    is moved inside the directory. The destination path must not already
+    exist.
+
+    If the destination already exists but is not a directory, it may be
+    overwritten depending on os.rename() semantics.
+
+    If the destination is on our current filesystem, then rename() is used.
+    Otherwise, src is copied to the destination and then removed.
+    A lot more could be done here...  A look at a mv.c shows a lot of
+    the issues this implementation glosses over.
+
+    """
+    real_dst = dst
+    if os.path.isdir(dst):
+        if _samefile(src, dst):
+            # We might be on a case insensitive filesystem,
+            # perform the rename anyway.
+            os.rename(src, dst)
+            return
+
+        real_dst = os.path.join(dst, _basename(src))
+        if os.path.exists(real_dst):
+            raise Error("Destination path '%s' already exists" % real_dst)
+    try:
+        os.rename(src, real_dst)
+    except OSError:
+        if os.path.isdir(src):
+            if _destinsrc(src, dst):
+                raise Error("Cannot move a directory '%s' into itself '%s'." % (src, dst))
+            copytree(src, real_dst, symlinks=True)
+            rmtree(src)
+        else:
+            copy2(src, real_dst)
+            os.unlink(src)
+
+def _destinsrc(src, dst):
+    src = abspath(src)
+    dst = abspath(dst)
+    if not src.endswith(os.path.sep):
+        src += os.path.sep
+    if not dst.endswith(os.path.sep):
+        dst += os.path.sep
+    return dst.startswith(src)
+
+def _get_gid(name):
+    """Returns a gid, given a group name."""
+    if getgrnam is None or name is None:
+        return None
+    try:
+        result = getgrnam(name)
+    except KeyError:
+        result = None
+    if result is not None:
+        return result[2]
+    return None
+
+def _get_uid(name):
+    """Returns an uid, given a user name."""
+    if getpwnam is None or name is None:
+        return None
+    try:
+        result = getpwnam(name)
+    except KeyError:
+        result = None
+    if result is not None:
+        return result[2]
+    return None
+
+def _make_tarball(base_name, base_dir, compress="gzip", verbose=0, dry_run=0,
+                  owner=None, group=None, logger=None):
+    """Create a (possibly compressed) tar file from all the files under
+    'base_dir'.
+
+    'compress' must be "gzip" (the default), "bzip2", or None.
+
+    'owner' and 'group' can be used to define an owner and a group for the
+    archive that is being built. If not provided, the current owner and group
+    will be used.
+
+    The output tar file will be named 'base_name' +  ".tar", possibly plus
+    the appropriate compression extension (".gz", or ".bz2").
+
+    Returns the output filename.
+    """
+    tar_compression = {'gzip': 'gz', None: ''}
+    compress_ext = {'gzip': '.gz'}
+
+    if _BZ2_SUPPORTED:
+        tar_compression['bzip2'] = 'bz2'
+        compress_ext['bzip2'] = '.bz2'
+
+    # flags for compression program, each element of list will be an argument
+    if compress is not None and compress not in compress_ext:
+        raise ValueError("bad value for 'compress', or compression format not "
+                         "supported : {0}".format(compress))
+
+    archive_name = base_name + '.tar' + compress_ext.get(compress, '')
+    archive_dir = os.path.dirname(archive_name)
+
+    if not os.path.exists(archive_dir):
+        if logger is not None:
+            logger.info("creating %s", archive_dir)
+        if not dry_run:
+            os.makedirs(archive_dir)
+
+    # creating the tarball
+    if logger is not None:
+        logger.info('Creating tar archive')
+
+    uid = _get_uid(owner)
+    gid = _get_gid(group)
+
+    def _set_uid_gid(tarinfo):
+        if gid is not None:
+            tarinfo.gid = gid
+            tarinfo.gname = group
+        if uid is not None:
+            tarinfo.uid = uid
+            tarinfo.uname = owner
+        return tarinfo
+
+    if not dry_run:
+        tar = tarfile.open(archive_name, 'w|%s' % tar_compression[compress])
+        try:
+            tar.add(base_dir, filter=_set_uid_gid)
+        finally:
+            tar.close()
+
+    return archive_name
+
+def _call_external_zip(base_dir, zip_filename, verbose=False, dry_run=False):
+    # XXX see if we want to keep an external call here
+    if verbose:
+        zipoptions = "-r"
+    else:
+        zipoptions = "-rq"
+    from distutils.errors import DistutilsExecError
+    from distutils.spawn import spawn
+    try:
+        spawn(["zip", zipoptions, zip_filename, base_dir], dry_run=dry_run)
+    except DistutilsExecError:
+        # XXX really should distinguish between "couldn't find
+        # external 'zip' command" and "zip failed".
+        raise ExecError("unable to create zip file '%s': "
+            "could neither import the 'zipfile' module nor "
+            "find a standalone zip utility") % zip_filename
+
+def _make_zipfile(base_name, base_dir, verbose=0, dry_run=0, logger=None):
+    """Create a zip file from all the files under 'base_dir'.
+
+    The output zip file will be named 'base_name' + ".zip".  Uses either the
+    "zipfile" Python module (if available) or the InfoZIP "zip" utility
+    (if installed and found on the default search path).  If neither tool is
+    available, raises ExecError.  Returns the name of the output zip
+    file.
+    """
+    zip_filename = base_name + ".zip"
+    archive_dir = os.path.dirname(base_name)
+
+    if not os.path.exists(archive_dir):
+        if logger is not None:
+            logger.info("creating %s", archive_dir)
+        if not dry_run:
+            os.makedirs(archive_dir)
+
+    # If zipfile module is not available, try spawning an external 'zip'
+    # command.
+    try:
+        import zipfile
+    except ImportError:
+        zipfile = None
+
+    if zipfile is None:
+        _call_external_zip(base_dir, zip_filename, verbose, dry_run)
+    else:
+        if logger is not None:
+            logger.info("creating '%s' and adding '%s' to it",
+                        zip_filename, base_dir)
+
+        if not dry_run:
+            zip = zipfile.ZipFile(zip_filename, "w",
+                                  compression=zipfile.ZIP_DEFLATED)
+
+            for dirpath, dirnames, filenames in os.walk(base_dir):
+                for name in filenames:
+                    path = os.path.normpath(os.path.join(dirpath, name))
+                    if os.path.isfile(path):
+                        zip.write(path, path)
+                        if logger is not None:
+                            logger.info("adding '%s'", path)
+            zip.close()
+
+    return zip_filename
+
+_ARCHIVE_FORMATS = {
+    'gztar': (_make_tarball, [('compress', 'gzip')], "gzip'ed tar-file"),
+    'bztar': (_make_tarball, [('compress', 'bzip2')], "bzip2'ed tar-file"),
+    'tar':   (_make_tarball, [('compress', None)], "uncompressed tar file"),
+    'zip':   (_make_zipfile, [], "ZIP file"),
+    }
+
+if _BZ2_SUPPORTED:
+    _ARCHIVE_FORMATS['bztar'] = (_make_tarball, [('compress', 'bzip2')],
+                                "bzip2'ed tar-file")
+
+def get_archive_formats():
+    """Returns a list of supported formats for archiving and unarchiving.
+
+    Each element of the returned sequence is a tuple (name, description)
+    """
+    formats = [(name, registry[2]) for name, registry in
+               _ARCHIVE_FORMATS.items()]
+    formats.sort()
+    return formats
+
+def register_archive_format(name, function, extra_args=None, description=''):
+    """Registers an archive format.
+
+    name is the name of the format. function is the callable that will be
+    used to create archives. If provided, extra_args is a sequence of
+    (name, value) tuples that will be passed as arguments to the callable.
+    description can be provided to describe the format, and will be returned
+    by the get_archive_formats() function.
+    """
+    if extra_args is None:
+        extra_args = []
+    if not isinstance(function, collections.Callable):
+        raise TypeError('The %s object is not callable' % function)
+    if not isinstance(extra_args, (tuple, list)):
+        raise TypeError('extra_args needs to be a sequence')
+    for element in extra_args:
+        if not isinstance(element, (tuple, list)) or len(element) !=2:
+            raise TypeError('extra_args elements are : (arg_name, value)')
+
+    _ARCHIVE_FORMATS[name] = (function, extra_args, description)
+
+def unregister_archive_format(name):
+    del _ARCHIVE_FORMATS[name]
+
+def make_archive(base_name, format, root_dir=None, base_dir=None, verbose=0,
+                 dry_run=0, owner=None, group=None, logger=None):
+    """Create an archive file (eg. zip or tar).
+
+    'base_name' is the name of the file to create, minus any format-specific
+    extension; 'format' is the archive format: one of "zip", "tar", "bztar"
+    or "gztar".
+
+    'root_dir' is a directory that will be the root directory of the
+    archive; ie. we typically chdir into 'root_dir' before creating the
+    archive.  'base_dir' is the directory where we start archiving from;
+    ie. 'base_dir' will be the common prefix of all files and
+    directories in the archive.  'root_dir' and 'base_dir' both default
+    to the current directory.  Returns the name of the archive file.
+
+    'owner' and 'group' are used when creating a tar archive. By default,
+    uses the current owner and group.
+    """
+    save_cwd = os.getcwd()
+    if root_dir is not None:
+        if logger is not None:
+            logger.debug("changing into '%s'", root_dir)
+        base_name = os.path.abspath(base_name)
+        if not dry_run:
+            os.chdir(root_dir)
+
+    if base_dir is None:
+        base_dir = os.curdir
+
+    kwargs = {'dry_run': dry_run, 'logger': logger}
+
+    try:
+        format_info = _ARCHIVE_FORMATS[format]
+    except KeyError:
+        raise ValueError("unknown archive format '%s'" % format)
+
+    func = format_info[0]
+    for arg, val in format_info[1]:
+        kwargs[arg] = val
+
+    if format != 'zip':
+        kwargs['owner'] = owner
+        kwargs['group'] = group
+
+    try:
+        filename = func(base_name, base_dir, **kwargs)
+    finally:
+        if root_dir is not None:
+            if logger is not None:
+                logger.debug("changing back to '%s'", save_cwd)
+            os.chdir(save_cwd)
+
+    return filename
+
+
+def get_unpack_formats():
+    """Returns a list of supported formats for unpacking.
+
+    Each element of the returned sequence is a tuple
+    (name, extensions, description)
+    """
+    formats = [(name, info[0], info[3]) for name, info in
+               _UNPACK_FORMATS.items()]
+    formats.sort()
+    return formats
+
+def _check_unpack_options(extensions, function, extra_args):
+    """Checks what gets registered as an unpacker."""
+    # first make sure no other unpacker is registered for this extension
+    existing_extensions = {}
+    for name, info in _UNPACK_FORMATS.items():
+        for ext in info[0]:
+            existing_extensions[ext] = name
+
+    for extension in extensions:
+        if extension in existing_extensions:
+            msg = '%s is already registered for "%s"'
+            raise RegistryError(msg % (extension,
+                                       existing_extensions[extension]))
+
+    if not isinstance(function, collections.Callable):
+        raise TypeError('The registered function must be a callable')
+
+
+def register_unpack_format(name, extensions, function, extra_args=None,
+                           description=''):
+    """Registers an unpack format.
+
+    `name` is the name of the format. `extensions` is a list of extensions
+    corresponding to the format.
+
+    `function` is the callable that will be
+    used to unpack archives. The callable will receive archives to unpack.
+    If it's unable to handle an archive, it needs to raise a ReadError
+    exception.
+
+    If provided, `extra_args` is a sequence of
+    (name, value) tuples that will be passed as arguments to the callable.
+    description can be provided to describe the format, and will be returned
+    by the get_unpack_formats() function.
+    """
+    if extra_args is None:
+        extra_args = []
+    _check_unpack_options(extensions, function, extra_args)
+    _UNPACK_FORMATS[name] = extensions, function, extra_args, description
+
+def unregister_unpack_format(name):
+    """Removes the pack format from the registery."""
+    del _UNPACK_FORMATS[name]
+
+def _ensure_directory(path):
+    """Ensure that the parent directory of `path` exists"""
+    dirname = os.path.dirname(path)
+    if not os.path.isdir(dirname):
+        os.makedirs(dirname)
+
+def _unpack_zipfile(filename, extract_dir):
+    """Unpack zip `filename` to `extract_dir`
+    """
+    try:
+        import zipfile
+    except ImportError:
+        raise ReadError('zlib not supported, cannot unpack this archive.')
+
+    if not zipfile.is_zipfile(filename):
+        raise ReadError("%s is not a zip file" % filename)
+
+    zip = zipfile.ZipFile(filename)
+    try:
+        for info in zip.infolist():
+            name = info.filename
+
+            # don't extract absolute paths or ones with .. in them
+            if name.startswith('/') or '..' in name:
+                continue
+
+            target = os.path.join(extract_dir, *name.split('/'))
+            if not target:
+                continue
+
+            _ensure_directory(target)
+            if not name.endswith('/'):
+                # file
+                data = zip.read(info.filename)
+                f = open(target, 'wb')
+                try:
+                    f.write(data)
+                finally:
+                    f.close()
+                    del data
+    finally:
+        zip.close()
+
+def _unpack_tarfile(filename, extract_dir):
+    """Unpack tar/tar.gz/tar.bz2 `filename` to `extract_dir`
+    """
+    try:
+        tarobj = tarfile.open(filename)
+    except tarfile.TarError:
+        raise ReadError(
+            "%s is not a compressed or uncompressed tar file" % filename)
+    try:
+        tarobj.extractall(extract_dir)
+    finally:
+        tarobj.close()
+
+_UNPACK_FORMATS = {
+    'gztar': (['.tar.gz', '.tgz'], _unpack_tarfile, [], "gzip'ed tar-file"),
+    'tar':   (['.tar'], _unpack_tarfile, [], "uncompressed tar file"),
+    'zip':   (['.zip'], _unpack_zipfile, [], "ZIP file")
+    }
+
+if _BZ2_SUPPORTED:
+    _UNPACK_FORMATS['bztar'] = (['.bz2'], _unpack_tarfile, [],
+                                "bzip2'ed tar-file")
+
+def _find_unpack_format(filename):
+    for name, info in _UNPACK_FORMATS.items():
+        for extension in info[0]:
+            if filename.endswith(extension):
+                return name
+    return None
+
+def unpack_archive(filename, extract_dir=None, format=None):
+    """Unpack an archive.
+
+    `filename` is the name of the archive.
+
+    `extract_dir` is the name of the target directory, where the archive
+    is unpacked. If not provided, the current working directory is used.
+
+    `format` is the archive format: one of "zip", "tar", or "gztar". Or any
+    other registered format. If not provided, unpack_archive will use the
+    filename extension and see if an unpacker was registered for that
+    extension.
+
+    In case none is found, a ValueError is raised.
+    """
+    if extract_dir is None:
+        extract_dir = os.getcwd()
+
+    if format is not None:
+        try:
+            format_info = _UNPACK_FORMATS[format]
+        except KeyError:
+            raise ValueError("Unknown unpack format '{0}'".format(format))
+
+        func = format_info[1]
+        func(filename, extract_dir, **dict(format_info[2]))
+    else:
+        # we need to look at the registered unpackers supported extensions
+        format = _find_unpack_format(filename)
+        if format is None:
+            raise ReadError("Unknown archive format '{0}'".format(filename))
+
+        func = _UNPACK_FORMATS[format][1]
+        kwargs = dict(_UNPACK_FORMATS[format][2])
+        func(filename, extract_dir, **kwargs)

get_obitools/getpackage/pip/_vendor/distlib/_backport/sysconfig.cfg

@@ -0,0 +1,84 @@
+[posix_prefix]
+# Configuration directories.  Some of these come straight out of the
+# configure script.  They are for implementing the other variables, not to
+# be used directly in [resource_locations].
+confdir = /etc
+datadir = /usr/share
+libdir = /usr/lib
+statedir = /var
+# User resource directory
+local = ~/.local/{distribution.name}
+
+stdlib = {base}/lib/python{py_version_short}
+platstdlib = {platbase}/lib/python{py_version_short}
+purelib = {base}/lib/python{py_version_short}/site-packages
+platlib = {platbase}/lib/python{py_version_short}/site-packages
+include = {base}/include/python{py_version_short}{abiflags}
+platinclude = {platbase}/include/python{py_version_short}{abiflags}
+data = {base}
+
+[posix_home]
+stdlib = {base}/lib/python
+platstdlib = {base}/lib/python
+purelib = {base}/lib/python
+platlib = {base}/lib/python
+include = {base}/include/python
+platinclude = {base}/include/python
+scripts = {base}/bin
+data = {base}
+
+[nt]
+stdlib = {base}/Lib
+platstdlib = {base}/Lib
+purelib = {base}/Lib/site-packages
+platlib = {base}/Lib/site-packages
+include = {base}/Include
+platinclude = {base}/Include
+scripts = {base}/Scripts
+data = {base}
+
+[os2]
+stdlib = {base}/Lib
+platstdlib = {base}/Lib
+purelib = {base}/Lib/site-packages
+platlib = {base}/Lib/site-packages
+include = {base}/Include
+platinclude = {base}/Include
+scripts = {base}/Scripts
+data = {base}
+
+[os2_home]
+stdlib = {userbase}/lib/python{py_version_short}
+platstdlib = {userbase}/lib/python{py_version_short}
+purelib = {userbase}/lib/python{py_version_short}/site-packages
+platlib = {userbase}/lib/python{py_version_short}/site-packages
+include = {userbase}/include/python{py_version_short}
+scripts = {userbase}/bin
+data = {userbase}
+
+[nt_user]
+stdlib = {userbase}/Python{py_version_nodot}
+platstdlib = {userbase}/Python{py_version_nodot}
+purelib = {userbase}/Python{py_version_nodot}/site-packages
+platlib = {userbase}/Python{py_version_nodot}/site-packages
+include = {userbase}/Python{py_version_nodot}/Include
+scripts = {userbase}/Scripts
+data = {userbase}
+
+[posix_user]
+stdlib = {userbase}/lib/python{py_version_short}
+platstdlib = {userbase}/lib/python{py_version_short}
+purelib = {userbase}/lib/python{py_version_short}/site-packages
+platlib = {userbase}/lib/python{py_version_short}/site-packages
+include = {userbase}/include/python{py_version_short}
+scripts = {userbase}/bin
+data = {userbase}
+
+[osx_framework_user]
+stdlib = {userbase}/lib/python
+platstdlib = {userbase}/lib/python
+purelib = {userbase}/lib/python/site-packages
+platlib = {userbase}/lib/python/site-packages
+include = {userbase}/include
+scripts = {userbase}/bin
+data = {userbase}

get_obitools/getpackage/pip/_vendor/distlib/_backport/sysconfig.py

@@ -0,0 +1,788 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012 The Python Software Foundation.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+"""Access to Python's configuration information."""
+
+import codecs
+import os
+import re
+import sys
+from os.path import pardir, realpath
+try:
+    import configparser
+except ImportError:
+    import ConfigParser as configparser
+
+
+__all__ = [
+    'get_config_h_filename',
+    'get_config_var',
+    'get_config_vars',
+    'get_makefile_filename',
+    'get_path',
+    'get_path_names',
+    'get_paths',
+    'get_platform',
+    'get_python_version',
+    'get_scheme_names',
+    'parse_config_h',
+]
+
+
+def _safe_realpath(path):
+    try:
+        return realpath(path)
+    except OSError:
+        return path
+
+
+if sys.executable:
+    _PROJECT_BASE = os.path.dirname(_safe_realpath(sys.executable))
+else:
+    # sys.executable can be empty if argv[0] has been changed and Python is
+    # unable to retrieve the real program name
+    _PROJECT_BASE = _safe_realpath(os.getcwd())
+
+if os.name == "nt" and "pcbuild" in _PROJECT_BASE[-8:].lower():
+    _PROJECT_BASE = _safe_realpath(os.path.join(_PROJECT_BASE, pardir))
+# PC/VS7.1
+if os.name == "nt" and "\\pc\\v" in _PROJECT_BASE[-10:].lower():
+    _PROJECT_BASE = _safe_realpath(os.path.join(_PROJECT_BASE, pardir, pardir))
+# PC/AMD64
+if os.name == "nt" and "\\pcbuild\\amd64" in _PROJECT_BASE[-14:].lower():
+    _PROJECT_BASE = _safe_realpath(os.path.join(_PROJECT_BASE, pardir, pardir))
+
+
+def is_python_build():
+    for fn in ("Setup.dist", "Setup.local"):
+        if os.path.isfile(os.path.join(_PROJECT_BASE, "Modules", fn)):
+            return True
+    return False
+
+_PYTHON_BUILD = is_python_build()
+
+_cfg_read = False
+
+def _ensure_cfg_read():
+    global _cfg_read
+    if not _cfg_read:
+        from ..resources import finder
+        backport_package = __name__.rsplit('.', 1)[0]
+        _finder = finder(backport_package)
+        _cfgfile = _finder.find('sysconfig.cfg')
+        assert _cfgfile, 'sysconfig.cfg exists'
+        with _cfgfile.as_stream() as s:
+            _SCHEMES.readfp(s)
+        if _PYTHON_BUILD:
+            for scheme in ('posix_prefix', 'posix_home'):
+                _SCHEMES.set(scheme, 'include', '{srcdir}/Include')
+                _SCHEMES.set(scheme, 'platinclude', '{projectbase}/.')
+
+        _cfg_read = True
+
+
+_SCHEMES = configparser.RawConfigParser()
+_VAR_REPL = re.compile(r'\{([^{]*?)\}')
+
+def _expand_globals(config):
+    _ensure_cfg_read()
+    if config.has_section('globals'):
+        globals = config.items('globals')
+    else:
+        globals = tuple()
+
+    sections = config.sections()
+    for section in sections:
+        if section == 'globals':
+            continue
+        for option, value in globals:
+            if config.has_option(section, option):
+                continue
+            config.set(section, option, value)
+    config.remove_section('globals')
+
+    # now expanding local variables defined in the cfg file
+    #
+    for section in config.sections():
+        variables = dict(config.items(section))
+
+        def _replacer(matchobj):
+            name = matchobj.group(1)
+            if name in variables:
+                return variables[name]
+            return matchobj.group(0)
+
+        for option, value in config.items(section):
+            config.set(section, option, _VAR_REPL.sub(_replacer, value))
+
+#_expand_globals(_SCHEMES)
+
+ # FIXME don't rely on sys.version here, its format is an implementation detail
+ # of CPython, use sys.version_info or sys.hexversion
+_PY_VERSION = sys.version.split()[0]
+_PY_VERSION_SHORT = sys.version[:3]
+_PY_VERSION_SHORT_NO_DOT = _PY_VERSION[0] + _PY_VERSION[2]
+_PREFIX = os.path.normpath(sys.prefix)
+_EXEC_PREFIX = os.path.normpath(sys.exec_prefix)
+_CONFIG_VARS = None
+_USER_BASE = None
+
+
+def _subst_vars(path, local_vars):
+    """In the string `path`, replace tokens like {some.thing} with the
+    corresponding value from the map `local_vars`.
+
+    If there is no corresponding value, leave the token unchanged.
+    """
+    def _replacer(matchobj):
+        name = matchobj.group(1)
+        if name in local_vars:
+            return local_vars[name]
+        elif name in os.environ:
+            return os.environ[name]
+        return matchobj.group(0)
+    return _VAR_REPL.sub(_replacer, path)
+
+
+def _extend_dict(target_dict, other_dict):
+    target_keys = target_dict.keys()
+    for key, value in other_dict.items():
+        if key in target_keys:
+            continue
+        target_dict[key] = value
+
+
+def _expand_vars(scheme, vars):
+    res = {}
+    if vars is None:
+        vars = {}
+    _extend_dict(vars, get_config_vars())
+
+    for key, value in _SCHEMES.items(scheme):
+        if os.name in ('posix', 'nt'):
+            value = os.path.expanduser(value)
+        res[key] = os.path.normpath(_subst_vars(value, vars))
+    return res
+
+
+def format_value(value, vars):
+    def _replacer(matchobj):
+        name = matchobj.group(1)
+        if name in vars:
+            return vars[name]
+        return matchobj.group(0)
+    return _VAR_REPL.sub(_replacer, value)
+
+
+def _get_default_scheme():
+    if os.name == 'posix':
+        # the default scheme for posix is posix_prefix
+        return 'posix_prefix'
+    return os.name
+
+
+def _getuserbase():
+    env_base = os.environ.get("PYTHONUSERBASE", None)
+
+    def joinuser(*args):
+        return os.path.expanduser(os.path.join(*args))
+
+    # what about 'os2emx', 'riscos' ?
+    if os.name == "nt":
+        base = os.environ.get("APPDATA") or "~"
+        if env_base:
+            return env_base
+        else:
+            return joinuser(base, "Python")
+
+    if sys.platform == "darwin":
+        framework = get_config_var("PYTHONFRAMEWORK")
+        if framework:
+            if env_base:
+                return env_base
+            else:
+                return joinuser("~", "Library", framework, "%d.%d" %
+                                sys.version_info[:2])
+
+    if env_base:
+        return env_base
+    else:
+        return joinuser("~", ".local")
+
+
+def _parse_makefile(filename, vars=None):
+    """Parse a Makefile-style file.
+
+    A dictionary containing name/value pairs is returned.  If an
+    optional dictionary is passed in as the second argument, it is
+    used instead of a new dictionary.
+    """
+    # Regexes needed for parsing Makefile (and similar syntaxes,
+    # like old-style Setup files).
+    _variable_rx = re.compile("([a-zA-Z][a-zA-Z0-9_]+)\s*=\s*(.*)")
+    _findvar1_rx = re.compile(r"\$\(([A-Za-z][A-Za-z0-9_]*)\)")
+    _findvar2_rx = re.compile(r"\${([A-Za-z][A-Za-z0-9_]*)}")
+
+    if vars is None:
+        vars = {}
+    done = {}
+    notdone = {}
+
+    with codecs.open(filename, encoding='utf-8', errors="surrogateescape") as f:
+        lines = f.readlines()
+
+    for line in lines:
+        if line.startswith('#') or line.strip() == '':
+            continue
+        m = _variable_rx.match(line)
+        if m:
+            n, v = m.group(1, 2)
+            v = v.strip()
+            # `$$' is a literal `$' in make
+            tmpv = v.replace('$$', '')
+
+            if "$" in tmpv:
+                notdone[n] = v
+            else:
+                try:
+                    v = int(v)
+                except ValueError:
+                    # insert literal `$'
+                    done[n] = v.replace('$$', '$')
+                else:
+                    done[n] = v
+
+    # do variable interpolation here
+    variables = list(notdone.keys())
+
+    # Variables with a 'PY_' prefix in the makefile. These need to
+    # be made available without that prefix through sysconfig.
+    # Special care is needed to ensure that variable expansion works, even
+    # if the expansion uses the name without a prefix.
+    renamed_variables = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS')
+
+    while len(variables) > 0:
+        for name in tuple(variables):
+            value = notdone[name]
+            m = _findvar1_rx.search(value) or _findvar2_rx.search(value)
+            if m is not None:
+                n = m.group(1)
+                found = True
+                if n in done:
+                    item = str(done[n])
+                elif n in notdone:
+                    # get it on a subsequent round
+                    found = False
+                elif n in os.environ:
+                    # do it like make: fall back to environment
+                    item = os.environ[n]
+
+                elif n in renamed_variables:
+                    if (name.startswith('PY_') and
+                        name[3:] in renamed_variables):
+                        item = ""
+
+                    elif 'PY_' + n in notdone:
+                        found = False
+
+                    else:
+                        item = str(done['PY_' + n])
+
+                else:
+                    done[n] = item = ""
+
+                if found:
+                    after = value[m.end():]
+                    value = value[:m.start()] + item + after
+                    if "$" in after:
+                        notdone[name] = value
+                    else:
+                        try:
+                            value = int(value)
+                        except ValueError:
+                            done[name] = value.strip()
+                        else:
+                            done[name] = value
+                        variables.remove(name)
+
+                        if (name.startswith('PY_') and
+                            name[3:] in renamed_variables):
+
+                            name = name[3:]
+                            if name not in done:
+                                done[name] = value
+
+            else:
+                # bogus variable reference (e.g. "prefix=$/opt/python");
+                # just drop it since we can't deal
+                done[name] = value
+                variables.remove(name)
+
+    # strip spurious spaces
+    for k, v in done.items():
+        if isinstance(v, str):
+            done[k] = v.strip()
+
+    # save the results in the global dictionary
+    vars.update(done)
+    return vars
+
+
+def get_makefile_filename():
+    """Return the path of the Makefile."""
+    if _PYTHON_BUILD:
+        return os.path.join(_PROJECT_BASE, "Makefile")
+    if hasattr(sys, 'abiflags'):
+        config_dir_name = 'config-%s%s' % (_PY_VERSION_SHORT, sys.abiflags)
+    else:
+        config_dir_name = 'config'
+    return os.path.join(get_path('stdlib'), config_dir_name, 'Makefile')
+
+
+def _init_posix(vars):
+    """Initialize the module as appropriate for POSIX systems."""
+    # load the installed Makefile:
+    makefile = get_makefile_filename()
+    try:
+        _parse_makefile(makefile, vars)
+    except IOError as e:
+        msg = "invalid Python installation: unable to open %s" % makefile
+        if hasattr(e, "strerror"):
+            msg = msg + " (%s)" % e.strerror
+        raise IOError(msg)
+    # load the installed pyconfig.h:
+    config_h = get_config_h_filename()
+    try:
+        with open(config_h) as f:
+            parse_config_h(f, vars)
+    except IOError as e:
+        msg = "invalid Python installation: unable to open %s" % config_h
+        if hasattr(e, "strerror"):
+            msg = msg + " (%s)" % e.strerror
+        raise IOError(msg)
+    # On AIX, there are wrong paths to the linker scripts in the Makefile
+    # -- these paths are relative to the Python source, but when installed
+    # the scripts are in another directory.
+    if _PYTHON_BUILD:
+        vars['LDSHARED'] = vars['BLDSHARED']
+
+
+def _init_non_posix(vars):
+    """Initialize the module as appropriate for NT"""
+    # set basic install directories
+    vars['LIBDEST'] = get_path('stdlib')
+    vars['BINLIBDEST'] = get_path('platstdlib')
+    vars['INCLUDEPY'] = get_path('include')
+    vars['SO'] = '.pyd'
+    vars['EXE'] = '.exe'
+    vars['VERSION'] = _PY_VERSION_SHORT_NO_DOT
+    vars['BINDIR'] = os.path.dirname(_safe_realpath(sys.executable))
+
+#
+# public APIs
+#
+
+
+def parse_config_h(fp, vars=None):
+    """Parse a config.h-style file.
+
+    A dictionary containing name/value pairs is returned.  If an
+    optional dictionary is passed in as the second argument, it is
+    used instead of a new dictionary.
+    """
+    if vars is None:
+        vars = {}
+    define_rx = re.compile("#define ([A-Z][A-Za-z0-9_]+) (.*)\n")
+    undef_rx = re.compile("/[*] #undef ([A-Z][A-Za-z0-9_]+) [*]/\n")
+
+    while True:
+        line = fp.readline()
+        if not line:
+            break
+        m = define_rx.match(line)
+        if m:
+            n, v = m.group(1, 2)
+            try:
+                v = int(v)
+            except ValueError:
+                pass
+            vars[n] = v
+        else:
+            m = undef_rx.match(line)
+            if m:
+                vars[m.group(1)] = 0
+    return vars
+
+
+def get_config_h_filename():
+    """Return the path of pyconfig.h."""
+    if _PYTHON_BUILD:
+        if os.name == "nt":
+            inc_dir = os.path.join(_PROJECT_BASE, "PC")
+        else:
+            inc_dir = _PROJECT_BASE
+    else:
+        inc_dir = get_path('platinclude')
+    return os.path.join(inc_dir, 'pyconfig.h')
+
+
+def get_scheme_names():
+    """Return a tuple containing the schemes names."""
+    return tuple(sorted(_SCHEMES.sections()))
+
+
+def get_path_names():
+    """Return a tuple containing the paths names."""
+    # xxx see if we want a static list
+    return _SCHEMES.options('posix_prefix')
+
+
+def get_paths(scheme=_get_default_scheme(), vars=None, expand=True):
+    """Return a mapping containing an install scheme.
+
+    ``scheme`` is the install scheme name. If not provided, it will
+    return the default scheme for the current platform.
+    """
+    _ensure_cfg_read()
+    if expand:
+        return _expand_vars(scheme, vars)
+    else:
+        return dict(_SCHEMES.items(scheme))
+
+
+def get_path(name, scheme=_get_default_scheme(), vars=None, expand=True):
+    """Return a path corresponding to the scheme.
+
+    ``scheme`` is the install scheme name.
+    """
+    return get_paths(scheme, vars, expand)[name]
+
+
+def get_config_vars(*args):
+    """With no arguments, return a dictionary of all configuration
+    variables relevant for the current platform.
+
+    On Unix, this means every variable defined in Python's installed Makefile;
+    On Windows and Mac OS it's a much smaller set.
+
+    With arguments, return a list of values that result from looking up
+    each argument in the configuration variable dictionary.
+    """
+    global _CONFIG_VARS
+    if _CONFIG_VARS is None:
+        _CONFIG_VARS = {}
+        # Normalized versions of prefix and exec_prefix are handy to have;
+        # in fact, these are the standard versions used most places in the
+        # distutils2 module.
+        _CONFIG_VARS['prefix'] = _PREFIX
+        _CONFIG_VARS['exec_prefix'] = _EXEC_PREFIX
+        _CONFIG_VARS['py_version'] = _PY_VERSION
+        _CONFIG_VARS['py_version_short'] = _PY_VERSION_SHORT
+        _CONFIG_VARS['py_version_nodot'] = _PY_VERSION[0] + _PY_VERSION[2]
+        _CONFIG_VARS['base'] = _PREFIX
+        _CONFIG_VARS['platbase'] = _EXEC_PREFIX
+        _CONFIG_VARS['projectbase'] = _PROJECT_BASE
+        try:
+            _CONFIG_VARS['abiflags'] = sys.abiflags
+        except AttributeError:
+            # sys.abiflags may not be defined on all platforms.
+            _CONFIG_VARS['abiflags'] = ''
+
+        if os.name in ('nt', 'os2'):
+            _init_non_posix(_CONFIG_VARS)
+        if os.name == 'posix':
+            _init_posix(_CONFIG_VARS)
+        # Setting 'userbase' is done below the call to the
+        # init function to enable using 'get_config_var' in
+        # the init-function.
+        if sys.version >= '2.6':
+            _CONFIG_VARS['userbase'] = _getuserbase()
+
+        if 'srcdir' not in _CONFIG_VARS:
+            _CONFIG_VARS['srcdir'] = _PROJECT_BASE
+        else:
+            _CONFIG_VARS['srcdir'] = _safe_realpath(_CONFIG_VARS['srcdir'])
+
+        # Convert srcdir into an absolute path if it appears necessary.
+        # Normally it is relative to the build directory.  However, during
+        # testing, for example, we might be running a non-installed python
+        # from a different directory.
+        if _PYTHON_BUILD and os.name == "posix":
+            base = _PROJECT_BASE
+            try:
+                cwd = os.getcwd()
+            except OSError:
+                cwd = None
+            if (not os.path.isabs(_CONFIG_VARS['srcdir']) and
+                base != cwd):
+                # srcdir is relative and we are not in the same directory
+                # as the executable. Assume executable is in the build
+                # directory and make srcdir absolute.
+                srcdir = os.path.join(base, _CONFIG_VARS['srcdir'])
+                _CONFIG_VARS['srcdir'] = os.path.normpath(srcdir)
+
+        if sys.platform == 'darwin':
+            kernel_version = os.uname()[2]  # Kernel version (8.4.3)
+            major_version = int(kernel_version.split('.')[0])
+
+            if major_version < 8:
+                # On Mac OS X before 10.4, check if -arch and -isysroot
+                # are in CFLAGS or LDFLAGS and remove them if they are.
+                # This is needed when building extensions on a 10.3 system
+                # using a universal build of python.
+                for key in ('LDFLAGS', 'BASECFLAGS',
+                        # a number of derived variables. These need to be
+                        # patched up as well.
+                        'CFLAGS', 'PY_CFLAGS', 'BLDSHARED'):
+                    flags = _CONFIG_VARS[key]
+                    flags = re.sub('-arch\s+\w+\s', ' ', flags)
+                    flags = re.sub('-isysroot [^ \t]*', ' ', flags)
+                    _CONFIG_VARS[key] = flags
+            else:
+                # Allow the user to override the architecture flags using
+                # an environment variable.
+                # NOTE: This name was introduced by Apple in OSX 10.5 and
+                # is used by several scripting languages distributed with
+                # that OS release.
+                if 'ARCHFLAGS' in os.environ:
+                    arch = os.environ['ARCHFLAGS']
+                    for key in ('LDFLAGS', 'BASECFLAGS',
+                        # a number of derived variables. These need to be
+                        # patched up as well.
+                        'CFLAGS', 'PY_CFLAGS', 'BLDSHARED'):
+
+                        flags = _CONFIG_VARS[key]
+                        flags = re.sub('-arch\s+\w+\s', ' ', flags)
+                        flags = flags + ' ' + arch
+                        _CONFIG_VARS[key] = flags
+
+                # If we're on OSX 10.5 or later and the user tries to
+                # compiles an extension using an SDK that is not present
+                # on the current machine it is better to not use an SDK
+                # than to fail.
+                #
+                # The major usecase for this is users using a Python.org
+                # binary installer  on OSX 10.6: that installer uses
+                # the 10.4u SDK, but that SDK is not installed by default
+                # when you install Xcode.
+                #
+                CFLAGS = _CONFIG_VARS.get('CFLAGS', '')
+                m = re.search('-isysroot\s+(\S+)', CFLAGS)
+                if m is not None:
+                    sdk = m.group(1)
+                    if not os.path.exists(sdk):
+                        for key in ('LDFLAGS', 'BASECFLAGS',
+                             # a number of derived variables. These need to be
+                             # patched up as well.
+                            'CFLAGS', 'PY_CFLAGS', 'BLDSHARED'):
+
+                            flags = _CONFIG_VARS[key]
+                            flags = re.sub('-isysroot\s+\S+(\s|$)', ' ', flags)
+                            _CONFIG_VARS[key] = flags
+
+    if args:
+        vals = []
+        for name in args:
+            vals.append(_CONFIG_VARS.get(name))
+        return vals
+    else:
+        return _CONFIG_VARS
+
+
+def get_config_var(name):
+    """Return the value of a single variable using the dictionary returned by
+    'get_config_vars()'.
+
+    Equivalent to get_config_vars().get(name)
+    """
+    return get_config_vars().get(name)
+
+
+def get_platform():
+    """Return a string that identifies the current platform.
+
+    This is used mainly to distinguish platform-specific build directories and
+    platform-specific built distributions.  Typically includes the OS name
+    and version and the architecture (as supplied by 'os.uname()'),
+    although the exact information included depends on the OS; eg. for IRIX
+    the architecture isn't particularly important (IRIX only runs on SGI
+    hardware), but for Linux the kernel version isn't particularly
+    important.
+
+    Examples of returned values:
+       linux-i586
+       linux-alpha (?)
+       solaris-2.6-sun4u
+       irix-5.3
+       irix64-6.2
+
+    Windows will return one of:
+       win-amd64 (64bit Windows on AMD64 (aka x86_64, Intel64, EM64T, etc)
+       win-ia64 (64bit Windows on Itanium)
+       win32 (all others - specifically, sys.platform is returned)
+
+    For other non-POSIX platforms, currently just returns 'sys.platform'.
+    """
+    if os.name == 'nt':
+        # sniff sys.version for architecture.
+        prefix = " bit ("
+        i = sys.version.find(prefix)
+        if i == -1:
+            return sys.platform
+        j = sys.version.find(")", i)
+        look = sys.version[i+len(prefix):j].lower()
+        if look == 'amd64':
+            return 'win-amd64'
+        if look == 'itanium':
+            return 'win-ia64'
+        return sys.platform
+
+    if os.name != "posix" or not hasattr(os, 'uname'):
+        # XXX what about the architecture? NT is Intel or Alpha,
+        # Mac OS is M68k or PPC, etc.
+        return sys.platform
+
+    # Try to distinguish various flavours of Unix
+    osname, host, release, version, machine = os.uname()
+
+    # Convert the OS name to lowercase, remove '/' characters
+    # (to accommodate BSD/OS), and translate spaces (for "Power Macintosh")
+    osname = osname.lower().replace('/', '')
+    machine = machine.replace(' ', '_')
+    machine = machine.replace('/', '-')
+
+    if osname[:5] == "linux":
+        # At least on Linux/Intel, 'machine' is the processor --
+        # i386, etc.
+        # XXX what about Alpha, SPARC, etc?
+        return  "%s-%s" % (osname, machine)
+    elif osname[:5] == "sunos":
+        if release[0] >= "5":           # SunOS 5 == Solaris 2
+            osname = "solaris"
+            release = "%d.%s" % (int(release[0]) - 3, release[2:])
+        # fall through to standard osname-release-machine representation
+    elif osname[:4] == "irix":              # could be "irix64"!
+        return "%s-%s" % (osname, release)
+    elif osname[:3] == "aix":
+        return "%s-%s.%s" % (osname, version, release)
+    elif osname[:6] == "cygwin":
+        osname = "cygwin"
+        rel_re = re.compile(r'[\d.]+')
+        m = rel_re.match(release)
+        if m:
+            release = m.group()
+    elif osname[:6] == "darwin":
+        #
+        # For our purposes, we'll assume that the system version from
+        # distutils' perspective is what MACOSX_DEPLOYMENT_TARGET is set
+        # to. This makes the compatibility story a bit more sane because the
+        # machine is going to compile and link as if it were
+        # MACOSX_DEPLOYMENT_TARGET.
+        cfgvars = get_config_vars()
+        macver = cfgvars.get('MACOSX_DEPLOYMENT_TARGET')
+
+        if True:
+            # Always calculate the release of the running machine,
+            # needed to determine if we can build fat binaries or not.
+
+            macrelease = macver
+            # Get the system version. Reading this plist is a documented
+            # way to get the system version (see the documentation for
+            # the Gestalt Manager)
+            try:
+                f = open('/System/Library/CoreServices/SystemVersion.plist')
+            except IOError:
+                # We're on a plain darwin box, fall back to the default
+                # behaviour.
+                pass
+            else:
+                try:
+                    m = re.search(r'<key>ProductUserVisibleVersion</key>\s*'
+                                  r'<string>(.*?)</string>', f.read())
+                finally:
+                    f.close()
+                if m is not None:
+                    macrelease = '.'.join(m.group(1).split('.')[:2])
+                # else: fall back to the default behaviour
+
+        if not macver:
+            macver = macrelease
+
+        if macver:
+            release = macver
+            osname = "macosx"
+
+            if ((macrelease + '.') >= '10.4.' and
+                '-arch' in get_config_vars().get('CFLAGS', '').strip()):
+                # The universal build will build fat binaries, but not on
+                # systems before 10.4
+                #
+                # Try to detect 4-way universal builds, those have machine-type
+                # 'universal' instead of 'fat'.
+
+                machine = 'fat'
+                cflags = get_config_vars().get('CFLAGS')
+
+                archs = re.findall('-arch\s+(\S+)', cflags)
+                archs = tuple(sorted(set(archs)))
+
+                if len(archs) == 1:
+                    machine = archs[0]
+                elif archs == ('i386', 'ppc'):
+                    machine = 'fat'
+                elif archs == ('i386', 'x86_64'):
+                    machine = 'intel'
+                elif archs == ('i386', 'ppc', 'x86_64'):
+                    machine = 'fat3'
+                elif archs == ('ppc64', 'x86_64'):
+                    machine = 'fat64'
+                elif archs == ('i386', 'ppc', 'ppc64', 'x86_64'):
+                    machine = 'universal'
+                else:
+                    raise ValueError(
+                       "Don't know machine value for archs=%r" % (archs,))
+
+            elif machine == 'i386':
+                # On OSX the machine type returned by uname is always the
+                # 32-bit variant, even if the executable architecture is
+                # the 64-bit variant
+                if sys.maxsize >= 2**32:
+                    machine = 'x86_64'
+
+            elif machine in ('PowerPC', 'Power_Macintosh'):
+                # Pick a sane name for the PPC architecture.
+                # See 'i386' case
+                if sys.maxsize >= 2**32:
+                    machine = 'ppc64'
+                else:
+                    machine = 'ppc'
+
+    return "%s-%s-%s" % (osname, release, machine)
+
+
+def get_python_version():
+    return _PY_VERSION_SHORT
+
+
+def _print_dict(title, data):
+    for index, (key, value) in enumerate(sorted(data.items())):
+        if index == 0:
+            print('%s: ' % (title))
+        print('\t%s = "%s"' % (key, value))
+
+
+def _main():
+    """Display all information sysconfig detains."""
+    print('Platform: "%s"' % get_platform())
+    print('Python version: "%s"' % get_python_version())
+    print('Current installation scheme: "%s"' % _get_default_scheme())
+    print()
+    _print_dict('Paths', get_paths())
+    print()
+    _print_dict('Variables', get_config_vars())
+
+
+if __name__ == '__main__':
+    _main()

get_obitools/getpackage/pip/_vendor/distlib/index.py

@@ -0,0 +1,488 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Vinay Sajip.
+# Licensed to the Python Software Foundation under a contributor agreement.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+import hashlib
+import logging
+import os
+import shutil
+import subprocess
+import tempfile
+try:
+    from threading import Thread
+except ImportError:
+    from dummy_threading import Thread
+
+from . import DistlibException
+from .compat import (HTTPBasicAuthHandler, Request, HTTPPasswordMgr,
+                     urlparse, build_opener, string_types)
+from .util import cached_property, zip_dir, ServerProxy
+
+logger = logging.getLogger(__name__)
+
+DEFAULT_INDEX = 'https://pypi.python.org/pypi'
+DEFAULT_REALM = 'pypi'
+
+class PackageIndex(object):
+    """
+    This class represents a package index compatible with PyPI, the Python
+    Package Index.
+    """
+
+    boundary = b'----------ThIs_Is_tHe_distlib_index_bouNdaRY_$'
+
+    def __init__(self, url=None):
+        """
+        Initialise an instance.
+
+        :param url: The URL of the index. If not specified, the URL for PyPI is
+                    used.
+        """
+        self.url = url or DEFAULT_INDEX
+        self.read_configuration()
+        scheme, netloc, path, params, query, frag = urlparse(self.url)
+        if params or query or frag or scheme not in ('http', 'https'):
+            raise DistlibException('invalid repository: %s' % self.url)
+        self.password_handler = None
+        self.ssl_verifier = None
+        self.gpg = None
+        self.gpg_home = None
+        self.rpc_proxy = None
+        with open(os.devnull, 'w') as sink:
+            for s in ('gpg2', 'gpg'):
+                try:
+                    rc = subprocess.check_call([s, '--version'], stdout=sink,
+                                               stderr=sink)
+                    if rc == 0:
+                        self.gpg = s
+                        break
+                except OSError:
+                    pass
+
+    def _get_pypirc_command(self):
+        """
+        Get the distutils command for interacting with PyPI configurations.
+        :return: the command.
+        """
+        from distutils.core import Distribution
+        from distutils.config import PyPIRCCommand
+        d = Distribution()
+        return PyPIRCCommand(d)
+
+    def read_configuration(self):
+        """
+        Read the PyPI access configuration as supported by distutils, getting
+        PyPI to do the acutal work. This populates ``username``, ``password``,
+        ``realm`` and ``url`` attributes from the configuration.
+        """
+        # get distutils to do the work
+        c = self._get_pypirc_command()
+        c.repository = self.url
+        cfg = c._read_pypirc()
+        self.username = cfg.get('username')
+        self.password = cfg.get('password')
+        self.realm = cfg.get('realm', 'pypi')
+        self.url = cfg.get('repository', self.url)
+
+    def save_configuration(self):
+        """
+        Save the PyPI access configuration. You must have set ``username`` and
+        ``password`` attributes before calling this method.
+
+        Again, distutils is used to do the actual work.
+        """
+        self.check_credentials()
+        # get distutils to do the work
+        c = self._get_pypirc_command()
+        c._store_pypirc(self.username, self.password)
+
+    def check_credentials(self):
+        """
+        Check that ``username`` and ``password`` have been set, and raise an
+        exception if not.
+        """
+        if self.username is None or self.password is None:
+            raise DistlibException('username and password must be set')
+        pm = HTTPPasswordMgr()
+        _, netloc, _, _, _, _ = urlparse(self.url)
+        pm.add_password(self.realm, netloc, self.username, self.password)
+        self.password_handler = HTTPBasicAuthHandler(pm)
+
+    def register(self, metadata):
+        """
+        Register a distribution on PyPI, using the provided metadata.
+
+        :param metadata: A :class:`Metadata` instance defining at least a name
+                         and version number for the distribution to be
+                         registered.
+        :return: The HTTP response received from PyPI upon submission of the
+                request.
+        """
+        self.check_credentials()
+        metadata.validate()
+        d = metadata.todict()
+        d[':action'] = 'verify'
+        request = self.encode_request(d.items(), [])
+        response = self.send_request(request)
+        d[':action'] = 'submit'
+        request = self.encode_request(d.items(), [])
+        return self.send_request(request)
+
+    def _reader(self, name, stream, outbuf):
+        """
+        Thread runner for reading lines of from a subprocess into a buffer.
+
+        :param name: The logical name of the stream (used for logging only).
+        :param stream: The stream to read from. This will typically a pipe
+                       connected to the output stream of a subprocess.
+        :param outbuf: The list to append the read lines to.
+        """
+        while True:
+            s = stream.readline()
+            if not s:
+                break
+            s = s.decode('utf-8').rstrip()
+            outbuf.append(s)
+            logger.debug('%s: %s' % (name, s))
+        stream.close()
+
+    def get_sign_command(self, filename, signer, sign_password):
+        """
+        Return a suitable command for signing a file.
+
+        :param filename: The pathname to the file to be signed.
+        :param signer: The identifier of the signer of the file.
+        :param sign_password: The passphrase for the signer's
+                              private key used for signing.
+        :return: The signing command as a list suitable to be
+                 passed to :class:`subprocess.Popen`.
+        """
+        cmd = [self.gpg, '--status-fd', '2', '--no-tty']
+        if self.gpg_home:
+            cmd.extend(['--homedir', self.gpg_home])
+        if sign_password is not None:
+            cmd.extend(['--batch', '--passphrase-fd', '0'])
+        td = tempfile.mkdtemp()
+        sf = os.path.join(td, os.path.basename(filename) + '.asc')
+        cmd.extend(['--detach-sign', '--armor', '--local-user',
+                    signer, '--output', sf, filename])
+        logger.debug('invoking: %s', ' '.join(cmd))
+        return cmd, sf
+
+    def run_command(self, cmd, input_data=None):
+        """
+        Run a command in a child process , passing it any input data specified.
+
+        :param cmd: The command to run.
+        :param input_data: If specified, this must be a byte string containing
+                           data to be sent to the child process.
+        :return: A tuple consisting of the subprocess' exit code, a list of
+                 lines read from the subprocess' ``stdout``, and a list of
+                 lines read from the subprocess' ``stderr``.
+        """
+        kwargs = {
+            'stdout': subprocess.PIPE,
+            'stderr': subprocess.PIPE,
+        }
+        if input_data is not None:
+            kwargs['stdin'] = subprocess.PIPE
+        stdout = []
+        stderr = []
+        p = subprocess.Popen(cmd, **kwargs)
+        # We don't use communicate() here because we may need to
+        # get clever with interacting with the command
+        t1 = Thread(target=self._reader, args=('stdout', p.stdout, stdout))
+        t1.start()
+        t2 = Thread(target=self._reader, args=('stderr', p.stderr, stderr))
+        t2.start()
+        if input_data is not None:
+            p.stdin.write(input_data)
+            p.stdin.close()
+
+        p.wait()
+        t1.join()
+        t2.join()
+        return p.returncode, stdout, stderr
+
+    def sign_file(self, filename, signer, sign_password):
+        """
+        Sign a file.
+
+        :param filename: The pathname to the file to be signed.
+        :param signer: The identifier of the signer of the file.
+        :param sign_password: The passphrase for the signer's
+                              private key used for signing.
+        :return: The absolute pathname of the file where the signature is
+                 stored.
+        """
+        cmd, sig_file = self.get_sign_command(filename, signer, sign_password)
+        rc, stdout, stderr = self.run_command(cmd,
+                                              sign_password.encode('utf-8'))
+        if rc != 0:
+            raise DistlibException('sign command failed with error '
+                                   'code %s' % rc)
+        return sig_file
+
+    def upload_file(self, metadata, filename, signer=None, sign_password=None,
+                    filetype='sdist', pyversion='source'):
+        """
+        Upload a release file to the index.
+
+        :param metadata: A :class:`Metadata` instance defining at least a name
+                         and version number for the file to be uploaded.
+        :param filename: The pathname of the file to be uploaded.
+        :param signer: The identifier of the signer of the file.
+        :param sign_password: The passphrase for the signer's
+                              private key used for signing.
+        :param filetype: The type of the file being uploaded. This is the
+                        distutils command which produced that file, e.g.
+                        ``sdist`` or ``bdist_wheel``.
+        :param pyversion: The version of Python which the release relates
+                          to. For code compatible with any Python, this would
+                          be ``source``, otherwise it would be e.g. ``3.2``.
+        :return: The HTTP response received from PyPI upon submission of the
+                request.
+        """
+        self.check_credentials()
+        if not os.path.exists(filename):
+            raise DistlibException('not found: %s' % filename)
+        metadata.validate()
+        d = metadata.todict()
+        sig_file = None
+        if signer:
+            if not self.gpg:
+                logger.warning('no signing program available - not signed')
+            else:
+                sig_file = self.sign_file(filename, signer, sign_password)
+        with open(filename, 'rb') as f:
+            file_data = f.read()
+        md5_digest = hashlib.md5(file_data).hexdigest()
+        sha256_digest = hashlib.sha256(file_data).hexdigest()
+        d.update({
+            ':action': 'file_upload',
+            'protcol_version': '1',
+            'filetype': filetype,
+            'pyversion': pyversion,
+            'md5_digest': md5_digest,
+            'sha256_digest': sha256_digest,
+        })
+        files = [('content', os.path.basename(filename), file_data)]
+        if sig_file:
+            with open(sig_file, 'rb') as f:
+                sig_data = f.read()
+            files.append(('gpg_signature', os.path.basename(sig_file),
+                         sig_data))
+            shutil.rmtree(os.path.dirname(sig_file))
+        request = self.encode_request(d.items(), files)
+        return self.send_request(request)
+
+    def upload_documentation(self, metadata, doc_dir):
+        """
+        Upload documentation to the index.
+
+        :param metadata: A :class:`Metadata` instance defining at least a name
+                         and version number for the documentation to be
+                         uploaded.
+        :param doc_dir: The pathname of the directory which contains the
+                        documentation. This should be the directory that
+                        contains the ``index.html`` for the documentation.
+        :return: The HTTP response received from PyPI upon submission of the
+                request.
+        """
+        self.check_credentials()
+        if not os.path.isdir(doc_dir):
+            raise DistlibException('not a directory: %r' % doc_dir)
+        fn = os.path.join(doc_dir, 'index.html')
+        if not os.path.exists(fn):
+            raise DistlibException('not found: %r' % fn)
+        metadata.validate()
+        name, version = metadata.name, metadata.version
+        zip_data = zip_dir(doc_dir).getvalue()
+        fields = [(':action', 'doc_upload'),
+                  ('name', name), ('version', version)]
+        files = [('content', name, zip_data)]
+        request = self.encode_request(fields, files)
+        return self.send_request(request)
+
+    def get_verify_command(self, signature_filename, data_filename):
+        """
+        Return a suitable command for verifying a file.
+
+        :param signature_filename: The pathname to the file containing the
+                                   signature.
+        :param data_filename: The pathname to the file containing the
+                              signed data.
+        :return: The verifying command as a list suitable to be
+                 passed to :class:`subprocess.Popen`.
+        """
+        cmd = [self.gpg, '--status-fd', '2', '--no-tty']
+        if self.gpg_home:
+            cmd.extend(['--homedir', self.gpg_home])
+        cmd.extend(['--verify', signature_filename, data_filename])
+        logger.debug('invoking: %s', ' '.join(cmd))
+        return cmd
+
+    def verify_signature(self, signature_filename, data_filename):
+        """
+        Verify a signature for a file.
+
+        :param signature_filename: The pathname to the file containing the
+                                   signature.
+        :param data_filename: The pathname to the file containing the
+                              signed data.
+        :return: True if the signature was verified, else False.
+        """
+        if not self.gpg:
+            raise DistlibException('verification unavailable because gpg '
+                                   'unavailable')
+        cmd = self.get_verify_command(signature_filename, data_filename)
+        rc, stdout, stderr = self.run_command(cmd)
+        if rc not in (0, 1):
+            raise DistlibException('verify command failed with error '
+                             'code %s' % rc)
+        return rc == 0
+
+    def download_file(self, url, destfile, digest=None, reporthook=None):
+        """
+        This is a convenience method for downloading a file from an URL.
+        Normally, this will be a file from the index, though currently
+        no check is made for this (i.e. a file can be downloaded from
+        anywhere).
+
+        The method is just like the :func:`urlretrieve` function in the
+        standard library, except that it allows digest computation to be
+        done during download and checking that the downloaded data
+        matched any expected value.
+
+        :param url: The URL of the file to be downloaded (assumed to be
+                    available via an HTTP GET request).
+        :param destfile: The pathname where the downloaded file is to be
+                         saved.
+        :param digest: If specified, this must be a (hasher, value)
+                       tuple, where hasher is the algorithm used (e.g.
+                       ``'md5'``) and ``value`` is the expected value.
+        :param reporthook: The same as for :func:`urlretrieve` in the
+                           standard library.
+        """
+        if digest is None:
+            digester = None
+            logger.debug('No digest specified')
+        else:
+            if isinstance(digest, (list, tuple)):
+                hasher, digest = digest
+            else:
+                hasher = 'md5'
+            digester = getattr(hashlib, hasher)()
+            logger.debug('Digest specified: %s' % digest)
+        # The following code is equivalent to urlretrieve.
+        # We need to do it this way so that we can compute the
+        # digest of the file as we go.
+        with open(destfile, 'wb') as dfp:
+            # addinfourl is not a context manager on 2.x
+            # so we have to use try/finally
+            sfp = self.send_request(Request(url))
+            try:
+                headers = sfp.info()
+                blocksize = 8192
+                size = -1
+                read = 0
+                blocknum = 0
+                if "content-length" in headers:
+                    size = int(headers["Content-Length"])
+                if reporthook:
+                    reporthook(blocknum, blocksize, size)
+                while True:
+                    block = sfp.read(blocksize)
+                    if not block:
+                        break
+                    read += len(block)
+                    dfp.write(block)
+                    if digester:
+                        digester.update(block)
+                    blocknum += 1
+                    if reporthook:
+                        reporthook(blocknum, blocksize, size)
+            finally:
+                sfp.close()
+
+        # check that we got the whole file, if we can
+        if size >= 0 and read < size:
+            raise DistlibException(
+                'retrieval incomplete: got only %d out of %d bytes'
+                % (read, size))
+        # if we have a digest, it must match.
+        if digester:
+            actual = digester.hexdigest()
+            if digest != actual:
+                raise DistlibException('%s digest mismatch for %s: expected '
+                                       '%s, got %s' % (hasher, destfile,
+                                                       digest, actual))
+            logger.debug('Digest verified: %s', digest)
+
+    def send_request(self, req):
+        """
+        Send a standard library :class:`Request` to PyPI and return its
+        response.
+
+        :param req: The request to send.
+        :return: The HTTP response from PyPI (a standard library HTTPResponse).
+        """
+        handlers = []
+        if self.password_handler:
+            handlers.append(self.password_handler)
+        if self.ssl_verifier:
+            handlers.append(self.ssl_verifier)
+        opener = build_opener(*handlers)
+        return opener.open(req)
+
+    def encode_request(self, fields, files):
+        """
+        Encode fields and files for posting to an HTTP server.
+
+        :param fields: The fields to send as a list of (fieldname, value)
+                       tuples.
+        :param files: The files to send as a list of (fieldname, filename,
+                      file_bytes) tuple.
+        """
+        # Adapted from packaging, which in turn was adapted from
+        # http://code.activestate.com/recipes/146306
+
+        parts = []
+        boundary = self.boundary
+        for k, values in fields:
+            if not isinstance(values, (list, tuple)):
+                values = [values]
+
+            for v in values:
+                parts.extend((
+                    b'--' + boundary,
+                    ('Content-Disposition: form-data; name="%s"' %
+                     k).encode('utf-8'),
+                    b'',
+                    v.encode('utf-8')))
+        for key, filename, value in files:
+            parts.extend((
+                b'--' + boundary,
+                ('Content-Disposition: form-data; name="%s"; filename="%s"' %
+                 (key, filename)).encode('utf-8'),
+                b'',
+                value))
+
+        parts.extend((b'--' + boundary + b'--', b''))
+
+        body = b'\r\n'.join(parts)
+        ct = b'multipart/form-data; boundary=' + boundary
+        headers = {
+            'Content-type': ct,
+            'Content-length': str(len(body))
+        }
+        return Request(self.url, body, headers)
+
+    def search(self, terms, operator=None):
+        if isinstance(terms, string_types):
+            terms = {'name': terms}
+        if self.rpc_proxy is None:
+            self.rpc_proxy = ServerProxy(self.url, timeout=3.0)
+        return self.rpc_proxy.search(terms, operator or 'and')

get_obitools/getpackage/pip/_vendor/distlib/manifest.py

@@ -0,0 +1,364 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012-2013 Python Software Foundation.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+"""
+Class representing the list of files in a distribution.
+
+Equivalent to distutils.filelist, but fixes some problems.
+"""
+import fnmatch
+import logging
+import os
+import re
+
+from . import DistlibException
+from .compat import fsdecode
+from .util import convert_path
+
+
+__all__ = ['Manifest']
+
+logger = logging.getLogger(__name__)
+
+# a \ followed by some spaces + EOL
+_COLLAPSE_PATTERN = re.compile('\\\w*\n', re.M)
+_COMMENTED_LINE = re.compile('#.*?(?=\n)|\n(?=$)', re.M | re.S)
+
+
+class Manifest(object):
+    """A list of files built by on exploring the filesystem and filtered by
+    applying various patterns to what we find there.
+    """
+
+    def __init__(self, base=None):
+        """
+        Initialise an instance.
+
+        :param base: The base directory to explore under.
+        """
+        self.base = os.path.abspath(os.path.normpath(base or os.getcwd()))
+        self.prefix = self.base + os.sep
+        self.allfiles = None
+        self.files = set()
+
+    #
+    # Public API
+    #
+
+    def findall(self):
+        """Find all files under the base and set ``allfiles`` to the absolute
+        pathnames of files found.
+        """
+        from stat import S_ISREG, S_ISDIR, S_ISLNK
+
+        self.allfiles = allfiles = []
+        root = self.base
+        stack = [root]
+        pop = stack.pop
+        push = stack.append
+
+        while stack:
+            root = pop()
+            names = os.listdir(root)
+
+            for name in names:
+                fullname = os.path.join(root, name)
+
+                # Avoid excess stat calls -- just one will do, thank you!
+                stat = os.stat(fullname)
+                mode = stat.st_mode
+                if S_ISREG(mode):
+                    allfiles.append(fsdecode(fullname))
+                elif S_ISDIR(mode) and not S_ISLNK(mode):
+                    push(fullname)
+
+    def add(self, item):
+        """
+        Add a file to the manifest.
+
+        :param item: The pathname to add. This can be relative to the base.
+        """
+        if not item.startswith(self.prefix):
+            item = os.path.join(self.base, item)
+        self.files.add(os.path.normpath(item))
+
+    def add_many(self, items):
+        """
+        Add a list of files to the manifest.
+
+        :param items: The pathnames to add. These can be relative to the base.
+        """
+        for item in items:
+            self.add(item)
+
+    def sorted(self, wantdirs=False):
+        """
+        Return sorted files in directory order
+        """
+
+        def add_dir(dirs, d):
+            dirs.add(d)
+            logger.debug('add_dir added %s', d)
+            if d != self.base:
+                parent, _ = os.path.split(d)
+                assert parent not in ('', '/')
+                add_dir(dirs, parent)
+
+        result = set(self.files)    # make a copy!
+        if wantdirs:
+            dirs = set()
+            for f in result:
+                add_dir(dirs, os.path.dirname(f))
+            result |= dirs
+        return [os.path.join(*path_tuple) for path_tuple in
+                sorted(os.path.split(path) for path in result)]
+
+    def clear(self):
+        """Clear all collected files."""
+        self.files = set()
+        self.allfiles = []
+
+    def process_directive(self, directive):
+        """
+        Process a directive which either adds some files from ``allfiles`` to
+        ``files``, or removes some files from ``files``.
+
+        :param directive: The directive to process. This should be in a format
+                     compatible with distutils ``MANIFEST.in`` files:
+
+                     http://docs.python.org/distutils/sourcedist.html#commands
+        """
+        # Parse the line: split it up, make sure the right number of words
+        # is there, and return the relevant words.  'action' is always
+        # defined: it's the first word of the line.  Which of the other
+        # three are defined depends on the action; it'll be either
+        # patterns, (dir and patterns), or (dirpattern).
+        action, patterns, thedir, dirpattern = self._parse_directive(directive)
+
+        # OK, now we know that the action is valid and we have the
+        # right number of words on the line for that action -- so we
+        # can proceed with minimal error-checking.
+        if action == 'include':
+            for pattern in patterns:
+                if not self._include_pattern(pattern, anchor=True):
+                    logger.warning('no files found matching %r', pattern)
+
+        elif action == 'exclude':
+            for pattern in patterns:
+                if not self._exclude_pattern(pattern, anchor=True):
+                    logger.warning('no previously-included files '
+                                   'found matching %r', pattern)
+
+        elif action == 'global-include':
+            for pattern in patterns:
+                if not self._include_pattern(pattern, anchor=False):
+                    logger.warning('no files found matching %r '
+                                   'anywhere in distribution', pattern)
+
+        elif action == 'global-exclude':
+            for pattern in patterns:
+                if not self._exclude_pattern(pattern, anchor=False):
+                    logger.warning('no previously-included files '
+                                   'matching %r found anywhere in '
+                                   'distribution', pattern)
+
+        elif action == 'recursive-include':
+            for pattern in patterns:
+                if not self._include_pattern(pattern, prefix=thedir):
+                    logger.warning('no files found matching %r '
+                                   'under directory %r', pattern, thedir)
+
+        elif action == 'recursive-exclude':
+            for pattern in patterns:
+                if not self._exclude_pattern(pattern, prefix=thedir):
+                    logger.warning('no previously-included files '
+                                   'matching %r found under directory %r',
+                                   pattern, thedir)
+
+        elif action == 'graft':
+            if not self._include_pattern(None, prefix=dirpattern):
+                logger.warning('no directories found matching %r',
+                               dirpattern)
+
+        elif action == 'prune':
+            if not self._exclude_pattern(None, prefix=dirpattern):
+                logger.warning('no previously-included directories found '
+                               'matching %r', dirpattern)
+        else:   # pragma: no cover
+            # This should never happen, as it should be caught in
+            # _parse_template_line
+            raise DistlibException(
+                'invalid action %r' % action)
+
+    #
+    # Private API
+    #
+
+    def _parse_directive(self, directive):
+        """
+        Validate a directive.
+        :param directive: The directive to validate.
+        :return: A tuple of action, patterns, thedir, dir_patterns
+        """
+        words = directive.split()
+        if len(words) == 1 and words[0] not in ('include', 'exclude',
+                                                'global-include',
+                                                'global-exclude',
+                                                'recursive-include',
+                                                'recursive-exclude',
+                                                'graft', 'prune'):
+            # no action given, let's use the default 'include'
+            words.insert(0, 'include')
+
+        action = words[0]
+        patterns = thedir = dir_pattern = None
+
+        if action in ('include', 'exclude',
+                      'global-include', 'global-exclude'):
+            if len(words) < 2:
+                raise DistlibException(
+                    '%r expects <pattern1> <pattern2> ...' % action)
+
+            patterns = [convert_path(word) for word in words[1:]]
+
+        elif action in ('recursive-include', 'recursive-exclude'):
+            if len(words) < 3:
+                raise DistlibException(
+                    '%r expects <dir> <pattern1> <pattern2> ...' % action)
+
+            thedir = convert_path(words[1])
+            patterns = [convert_path(word) for word in words[2:]]
+
+        elif action in ('graft', 'prune'):
+            if len(words) != 2:
+                raise DistlibException(
+                    '%r expects a single <dir_pattern>' % action)
+
+            dir_pattern = convert_path(words[1])
+
+        else:
+            raise DistlibException('unknown action %r' % action)
+
+        return action, patterns, thedir, dir_pattern
+
+    def _include_pattern(self, pattern, anchor=True, prefix=None,
+                         is_regex=False):
+        """Select strings (presumably filenames) from 'self.files' that
+        match 'pattern', a Unix-style wildcard (glob) pattern.
+
+        Patterns are not quite the same as implemented by the 'fnmatch'
+        module: '*' and '?'  match non-special characters, where "special"
+        is platform-dependent: slash on Unix; colon, slash, and backslash on
+        DOS/Windows; and colon on Mac OS.
+
+        If 'anchor' is true (the default), then the pattern match is more
+        stringent: "*.py" will match "foo.py" but not "foo/bar.py".  If
+        'anchor' is false, both of these will match.
+
+        If 'prefix' is supplied, then only filenames starting with 'prefix'
+        (itself a pattern) and ending with 'pattern', with anything in between
+        them, will match.  'anchor' is ignored in this case.
+
+        If 'is_regex' is true, 'anchor' and 'prefix' are ignored, and
+        'pattern' is assumed to be either a string containing a regex or a
+        regex object -- no translation is done, the regex is just compiled
+        and used as-is.
+
+        Selected strings will be added to self.files.
+
+        Return True if files are found.
+        """
+        # XXX docstring lying about what the special chars are?
+        found = False
+        pattern_re = self._translate_pattern(pattern, anchor, prefix, is_regex)
+
+        # delayed loading of allfiles list
+        if self.allfiles is None:
+            self.findall()
+
+        for name in self.allfiles:
+            if pattern_re.search(name):
+                self.files.add(name)
+                found = True
+        return found
+
+    def _exclude_pattern(self, pattern, anchor=True, prefix=None,
+                         is_regex=False):
+        """Remove strings (presumably filenames) from 'files' that match
+        'pattern'.
+
+        Other parameters are the same as for 'include_pattern()', above.
+        The list 'self.files' is modified in place. Return True if files are
+        found.
+
+        This API is public to allow e.g. exclusion of SCM subdirs, e.g. when
+        packaging source distributions
+        """
+        found = False
+        pattern_re = self._translate_pattern(pattern, anchor, prefix, is_regex)
+        for f in list(self.files):
+            if pattern_re.search(f):
+                self.files.remove(f)
+                found = True
+        return found
+
+    def _translate_pattern(self, pattern, anchor=True, prefix=None,
+                           is_regex=False):
+        """Translate a shell-like wildcard pattern to a compiled regular
+        expression.
+
+        Return the compiled regex.  If 'is_regex' true,
+        then 'pattern' is directly compiled to a regex (if it's a string)
+        or just returned as-is (assumes it's a regex object).
+        """
+        if is_regex:
+            if isinstance(pattern, str):
+                return re.compile(pattern)
+            else:
+                return pattern
+
+        if pattern:
+            pattern_re = self._glob_to_re(pattern)
+        else:
+            pattern_re = ''
+
+        base = re.escape(os.path.join(self.base, ''))
+        if prefix is not None:
+            # ditch end of pattern character
+            empty_pattern = self._glob_to_re('')
+            prefix_re = self._glob_to_re(prefix)[:-len(empty_pattern)]
+            sep = os.sep
+            if os.sep == '\\':
+                sep = r'\\'
+            pattern_re = '^' + base + sep.join((prefix_re,
+                                                '.*' + pattern_re))
+        else:                               # no prefix -- respect anchor flag
+            if anchor:
+                pattern_re = '^' + base + pattern_re
+
+        return re.compile(pattern_re)
+
+    def _glob_to_re(self, pattern):
+        """Translate a shell-like glob pattern to a regular expression.
+
+        Return a string containing the regex.  Differs from
+        'fnmatch.translate()' in that '*' does not match "special characters"
+        (which are platform-specific).
+        """
+        pattern_re = fnmatch.translate(pattern)
+
+        # '?' and '*' in the glob pattern become '.' and '.*' in the RE, which
+        # IMHO is wrong -- '?' and '*' aren't supposed to match slash in Unix,
+        # and by extension they shouldn't match such "special characters" under
+        # any OS.  So change all non-escaped dots in the RE to match any
+        # character except the special characters (currently: just os.sep).
+        sep = os.sep
+        if os.sep == '\\':
+            # we're using a regex to manipulate a regex, so we need
+            # to escape the backslash twice
+            sep = r'\\\\'
+        escaped = r'\1[^%s]' % sep
+        pattern_re = re.sub(r'((?<!\\)(\\\\)*)\.', escaped, pattern_re)
+        return pattern_re

get_obitools/getpackage/pip/_vendor/distlib/markers.py

@@ -0,0 +1,190 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012-2013 Vinay Sajip.
+# Licensed to the Python Software Foundation under a contributor agreement.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+"""Parser for the environment markers micro-language defined in PEP 345."""
+
+import ast
+import os
+import sys
+import platform
+
+from .compat import python_implementation, string_types
+from .util import in_venv
+
+__all__ = ['interpret']
+
+
+class Evaluator(object):
+    """
+    A limited evaluator for Python expressions.
+    """
+
+    operators = {
+        'eq': lambda x, y: x == y,
+        'gt': lambda x, y: x > y,
+        'gte': lambda x, y: x >= y,
+        'in': lambda x, y: x in y,
+        'lt': lambda x, y: x < y,
+        'lte': lambda x, y: x <= y,
+        'not': lambda x: not x,
+        'noteq': lambda x, y: x != y,
+        'notin': lambda x, y: x not in y,
+    }
+
+    allowed_values = {
+        'sys_platform': sys.platform,
+        'python_version': '%s.%s' % sys.version_info[:2],
+        # parsing sys.platform is not reliable, but there is no other
+        # way to get e.g. 2.7.2+, and the PEP is defined with sys.version
+        'python_full_version': sys.version.split(' ', 1)[0],
+        'os_name': os.name,
+        'platform_in_venv': str(in_venv()),
+        'platform_release': platform.release(),
+        'platform_version': platform.version(),
+        'platform_machine': platform.machine(),
+        'platform_python_implementation': python_implementation(),
+    }
+
+    def __init__(self, context=None):
+        """
+        Initialise an instance.
+
+        :param context: If specified, names are looked up in this mapping.
+        """
+        self.context = context or {}
+        self.source = None
+
+    def get_fragment(self, offset):
+        """
+        Get the part of the source which is causing a problem.
+        """
+        fragment_len = 10
+        s = '%r' % (self.source[offset:offset + fragment_len])
+        if offset + fragment_len < len(self.source):
+            s += '...'
+        return s
+
+    def get_handler(self, node_type):
+        """
+        Get a handler for the specified AST node type.
+        """
+        return getattr(self, 'do_%s' % node_type, None)
+
+    def evaluate(self, node, filename=None):
+        """
+        Evaluate a source string or node, using ``filename`` when
+        displaying errors.
+        """
+        if isinstance(node, string_types):
+            self.source = node
+            kwargs = {'mode': 'eval'}
+            if filename:
+                kwargs['filename'] = filename
+            try:
+                node = ast.parse(node, **kwargs)
+            except SyntaxError as e:
+                s = self.get_fragment(e.offset)
+                raise SyntaxError('syntax error %s' % s)
+        node_type = node.__class__.__name__.lower()
+        handler = self.get_handler(node_type)
+        if handler is None:
+            if self.source is None:
+                s = '(source not available)'
+            else:
+                s = self.get_fragment(node.col_offset)
+            raise SyntaxError("don't know how to evaluate %r %s" % (
+                node_type, s))
+        return handler(node)
+
+    def get_attr_key(self, node):
+        assert isinstance(node, ast.Attribute), 'attribute node expected'
+        return '%s.%s' % (node.value.id, node.attr)
+
+    def do_attribute(self, node):
+        if not isinstance(node.value, ast.Name):
+            valid = False
+        else:
+            key = self.get_attr_key(node)
+            valid = key in self.context or key in self.allowed_values
+        if not valid:
+            raise SyntaxError('invalid expression: %s' % key)
+        if key in self.context:
+            result = self.context[key]
+        else:
+            result = self.allowed_values[key]
+        return result
+
+    def do_boolop(self, node):
+        result = self.evaluate(node.values[0])
+        is_or = node.op.__class__ is ast.Or
+        is_and = node.op.__class__ is ast.And
+        assert is_or or is_and
+        if (is_and and result) or (is_or and not result):
+            for n in node.values[1:]:
+                result = self.evaluate(n)
+                if (is_or and result) or (is_and and not result):
+                    break
+        return result
+
+    def do_compare(self, node):
+        def sanity_check(lhsnode, rhsnode):
+            valid = True
+            if isinstance(lhsnode, ast.Str) and isinstance(rhsnode, ast.Str):
+                valid = False
+            #elif (isinstance(lhsnode, ast.Attribute)
+            #      and isinstance(rhsnode, ast.Attribute)):
+            #    klhs = self.get_attr_key(lhsnode)
+            #    krhs = self.get_attr_key(rhsnode)
+            #    valid = klhs != krhs
+            if not valid:
+                s = self.get_fragment(node.col_offset)
+                raise SyntaxError('Invalid comparison: %s' % s)
+
+        lhsnode = node.left
+        lhs = self.evaluate(lhsnode)
+        result = True
+        for op, rhsnode in zip(node.ops, node.comparators):
+            sanity_check(lhsnode, rhsnode)
+            op = op.__class__.__name__.lower()
+            if op not in self.operators:
+                raise SyntaxError('unsupported operation: %r' % op)
+            rhs = self.evaluate(rhsnode)
+            result = self.operators[op](lhs, rhs)
+            if not result:
+                break
+            lhs = rhs
+            lhsnode = rhsnode
+        return result
+
+    def do_expression(self, node):
+        return self.evaluate(node.body)
+
+    def do_name(self, node):
+        valid = False
+        if node.id in self.context:
+            valid = True
+            result = self.context[node.id]
+        elif node.id in self.allowed_values:
+            valid = True
+            result = self.allowed_values[node.id]
+        if not valid:
+            raise SyntaxError('invalid expression: %s' % node.id)
+        return result
+
+    def do_str(self, node):
+        return node.s
+
+
+def interpret(marker, execution_context=None):
+    """
+    Interpret a marker and return a result depending on environment.
+
+    :param marker: The marker to interpret.
+    :type marker: str
+    :param execution_context: The context used for name lookup.
+    :type execution_context: mapping
+    """
+    return Evaluator(execution_context).evaluate(marker.strip())

get_obitools/getpackage/pip/_vendor/distlib/resources.py

@@ -0,0 +1,317 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Vinay Sajip.
+# Licensed to the Python Software Foundation under a contributor agreement.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+from __future__ import unicode_literals
+
+import bisect
+import io
+import logging
+import os
+import pkgutil
+import shutil
+import sys
+import types
+import zipimport
+
+from . import DistlibException
+from .util import cached_property, get_cache_base, path_to_cache_dir, Cache
+
+logger = logging.getLogger(__name__)
+
+
+cache = None    # created when needed
+
+
+class ResourceCache(Cache):
+    def __init__(self, base=None):
+        if base is None:
+            # Use native string to avoid issues on 2.x: see Python #20140.
+            base = os.path.join(get_cache_base(), str('resource-cache'))
+        super(ResourceCache, self).__init__(base)
+
+    def is_stale(self, resource, path):
+        """
+        Is the cache stale for the given resource?
+
+        :param resource: The :class:`Resource` being cached.
+        :param path: The path of the resource in the cache.
+        :return: True if the cache is stale.
+        """
+        # Cache invalidation is a hard problem :-)
+        return True
+
+    def get(self, resource):
+        """
+        Get a resource into the cache,
+
+        :param resource: A :class:`Resource` instance.
+        :return: The pathname of the resource in the cache.
+        """
+        prefix, path = resource.finder.get_cache_info(resource)
+        if prefix is None:
+            result = path
+        else:
+            result = os.path.join(self.base, self.prefix_to_dir(prefix), path)
+            dirname = os.path.dirname(result)
+            if not os.path.isdir(dirname):
+                os.makedirs(dirname)
+            if not os.path.exists(result):
+                stale = True
+            else:
+                stale = self.is_stale(resource, path)
+            if stale:
+                # write the bytes of the resource to the cache location
+                with open(result, 'wb') as f:
+                    f.write(resource.bytes)
+        return result
+
+
+class ResourceBase(object):
+    def __init__(self, finder, name):
+        self.finder = finder
+        self.name = name
+
+
+class Resource(ResourceBase):
+    """
+    A class representing an in-package resource, such as a data file. This is
+    not normally instantiated by user code, but rather by a
+    :class:`ResourceFinder` which manages the resource.
+    """
+    is_container = False        # Backwards compatibility
+
+    def as_stream(self):
+        """
+        Get the resource as a stream.
+
+        This is not a property to make it obvious that it returns a new stream
+        each time.
+        """
+        return self.finder.get_stream(self)
+
+    @cached_property
+    def file_path(self):
+        global cache
+        if cache is None:
+            cache = ResourceCache()
+        return cache.get(self)
+
+    @cached_property
+    def bytes(self):
+        return self.finder.get_bytes(self)
+
+    @cached_property
+    def size(self):
+        return self.finder.get_size(self)
+
+
+class ResourceContainer(ResourceBase):
+    is_container = True     # Backwards compatibility
+
+    @cached_property
+    def resources(self):
+        return self.finder.get_resources(self)
+
+
+class ResourceFinder(object):
+    """
+    Resource finder for file system resources.
+    """
+    def __init__(self, module):
+        self.module = module
+        self.loader = getattr(module, '__loader__', None)
+        self.base = os.path.dirname(getattr(module, '__file__', ''))
+
+    def _adjust_path(self, path):
+        return os.path.realpath(path)
+
+    def _make_path(self, resource_name):
+        parts = resource_name.split('/')
+        parts.insert(0, self.base)
+        result = os.path.join(*parts)
+        return self._adjust_path(result)
+
+    def _find(self, path):
+        return os.path.exists(path)
+
+    def get_cache_info(self, resource):
+        return None, resource.path
+
+    def find(self, resource_name):
+        path = self._make_path(resource_name)
+        if not self._find(path):
+            result = None
+        else:
+            if self._is_directory(path):
+                result = ResourceContainer(self, resource_name)
+            else:
+                result = Resource(self, resource_name)
+            result.path = path
+        return result
+
+    def get_stream(self, resource):
+        return open(resource.path, 'rb')
+
+    def get_bytes(self, resource):
+        with open(resource.path, 'rb') as f:
+            return f.read()
+
+    def get_size(self, resource):
+        return os.path.getsize(resource.path)
+
+    def get_resources(self, resource):
+        def allowed(f):
+            return f != '__pycache__' and not f.endswith(('.pyc', '.pyo'))
+        return set([f for f in os.listdir(resource.path) if allowed(f)])
+
+    def is_container(self, resource):
+        return self._is_directory(resource.path)
+
+    _is_directory = staticmethod(os.path.isdir)
+
+
+class ZipResourceFinder(ResourceFinder):
+    """
+    Resource finder for resources in .zip files.
+    """
+    def __init__(self, module):
+        super(ZipResourceFinder, self).__init__(module)
+        archive = self.loader.archive
+        self.prefix_len = 1 + len(archive)
+        # PyPy doesn't have a _files attr on zipimporter, and you can't set one
+        if hasattr(self.loader, '_files'):
+            self._files = self.loader._files
+        else:
+            self._files = zipimport._zip_directory_cache[archive]
+        self.index = sorted(self._files)
+
+    def _adjust_path(self, path):
+        return path
+
+    def _find(self, path):
+        path = path[self.prefix_len:]
+        if path in self._files:
+            result = True
+        else:
+            if path and path[-1] != os.sep:
+                path = path + os.sep
+            i = bisect.bisect(self.index, path)
+            try:
+                result = self.index[i].startswith(path)
+            except IndexError:
+                result = False
+        if not result:
+            logger.debug('_find failed: %r %r', path, self.loader.prefix)
+        else:
+            logger.debug('_find worked: %r %r', path, self.loader.prefix)
+        return result
+
+    def get_cache_info(self, resource):
+        prefix = self.loader.archive
+        path = resource.path[1 + len(prefix):]
+        return prefix, path
+
+    def get_bytes(self, resource):
+        return self.loader.get_data(resource.path)
+
+    def get_stream(self, resource):
+        return io.BytesIO(self.get_bytes(resource))
+
+    def get_size(self, resource):
+        path = resource.path[self.prefix_len:]
+        return self._files[path][3]
+
+    def get_resources(self, resource):
+        path = resource.path[self.prefix_len:]
+        if path and path[-1] != os.sep:
+            path += os.sep
+        plen = len(path)
+        result = set()
+        i = bisect.bisect(self.index, path)
+        while i < len(self.index):
+            if not self.index[i].startswith(path):
+                break
+            s = self.index[i][plen:]
+            result.add(s.split(os.sep, 1)[0])   # only immediate children
+            i += 1
+        return result
+
+    def _is_directory(self, path):
+        path = path[self.prefix_len:]
+        if path and path[-1] != os.sep:
+            path += os.sep
+        i = bisect.bisect(self.index, path)
+        try:
+            result = self.index[i].startswith(path)
+        except IndexError:
+            result = False
+        return result
+
+_finder_registry = {
+    type(None): ResourceFinder,
+    zipimport.zipimporter: ZipResourceFinder
+}
+
+try:
+    import _frozen_importlib
+    _finder_registry[_frozen_importlib.SourceFileLoader] = ResourceFinder
+    _finder_registry[_frozen_importlib.FileFinder] = ResourceFinder
+except (ImportError, AttributeError):
+    pass
+
+
+def register_finder(loader, finder_maker):
+    _finder_registry[type(loader)] = finder_maker
+
+_finder_cache = {}
+
+
+def finder(package):
+    """
+    Return a resource finder for a package.
+    :param package: The name of the package.
+    :return: A :class:`ResourceFinder` instance for the package.
+    """
+    if package in _finder_cache:
+        result = _finder_cache[package]
+    else:
+        if package not in sys.modules:
+            __import__(package)
+        module = sys.modules[package]
+        path = getattr(module, '__path__', None)
+        if path is None:
+            raise DistlibException('You cannot get a finder for a module, '
+                                   'only for a package')
+        loader = getattr(module, '__loader__', None)
+        finder_maker = _finder_registry.get(type(loader))
+        if finder_maker is None:
+            raise DistlibException('Unable to locate finder for %r' % package)
+        result = finder_maker(module)
+        _finder_cache[package] = result
+    return result
+
+
+_dummy_module = types.ModuleType(str('__dummy__'))
+
+
+def finder_for_path(path):
+    """
+    Return a resource finder for a path, which should represent a container.
+
+    :param path: The path.
+    :return: A :class:`ResourceFinder` instance for the path.
+    """
+    result = None
+    # calls any path hooks, gets importer into cache
+    pkgutil.get_importer(path)
+    loader = sys.path_importer_cache.get(path)
+    finder = _finder_registry.get(type(loader))
+    if finder:
+        module = _dummy_module
+        module.__file__ = os.path.join(path, '')
+        module.__loader__ = loader
+        result = finder(module)
+    return result

get_obitools/getpackage/pip/_vendor/distlib/scripts.py

@@ -0,0 +1,323 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2013 Vinay Sajip.
+# Licensed to the Python Software Foundation under a contributor agreement.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+from io import BytesIO
+import logging
+import os
+import re
+import struct
+import sys
+
+from .compat import sysconfig, fsencode, detect_encoding, ZipFile
+from .resources import finder
+from .util import (FileOperator, get_export_entry, convert_path,
+                   get_executable, in_venv)
+
+logger = logging.getLogger(__name__)
+
+_DEFAULT_MANIFEST = '''
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<assembly xmlns="urn:schemas-microsoft-com:asm.v1" manifestVersion="1.0">
+ <assemblyIdentity version="1.0.0.0"
+ processorArchitecture="X86"
+ name="%s"
+ type="win32"/>
+
+ <!-- Identify the application security requirements. -->
+ <trustInfo xmlns="urn:schemas-microsoft-com:asm.v3">
+ <security>
+ <requestedPrivileges>
+ <requestedExecutionLevel level="asInvoker" uiAccess="false"/>
+ </requestedPrivileges>
+ </security>
+ </trustInfo>
+</assembly>'''.strip()
+
+# check if Python is called on the first line with this expression
+FIRST_LINE_RE = re.compile(b'^#!.*pythonw?[0-9.]*([ \t].*)?$')
+SCRIPT_TEMPLATE = '''# -*- coding: utf-8 -*-
+if __name__ == '__main__':
+    import sys, re
+
+    def _resolve(module, func):
+        __import__(module)
+        mod = sys.modules[module]
+        parts = func.split('.')
+        result = getattr(mod, parts.pop(0))
+        for p in parts:
+            result = getattr(result, p)
+        return result
+
+    try:
+        sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+
+        func = _resolve('%(module)s', '%(func)s')
+        rc = func() # None interpreted as 0
+    except Exception as e:  # only supporting Python >= 2.6
+        sys.stderr.write('%%s\\n' %% e)
+        rc = 1
+    sys.exit(rc)
+'''
+
+
+class ScriptMaker(object):
+    """
+    A class to copy or create scripts from source scripts or callable
+    specifications.
+    """
+    script_template = SCRIPT_TEMPLATE
+
+    executable = None  # for shebangs
+
+    def __init__(self, source_dir, target_dir, add_launchers=True,
+                 dry_run=False, fileop=None):
+        self.source_dir = source_dir
+        self.target_dir = target_dir
+        self.add_launchers = add_launchers
+        self.force = False
+        self.clobber = False
+        # It only makes sense to set mode bits on POSIX.
+        self.set_mode = (os.name == 'posix')
+        self.variants = set(('', 'X.Y'))
+        self._fileop = fileop or FileOperator(dry_run)
+
+    def _get_alternate_executable(self, executable, options):
+        if options.get('gui', False) and os.name == 'nt':
+            dn, fn = os.path.split(executable)
+            fn = fn.replace('python', 'pythonw')
+            executable = os.path.join(dn, fn)
+        return executable
+
+    def _get_shebang(self, encoding, post_interp=b'', options=None):
+        enquote = True
+        if self.executable:
+            executable = self.executable
+            enquote = False     # assume this will be taken care of
+        elif not sysconfig.is_python_build():
+            executable = get_executable()
+        elif in_venv():
+            executable = os.path.join(sysconfig.get_path('scripts'),
+                            'python%s' % sysconfig.get_config_var('EXE'))
+        else:
+            executable = os.path.join(
+                sysconfig.get_config_var('BINDIR'),
+               'python%s%s' % (sysconfig.get_config_var('VERSION'),
+                               sysconfig.get_config_var('EXE')))
+        if options:
+            executable = self._get_alternate_executable(executable, options)
+
+        # If the user didn't specify an executable, it may be necessary to
+        # cater for executable paths with spaces (not uncommon on Windows)
+        if enquote and ' ' in executable:
+            executable = '"%s"' % executable
+        executable = fsencode(executable)
+        shebang = b'#!' + executable + post_interp + b'\n'
+        # Python parser starts to read a script using UTF-8 until
+        # it gets a #coding:xxx cookie. The shebang has to be the
+        # first line of a file, the #coding:xxx cookie cannot be
+        # written before. So the shebang has to be decodable from
+        # UTF-8.
+        try:
+            shebang.decode('utf-8')
+        except UnicodeDecodeError:
+            raise ValueError(
+                'The shebang (%r) is not decodable from utf-8' % shebang)
+        # If the script is encoded to a custom encoding (use a
+        # #coding:xxx cookie), the shebang has to be decodable from
+        # the script encoding too.
+        if encoding != 'utf-8':
+            try:
+                shebang.decode(encoding)
+            except UnicodeDecodeError:
+                raise ValueError(
+                    'The shebang (%r) is not decodable '
+                    'from the script encoding (%r)' % (shebang, encoding))
+        return shebang
+
+    def _get_script_text(self, entry):
+        return self.script_template % dict(module=entry.prefix,
+                                           func=entry.suffix)
+
+    manifest = _DEFAULT_MANIFEST
+
+    def get_manifest(self, exename):
+        base = os.path.basename(exename)
+        return self.manifest % base
+
+    def _write_script(self, names, shebang, script_bytes, filenames, ext):
+        use_launcher = self.add_launchers and os.name == 'nt'
+        linesep = os.linesep.encode('utf-8')
+        if not use_launcher:
+            script_bytes = shebang + linesep + script_bytes
+        else:
+            if ext == 'py':
+                launcher = self._get_launcher('t')
+            else:
+                launcher = self._get_launcher('w')
+            stream = BytesIO()
+            with ZipFile(stream, 'w') as zf:
+                zf.writestr('__main__.py', script_bytes)
+            zip_data = stream.getvalue()
+            script_bytes = launcher + shebang + linesep + zip_data
+        for name in names:
+            outname = os.path.join(self.target_dir, name)
+            if use_launcher:
+                n, e = os.path.splitext(outname)
+                if e.startswith('.py'):
+                    outname = n
+                outname = '%s.exe' % outname
+                try:
+                    self._fileop.write_binary_file(outname, script_bytes)
+                except Exception:
+                    # Failed writing an executable - it might be in use.
+                    logger.warning('Failed to write executable - trying to '
+                                   'use .deleteme logic')
+                    dfname = '%s.deleteme' % outname
+                    if os.path.exists(dfname):
+                        os.remove(dfname)       # Not allowed to fail here
+                    os.rename(outname, dfname)  # nor here
+                    self._fileop.write_binary_file(outname, script_bytes)
+                    logger.debug('Able to replace executable using '
+                                 '.deleteme logic')
+                    try:
+                        os.remove(dfname)
+                    except Exception:
+                        pass    # still in use - ignore error
+            else:
+                if os.name == 'nt' and not outname.endswith('.' + ext):
+                    outname = '%s.%s' % (outname, ext)
+                if os.path.exists(outname) and not self.clobber:
+                    logger.warning('Skipping existing file %s', outname)
+                    continue
+                self._fileop.write_binary_file(outname, script_bytes)
+                if self.set_mode:
+                    self._fileop.set_executable_mode([outname])
+            filenames.append(outname)
+
+    def _make_script(self, entry, filenames, options=None):
+        shebang = self._get_shebang('utf-8', options=options)
+        script = self._get_script_text(entry).encode('utf-8')
+        name = entry.name
+        scriptnames = set()
+        if '' in self.variants:
+            scriptnames.add(name)
+        if 'X' in self.variants:
+            scriptnames.add('%s%s' % (name, sys.version[0]))
+        if 'X.Y' in self.variants:
+            scriptnames.add('%s-%s' % (name, sys.version[:3]))
+        if options and options.get('gui', False):
+            ext = 'pyw'
+        else:
+            ext = 'py'
+        self._write_script(scriptnames, shebang, script, filenames, ext)
+
+    def _copy_script(self, script, filenames):
+        adjust = False
+        script = os.path.join(self.source_dir, convert_path(script))
+        outname = os.path.join(self.target_dir, os.path.basename(script))
+        if not self.force and not self._fileop.newer(script, outname):
+            logger.debug('not copying %s (up-to-date)', script)
+            return
+
+        # 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, 'rb')
+        except IOError:
+            if not self.dry_run:
+                raise
+            f = None
+        else:
+            encoding, lines = detect_encoding(f.readline)
+            f.seek(0)
+            first_line = f.readline()
+            if not first_line:
+                logger.warning('%s: %s is an empty file (skipping)',
+                               self.get_command_name(),  script)
+                return
+
+            match = FIRST_LINE_RE.match(first_line.replace(b'\r\n', b'\n'))
+            if match:
+                adjust = True
+                post_interp = match.group(1) or b''
+
+        if not adjust:
+            if f:
+                f.close()
+            self._fileop.copy_file(script, outname)
+            if self.set_mode:
+                self._fileop.set_executable_mode([outname])
+            filenames.append(outname)
+        else:
+            logger.info('copying and adjusting %s -> %s', script,
+                        self.target_dir)
+            if not self._fileop.dry_run:
+                shebang = self._get_shebang(encoding, post_interp)
+                if b'pythonw' in first_line:
+                    ext = 'pyw'
+                else:
+                    ext = 'py'
+                n = os.path.basename(outname)
+                self._write_script([n], shebang, f.read(), filenames, ext)
+            if f:
+                f.close()
+
+    @property
+    def dry_run(self):
+        return self._fileop.dry_run
+
+    @dry_run.setter
+    def dry_run(self, value):
+        self._fileop.dry_run = value
+
+    if os.name == 'nt':
+        # Executable launcher support.
+        # Launchers are from https://bitbucket.org/vinay.sajip/simple_launcher/
+
+        def _get_launcher(self, kind):
+            if struct.calcsize('P') == 8:   # 64-bit
+                bits = '64'
+            else:
+                bits = '32'
+            name = '%s%s.exe' % (kind, bits)
+            # Issue 31: don't hardcode an absolute package name, but
+            # determine it relative to the current package
+            distlib_package = __name__.rsplit('.', 1)[0]
+            result = finder(distlib_package).find(name).bytes
+            return result
+
+    # Public API follows
+
+    def make(self, specification, options=None):
+        """
+        Make a script.
+
+        :param specification: The specification, which is either a valid export
+                              entry specification (to make a script from a
+                              callable) or a filename (to make a script by
+                              copying from a source location).
+        :param options: A dictionary of options controlling script generation.
+        :return: A list of all absolute pathnames written to.
+        """
+        filenames = []
+        entry = get_export_entry(specification)
+        if entry is None:
+            self._copy_script(specification, filenames)
+        else:
+            self._make_script(entry, filenames, options=options)
+        return filenames
+
+    def make_multiple(self, specifications, options=None):
+        """
+        Take a list of specifications and make scripts from them,
+        :param specifications: A list of specifications.
+        :return: A list of all absolute pathnames written to,
+        """
+        filenames = []
+        for specification in specifications:
+            filenames.extend(self.make(specification, options))
+        return filenames

get_obitools/getpackage/pip/_vendor/distlib/version.py

@@ -0,0 +1,721 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2012-2013 The Python Software Foundation.
+# See LICENSE.txt and CONTRIBUTORS.txt.
+#
+"""
+Implementation of a flexible versioning scheme providing support for PEP-386,
+distribute-compatible and semantic versioning.
+"""
+
+import logging
+import re
+
+from .compat import string_types
+
+__all__ = ['NormalizedVersion', 'NormalizedMatcher',
+           'LegacyVersion', 'LegacyMatcher',
+           'SemanticVersion', 'SemanticMatcher',
+           'UnsupportedVersionError', 'get_scheme']
+
+logger = logging.getLogger(__name__)
+
+
+class UnsupportedVersionError(ValueError):
+    """This is an unsupported version."""
+    pass
+
+
+class Version(object):
+    def __init__(self, s):
+        self._string = s = s.strip()
+        self._parts = parts = self.parse(s)
+        assert isinstance(parts, tuple)
+        assert len(parts) > 0
+
+    def parse(self, s):
+        raise NotImplementedError('please implement in a subclass')
+
+    def _check_compatible(self, other):
+        if type(self) != type(other):
+            raise TypeError('cannot compare %r and %r' % (self, other))
+
+    def __eq__(self, other):
+        self._check_compatible(other)
+        return self._parts == other._parts
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def __lt__(self, other):
+        self._check_compatible(other)
+        return self._parts < other._parts
+
+    def __gt__(self, other):
+        return not (self.__lt__(other) or self.__eq__(other))
+
+    def __le__(self, other):
+        return self.__lt__(other) or self.__eq__(other)
+
+    def __ge__(self, other):
+        return self.__gt__(other) or self.__eq__(other)
+
+    # See http://docs.python.org/reference/datamodel#object.__hash__
+    def __hash__(self):
+        return hash(self._parts)
+
+    def __repr__(self):
+        return "%s('%s')" % (self.__class__.__name__, self._string)
+
+    def __str__(self):
+        return self._string
+
+    @property
+    def is_prerelease(self):
+        raise NotImplementedError('Please implement in subclasses.')
+
+
+class Matcher(object):
+    version_class = None
+
+    dist_re = re.compile(r"^(\w[\s\w'.-]*)(\((.*)\))?")
+    comp_re = re.compile(r'^(<=|>=|<|>|!=|==|~=)?\s*([^\s,]+)$')
+    num_re = re.compile(r'^\d+(\.\d+)*$')
+
+    # value is either a callable or the name of a method
+    _operators = {
+        '<': lambda v, c, p: v < c,
+        '>': lambda v, c, p: v > c,
+        '<=': lambda v, c, p: v == c or v < c,
+        '>=': lambda v, c, p: v == c or v > c,
+        '==': lambda v, c, p: v == c,
+        # by default, compatible => >=.
+        '~=': lambda v, c, p: v == c or v > c,
+        '!=': lambda v, c, p: v != c,
+    }
+
+    def __init__(self, s):
+        if self.version_class is None:
+            raise ValueError('Please specify a version class')
+        self._string = s = s.strip()
+        m = self.dist_re.match(s)
+        if not m:
+            raise ValueError('Not valid: %r' % s)
+        groups = m.groups('')
+        self.name = groups[0].strip()
+        self.key = self.name.lower()    # for case-insensitive comparisons
+        clist = []
+        if groups[2]:
+            constraints = [c.strip() for c in groups[2].split(',')]
+            for c in constraints:
+                m = self.comp_re.match(c)
+                if not m:
+                    raise ValueError('Invalid %r in %r' % (c, s))
+                groups = m.groups()
+                op = groups[0] or '~='
+                s = groups[1]
+                if s.endswith('.*'):
+                    if op not in ('==', '!='):
+                        raise ValueError('\'.*\' not allowed for '
+                                         '%r constraints' % op)
+                    # Could be a partial version (e.g. for '2.*') which
+                    # won't parse as a version, so keep it as a string
+                    vn, prefix = s[:-2], True
+                    if not self.num_re.match(vn):
+                        # Just to check that vn is a valid version
+                        self.version_class(vn)
+                else:
+                    # Should parse as a version, so we can create an
+                    # instance for the comparison
+                    vn, prefix = self.version_class(s), False
+                clist.append((op, vn, prefix))
+        self._parts = tuple(clist)
+
+    def match(self, version):
+        """
+        Check if the provided version matches the constraints.
+
+        :param version: The version to match against this instance.
+        :type version: Strring or :class:`Version` instance.
+        """
+        if isinstance(version, string_types):
+            version = self.version_class(version)
+        for operator, constraint, prefix in self._parts:
+            f = self._operators.get(operator)
+            if isinstance(f, string_types):
+                f = getattr(self, f)
+            if not f:
+                msg = ('%r not implemented '
+                       'for %s' % (operator, self.__class__.__name__))
+                raise NotImplementedError(msg)
+            if not f(version, constraint, prefix):
+                return False
+        return True
+
+    @property
+    def exact_version(self):
+        result = None
+        if len(self._parts) == 1 and self._parts[0][0] == '==':
+            result = self._parts[0][1]
+        return result
+
+    def _check_compatible(self, other):
+        if type(self) != type(other) or self.name != other.name:
+            raise TypeError('cannot compare %s and %s' % (self, other))
+
+    def __eq__(self, other):
+        self._check_compatible(other)
+        return self.key == other.key and self._parts == other._parts
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    # See http://docs.python.org/reference/datamodel#object.__hash__
+    def __hash__(self):
+        return hash(self.