[Biopython] problem building with pip

[David Koppstein]

Hio,

First time biopythoner here. I just wanted to mention that installing 
with pip fails with the following error. I was able to fix it by 
commenting out line 546 of req.py, which lives in 
$YOUR_LIBRARY_DIRECTORY/python/2.7.1/lib/python2.7/site-packages/pip-0.8.2-py2.7.egg/pip/

I think it would be nice to include the 
"--single-version-externally-managed" option in the install script so 
that biopython can be installed using pip.

Looking forward to using biopython (and for python3 support whenever 
numpy and scipy get their act together...)!

Best,
David
-----------------

# req.py

......

     def install(self, install_options, global_options=()):
         if self.editable:
             self.install_editable(install_options, global_options)
             return
         temp_location = tempfile.mkdtemp('-record', 'pip-')
         record_filename = os.path.join(temp_location, 
'install-record.txt')
         try:

             install_args = [
                 sys.executable, '-c',
                 "import setuptools;__file__=%r;"\
                 "execfile(__file__)" % self.setup_py] +\
                 list(global_options) + [
                 'install',
                 
#'--single-version-externally-managed',                                   # 
commented line
                 '--record', record_filename]




----------------

# error message

   Running setup.py install for biopython
     usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
        or: -c --help [cmd1 cmd2 ...]
        or: -c --help-commands
        or: -c cmd --help

     error: option --single-version-externally-managed not recognized
     Complete output from command 
/usr/local/Cellar/python/2.7.1/bin/python -c "import 
setuptools;__file__='/usr/local/var/pip/build/biopython/setup.py';execfile(__file__)" 
install --single-version-externally-managed --record 
/var/folders/Oa/OajmBH+JHBaJJ5JEOfVFSE+++TI/-Tmp-/pip-jjEn53-record/install-record.txt:
     usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]

    or: -c --help [cmd1 cmd2 ...]

    or: -c --help-commands

    or: -c cmd --help



error: option --single-version-externally-managed not recognized

----------------------------------------
Command /usr/local/Cellar/python/2.7.1/bin/python -c "import 
setuptools;__file__='/usr/local/var/pip/build/biopython/setup.py';execfile(__file__)" 
install --single-version-externally-managed --record 
/var/folders/Oa/OajmBH+JHBaJJ5JEOfVFSE+++TI/-Tmp-/pip-jjEn53-record/install-record.txt 
failed with error code 1
Storing complete log in /usr/local/var/pip/pip.log

-- 
David Koppstein
MIT Biology
Graduate Student, Bartel Lab
Whitehead Institute, Room 629a
9 Cambridge Center
Cambridge, MA 02142
Cell: (609) 933-3952