[Biopython-dev] NumPy dialog when Biopython installed from automated programs

[Connor McCoy]

Hello,

About a year ago, pip support came up on the list:

http://biopython.org/pipermail/biopython-dev/2011-October/009234.html

I remember this being resolved, but when I try to install biopython with
pip, it fails:

    $ testenv/bin/pip install biopython

    Downloading/unpacking biopython
      Running setup.py egg_info for package biopython

        warning: no previously-included files matching '.cvsignore' found
under directory '*'
        warning: no previously-included files matching '*.pyc' found under
directory '*'
    Installing collected packages: biopython
      Running setup.py install for biopython

        Numerical Python (NumPy) is not installed.

        This package is required for many Biopython features.  Please
install
        it before you install Biopython. You can install Biopython anyway,
but
        anything dependent on NumPy will not work. If you do this, and later
        install NumPy, you should then re-install Biopython.

        You can find NumPy at http://numpy.scipy.org

        Complete output from command
/home/cmccoy/development/seqmagick/testenv/bin/python -c "import
setuptools;__file__='/home/cmccoy/development/seqmagick/testenv/build/biopython/set
    up.py';exec(compile(open(__file__).read().replace('\r\n', '\n'),
__file__, 'exec'))" install --single-version-externally-managed --record
/tmp/pip-wc___H-record/install-record.txt -
    -install-headers
/home/cmccoy/development/seqmagick/testenv/include/site/python2.7:
        running install



    Numerical Python (NumPy) is not installed.



    This package is required for many Biopython features.  Please install

    it before you install Biopython. You can install Biopython anyway, but

    anything dependent on NumPy will not work. If you do this, and later

    install NumPy, you should then re-install Biopython.



    You can find NumPy at http://numpy.scipy.org



    ----------------------------------------
    Command /home/cmccoy/development/seqmagick/testenv/bin/python -c
"import
setuptools;__file__='/home/cmccoy/development/seqmagick/testenv/build/biopython/setup.py';exec(compile(open(
    __file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install
--single-version-externally-managed --record
/tmp/pip-wc___H-record/install-record.txt --install-headers /home/cm
    ccoy/development/seqmagick/testenv/include/site/python2.7 failed with
error code 255 in /home/cmccoy/development/seqmagick/testenv/build/biopython
    Storing complete log in /home/cmccoy/.pip/pip.log


Same for libraries which list biopython in `install_requires`.

Does anyone know of a way around this?

Thanks,
Connor

-- 
Connor McCoy
Fred Hutchinson Cancer Research Center
1100 Fairview Ave N.
Seattle, WA 98109-1924
cmccoy at fhcrc.org