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

[Peter Cock]

On Thu, Oct 25, 2012 at 10:36 PM, Connor McCoy <cmccoy at fhcrc.org> wrote:
> 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

Hi Connor,

This is probably a question for Brad - I don't use pip.

Was it sitting stalled at the prompt from Biopython's setup.py?
"Do you want to continue this installation? (y/N)" or from pip?
i.e. What was at the end of the complete log?

In terms of a quick workaround, what we use under TravisCI
(where most of the targets don't have numpy installed) is
piping a yes on stdin, e.g.

$ /usr/bin/yes | python setup.py install

Peter