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

[Peter Cock]

On Thu, Nov 17, 2011 at 12:00 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Peter and Eric;
> I wanted to follow up about the patch to automate Biopython installs
> from easy_install and pip when NumPu is not present:
>
> https://github.com/chapmanb/biopython/commit/be53d850d721fc82af81bedcd9fb9034b0a2099b
>
> You'd both reviewed it, and the only holdup was a warning message when
> setuptools is not installed:
>
>> $ jython setup.py install
>> /Users/pjcock/jython2.5.2/Lib/distutils/dist.py:263: UserWarning:
>> Unknown distribution option: 'install_requires'
>>   warnings.warn(msg)
>
> We'd discussed some other options like including setuptools and
> installing it, ignoring the warning, or ignoring it since it is not
> problematic.
>
> My lazy side says ignoring it is fine, but if you want to explicitly
> turn it off we can use this around the setup call:
>
> with warnings.catch_warnings():
>    warnings.simplefilter("ignore")
>
> Happy to handle it however you prefer but I'd love to get this in,
> Brad

How about this to avoid the warning by not passing the argument?
https://github.com/peterjc/biopython/commit/78b965f48939c7395aab6e0919b86686443f640e

Note I rebased to the current master.

If you and Eric are happy with that, I guess we can check it in
and see how the build slaves like it...

Peter