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

[Peter Cock]

On Thu, Oct 13, 2011 at 3:05 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Hi all;
> Biopython's setup.py currently has an interactive question/answer
> session to remind users to optionally install NumPy if it's not
> present. This is useful for by-hand installations, but problematic with
> automated installers.
>
> One useful feature of setuptools is the 'install_requires' attribute in
> setup.py. This allows your programs to define the requirements and have
> them automatically installed from PyPi. It's a great way to include
> useful libraries without having to fret excessively about users
> installing dependencies.
>
> Unfortunately if you use install_requires with Biopython, and NumPy is
> not installed, automated scripts will get stuck in the question/answer
> dialog. To resolve this issue, I wrote a small patch that adds NumPy to
> Biopython's install_requires and skips the Q/A only in cases where it is
> installed via pip or easy_install:
>
> https://github.com/chapmanb/biopython/commit/be53d850d721fc82af81bedcd9fb9034b0a2099b
>
> If someone is able to review this, it would be great to get it into
> Biopython for the next release.
>
> Brad

I can appreciate the usefulness of this, but don't know enough
about pip and easy_install to comment on the implementation.

Anyone else?

Peter