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

[Brad Chapman]

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