[Biopython-dev] Fwd: [biopython] Fix Biopython installation with pip (#172)

Peter Cock p.j.a.cock at googlemail.com
Fri Mar 29 11:54:33 UTC 2013

Hi Brad,

This sounds sensible in principle - it just needs some hands on testing
on various systems - any volunteers who use PIP and virtual envs?



---------- Forwarded message ----------
From: Brad Chapman <notifications at github.com>
Date: Fri, Mar 29, 2013 at 11:47 AM
Subject: [biopython] Fix Biopython installation with pip (#172)
To: biopython/biopython <biopython at noreply.github.com>

Hi all;
This is yet another take on making Biopython install nicely with pip
in virtual environments. This avoids adding numpy as an explicit
dependency and instead uses it if present or skips it if not.

The problem with the previous install_requires approach is that pip
doesn't build and install all requirements before setting up
Biopython, so Biopython will fail with a numpy missing error.
Additionally, our old approach drags in numpy so creates a heavyweight
dependency for isolated environments.

The new approach requires users to explicitly install numpy if needed
but doesn't penalize them if it's not present.

I submitted as a pull request for documentation and feedback from
anyone. If y'all agree, merge away. Thanks,


You can merge this Pull Request by running

  git pull https://github.com/chapmanb/biopython master

Or view, comment on, or merge it at:


Commit Summary

Improve Biopython installation with pip: avoid including numpy as
dependency when automated. Instead explicitly avoid needing numpy
installed to continue
Add helpful comment on pip dependency management

File Changes

M setup.py (38)

Patch Links:


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