[Biopython-dev] Optional libraries in README file (etc)

Eric Talevich eric.talevich at gmail.com
Tue Feb 21 14:53:20 UTC 2012

On Mon, Feb 20, 2012 at 6:06 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi all,
> Do we need to have a new section in the README file for other soft
> dependencies like NetworkX? This file is now especially important
> as it gets shown on github for the project:
> https://github.com/biopython/biopython/blob/master/README

It would be good to have this info in the README. These would also be
meaningful entries in the Debian package for Biopython, where soft
dependencies would go in the "Suggests" field and probably just NumPy would
go in "Recommends".

A couple soft dependencies not listed in the README are networkx (which in
turn depends on pygraphviz|pydot and graphviz in Debian) and
matplotlib|pylab, both for Bio.Phylo._utils.

> Similarly, does the long installation manual need some work?
> https://github.com/biopython/biopython/blob/master/Doc/install/Installation.tex
> http://biopython.org/DIST/docs/install/Installation.html
> http://biopython.org/DIST/docs/install/Installation.pdf
 I guess mxTextTools can probably go, now. Does MMCIFlex still work?

The easy_install and pip approaches for installing Biopython and its
dependencies should probably be prominent. Maybe an extra layer of nesting
in the outline, like:

1. Installing Python
2. Installing pre-built packages (the easy way)
 - PyPI & pip / easy_install
 - On Linux: Biopython and NumPy are packaged for Ubuntu/Debian and
presumably other Linux distros
3. Installing from source
 - Dependencies
 - Biopython
 - Installing with non-admin permissions (Unix/Mac)
4. Testing
5. Third-party tools


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