[Biopython-dev] List of Biopython dependencies

Tiago Antão tiagoantao at gmail.com
Thu Jan 9 09:02:25 UTC 2014

Hi all,

What I am trying to do is to get a list of stuff that assures that
biopython is tested top to bottom. This in order to assure QA for releases
and a complete and stable test framework.
I am also trying to create a VM machine for testing (based on CloudBioLinux
- with Brad's help), so that anyone can do a full test and there is a
complete VM with everything needed out-of-the-box.
It so happens that I have been travelling since mid-December (back in
office on Monday) and things have been mostly frozen (restarting next week).

The format for the list is really not much important, but it has a
completely different slant from the requirements page: it is meant for
developers and testing, etc. Whatever you guys prefer is fine by me. I just
plan to review the list top-to-bottom and assure that it is complete and


On 8 January 2014 22:51, Eric Talevich <eric.talevich at gmail.com> wrote:

> On Wed, Jan 8, 2014 at 1:55 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
>> On Wednesday, January 8, 2014, Eric Talevich wrote:
>>> Folks,
>>> It appears that there are two lists of Biopython dependencies on the
>>> wiki:
>>> http://biopython.org/wiki/List_of_applications_executed_via_Biopython
>>> http://biopython.org/wiki/Download#Required_Software
>>> There is potential for confusion here. Shall we merge these lists on the
>>> Download page?
>> Tiago started the list of applications page while updating the
>> buildbots - it is as noted a work in progress. Maybe it should
>> be just command line applications, which can then be linked
>> to from the downloads page?
> So the list of command line applications on the Download page would be
> moved to the separate Wiki page? Seems reasonable if the list is long.
> We could follow Debian's approach of splitting the list into Depends
>>> (strict requirements, e.g. Python), Recommended (non-essential but
>>> important, e.g. numpy and reportlab), and Suggested (everything else).
>> That split makes sense for libraries, but is it also sensible
>> for command line applications Biopython can call?
> The sub-headings could be:
> - Required software
> - Recommended Python libraries [needed to enable significant functionality]
> - Additional Python libraries [used by individual Biopython modules for
> additional features]
> "In addition Biopython includes wrapper code for calling a number of third
> party command line tools [link]"
> I imagine this format would be useful to sysadmins (and maybe distro
> package maintainers, too). But it may be just as well to merge the
> "required" and "recommended" lists and just note caveats inline as is
> currently done.

"The truth may be out there, but the lies are already in your head" - Terry

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