[Biopython-dev] Biopython 1.70 plans

Peter Cock p.j.a.cock at googlemail.com
Mon Jul 3 17:39:50 UTC 2017

Hello all,

Michael & Adil: Those deprecations are now done, thanks:

Given a recent pip/numpy query, I'd like someone to
review at a further change to setup.py regarding our
NumPy dependency:


This would make NumPy a hard requirement (except on
Jython which we plan to drop, and IronPython which
as far as I know has not been tested with Biopython for
quite some time and is even less important).

This would also switch from requirements.txt to putting
the dependency in setup.py (since we now use setuptools
in place of distutils).

Otherwise I think we're about ready for Biopython 1.70
(there are a few nearly ready pull requests which might
make it in as well), which I'd like to try to do this week.


On Mon, Jun 26, 2017 at 1:57 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> > Otherwise, I don't think there is anything worth delaying the
>> > release for.
>> We could include deprecating Bio.NeutralNetwork and Bio.GA
>> as well:
>> https://github.com/biopython/biopython/pull/1292
>> http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021780.html
>> http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021783.html
> Yes let's do that. It will help to clean up the code base.
> Best,
> -Michiel

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