[Biopython] Biopython Project Update 20019, was: [Bosc-announce] BOSC 2019 Call for Abstracts

Wed May 15 15:18:38 UTC 2019

Dear Biopythoneers,

I've put together an abstract for BOSC 2019 (PDF attached, plain text below)
for any quick comments before I submit it later today. There may be a chance
to tweak this during the abstract review process, if for example I've forgotten
something or someone important.

The source is currently here, on what was originally a fork of Bow's
repository -
which we're going to move under the Biopython GitHub account shortly:

https://github.com/peterjc/talks/blob/master/2019_BOSC/abstract/abstract.tex

Peter

--

The Biopython Project is a long-running distributed collaborative
effort, supported by the Open Bioinformatics Foundation, which
develops a freely available Python library for biological computation
[1]. This talk will look ahead to the year to come, and give a summary
of the project news since the 1.72 release in June 2018, and the talk
at GCCBOSC 2018.

While there were no major new modules introduced in Biopython 1.73
(December 2018) or Biopython 1.74 (expected May/June 2019), there have
been lots of incremental improvements. In terms of lines of code
changed, a substantial proportion have been in-line documentation
(Python docstrings), used to generate human readable API
documentation. While we are still using epydoc for this, our
continuous integration system has been generating more modern HTML
output using Sphinx, which we hope to host on our domain, or at Read
The Docs, making this work much more visible to the world. We have
been using the tool flake8 with various plugins for this (as well as
checking coding style), showing a steady improvement in best practice
compliance - every public API should be documented this year.

In 2017 we started a re-licensing plan, to transition away from our
liberal but unique Biopython License Agreement to the similar but very
widely used 3-Clause BSD License. We are reviewing the code base
authorship file-by-file, to gradually dual license the entire project.
All new contributions are dual licensed, and currently half the Python
files in the main library have been dual licensed.

Another important going effort is improving the unit test coverage.
Sadly This is currently fairly static at about 85% (excluding online
tests), but can be viewed online at CodeCov.io.

We are using GitHub-integrated continuous integration testing on Linux
(using TravisCI) and Windows (using AppVeyor), including enforcing the
Python PEP8 and PEP257 coding style guidelines. We hope to be able to
recommend a simple git pre-commit hook for our contributors shortly,
and have discussed the idea of adopting the new yet popular Python
code formatting style tool black to reduce the human time costs in
writing compliant code.

Looking further ahead, in 2020, in line with most major scientific
Python libraries, we will be dropping support for Python 2. See
https://python3statement.org/

Finally, since our last update talk in June 2018, Biopython has had 32
named contributors including 14 newcomers. This reflects our policy of
trying to encourage even small contributions. This brings our total
named contributor count to 248 since the project began, and looks
likely to break 250 by our 20th Birthday in August 2019.

References

[1] Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J.,
Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., de
Hoon, M.J. (2009) Biopython: freely available Python tools for
computational molecular biology and bioinformatics. Bioinformatics
25(11) 1422-3. doi:10.1093/bioinformatics/btp163

On Wed, May 15, 2019 at 8:58 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Hello all,
>
> I intend to put together a Biopython Project Update 2019 abstract for a
> BOSC 2019 Late Breaking Lightning Talk (i.e. 5mins), the deadline for
> which is TODAY.
>
> https://www.open-bio.org/events/bosc/
>
> This will include the imminent Biopython 1.74 release, which we should
> try to get ready soon. Separate emails on that later.
>
> Thanks,
>
> Peter
>
> On Tue, Apr 9, 2019 at 9:11 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >
> > No talk volunteers? The deadline for abstract submission is this Thursday (see below), unless we go for a lightning talk only which might be appropriate?
> >
> > Peter
> >
> > On Wed, 13 Mar 2019 at 13:20, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >>
> >> Dear Biopythoneers,
> >>
> >> Speaking as part of the BOSC organising committee, please
> >> come to Basel this summer and submit your open source
> >> bioinformatics abstracts soon.
> >>
> >> Speaking as a Biopython developer, we should start planning
> >> our traditional annual Biopython Project Update talk. As usual,
> >> are there any volunteers from our contributors who would like
> >> to present this? If not, I am hoping to be there myself.
> >>
> >> We have templates for the abstracts submitted in recent years,
> >> and slide decks too - have a look at some of the past talk slides
> >> and videos if you are interested:
> >>
> >> https://gccbosc2018.sched.com/event/EivJ/biopython-project-update-2018
> >> https://www.open-bio.org/wiki/BOSC_2017_Schedule
> >> https://www.open-bio.org/wiki/BOSC_2016_Schedule
> >> https://www.open-bio.org/wiki/BOSC_2015_Schedule
> >> etc
> >>
> >> Thank you,
> >>
> >> Peter
> >>
> >>
> >
> > ---------- Forwarded message ---------
> > From: BOSC 2019 <boscannounce2019 at gmail.com>
> > Date: Tue, 9 Apr 2019 at 05:32
> > Subject: [BOSC] BOSC abstract deadline is this Thursday (April 11)!
> > To: <bosc at open-bio.org>
> >
> >
> > Hi all,
> >
> >
> > [Apologies if you get this message more than once! Google didn't like the messages we sent from the open-bio.org mailing list, so we're trying something different for now.]
> >
> > If you’re hoping to give a full-length talk at BOSC 2019, don’t forget to submit your abstract by Thursday, April 11! The later deadline (May 15) is just for posters and late-breaking lightning talks.
> >
> >
> > Please note: although BOSC has often granted extensions, ISMB does not plan to do this, so be sure to get your abstract in by 11:59 Hawaii Time on April 11!
> >
> >
> > Key Dates
> >
> > April 11, 2019: Deadline for submitting talk/poster abstracts
> >
> > April 15: OBF travel fellowship application deadline
> >
> > May 9: First-round authors notified about talk/poster acceptance
> >
> > May 15: Late poster / late-breaking lightning talk abstract deadline
> >
> > May 23: Late poster / late-breaking lightning talk authors notified
> >
> > July 21-25, 2019: ISMB/ECCB 2019, Basel, Switzerland
> >
> > July 24-25 (last two days of ISMB): BOSC 2019, Basel, Switzerland
> >
> > July 26-27: CollaborationFest (CoFest) 2019, Basel
> >
> >
> > Check out our NEW website: https://www.open-bio.org/events/bosc/ !
> >
> >
> > We hope to see you in Basel!
> >
> >
> >     --The BOSC 2019 Organizing Committee
> >
> >
> >>
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