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

Wed May 15 16:20:16 UTC 2019

Revised slightly with input from Christian, thank you. The plain text
is now here:

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

That will become an official biopython repository on GitHub shortly...

Peter

On Wed, May 15, 2019 at 4:51 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Cut down to 200 words for the online submission, longer PDF attached too:
>
> <start>
>
> Biopython is a long-running distributed collaborative effort, a freely
> available Python library for biological computation. We summarise
> recent project news, and look ahead.
>
> Releases 1.73 (December 2018) and 1.74 (expected May/June 2019) had
> incremental improvements, especially on the in-line API documentation.
> Every public API should be documented this year.
>
> In 2017 we started a transition away from our liberal but unique
> Biopython License Agreement to the similar but very widely used
> 3-Clause BSD License. Already half the files in the main library have
> been dual licensed after reviewing authorship, and all new
> contributions are dual licensed.
>
> Improving test coverage is ongoing, currently fairly static at 85%
> (excluding online tests). Tests and Python PEP8/PEP257 style are
> checked with continuous integration on Linux (TravisCI) and Windows
> (AppVeyor). We may adopt Python code formatting style tool black to
> reduce human time writing compliant code.
>
> In 2020, in line with other scientific Python libraries, we will drop
> Python 2 support.
>
> In the last year Biopython had 32 named contributors, including 14
> newcomers. This reflects our policy of trying to encourage even small
> contributions. We expect reach 250 contributors by our 20th Birthday
> in August 2019.
>
> <end>
>
> This has been submitted, but until the submissions close tonight I
> should be able to tweak it.
>
> Peter
>
> On Wed, May 15, 2019 at 4:26 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >
> > Curses, over double the 200 word limit on the new ISCB shared abstract
> > submission system.
> > The PDF is fine, but lots of editing required...
> >
> > Peter
> >
> > On Wed, May 15, 2019 at 4:18 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > >
> > > 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
> > > > >
> > > > >
> > > > >>