[Biopython] Support for Xdna, SnapGene and GCK formats

[Peter Cock]

This looks ready to merge - if there are no further comments or
suggestions, I'll aim to do this at the end of the week.

Peter

On Tue, Aug 6, 2019 at 7:46 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Damien's pull request is here:
>
> https://github.com/biopython/biopython/pull/2204
>
> Peter
>
> On Thu, Aug 1, 2019 at 1:29 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >
> > On Thu, Aug 1, 2019 at 1:19 PM Damien Goutte-Gattat
> > <dgouttegattat at incenp.org> wrote:
> > >
> > > On Thu, Aug 01, 2019 at 10:01:22AM +0100, Peter Cock wrote:
> > > >> All the GCK files I have come from the "Drosophila Gateway Vector
> > > >> Collection" [1]; those files are not explicitly released under any free
> > > >> license (in fact there are no license terms at all), so I don't think we
> > > >> could bundle even one of them with the Biopython's source code, even if
> > > >> it is just to serve as a test file.
> > > >
> > > >The website [1] had a fairly liberal copyright statement at the bottom,
> > > >suggesting a sample file could be used with attribution (e.g. in the git
> > > >check in comment and where the test or example code used it)?
> > >
> > > The notice states "You are free to use the information contained on this
> > > page for non-profit purpose [...]". I am not sure this would be
> > > compatible with either the 3-clause BSD license or the Biopython License
> > > Agreement (neither of them excluding any kind of for-profit use).
> > >
> > > I am also slightly concerned by the following statement: "Portions of
> > > the material contained in the Drosophila Gateway Vector collection are
> > > subject to international patents [...]". I guess this refers to the
> > > vectors themselves and not merely to files containing their sequences,
> > > but I wonder if that could be subject to interpretation.
> > >
> > > Obviously I am no lawyer, so maybe I am just worrying too much. :)
> >
> > Sadly I think you are right. I was thinking just about the immediate (and
> > to me clearly non-profit) step of validating Biopython functionality - there
> > is definitely a problem in redistribution to anyone using Biopython in a
> > for-profit setting, unless one sample file is judged fair use (and that is
> > a legal grey area).
> >
> > > >Damien, you evidently know a lot more about email headers etc than me.
> > > >Are you also familiar with mailman, and how it might be better configured
> > > >on this specific point?
> > >
> > > Yes.
> > >
> > > Basically there's two options.
> > >
> > > ...
> > >
> > > Unfortunately, `from_is_list` has been introduced in Mailman 2.1.16 and
> > > `dmarc_moderation_action` in Mailman 2.1.18, but mailman.open-bio.org is
> > > running Mailman 2.1.15, so an upgrade would be needed before we can
> > > adopt that approach.
> >
> > That seems worth looking at - I will forward this to the OBF mailman team.
> >
> > Thank you,
> >
> > Peter