Re: [Bioperl-l] Fate of Bio::Perl newbie module?
Carnë Draug
>
> I see that the Bio::Perl newbie module was removed in 1.7.3, but I
> can't find the successor on CPAN or GitHub.
>
> Any hints?
The Bio::Perl module is on the Bio-Procedural repository [1]. No one
has picked up its maintenance and remains unreleased so you won't find
it on CPAN.
David
[1] https://github.com/bioperl/Bio-Procedural
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Carnë Draug
>
> Hi Carnė,
>
> On Wed, Nov 27, 2019 at 10:34:19AM +0000, Carnė Draug wrote:
> >
> > The Bio::Perl module is on the Bio-Procedural repository [1]. No one
> > has picked up its maintenance and remains unreleased so you won't find
> > it on CPAN.
>
I'm sorry but I can't.
> If not could you give some
> short intro what is needed to do to get that module back on CPAN?
Sure. Someone will need to show interest on take over maintenance of
it. To do so, I would open an issue on the repo [2] saying that I was
interested. This person will need a PAUSE account [3]. The admin of
the BIOPERLML on PAUSE (that's cjfields) will need to give permissions
to that person.
The distribution is already setup to be released with bioperl's dzil
plugin bundle [4]. The instructions are there.
I think a maintainer should at least address issues #1 [5] and #2 [6]
before making the release.
Also, beware of the following optional dependencies which are not part
of the core BioPerl distribution (not sure if already packaged in
Debian):
* Bio::DB::EMBL
* Bio::DB::GenBank
* Bio::DB::GenPept
* Bio::DB::RefSeq
* Bio::Tools::Run::RemoteBlast
As well as these also optional dependencies which are also not on CPAN
yet:
* Bio::DB::RefSeq [7]
* Bio::DB::SwissProt [8]
David
[2] https://github.com/bioperl/Bio-Procedural/issues/
[3] https://pause.perl.org/pause/query
[4] https://metacpan.org/pod/Dist::Zilla::PluginBundle::BioPerl#Pushing-releases
[5] https://github.com/bioperl/Bio-Procedural/issues/1
[6] https://github.com/bioperl/Bio-Procedural/issues/2
[7] https://github.com/bioperl/Bio-DB-RefSeq
[8] https://github.com/bioperl/Bio-DB-SwissProt
Carnë Draug
>
> Hi,
>
> On Wed, Nov 27, 2019 at 12:08:08PM +0000, Carnė Draug wrote:
> > On Wed, 27 Nov 2019 at 10:52, Andreas Tille <and...@an3as.eu> wrote:
> > > > The Bio::Perl module is on the Bio-Procedural repository [1]. No one
> > > > has picked up its maintenance and remains unreleased so you won't find
> > > > it on CPAN.
> > >
> > > Would you volunteer to take over this one?
> >
> > I'm sorry but I can't.
> >
> > > If not could you give some
> > > short intro what is needed to do to get that module back on CPAN?
> >
> > Sure. Someone will need to show interest on take over maintenance of
> > it. To do so, I would open an issue on the repo [2] saying that I was
> > interested. This person will need a PAUSE account [3]. The admin of
> > the BIOPERLML on PAUSE (that's cjfields) will need to give permissions
> > to that person.
> >
> > The distribution is already setup to be released with bioperl's dzil
> > plugin bundle [4]. The instructions are there.
> >
> > I think a maintainer should at least address issues #1 [5] and #2 [6]
> > before making the release.
>
> to complex since even if I make it through the procedure I could not
> take over any maintenance of a Perl module.
I didn't realise you were asking instructions for you. I wrote them
thinking of someone that could maintain a Perl module.
> > Also, beware of the following optional dependencies which are not part
> > of the core BioPerl distribution (not sure if already packaged in
> > Debian):
> >
> > * Bio::DB::EMBL
> > * Bio::DB::GenBank
> > * Bio::DB::GenPept
> > * Bio::DB::RefSeq
> > * Bio::Tools::Run::RemoteBlast
> >
> > As well as these also optional dependencies which are also not on CPAN
> > yet:
> >
> > * Bio::DB::RefSeq [7]
> > * Bio::DB::SwissProt [8]
>
> Adding some other lib#AvailableOnCPAN#-perl package seems to be a
> feasible thing to do, thought. Also if there is some maintained
> upstream source outside CPAN should be fine.
>
> So the question is:
>
> Do we have some Perl programmer in the Debian Med team who is
> willing to follow the procedure described above?
>
> If the answer is no, what do we do to salvage packages like prokka and
> possibly others since it seems the old bioperl is broken appart that
> strongly that other packages relying on it will be broken as well. Is
> the answer that we revert the version bump any rely on the old
> monolithic bioperl or should we talk about the problem with upstreams of
> prokka (and may be others) to change their code to only use maintained
> bioperl modules?
On Perl, a distribution will depend on a set of modules not on other
distributions. So something like roary does not list the BioPerl
distribution as dependency, it lists modules like Bio::SeqIO. So as
long as roary keeps using maintained modules, meaning released, it
will work, no matter which way bioperl gets split apart.
I think speaking with upstream of prokka, roary, and others may be
best approach since this is not a Debian only problem. All their
users will face the same issue. As perl programmers and users of
those modules they are in a good position to take over maintenance of
the bioperl modules they need which them someone on Debian Med team
could package. Or they can replace their use of the unmaintained
bioperl modules.
I'm sorry I can't offer more help than comments, opinion, and
direction if you want.
David
Fields, Christopher J
I agree re: having discussions with the developers of packages using bioperl modules for releases is needed; this has been somewhat started with Torsten re: prokka. It sounds as if the distribution is being pulled in via 'cpanm Bio::Perl'?
chris
Fields, Christopher J
chris
Christopher Fields
Not a problem Michael. I also pushed a new Bio::DB::NCBIHelper, which updated a few missing dependencies.
chris
From: Michael Crusoe <michael...@gmail.com>
Date: Monday, December 2, 2019 at 10:05 AM
To: Andreas Tille <and...@fam-tille.de>
Cc: Chris Fields <cjfi...@illinois.edu>, Carnë Draug <carandr...@gmail.com>, Debian Med Project List <debia...@lists.debian.org>, bioperl mailing list <biop...@mailman.open-bio.org>
Subject: Re: [Bioperl-l] Fate of Bio::Perl newbie module?
On Fri, Nov 29, 2019 at 09:11:41PM +0000, Fields, Christopher J wrote:
> Just a quick update: I have pushed a quick release of Bio::DB::SwissProt, Bio::DB::RefSeq, and Bio::Procedural (which contains Bio::Perl) to CPAN. I'm awaiting CPAN testing for the Bio::Procedural module (this will show up here: http://matrix.cpantesters.org/?dist=Bio-Procedural); the others seem to be passing.
Thanks for the update. I need to admit I personally can not match these
modules to the old bioperl package and what might be missing in the new
what is needed for reverse dependencies. I've consulted
codesearch.debian.net. I have not found any reference to
Bio::Procedural.
Hey Andreas,
The Bio-Procedural distribution includes the "Bio::Perl" module: https://metacpan.org/pod/Bio::Perl
Looks like all the new distributions are live on CPAN, thanks Chris!
--
Michael R. Crusoe