On 1 April 2013 04:28, Fields, Christopher J wrote:
> On Mar 31, 2013, at 9:05 PM, Carnë Draug
>> On 1 April 2013 01:34, Fields, Christopher J
>>> I agree. Another approach might be to cleave off a section that you
could mould into your own; this could be done for bioperl-run,
>> Why did the project ran out of time 2 years ago? The blog posts about
>> it are very few and don't sound too bad. It mentions having prepared a
>> couple of them, but none was actually ever released. Instead, the
>> source was also kept in bioperl-live and seems to have already
>> branched. Is there any reason for this? It was my understanding that
>> splitting the project is still desirable, from a discussion back in
>> it just happens that no one has picked it up yet.
> The project actually made a lot of headway; the particular pieces moved
out (Bio::Root, Bio::Factory, etc) worked fine, but we never followed up on
exactly what to do next on master branch. It's perfectly feasible for
someone to go ahead and finish the initial part of that (in fact, I believe
there were some branches that started along this path but never merged back
Can I merge any branching between these and bioperl-live and set them
up so you only have to run dzil on their repos?
>> I think splitting bioperl-live into subdistributions and make a new
>> 1.70 release of each of them is perfectly doable over a summer. And I
>> say this after having split and release Bio-Biblio. This is one of my
>> itches with BioPerl. I have been using it for almost 3 years, but have
>> never seen a release. I would like to make new releases of everything,
>> no changes at the start, but take them to the point that "dzil
>> release" does everything. Make it really easy for anyone to come in
>> and contribute and even easier for a maintainer to make a new release
>> after receiving a contribution. Is this desirable for the project?
> Hilmar's point is pretty valid, namely that a case would have to be made
as to why the initial run at it wasn't completed, or why it would work
better this time. We're not suggesting that this can't be done, but the
above point would have to be answered.
The only reason why I claim to be able to finish this is that I'm very
well familiar with both BioPerl and the tools to make the split. Plus,
I already split one (and trying to split another) to get a clear idea
what it involves.
> Frankly, the project has been pretty reliant on me for releases, so it's
perfectly valid to point out the modules haven't made it out yet b/c I
haven't made a release since then. From that point of view, this would be
a continuation of that work, maybe with the intent/focus on making code
releases much easier.
As a maintainer of another FOSS gigantic project that is also a
collection of libraries, I can relate to this. Of course it can be
much more interesting to write new sexy code and add it to the huge
pile of modules already in bioperl-live but I want to make it easier
for others to develop on BioPerl. Comparing with chemistry, I want
this to be the equivalent of a catalyst for the development, rather
than another reactant.
> Regarding updating Bioperl to use Dist::Zilla amongst other modern perl
tools (Moose included), yes, it is very much our wish/intent to have this,
in any way possible. But I don't think we can call it BioPerl v1.7, simply
based on past release cycles; we're somewhat bound by deprecations, etc.
We really need a clean break.
> So, my general feeling is that while we are cleaving out code and
releasing the independent dist and core, we should re-christen core as 1.9
(e.g. pre-v2). We move to v2 when we feel we're at the right point. Each
of the individual distributions would have to start with their own
versions, anything greater than the point where they left the core/live
distribution should work. I agree with you in that I don't think it would
take a long time, but we also have bioperl-run in the mix (and in many
cases it would make sense to combine wrappers with the proper parsers), so
simply cleaving out from one repo may not be the best approach.
> With that in mind, my point was meant to indicate we can also start
afresh with a section of the code that you would like to focus on, using
some of the same ideas (pulling out the relevant modules you want to work
on). This might be an attainable goal in the minds of GSoC reviewers and
might suit your particular needs (for instance, if you had a research
project reliant on such code). I'm supportive either way, and I don't
think you'll have a problem finding a mentor if you need one.
I suggested 1.70 only because it has no change. And it won't be
BioPerl 1.7. It would be Bio-Seq, Bio-Align, Bio-Popgen, etc v 1.70.
These smaller distributions can then stay as they are or evolve into
2.0 if their maintainers are so interested. I saw biome and liked it,
but is the plan to make a BioPerl 2.00 written in Moose? Won't that
path take us to the same place we are now in a couple of years? Won't
it be better to make the split now, and make the clean break on each
Would you be available to talk about this on #bioperl? I'm online
there most of the time.