[Bioperl-l] New distribution Bio-Tools-Phylo-PAML

[Carnë Draug]

> On Fri, Sep 8, 2017 at 8:32 AM Fields, Christopher J <cjfields at illinois.edu> wrote:
> > On Sep 7, 2017, at 2:12 PM, Carnë Draug <carandraug+dev at gmail.com>  wrote:
>>>
>>> Hi
>>>
>>> I have been preparing a new distribution for Bio::Tools::Phylo::PAML
>>> and related modules [1] which I would like to make a release of.
>>>
>>> To avoid clashes with existing installations, I would like to have a
>>> new release of bioperl-live and bioperl-run soon.  Is this possible?
>>> I already have commits ready for bioperl-live and bioperl-run that
>>> will remove the files.
>>>
>>> On a related topic, I updated the instructions on how to prepare a new
>>> perl distribution from a subset of modules [2] and made a new release
>>> of the bioperl distzilla plugin bundle [3] (will take a few hours
>>> before it is indexed in metacpan).
>>>
>>> Carnë
>>>
>>> [1] https://github.com/bioperl/Bio-Tools-Phylo-PAML
>>> [2] http://bioperl.org/howtos/split-new-distribution.html
>>> [3] https://metacpan.org/pod/Dist::Zilla::PluginBundle::BioPerl
>>>
>>
>>
>> I personally think splitting these out into a separate PAML-specific
>> distribution is a great idea, variations with PAML has always been hard to
>> keep up with.  I’ll have a look at the documentation as well, if there is a
>> way to do this for each Bio::Tools application it paves the way for
>> combining the wrappers and parsers into separate distributions if needed.
>>
>> Jason, you’re listed as key contributor for bioperl PAML development, any
>> thoughts?
>>
>> Chris
>>

On 8 September 2017 at 17:45, Jason Stajich <jason.stajich at ucr.edu> wrote:
> Prob package the Run and parser code in same distr as well I think?

That's what I have done.  See https://github.com/bioperl/Bio-Tools-Phylo-PAML

> On Fri, Sep 8, 2017 at 9:44 AM Jason Stajich <jason.stajich at ucr.edu> wrote:
> Absolutely. A separate package here makes
> Complete sense and wouid hopefully make it easier to fix and update as
> needed. Is anyone actively willing to maintain format chasing of PAML?
>

I can confirm that it is broken for the latest version.  As part of
the split I removed the conditions on the tests and they started to
fail immediately.

Despite the issue, I would prefer to have one release first without
any code changes.  Any fixing should be done on a follow up release.

Carnë