New distribution Bio-Tools-Phylo-PAML

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New distribution Bio-Tools-Phylo-PAML

Carnë Draug-2
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

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Re: New distribution Bio-Tools-Phylo-PAML

Fields, Christopher J
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 Sep 7, 2017, at 2:12 PM, Carnë Draug <[hidden email]> 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


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Re: New distribution Bio-Tools-Phylo-PAML

Carnë Draug-2
> On Fri, Sep 8, 2017 at 8:32 AM Fields, Christopher J <[hidden email]> wrote:
> > On Sep 7, 2017, at 2:12 PM, Carnë Draug <[hidden email]>  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 <[hidden email]> 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 <[hidden email]> 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

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Re: New distribution Bio-Tools-Phylo-PAML

Fields, Christopher J
In reply to this post by Fields, Christopher J
Yep, that’s what Carnë set up: https://github.com/bioperl/Bio-Tools-Phylo-PAML

Carnë, can you go ahead and merge the commits removing these?  I can work on a version bump, and at least get a new 1.7.x point release out.

Chris

On Sep 8, 2017, at 11:45 AM, Jason Stajich <[hidden email]> wrote:

Prob package the Run and parser code in same distr as well I think?

Jason 

On Fri, Sep 8, 2017 at 9:44 AM Jason Stajich <[hidden email]> 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? 


On Fri, Sep 8, 2017 at 8:32 AM Fields, Christopher J <[hidden email]> wrote:
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 Sep 7, 2017, at 2:12 PM, Carnë Draug <[hidden email]> 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

--
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Jason Stajich - UC Riverside
http://lab.stajich.org
--
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Jason Stajich - UC Riverside
http://lab.stajich.org


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Re: New distribution Bio-Tools-Phylo-PAML

Carnë Draug-2
On 8 September 2017 at 20:33, Fields, Christopher J
<[hidden email]> wrote:
> Yep, that’s what Carnë set up:
> https://github.com/bioperl/Bio-Tools-Phylo-PAML
>
> Carnë, can you go ahead and merge the commits removing these?  I can work on
> a version bump, and at least get a new 1.7.x point release out.

Done.

https://github.com/bioperl/bioperl-live/commit/1e64ab3dd676ba40af91e7924a8d1737e9e3e87c
https://github.com/bioperl/bioperl-run/commit/e8e011989c5d35e1b467a1ca1380e93fbde58bf1

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