[Bioperl-l] Proposal for bioperl-run

[Mark A. Jensen]

Hearing no objections, I've merged topic/move_WrapperBase with master. 
I will proceed to remove WrapperBase and friends from bioperl-live.
MAJ
On 2014-08-23 15:29, Mark A. Jensen wrote:
> All,
> Can people have a look at bioperl/bioperl-run branch
> topic/move_WrapperBase
> (https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase)
> and see what they think. I used filter-branch to generate a (local
> clone of) bioperl-live containing only Bio/Tools/Run and t/tools, 
> then
> merged this into a topic/move_WrapperBase branch of bioperl-run. If
> this looks ok, give me the signal and I will merge into master. Next
> step would be to remove these items from bioperl-live.
>
> thanks MAJ
>
>
> On 2014-08-22 12:59, Fields, Christopher J wrote:
>> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossandón
>> <fossandonc at hotmail.com> wrote:
>>
>>> I have also looked
>>>
>>> I don't mind the moving of those modules but I would like to ask 
>>> something. Any future updates to the moved modules should also be 
>>> added, if possible, to the modules that will remain v1.6.x branch? Or 
>>> their development would be freezed?? Or should they also be removed 
>>> from there too??
>>
>> No updates to 1.6.x if they have been moved out (with the exception
>> of Bio::Root).
>>
>> We need to end-of-life 1.6.x at some point.  It's worth having a
>> meeting to talk about what needs to be done and to maybe discuss
>> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe
>> see who wants to participate...
>>
>>> I've been keeping the synchronicity of updated modules that were 
>>> moved out of -live into their own repo with their versions in v1.6.x 
>>> branch (like Root and Coordinate), but the synch of WrapperBase when 
>>> mixed into other existing repo like Run will depend on if it start to 
>>> depend on code of other Run modules or not.
>>
>> WrapperBase is essentially the common core for all the wrappers (a
>> few don’t use it, but most do).  So it really belongs in 
>> bioperl-run,
>> as well as StandAloneBlast.  The only real reason this and the other
>> Tool::Run modules were in bioperl-live was legacy, but I think this
>> hampers bioperl-run development frankly, as it relies on 
>> bioperl-live
>> (via WrapperBase).  If all the wrapper code were part of bioperl-run
>> fixes would be much easier to make and release independently.
>>
>>> On a side note, I just realized that there is an empty "hmmer3.pm" 
>>> file in "bioperl-live/Bio/Tools/Run"... It seems to have been added 
>>> already empty in 
>>> https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, 
>>> maybe by mistake. It appears to be the only empty file in the repo. 
>>> Should I delete it??
>>
>> Yes, go ahead and do that.
>>
>> -c
>>
>>> Cheers,
>>>
>>> Francisco J. Ossandon
>>>
>>> -----Mensaje original-----
>>> De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org 
>>> [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] 
>>> En nombre de Mark A. Jensen
>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>> Para: Fields, Christopher J
>>> CC: George Hartzell; bioperl-l at mailman.open-bio.org
>>> Asunto: Re: [Bioperl-l] Proposal for bioperl-run
>>>
>>> Thanks Chris-- yes, you must be right. I just did a quick grep for 
>>> "StandAloneBlast" in the modules. I will verify and leave bl2seq 
>>> alone.
>>> Will do everything in branches and then give the signal- cheers MAJ 
>>> On 2014-08-21 23:50, Fields, Christopher J wrote:
>>>> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
>>>> wrote:
>>>>
>>>>> Mark A. Jensen writes:
>>>>>> [...]
>>>>>> My simple proposal is to move these three modules from 
>>>>>> bioperl-live
>>>>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on 
>>>>>> StandAloneBlast,
>>>>>> btw).
>>>>>>
>>>>>> Thoughts?
>>>>>> [...]
>>>>>
>>>>> Speaking from a safe distance, that sounds *wonderful*.
>>>>>
>>>>> g.
>>>>
>>>> Agreed.  Also, I think you mean that StandAloneBlast has a 
>>>> dependency
>>>> on AlignIO::bl2seq, not the other way around, correct? At least, I
>>>> didn’t see anything there.
>>>>
>>>> If no one objects to it (give it a day), I say go ahead and move 
>>>> it
>>>> over.
>>>>
>>>> chris
>>>
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>>
>>
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