[Bioperl-l] Proposal for bioperl-run

[Mark A. Jensen]

WrapperBase and friends removed from bioperl-live; Travis built 
successfully at #486.
MAJ
On 2014-08-25 22:08, Mark A. Jensen wrote:
> 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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