Proposal for bioperl-run

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Proposal for bioperl-run

Mark A. Jensen
All,
I'm starting to look at cleaning up bioperl-run so that, e.g., tests
don't bork without a reasonable error message, are skipped
appropriately, etc. As I do this, I'm finding that to fix certain
issues, I need to consider mods to Bio::Tools::Run::WrapperBase and
friends. Alas, these are in the bioperl-live distro!

Now, grepping for 'WrapperBase' in bioperl-live modules reveals only
two that mention it:

Bio/Tools/Run/WrapperBase/CommandExts.pm
Bio/Tools/Run/StandAloneBlast.pm
Bio/Tools/Run/WrapperBase.pm

My simple proposal is to move these three modules from bioperl-live to
bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw).

Thoughts?
MAJ

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Re: Proposal for bioperl-run

George Hartzell-2
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.

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Re: Proposal for bioperl-run

Fields, Christopher J
On Aug 21, 2014, at 9:37 PM, George Hartzell <[hidden email]> 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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Re: Proposal for bioperl-run

Mark A. Jensen
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 <[hidden email]>
> 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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Re: Proposal for bioperl-run

Fields, Christopher J
Actually, it might be better to have all the BLAST-related stuff as one distribution, unless we can get bioperl-run installing much more cleanly (little overhead with few dependencies).  Is that what you want to do?  If so: cool!

You should have commit to bioperl-run BTW, you are listed as part of the developer team.

chris

On Aug 22, 2014, at 7:09 AM, Mark A. Jensen <[hidden email]> wrote:

> 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 <[hidden email]> 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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Re: Proposal for bioperl-run

Francisco J. Ossandón
In reply to this post by Fields, Christopher J
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??

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.

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??

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces+fossandonc=[hidden email] [mailto:bioperl-l-bounces+fossandonc=[hidden email]] En nombre de Mark A. Jensen
Enviado el: viernes, 22 de agosto de 2014 8:09
Para: Fields, Christopher J
CC: George Hartzell; [hidden email]
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 <[hidden email]>
> 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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Re: Proposal for bioperl-run

Mark A. Jensen
In reply to this post by Fields, Christopher J

Yeah, the cleanly part is what I hope to make happen, maybe splitting blast out makes sense there too. Will give it a go
MAJ


On Fri, Aug 22, 2014 at 11:47 AM, Fields, Christopher J <[hidden email]> wrote:

Actually, it might be better to have all the BLAST-related stuff as one distribution, unless we can get bioperl-run installing much more cleanly (little overhead with few dependencies).  Is that what you want to do?  If so: cool!

You should have commit to bioperl-run BTW, you are listed as part of the developer team.

chris

On Aug 22, 2014, at 7:09 AM, Mark A. Jensen <[hidden email]> wrote:

> 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 <[hidden email]> 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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Re: Proposal for bioperl-run

Fields, Christopher J
In reply to this post by Francisco J. Ossandón
On Aug 22, 2014, at 10:50 AM, Francisco J. Ossandón <[hidden email]> 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=[hidden email] [mailto:bioperl-l-bounces+fossandonc=[hidden email]] En nombre de Mark A. Jensen
> Enviado el: viernes, 22 de agosto de 2014 8:09
> Para: Fields, Christopher J
> CC: George Hartzell; [hidden email]
> 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 <[hidden email]>
>> 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
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>


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Re: Proposal for bioperl-run

Mark A. Jensen
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
> <[hidden email]> 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=[hidden email]
>> [mailto:bioperl-l-bounces+fossandonc=[hidden email]]
>> En nombre de Mark A. Jensen
>> Enviado el: viernes, 22 de agosto de 2014 8:09
>> Para: Fields, Christopher J
>> CC: George Hartzell; [hidden email]
>> 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 <[hidden email]>
>>> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: 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
>> <[hidden email]> 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=[hidden email]
>>> [mailto:bioperl-l-bounces+fossandonc=[hidden email]]
>>> En nombre de Mark A. Jensen
>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>> Para: Fields, Christopher J
>>> CC: George Hartzell; [hidden email]
>>> 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 <[hidden email]>
>>>> 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: 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
>>> <[hidden email]> 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=[hidden email]
>>>> [mailto:bioperl-l-bounces+fossandonc=[hidden email]]
>>>> En nombre de Mark A. Jensen
>>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>>> Para: Fields, Christopher J
>>>> CC: George Hartzell; [hidden email]
>>>> 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
>>>>> <[hidden email]>
>>>>> 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
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [hidden email]
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
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>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
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Re: Proposal for bioperl-run

Fields, Christopher J
\o/

Not sure but we should probably set up Travis-CI tests for bioperl-run; lots of apps available via apt.

-c

On Aug 25, 2014, at 9:46 PM, Mark A. Jensen <[hidden email]> wrote:

> 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
>>>> <[hidden email]> 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=[hidden email] [mailto:bioperl-l-bounces+fossandonc=[hidden email]] En nombre de Mark A. Jensen
>>>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>>>> Para: Fields, Christopher J
>>>>> CC: George Hartzell; [hidden email]
>>>>> 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 <[hidden email]>
>>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> [hidden email]
>>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [hidden email]
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: Proposal for bioperl-run

Mark A. Jensen
That's a great thought. For my next trick, I was planning ot think
about https://github.com/bioperl/bioperl-run/issues/11 - how to deal
with dependencies within BioPerl given the splits. I can include setting
up travis to test in these thoughts (and perhaps actions)-- unless
someone else is already working on this...
MAJ

On 2014-08-26 00:27, Fields, Christopher J wrote:

> \o/
>
> Not sure but we should probably set up Travis-CI tests for
> bioperl-run; lots of apps available via apt.
>
> -c
>
> On Aug 25, 2014, at 9:46 PM, Mark A. Jensen <[hidden email]>
> wrote:
>
>> 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
>>>>> <[hidden email]> 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=[hidden email]
>>>>>> [mailto:bioperl-l-bounces+fossandonc=[hidden email]]
>>>>>> En nombre de Mark A. Jensen
>>>>>> Enviado el: viernes, 22 de agosto de 2014 8:09
>>>>>> Para: Fields, Christopher J
>>>>>> CC: George Hartzell; [hidden email]
>>>>>> 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
>>>>>>> <[hidden email]>
>>>>>>> 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
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> [hidden email]
>>>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> [hidden email]
>>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [hidden email]
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
>
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