From andreas at sdsc.edu  Thu Aug  2 19:52:22 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 2 Aug 2012 16:52:22 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
Message-ID: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>

Hi,

I was wondering how people feel about migrating the BioJava  svn
repository and starting to use github for the trunk development?
(Currently github is only a read-only copy of our developer svn).

Any opinions?

Andreas

From biojava at hannes.oib.com  Thu Aug  2 23:11:23 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Fri, 3 Aug 2012 05:11:23 +0200
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
Message-ID: <CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>

On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> I was wondering how people feel about migrating the BioJava  svn
> repository and starting to use github for the trunk development?
> (Currently github is only a read-only copy of our developer svn).
>
> Any opinions?
>
> Andreas

I'm in favor - git pull requests make submitting patches so much easier, IMHO.

Hannes

From daniel.quest at gmail.com  Fri Aug  3 00:14:51 2012
From: daniel.quest at gmail.com (daniel.quest at gmail.com)
Date: Thu, 2 Aug 2012 23:14:51 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
Message-ID: <18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>

Github ==awesome.  
Go for it and let the social coding begin

Dan

Sent from my iPhone

On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:

> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi,
>> 
>> I was wondering how people feel about migrating the BioJava  svn
>> repository and starting to use github for the trunk development?
>> (Currently github is only a read-only copy of our developer svn).
>> 
>> Any opinions?
>> 
>> Andreas
> 
> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
> 
> Hannes
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From jttkim at googlemail.com  Fri Aug  3 08:47:04 2012
From: jttkim at googlemail.com (Jan T Kim)
Date: Fri, 3 Aug 2012 13:47:04 +0100
Subject: [Biojava-l] Are there EJB entities for BioSQL?
Message-ID: <20120803124703.GB3415@paxarchia.galaxy.uni>

Dear All,

is there a set of EJB 3 entities that correspond to BioSQL available?
I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
is that the recommended ORM solution?

Personally, I'd prefer a set of classes, with the suitable annotations
from the javax.persistence package applied (@Entity, @Id etc.) to match
the BioSQL tables.

Apparently there have been initiatives in this direction (e.g. [3]), has
any of these made it into mainstream BioJava? If not, why not?

Best regards, Jan

[1] http://biojava.org/wiki/BioJava:BioJavaXDocs
[2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
[3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*

From heuermh at gmail.com  Fri Aug  3 11:57:25 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Fri, 3 Aug 2012 10:57:25 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
Message-ID: <CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>

-0

I use github for quite a few personal things and mercurial via Google
Code on a different project and while I think there are some benefits
to the distributed model I don't understand how it would work from the
point of view of a release manager.  Does anyone have any pointers to
documentation on how to manage and cut a release from a distributed
repository?

With the current svn mirror on github, developers can already fork and
create pull requests, they just need to be applied back to the svn
repository.  Is there any advantage to moving the repository to
github?  Are there any people who will start contributing because the
repository is on github that are unwilling to do so with the current
model (send patches to the mailing list or issue tracker)?

My current client just started a new project on Google Code and we had
a similar conversation:  subversion on Google Code vs. git/mercurial
on Google Code vs. git at github vs. subversion on Google Code + read
only git mirror at github vs. subversion on Google Code + read/write
git mirror at github.  In the end we went with subversion on Google
Code with possibility of git mirror later because we understand how
the Maven release process works with subversion and we liked the issue
tracker at Google Code a lot better than the one at github.

   michael


On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
> Github ==awesome.
> Go for it and let the social coding begin
>
> Dan
>
> Sent from my iPhone
>
> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:
>
>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi,
>>>
>>> I was wondering how people feel about migrating the BioJava  svn
>>> repository and starting to use github for the trunk development?
>>> (Currently github is only a read-only copy of our developer svn).
>>>
>>> Any opinions?
>>>
>>> Andreas
>>
>> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
>>
>> Hannes


From p.j.a.cock at googlemail.com  Fri Aug  3 12:01:49 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 3 Aug 2012 17:01:49 +0100
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
Message-ID: <CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>

On Fri, Aug 3, 2012 at 4:57 PM, Michael Heuer <heuermh at gmail.com> wrote:
> -0
>
> I use github for quite a few personal things and mercurial via Google
> Code on a different project and while I think there are some benefits
> to the distributed model I don't understand how it would work from the
> point of view of a release manager.  Does anyone have any pointers to
> documentation on how to manage and cut a release from a distributed
> repository?
>
> With the current svn mirror on github, developers can already fork and
> create pull requests, they just need to be applied back to the svn
> repository.  Is there any advantage to moving the repository to
> github?  Are there any people who will start contributing because the
> repository is on github that are unwilling to do so with the current
> model (send patches to the mailing list or issue tracker)?
>
> My current client just started a new project on Google Code and we had
> a similar conversation:  subversion on Google Code vs. git/mercurial
> on Google Code vs. git at github vs. subversion on Google Code + read
> only git mirror at github vs. subversion on Google Code + read/write
> git mirror at github.  In the end we went with subversion on Google
> Code with possibility of git mirror later because we understand how
> the Maven release process works with subversion and we liked the issue
> tracker at Google Code a lot better than the one at github.
>
>    michael

I don't know if it would help, but GitHub can mimic SVN from a git
repository:

https://github.com/blog/626-announcing-svn-support
https://github.com/blog/966-improved-subversion-client-support

Peter

From heuermh at gmail.com  Fri Aug  3 12:08:32 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Fri, 3 Aug 2012 11:08:32 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
Message-ID: <CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>

On Fri, Aug 3, 2012 at 11:01 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Aug 3, 2012 at 4:57 PM, Michael Heuer <heuermh at gmail.com> wrote:
>> -0
>>
>> I use github for quite a few personal things and mercurial via Google
>> Code on a different project and while I think there are some benefits
>> to the distributed model I don't understand how it would work from the
>> point of view of a release manager.  Does anyone have any pointers to
>> documentation on how to manage and cut a release from a distributed
>> repository?
>>
>> With the current svn mirror on github, developers can already fork and
>> create pull requests, they just need to be applied back to the svn
>> repository.  Is there any advantage to moving the repository to
>> github?  Are there any people who will start contributing because the
>> repository is on github that are unwilling to do so with the current
>> model (send patches to the mailing list or issue tracker)?
>>
>> My current client just started a new project on Google Code and we had
>> a similar conversation:  subversion on Google Code vs. git/mercurial
>> on Google Code vs. git at github vs. subversion on Google Code + read
>> only git mirror at github vs. subversion on Google Code + read/write
>> git mirror at github.  In the end we went with subversion on Google
>> Code with possibility of git mirror later because we understand how
>> the Maven release process works with subversion and we liked the issue
>> tracker at Google Code a lot better than the one at github.
>>
>>    michael
>
> I don't know if it would help, but GitHub can mimic SVN from a git
> repository:
>
> https://github.com/blog/626-announcing-svn-support
> https://github.com/blog/966-improved-subversion-client-support

Thanks, Peter, think my head just exploded.  :)

   michael

From andreas at sdsc.edu  Fri Aug  3 17:21:01 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 14:21:01 -0700
Subject: [Biojava-l] Are there EJB entities for BioSQL?
In-Reply-To: <20120803124703.GB3415@paxarchia.galaxy.uni>
References: <20120803124703.GB3415@paxarchia.galaxy.uni>
Message-ID: <CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>

Hi Jan,

There is no biosql ORM mapping for biojava 3 currently. If you need
something like that you would need to use biojava 1 or patch biojava
3...

Andreas



On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> Dear All,
>
> is there a set of EJB 3 entities that correspond to BioSQL available?
> I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
> is that the recommended ORM solution?
>
> Personally, I'd prefer a set of classes, with the suitable annotations
> from the javax.persistence package applied (@Entity, @Id etc.) to match
> the BioSQL tables.
>
> Apparently there have been initiatives in this direction (e.g. [3]), has
> any of these made it into mainstream BioJava? If not, why not?
>
> Best regards, Jan
>
> [1] http://biojava.org/wiki/BioJava:BioJavaXDocs
> [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
> [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
> --
>  +- Jan T. Kim -------------------------------------------------------+
>  |             email: jttkim at gmail.com                                |
>  |             WWW:   http://www.jtkim.dreamhosters.com/              |
>  *-----=<  hierarchical systems are for files, not for humans  >=-----*
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From andreas at sdsc.edu  Fri Aug  3 17:54:48 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 14:54:48 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
	<CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
Message-ID: <CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>

Does anybody actively use the combination Eclipse-Maven-Git ? How good
are the eclipse plugins?

Andreas

From micha at sammeth.net  Fri Aug  3 18:09:47 2012
From: micha at sammeth.net (Micha)
Date: Sat, 4 Aug 2012 00:09:47 +0200
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
	<CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
	<CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>
Message-ID: <CANnPB=hKi6bU1jAGDj3iX0sx0wiunfPuARMsGSGLsh8dPnhn3Q@mail.gmail.com>

Hi Andreas,

we moved away from eclipse when switching to git. I remember that in the
end we used the git command mostly from the command line, and also then
there were update/refresh problems in the ide.

These experiences are from about 3 month ago, maybe the situation improved
recently.

cheers, micha


On Fri, Aug 3, 2012 at 11:54 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Does anybody actively use the combination Eclipse-Maven-Git ? How good
> are the eclipse plugins?
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From andreas at sdsc.edu  Fri Aug  3 18:26:11 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 15:26:11 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CANnPB=hKi6bU1jAGDj3iX0sx0wiunfPuARMsGSGLsh8dPnhn3Q@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
	<CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
	<CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>
	<CANnPB=hKi6bU1jAGDj3iX0sx0wiunfPuARMsGSGLsh8dPnhn3Q@mail.gmail.com>
Message-ID: <CALthepx3yRZ1K_UoG3B+MBsPTW9XFf469y0SRiO4G69724RwNQ@mail.gmail.com>

Did you use egit as your eclipse plugin?  http://www.eclipse.org/egit/

Andreas

On Fri, Aug 3, 2012 at 3:09 PM, Micha <micha at sammeth.net> wrote:
> Hi Andreas,
>
> we moved away from eclipse when switching to git. I remember that in the end
> we used the git command mostly from the command line, and also then there
> were update/refresh problems in the ide.
>
> These experiences are from about 3 month ago, maybe the situation improved
> recently.
>
> cheers, micha
>
>
> On Fri, Aug 3, 2012 at 11:54 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>> Does anybody actively use the combination Eclipse-Maven-Git ? How good
>> are the eclipse plugins?
>>
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

From andreas at sdsc.edu  Fri Aug  3 19:00:49 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 16:00:49 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
Message-ID: <CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>

Hi Michael,

About the question how to cut a release from a distributed repository:
I found this article an interesting read:

http://nvie.com/posts/a-successful-git-branching-model/

Andreas


On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com> wrote:
> -0
>
> I use github for quite a few personal things and mercurial via Google
> Code on a different project and while I think there are some benefits
> to the distributed model I don't understand how it would work from the
> point of view of a release manager.  Does anyone have any pointers to
> documentation on how to manage and cut a release from a distributed
> repository?
>
> With the current svn mirror on github, developers can already fork and
> create pull requests, they just need to be applied back to the svn
> repository.  Is there any advantage to moving the repository to
> github?  Are there any people who will start contributing because the
> repository is on github that are unwilling to do so with the current
> model (send patches to the mailing list or issue tracker)?
>
> My current client just started a new project on Google Code and we had
> a similar conversation:  subversion on Google Code vs. git/mercurial
> on Google Code vs. git at github vs. subversion on Google Code + read
> only git mirror at github vs. subversion on Google Code + read/write
> git mirror at github.  In the end we went with subversion on Google
> Code with possibility of git mirror later because we understand how
> the Maven release process works with subversion and we liked the issue
> tracker at Google Code a lot better than the one at github.
>
>    michael
>
>
> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
>> Github ==awesome.
>> Go for it and let the social coding begin
>>
>> Dan
>>
>> Sent from my iPhone
>>
>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:
>>
>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>> Hi,
>>>>
>>>> I was wondering how people feel about migrating the BioJava  svn
>>>> repository and starting to use github for the trunk development?
>>>> (Currently github is only a read-only copy of our developer svn).
>>>>
>>>> Any opinions?
>>>>
>>>> Andreas
>>>
>>> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
>>>
>>> Hannes
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From heuermh at gmail.com  Fri Aug  3 19:11:55 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Fri, 3 Aug 2012 18:11:55 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
Message-ID: <CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>

Thanks, Andreas, that is a good document.

One problem we might face is that some of the repository operations
are performed by the maven release plugin itself and then we're at the
mercy of the implementers of that plugin to have done it correctly.

   michael


On Fri, Aug 3, 2012 at 6:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michael,
>
> About the question how to cut a release from a distributed repository:
> I found this article an interesting read:
>
> http://nvie.com/posts/a-successful-git-branching-model/
>
> Andreas
>
>
> On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com> wrote:
>> -0
>>
>> I use github for quite a few personal things and mercurial via Google
>> Code on a different project and while I think there are some benefits
>> to the distributed model I don't understand how it would work from the
>> point of view of a release manager.  Does anyone have any pointers to
>> documentation on how to manage and cut a release from a distributed
>> repository?
>>
>> With the current svn mirror on github, developers can already fork and
>> create pull requests, they just need to be applied back to the svn
>> repository.  Is there any advantage to moving the repository to
>> github?  Are there any people who will start contributing because the
>> repository is on github that are unwilling to do so with the current
>> model (send patches to the mailing list or issue tracker)?
>>
>> My current client just started a new project on Google Code and we had
>> a similar conversation:  subversion on Google Code vs. git/mercurial
>> on Google Code vs. git at github vs. subversion on Google Code + read
>> only git mirror at github vs. subversion on Google Code + read/write
>> git mirror at github.  In the end we went with subversion on Google
>> Code with possibility of git mirror later because we understand how
>> the Maven release process works with subversion and we liked the issue
>> tracker at Google Code a lot better than the one at github.
>>
>>    michael
>>
>>
>> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
>>> Github ==awesome.
>>> Go for it and let the social coding begin
>>>
>>> Dan
>>>
>>> Sent from my iPhone
>>>
>>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:
>>>
>>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>>> Hi,
>>>>>
>>>>> I was wondering how people feel about migrating the BioJava  svn
>>>>> repository and starting to use github for the trunk development?
>>>>> (Currently github is only a read-only copy of our developer svn).
>>>>>
>>>>> Any opinions?
>>>>>
>>>>> Andreas
>>>>
>>>> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
>>>>
>>>> Hannes
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l


From sbliven at ucsd.edu  Fri Aug  3 23:54:08 2012
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Fri, 3 Aug 2012 20:54:08 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
	<CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>
Message-ID: <CA+P6ar=GUcPf9=Rm=0fSrXrykm2ObtvQjk2QBSNkLkw+sJnaew@mail.gmail.com>

I'm all for it, provided (as others have mentioned)

   1. Eclipse support is now good enough for day-to-day stuff (maybe
   falling back to command line for complicated merges and branches)
   2. It integrates with Maven for releases

I was also slightly concerned with the overhead of storing the full git
repository. Surprisingly, a git checkout doesn't have that much more
overhead than a SVN checkout, despite storing full histories for each file.

Biojava trunk checkout
Bare files: 29MB
SVN checkout: 60MB (107% overhead)
GIT checkout: 74MB (155% overhead)
However, GIT did take substantially longer to download from github than SVN
took from the biojava server. Since server speeds likely differ
significantly, that's not apples-to-apples, but it might be realistic.

SVN checkout: 1m9.333s
GIT checkout: 4m50.871s

Overall I'm in favor of making the switch.

-Spencer



On Fri, Aug 3, 2012 at 4:11 PM, Michael Heuer <heuermh at gmail.com> wrote:

> Thanks, Andreas, that is a good document.
>
> One problem we might face is that some of the repository operations
> are performed by the maven release plugin itself and then we're at the
> mercy of the implementers of that plugin to have done it correctly.
>
>    michael
>
>
> On Fri, Aug 3, 2012 at 6:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> > Hi Michael,
> >
> > About the question how to cut a release from a distributed repository:
> > I found this article an interesting read:
> >
> > http://nvie.com/posts/a-successful-git-branching-model/
> >
> > Andreas
> >
> >
> > On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com> wrote:
> >> -0
> >>
> >> I use github for quite a few personal things and mercurial via Google
> >> Code on a different project and while I think there are some benefits
> >> to the distributed model I don't understand how it would work from the
> >> point of view of a release manager.  Does anyone have any pointers to
> >> documentation on how to manage and cut a release from a distributed
> >> repository?
> >>
> >> With the current svn mirror on github, developers can already fork and
> >> create pull requests, they just need to be applied back to the svn
> >> repository.  Is there any advantage to moving the repository to
> >> github?  Are there any people who will start contributing because the
> >> repository is on github that are unwilling to do so with the current
> >> model (send patches to the mailing list or issue tracker)?
> >>
> >> My current client just started a new project on Google Code and we had
> >> a similar conversation:  subversion on Google Code vs. git/mercurial
> >> on Google Code vs. git at github vs. subversion on Google Code + read
> >> only git mirror at github vs. subversion on Google Code + read/write
> >> git mirror at github.  In the end we went with subversion on Google
> >> Code with possibility of git mirror later because we understand how
> >> the Maven release process works with subversion and we liked the issue
> >> tracker at Google Code a lot better than the one at github.
> >>
> >>    michael
> >>
> >>
> >> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
> >>> Github ==awesome.
> >>> Go for it and let the social coding begin
> >>>
> >>> Dan
> >>>
> >>> Sent from my iPhone
> >>>
> >>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<
> biojava at hannes.oib.com> wrote:
> >>>
> >>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu>
> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> I was wondering how people feel about migrating the BioJava  svn
> >>>>> repository and starting to use github for the trunk development?
> >>>>> (Currently github is only a read-only copy of our developer svn).
> >>>>>
> >>>>> Any opinions?
> >>>>>
> >>>>> Andreas
> >>>>
> >>>> I'm in favor - git pull requests make submitting patches so much
> easier, IMHO.
> >>>>
> >>>> Hannes
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jttkim at googlemail.com  Mon Aug  6 05:10:04 2012
From: jttkim at googlemail.com (Jan T Kim)
Date: Mon, 6 Aug 2012 10:10:04 +0100
Subject: [Biojava-l] Are there EJB entities for BioSQL?
In-Reply-To: <CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>
References: <20120803124703.GB3415@paxarchia.galaxy.uni>
	<CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>
Message-ID: <20120806091003.GA3404@paxarchia.galaxy.uni>

Hi Andreas and All,

On Fri, Aug 03, 2012 at 02:21:01PM -0700, Andreas Prlic wrote:
> Hi Jan,
> 
> There is no biosql ORM mapping for biojava 3 currently. If you need
> something like that you would need to use biojava 1 or patch biojava
> 3...

ok -- so is there any general suggestion / recommendation / best
practice for building applications that involve handling annotated
sequence data and a web UI?

Best regards, Jan


> Andreas
> 
> 
> 
> On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> > Dear All,
> >
> > is there a set of EJB 3 entities that correspond to BioSQL available?
> > I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
> > is that the recommended ORM solution?
> >
> > Personally, I'd prefer a set of classes, with the suitable annotations
> > from the javax.persistence package applied (@Entity, @Id etc.) to match
> > the BioSQL tables.
> >
> > Apparently there have been initiatives in this direction (e.g. [3]), has
> > any of these made it into mainstream BioJava? If not, why not?
> >
> > Best regards, Jan
> >
> > [1] http://biojava.org/wiki/BioJava:BioJavaXDocs
> > [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
> > [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
> > --
> >  +- Jan T. Kim -------------------------------------------------------+
> >  |             email: jttkim at gmail.com                                |
> >  |             WWW:   http://www.jtkim.dreamhosters.com/              |
> >  *-----=<  hierarchical systems are for files, not for humans  >=-----*
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*

From andreas at sdsc.edu  Tue Aug  7 23:08:35 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 7 Aug 2012 20:08:35 -0700
Subject: [Biojava-l] Are there EJB entities for BioSQL?
In-Reply-To: <20120806091003.GA3404@paxarchia.galaxy.uni>
References: <20120803124703.GB3415@paxarchia.galaxy.uni>
	<CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>
	<20120806091003.GA3404@paxarchia.galaxy.uni>
Message-ID: <CALthepznaGXHsY4VRZ=JSeXqsGDrPZZbwwypdughPgBt_bWZcQ@mail.gmail.com>

Hi Jan,

that really depends on what you want to do. My first response based on
your comment would be to take a look at the Distributed Annotation
System and the various DAS clients. We can say more if you tell us a
bit more specific what your intention is.

Andreas


On Mon, Aug 6, 2012 at 2:10 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> Hi Andreas and All,
>
> On Fri, Aug 03, 2012 at 02:21:01PM -0700, Andreas Prlic wrote:
>> Hi Jan,
>>
>> There is no biosql ORM mapping for biojava 3 currently. If you need
>> something like that you would need to use biojava 1 or patch biojava
>> 3...
>
> ok -- so is there any general suggestion / recommendation / best
> practice for building applications that involve handling annotated
> sequence data and a web UI?
>
> Best regards, Jan
>
>
>> Andreas
>>
>>
>>
>> On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <jttkim at googlemail.com> wrote:
>> > Dear All,
>> >
>> > is there a set of EJB 3 entities that correspond to BioSQL available?
>> > I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
>> > is that the recommended ORM solution?
>> >
>> > Personally, I'd prefer a set of classes, with the suitable annotations
>> > from the javax.persistence package applied (@Entity, @Id etc.) to match
>> > the BioSQL tables.
>> >
>> > Apparently there have been initiatives in this direction (e.g. [3]), has
>> > any of these made it into mainstream BioJava? If not, why not?
>> >
>> > Best regards, Jan
>> >
>> > [1] http://biojava.org/wiki/BioJava:BioJavaXDocs
>> > [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
>> > [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
>> > --
>> >  +- Jan T. Kim -------------------------------------------------------+
>> >  |             email: jttkim at gmail.com                                |
>> >  |             WWW:   http://www.jtkim.dreamhosters.com/              |
>> >  *-----=<  hierarchical systems are for files, not for humans  >=-----*
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
>  +- Jan T. Kim -------------------------------------------------------+
>  |             email: jttkim at gmail.com                                |
>  |             WWW:   http://www.jtkim.dreamhosters.com/              |
>  *-----=<  hierarchical systems are for files, not for humans  >=-----*
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From sbliven at ucsd.edu  Wed Aug  8 04:03:26 2012
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 8 Aug 2012 01:03:26 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CA+P6ar=GUcPf9=Rm=0fSrXrykm2ObtvQjk2QBSNkLkw+sJnaew@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
	<CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>
	<CA+P6ar=GUcPf9=Rm=0fSrXrykm2ObtvQjk2QBSNkLkw+sJnaew@mail.gmail.com>
Message-ID: <CA+P6arnDu81eYWTc_BT5T+0saZqArvXFcHjQ3FEXOZS0UCXHOw@mail.gmail.com>

I thought people here might be interested to know that Rosetta is currently
switching from SVN to GIT. They have a pretty complicated build
configuration, but GIT seems up to the challenge. They had an interesting
list of benefits drafted on the internal Baker
wiki<http://docu.bakerlab.org/doku.php?id=proposed_changes:switch_to_git>I
thought would be interesting to share:

End User ( You only use the binaries)

   - Your database version will always match the binary version ( so no
   more segfaults because your database is different)
   - You can switch to other people's patched databases easily!

 Infrequent Developers( A commit every so often )

   - Everything from End User applies
   - You can update every day *SAFELY*
   - You can work locally, and never actually commit your changes if you
   don't want to ( but still benefit from having version control, rollbacks,
   etc.)
   - You benefit from other people's uncommited changes( see below )
   - Committing your small change is much easier because you don't
*MERGE*with trunk, you
   *PATCH **ON TOP* of trunk
   - Workflow stays pretty much the same

 Frequent Developers

   - Everything from Infrequent Developers applies
   - You can create many local branches, one for each feature or bugfix
   - When you commit, you commit a whole branch at a time, which makes
      reading history very easy
       - You can update your local branch on *TOP* of the trunk
   - By applying your local branch as a series of patches, conflict
      resolution is MUCH easier (no enormous merge conflict resolutions)
       - Everyone's local branch is completely visible to you, allowing you
   to share uncommited changes very easily
   - Workflow changes quite a bit, but for the better

 Repository Manager

   - Other than setting up initial users, you don't have to do anything
   - Automated testing handles rejections of commits


Cheers,

Spencer



On Fri, Aug 3, 2012 at 8:54 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>
> I'm all for it, provided (as others have mentioned)
>
> Eclipse support is now good enough for day-to-day stuff (maybe falling
back to command line for complicated merges and branches)
> It integrates with Maven for releases
>
> I was also slightly concerned with the overhead of storing the full git
repository. Surprisingly, a git checkout doesn't have that much more
overhead than a SVN checkout, despite storing full histories for each file.
>
> Biojava trunk checkout
> Bare files: 29MB
> SVN checkout: 60MB (107% overhead)
> GIT checkout: 74MB (155% overhead)
>
> However, GIT did take substantially longer to download from github than
SVN took from the biojava server. Since server speeds likely differ
significantly, that's not apples-to-apples, but it might be realistic.
>
> SVN checkout: 1m9.333s
> GIT checkout: 4m50.871s
>
> Overall I'm in favor of making the switch.
>
> -Spencer
>
>
>
>
> On Fri, Aug 3, 2012 at 4:11 PM, Michael Heuer <heuermh at gmail.com> wrote:
>>
>> Thanks, Andreas, that is a good document.
>>
>> One problem we might face is that some of the repository operations
>> are performed by the maven release plugin itself and then we're at the
>> mercy of the implementers of that plugin to have done it correctly.
>>
>>    michael
>>
>>
>> On Fri, Aug 3, 2012 at 6:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > Hi Michael,
>> >
>> > About the question how to cut a release from a distributed repository:
>> > I found this article an interesting read:
>> >
>> > http://nvie.com/posts/a-successful-git-branching-model/
>> >
>> > Andreas
>> >
>> >
>> > On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com>
wrote:
>> >> -0
>> >>
>> >> I use github for quite a few personal things and mercurial via Google
>> >> Code on a different project and while I think there are some benefits
>> >> to the distributed model I don't understand how it would work from the
>> >> point of view of a release manager.  Does anyone have any pointers to
>> >> documentation on how to manage and cut a release from a distributed
>> >> repository?
>> >>
>> >> With the current svn mirror on github, developers can already fork and
>> >> create pull requests, they just need to be applied back to the svn
>> >> repository.  Is there any advantage to moving the repository to
>> >> github?  Are there any people who will start contributing because the
>> >> repository is on github that are unwilling to do so with the current
>> >> model (send patches to the mailing list or issue tracker)?
>> >>
>> >> My current client just started a new project on Google Code and we had
>> >> a similar conversation:  subversion on Google Code vs. git/mercurial
>> >> on Google Code vs. git at github vs. subversion on Google Code + read
>> >> only git mirror at github vs. subversion on Google Code + read/write
>> >> git mirror at github.  In the end we went with subversion on Google
>> >> Code with possibility of git mirror later because we understand how
>> >> the Maven release process works with subversion and we liked the issue
>> >> tracker at Google Code a lot better than the one at github.
>> >>
>> >>    michael
>> >>
>> >>
>> >> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
>> >>> Github ==awesome.
>> >>> Go for it and let the social coding begin
>> >>>
>> >>> Dan
>> >>>
>> >>> Sent from my iPhone
>> >>>
>> >>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<
biojava at hannes.oib.com> wrote:
>> >>>
>> >>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu>
wrote:
>> >>>>> Hi,
>> >>>>>
>> >>>>> I was wondering how people feel about migrating the BioJava  svn
>> >>>>> repository and starting to use github for the trunk development?
>> >>>>> (Currently github is only a read-only copy of our developer svn).
>> >>>>>
>> >>>>> Any opinions?
>> >>>>>
>> >>>>> Andreas
>> >>>>
>> >>>> I'm in favor - git pull requests make submitting patches so much
easier, IMHO.
>> >>>>
>> >>>> Hannes
>> >>
>> >> _______________________________________________
>> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From andreas at sdsc.edu  Fri Aug 10 11:46:50 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 10 Aug 2012 08:46:50 -0700
Subject: [Biojava-l] new BioJava paper published
Message-ID: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>

Hi,

I am pleased to announce that the latest BioJava paper describing the
version 3 series has been published and is now available online.

Thanks to all developers for their contributions, it would not have
been possible without them!

Andreas


Abstract:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

PDF:

http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

Citation:

BioJava: an open-source framework for bioinformatics in 2012

Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis

Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494

From power3d at gmail.com  Fri Aug 10 12:47:27 2012
From: power3d at gmail.com (Tony Power)
Date: Fri, 10 Aug 2012 17:47:27 +0100
Subject: [Biojava-l] new BioJava paper published
In-Reply-To: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>
References: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>
Message-ID: <CAMNg4HjufdC6dXVZZVKcXWJqAOfZPR9r=e2YF0eNdBQvJE32OA@mail.gmail.com>

Congratulations.

Tony

On Fri, Aug 10, 2012 at 4:46 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> I am pleased to announce that the latest BioJava paper describing the
> version 3 series has been published and is now available online.
>
> Thanks to all developers for their contributions, it would not have
> been possible without them!
>
> Andreas
>
>
> Abstract:
>
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref
>
> PDF:
>
> http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref
>
> Citation:
>
> BioJava: an open-source framework for bioinformatics in 2012
>
> Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
> Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
> Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
> Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
>
> Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From jprocter at compbio.dundee.ac.uk  Mon Aug 13 03:34:19 2012
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Mon, 13 Aug 2012 08:34:19 +0100
Subject: [Biojava-l] [Biojava-dev]  new BioJava paper published
In-Reply-To: <CAMNg4HjufdC6dXVZZVKcXWJqAOfZPR9r=e2YF0eNdBQvJE32OA@mail.gmail.com>
References: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>
	<CAMNg4HjufdC6dXVZZVKcXWJqAOfZPR9r=e2YF0eNdBQvJE32OA@mail.gmail.com>
Message-ID: <5028ADFB.5010906@compbio.dundee.ac.uk>

Hi bj3 developers!

> On Fri, Aug 10, 2012 at 4:46 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi,
>>
>> I am pleased to announce that the latest BioJava paper describing the
>> version 3 series has been published and is now available online.
>>
>> Thanks to all developers for their contributions, it would not have
>> been possible without them!

And I must say, it is really nice to see v3 in print .. you should all 
be proud!

Jim.



From ralf at ark.in-berlin.de  Wed Aug 29 03:38:20 2012
From: ralf at ark.in-berlin.de (ralf at ark.in-berlin.de)
Date: Wed, 29 Aug 2012 09:38:20 +0200
Subject: [Biojava-l] issues with mailman
In-Reply-To: <20120824165821.GA3008@ark.in-berlin.de>
References: <20120824165821.GA3008@ark.in-berlin.de>
Message-ID: <20120829073820.GB2440@ark.in-berlin.de>

Hello,
it appears mailman won't send password reminders,
also Noscript complained about a "potential cross-site
scripting (XSS) attempt from http://biojava.org"...
When trying to subscribe it complains about invalid email,
and finally, two mails to this list have not appeared
in one of the moderator's mailbox.

So, there appears to be something wrong...

Thanks to Andreas for subscribing me manually.



From ralf at ark.in-berlin.de  Wed Aug 29 04:21:41 2012
From: ralf at ark.in-berlin.de (ralf at ark.in-berlin.de)
Date: Wed, 29 Aug 2012 10:21:41 +0200
Subject: [Biojava-l] issues with mailman
In-Reply-To: <CAKVJ-_6o+kfXtFyWfEnMvLbA40QyM87VbaB7UXjn4dcZidc_NA@mail.gmail.com>
References: <20120824165821.GA3008@ark.in-berlin.de>
	<20120829073820.GB2440@ark.in-berlin.de>
	<CAKVJ-_6o+kfXtFyWfEnMvLbA40QyM87VbaB7UXjn4dcZidc_NA@mail.gmail.com>
Message-ID: <20120829082141.GA2659@ark.in-berlin.de>

On Wed, Aug 29, 2012 at 09:00:00AM +0100, Peter Cock wrote:
> On Wednesday, August 29, 2012, wrote:
> > also Noscript complained about a "potential cross-site
> > scripting (XSS) attempt from http://biojava.org"...
> 
> Was that from an open-bio.org URL? It is actually
> the same server for BioJava.org so I can imagine
> how an apparent cross-site scripting attempt
> might happen.

The offending page: 
http://lists.open-bio.org/mailman/options/biojava-l

Details:
[NoScript XSS] Sanitized suspicious upload to
[http://lists.open-bio.org/mailman/options/biojava-l] from
[http://www.biojava.org/mailman/listinfo/biojava-l]: transformed into a
download-only GET request.

If this is a Noscript bug, give me a hint, I have no idea
about such things.


ralf


From p.j.a.cock at googlemail.com  Wed Aug 29 04:44:19 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Aug 2012 09:44:19 +0100
Subject: [Biojava-l] issues with mailman
In-Reply-To: <20120829082141.GA2659@ark.in-berlin.de>
References: <20120824165821.GA3008@ark.in-berlin.de>
	<20120829073820.GB2440@ark.in-berlin.de>
	<CAKVJ-_6o+kfXtFyWfEnMvLbA40QyM87VbaB7UXjn4dcZidc_NA@mail.gmail.com>
	<20120829082141.GA2659@ark.in-berlin.de>
Message-ID: <CAKVJ-_4R+=WXm3e79WTEAW38Ts3bvabj+vazt-nFZtZegcxa3w@mail.gmail.com>

On Wed, Aug 29, 2012 at 9:21 AM, ralf at ark.in-berlin.de
<ralf at ark.in-berlin.de> wrote:
> On Wed, Aug 29, 2012 at 09:00:00AM +0100, Peter Cock wrote:
>> On Wednesday, August 29, 2012, wrote:
>> > also Noscript complained about a "potential cross-site
>> > scripting (XSS) attempt from http://biojava.org"...
>>
>> Was that from an open-bio.org URL? It is actually
>> the same server for BioJava.org so I can imagine
>> how an apparent cross-site scripting attempt
>> might happen.
>
> The offending page:
> http://lists.open-bio.org/mailman/options/biojava-l
>
> Details:
> [NoScript XSS] Sanitized suspicious upload to
> [http://lists.open-bio.org/mailman/options/biojava-l] from
> [http://www.biojava.org/mailman/listinfo/biojava-l]: transformed into a
> download-only GET request.
>
> If this is a Noscript bug, give me a hint, I have no idea
> about such things.
>
> ralf

I think it is harmless, notice both these URLs work:
http://www.biojava.org/mailman/options/biojava-l
http://lists.open-bio.org/mailman/options/biojava-l
but they both submit the form to lists.open-bio.org.

So technically the Noscript warning is correct - if
you use the www.biojava.org address it is sending
the information to lists.open-bio.org (both are OBF
servers, although under different domain names).

Similarly you can send send to this mailing list as
biojava-l at lists.open-bio.org or biojava-l at biojava.org

Peter

From andreas at sdsc.edu  Thu Aug  2 23:52:22 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 2 Aug 2012 16:52:22 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
Message-ID: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>

Hi,

I was wondering how people feel about migrating the BioJava  svn
repository and starting to use github for the trunk development?
(Currently github is only a read-only copy of our developer svn).

Any opinions?

Andreas


From biojava at hannes.oib.com  Fri Aug  3 03:11:23 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Fri, 3 Aug 2012 05:11:23 +0200
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
Message-ID: <CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>

On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> I was wondering how people feel about migrating the BioJava  svn
> repository and starting to use github for the trunk development?
> (Currently github is only a read-only copy of our developer svn).
>
> Any opinions?
>
> Andreas

I'm in favor - git pull requests make submitting patches so much easier, IMHO.

Hannes


From daniel.quest at gmail.com  Fri Aug  3 04:14:51 2012
From: daniel.quest at gmail.com (daniel.quest at gmail.com)
Date: Thu, 2 Aug 2012 23:14:51 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
Message-ID: <18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>

Github ==awesome.  
Go for it and let the social coding begin

Dan

Sent from my iPhone

On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:

> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi,
>> 
>> I was wondering how people feel about migrating the BioJava  svn
>> repository and starting to use github for the trunk development?
>> (Currently github is only a read-only copy of our developer svn).
>> 
>> Any opinions?
>> 
>> Andreas
> 
> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
> 
> Hannes
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From jttkim at googlemail.com  Fri Aug  3 12:47:04 2012
From: jttkim at googlemail.com (Jan T Kim)
Date: Fri, 3 Aug 2012 13:47:04 +0100
Subject: [Biojava-l] Are there EJB entities for BioSQL?
Message-ID: <20120803124703.GB3415@paxarchia.galaxy.uni>

Dear All,

is there a set of EJB 3 entities that correspond to BioSQL available?
I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
is that the recommended ORM solution?

Personally, I'd prefer a set of classes, with the suitable annotations
from the javax.persistence package applied (@Entity, @Id etc.) to match
the BioSQL tables.

Apparently there have been initiatives in this direction (e.g. [3]), has
any of these made it into mainstream BioJava? If not, why not?

Best regards, Jan

[1] http://biojava.org/wiki/BioJava:BioJavaXDocs
[2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
[3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*


From heuermh at gmail.com  Fri Aug  3 15:57:25 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Fri, 3 Aug 2012 10:57:25 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
Message-ID: <CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>

-0

I use github for quite a few personal things and mercurial via Google
Code on a different project and while I think there are some benefits
to the distributed model I don't understand how it would work from the
point of view of a release manager.  Does anyone have any pointers to
documentation on how to manage and cut a release from a distributed
repository?

With the current svn mirror on github, developers can already fork and
create pull requests, they just need to be applied back to the svn
repository.  Is there any advantage to moving the repository to
github?  Are there any people who will start contributing because the
repository is on github that are unwilling to do so with the current
model (send patches to the mailing list or issue tracker)?

My current client just started a new project on Google Code and we had
a similar conversation:  subversion on Google Code vs. git/mercurial
on Google Code vs. git at github vs. subversion on Google Code + read
only git mirror at github vs. subversion on Google Code + read/write
git mirror at github.  In the end we went with subversion on Google
Code with possibility of git mirror later because we understand how
the Maven release process works with subversion and we liked the issue
tracker at Google Code a lot better than the one at github.

   michael


On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
> Github ==awesome.
> Go for it and let the social coding begin
>
> Dan
>
> Sent from my iPhone
>
> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:
>
>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi,
>>>
>>> I was wondering how people feel about migrating the BioJava  svn
>>> repository and starting to use github for the trunk development?
>>> (Currently github is only a read-only copy of our developer svn).
>>>
>>> Any opinions?
>>>
>>> Andreas
>>
>> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
>>
>> Hannes



From p.j.a.cock at googlemail.com  Fri Aug  3 16:01:49 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 3 Aug 2012 17:01:49 +0100
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
Message-ID: <CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>

On Fri, Aug 3, 2012 at 4:57 PM, Michael Heuer <heuermh at gmail.com> wrote:
> -0
>
> I use github for quite a few personal things and mercurial via Google
> Code on a different project and while I think there are some benefits
> to the distributed model I don't understand how it would work from the
> point of view of a release manager.  Does anyone have any pointers to
> documentation on how to manage and cut a release from a distributed
> repository?
>
> With the current svn mirror on github, developers can already fork and
> create pull requests, they just need to be applied back to the svn
> repository.  Is there any advantage to moving the repository to
> github?  Are there any people who will start contributing because the
> repository is on github that are unwilling to do so with the current
> model (send patches to the mailing list or issue tracker)?
>
> My current client just started a new project on Google Code and we had
> a similar conversation:  subversion on Google Code vs. git/mercurial
> on Google Code vs. git at github vs. subversion on Google Code + read
> only git mirror at github vs. subversion on Google Code + read/write
> git mirror at github.  In the end we went with subversion on Google
> Code with possibility of git mirror later because we understand how
> the Maven release process works with subversion and we liked the issue
> tracker at Google Code a lot better than the one at github.
>
>    michael

I don't know if it would help, but GitHub can mimic SVN from a git
repository:

https://github.com/blog/626-announcing-svn-support
https://github.com/blog/966-improved-subversion-client-support

Peter


From heuermh at gmail.com  Fri Aug  3 16:08:32 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Fri, 3 Aug 2012 11:08:32 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
Message-ID: <CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>

On Fri, Aug 3, 2012 at 11:01 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Aug 3, 2012 at 4:57 PM, Michael Heuer <heuermh at gmail.com> wrote:
>> -0
>>
>> I use github for quite a few personal things and mercurial via Google
>> Code on a different project and while I think there are some benefits
>> to the distributed model I don't understand how it would work from the
>> point of view of a release manager.  Does anyone have any pointers to
>> documentation on how to manage and cut a release from a distributed
>> repository?
>>
>> With the current svn mirror on github, developers can already fork and
>> create pull requests, they just need to be applied back to the svn
>> repository.  Is there any advantage to moving the repository to
>> github?  Are there any people who will start contributing because the
>> repository is on github that are unwilling to do so with the current
>> model (send patches to the mailing list or issue tracker)?
>>
>> My current client just started a new project on Google Code and we had
>> a similar conversation:  subversion on Google Code vs. git/mercurial
>> on Google Code vs. git at github vs. subversion on Google Code + read
>> only git mirror at github vs. subversion on Google Code + read/write
>> git mirror at github.  In the end we went with subversion on Google
>> Code with possibility of git mirror later because we understand how
>> the Maven release process works with subversion and we liked the issue
>> tracker at Google Code a lot better than the one at github.
>>
>>    michael
>
> I don't know if it would help, but GitHub can mimic SVN from a git
> repository:
>
> https://github.com/blog/626-announcing-svn-support
> https://github.com/blog/966-improved-subversion-client-support

Thanks, Peter, think my head just exploded.  :)

   michael


From andreas at sdsc.edu  Fri Aug  3 21:21:01 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 14:21:01 -0700
Subject: [Biojava-l] Are there EJB entities for BioSQL?
In-Reply-To: <20120803124703.GB3415@paxarchia.galaxy.uni>
References: <20120803124703.GB3415@paxarchia.galaxy.uni>
Message-ID: <CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>

Hi Jan,

There is no biosql ORM mapping for biojava 3 currently. If you need
something like that you would need to use biojava 1 or patch biojava
3...

Andreas



On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> Dear All,
>
> is there a set of EJB 3 entities that correspond to BioSQL available?
> I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
> is that the recommended ORM solution?
>
> Personally, I'd prefer a set of classes, with the suitable annotations
> from the javax.persistence package applied (@Entity, @Id etc.) to match
> the BioSQL tables.
>
> Apparently there have been initiatives in this direction (e.g. [3]), has
> any of these made it into mainstream BioJava? If not, why not?
>
> Best regards, Jan
>
> [1] http://biojava.org/wiki/BioJava:BioJavaXDocs
> [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
> [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
> --
>  +- Jan T. Kim -------------------------------------------------------+
>  |             email: jttkim at gmail.com                                |
>  |             WWW:   http://www.jtkim.dreamhosters.com/              |
>  *-----=<  hierarchical systems are for files, not for humans  >=-----*
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From andreas at sdsc.edu  Fri Aug  3 21:54:48 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 14:54:48 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
	<CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
Message-ID: <CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>

Does anybody actively use the combination Eclipse-Maven-Git ? How good
are the eclipse plugins?

Andreas


From micha at sammeth.net  Fri Aug  3 22:09:47 2012
From: micha at sammeth.net (Micha)
Date: Sat, 4 Aug 2012 00:09:47 +0200
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
	<CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
	<CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>
Message-ID: <CANnPB=hKi6bU1jAGDj3iX0sx0wiunfPuARMsGSGLsh8dPnhn3Q@mail.gmail.com>

Hi Andreas,

we moved away from eclipse when switching to git. I remember that in the
end we used the git command mostly from the command line, and also then
there were update/refresh problems in the ide.

These experiences are from about 3 month ago, maybe the situation improved
recently.

cheers, micha


On Fri, Aug 3, 2012 at 11:54 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Does anybody actively use the combination Eclipse-Maven-Git ? How good
> are the eclipse plugins?
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From andreas at sdsc.edu  Fri Aug  3 22:26:11 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 15:26:11 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CANnPB=hKi6bU1jAGDj3iX0sx0wiunfPuARMsGSGLsh8dPnhn3Q@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CAKVJ-_6fD6CDexAubRyJ+bLGbkuRc06rWFxgOw8xj7HWiCje9Q@mail.gmail.com>
	<CAOjYwMzDZPxsC0BfZhCEmAHMePXiPPYc1bR5axdmBSpKgbZ89g@mail.gmail.com>
	<CALthepw_kNAdtAT72JmRvQScbvU-0EwE0gJYZRqM4O=WOaN8zg@mail.gmail.com>
	<CANnPB=hKi6bU1jAGDj3iX0sx0wiunfPuARMsGSGLsh8dPnhn3Q@mail.gmail.com>
Message-ID: <CALthepx3yRZ1K_UoG3B+MBsPTW9XFf469y0SRiO4G69724RwNQ@mail.gmail.com>

Did you use egit as your eclipse plugin?  http://www.eclipse.org/egit/

Andreas

On Fri, Aug 3, 2012 at 3:09 PM, Micha <micha at sammeth.net> wrote:
> Hi Andreas,
>
> we moved away from eclipse when switching to git. I remember that in the end
> we used the git command mostly from the command line, and also then there
> were update/refresh problems in the ide.
>
> These experiences are from about 3 month ago, maybe the situation improved
> recently.
>
> cheers, micha
>
>
> On Fri, Aug 3, 2012 at 11:54 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>> Does anybody actively use the combination Eclipse-Maven-Git ? How good
>> are the eclipse plugins?
>>
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From andreas at sdsc.edu  Fri Aug  3 23:00:49 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 3 Aug 2012 16:00:49 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
Message-ID: <CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>

Hi Michael,

About the question how to cut a release from a distributed repository:
I found this article an interesting read:

http://nvie.com/posts/a-successful-git-branching-model/

Andreas


On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com> wrote:
> -0
>
> I use github for quite a few personal things and mercurial via Google
> Code on a different project and while I think there are some benefits
> to the distributed model I don't understand how it would work from the
> point of view of a release manager.  Does anyone have any pointers to
> documentation on how to manage and cut a release from a distributed
> repository?
>
> With the current svn mirror on github, developers can already fork and
> create pull requests, they just need to be applied back to the svn
> repository.  Is there any advantage to moving the repository to
> github?  Are there any people who will start contributing because the
> repository is on github that are unwilling to do so with the current
> model (send patches to the mailing list or issue tracker)?
>
> My current client just started a new project on Google Code and we had
> a similar conversation:  subversion on Google Code vs. git/mercurial
> on Google Code vs. git at github vs. subversion on Google Code + read
> only git mirror at github vs. subversion on Google Code + read/write
> git mirror at github.  In the end we went with subversion on Google
> Code with possibility of git mirror later because we understand how
> the Maven release process works with subversion and we liked the issue
> tracker at Google Code a lot better than the one at github.
>
>    michael
>
>
> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
>> Github ==awesome.
>> Go for it and let the social coding begin
>>
>> Dan
>>
>> Sent from my iPhone
>>
>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:
>>
>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>> Hi,
>>>>
>>>> I was wondering how people feel about migrating the BioJava  svn
>>>> repository and starting to use github for the trunk development?
>>>> (Currently github is only a read-only copy of our developer svn).
>>>>
>>>> Any opinions?
>>>>
>>>> Andreas
>>>
>>> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
>>>
>>> Hannes
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From heuermh at gmail.com  Fri Aug  3 23:11:55 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Fri, 3 Aug 2012 18:11:55 -0500
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
Message-ID: <CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>

Thanks, Andreas, that is a good document.

One problem we might face is that some of the repository operations
are performed by the maven release plugin itself and then we're at the
mercy of the implementers of that plugin to have done it correctly.

   michael


On Fri, Aug 3, 2012 at 6:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michael,
>
> About the question how to cut a release from a distributed repository:
> I found this article an interesting read:
>
> http://nvie.com/posts/a-successful-git-branching-model/
>
> Andreas
>
>
> On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com> wrote:
>> -0
>>
>> I use github for quite a few personal things and mercurial via Google
>> Code on a different project and while I think there are some benefits
>> to the distributed model I don't understand how it would work from the
>> point of view of a release manager.  Does anyone have any pointers to
>> documentation on how to manage and cut a release from a distributed
>> repository?
>>
>> With the current svn mirror on github, developers can already fork and
>> create pull requests, they just need to be applied back to the svn
>> repository.  Is there any advantage to moving the repository to
>> github?  Are there any people who will start contributing because the
>> repository is on github that are unwilling to do so with the current
>> model (send patches to the mailing list or issue tracker)?
>>
>> My current client just started a new project on Google Code and we had
>> a similar conversation:  subversion on Google Code vs. git/mercurial
>> on Google Code vs. git at github vs. subversion on Google Code + read
>> only git mirror at github vs. subversion on Google Code + read/write
>> git mirror at github.  In the end we went with subversion on Google
>> Code with possibility of git mirror later because we understand how
>> the Maven release process works with subversion and we liked the issue
>> tracker at Google Code a lot better than the one at github.
>>
>>    michael
>>
>>
>> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
>>> Github ==awesome.
>>> Go for it and let the social coding begin
>>>
>>> Dan
>>>
>>> Sent from my iPhone
>>>
>>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<biojava at hannes.oib.com> wrote:
>>>
>>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>>> Hi,
>>>>>
>>>>> I was wondering how people feel about migrating the BioJava  svn
>>>>> repository and starting to use github for the trunk development?
>>>>> (Currently github is only a read-only copy of our developer svn).
>>>>>
>>>>> Any opinions?
>>>>>
>>>>> Andreas
>>>>
>>>> I'm in favor - git pull requests make submitting patches so much easier, IMHO.
>>>>
>>>> Hannes
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l



From sbliven at ucsd.edu  Sat Aug  4 03:54:08 2012
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Fri, 3 Aug 2012 20:54:08 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
	<CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>
Message-ID: <CA+P6ar=GUcPf9=Rm=0fSrXrykm2ObtvQjk2QBSNkLkw+sJnaew@mail.gmail.com>

I'm all for it, provided (as others have mentioned)

   1. Eclipse support is now good enough for day-to-day stuff (maybe
   falling back to command line for complicated merges and branches)
   2. It integrates with Maven for releases

I was also slightly concerned with the overhead of storing the full git
repository. Surprisingly, a git checkout doesn't have that much more
overhead than a SVN checkout, despite storing full histories for each file.

Biojava trunk checkout
Bare files: 29MB
SVN checkout: 60MB (107% overhead)
GIT checkout: 74MB (155% overhead)
However, GIT did take substantially longer to download from github than SVN
took from the biojava server. Since server speeds likely differ
significantly, that's not apples-to-apples, but it might be realistic.

SVN checkout: 1m9.333s
GIT checkout: 4m50.871s

Overall I'm in favor of making the switch.

-Spencer



On Fri, Aug 3, 2012 at 4:11 PM, Michael Heuer <heuermh at gmail.com> wrote:

> Thanks, Andreas, that is a good document.
>
> One problem we might face is that some of the repository operations
> are performed by the maven release plugin itself and then we're at the
> mercy of the implementers of that plugin to have done it correctly.
>
>    michael
>
>
> On Fri, Aug 3, 2012 at 6:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> > Hi Michael,
> >
> > About the question how to cut a release from a distributed repository:
> > I found this article an interesting read:
> >
> > http://nvie.com/posts/a-successful-git-branching-model/
> >
> > Andreas
> >
> >
> > On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com> wrote:
> >> -0
> >>
> >> I use github for quite a few personal things and mercurial via Google
> >> Code on a different project and while I think there are some benefits
> >> to the distributed model I don't understand how it would work from the
> >> point of view of a release manager.  Does anyone have any pointers to
> >> documentation on how to manage and cut a release from a distributed
> >> repository?
> >>
> >> With the current svn mirror on github, developers can already fork and
> >> create pull requests, they just need to be applied back to the svn
> >> repository.  Is there any advantage to moving the repository to
> >> github?  Are there any people who will start contributing because the
> >> repository is on github that are unwilling to do so with the current
> >> model (send patches to the mailing list or issue tracker)?
> >>
> >> My current client just started a new project on Google Code and we had
> >> a similar conversation:  subversion on Google Code vs. git/mercurial
> >> on Google Code vs. git at github vs. subversion on Google Code + read
> >> only git mirror at github vs. subversion on Google Code + read/write
> >> git mirror at github.  In the end we went with subversion on Google
> >> Code with possibility of git mirror later because we understand how
> >> the Maven release process works with subversion and we liked the issue
> >> tracker at Google Code a lot better than the one at github.
> >>
> >>    michael
> >>
> >>
> >> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
> >>> Github ==awesome.
> >>> Go for it and let the social coding begin
> >>>
> >>> Dan
> >>>
> >>> Sent from my iPhone
> >>>
> >>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<
> biojava at hannes.oib.com> wrote:
> >>>
> >>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu>
> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> I was wondering how people feel about migrating the BioJava  svn
> >>>>> repository and starting to use github for the trunk development?
> >>>>> (Currently github is only a read-only copy of our developer svn).
> >>>>>
> >>>>> Any opinions?
> >>>>>
> >>>>> Andreas
> >>>>
> >>>> I'm in favor - git pull requests make submitting patches so much
> easier, IMHO.
> >>>>
> >>>> Hannes
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jttkim at googlemail.com  Mon Aug  6 09:10:04 2012
From: jttkim at googlemail.com (Jan T Kim)
Date: Mon, 6 Aug 2012 10:10:04 +0100
Subject: [Biojava-l] Are there EJB entities for BioSQL?
In-Reply-To: <CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>
References: <20120803124703.GB3415@paxarchia.galaxy.uni>
	<CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>
Message-ID: <20120806091003.GA3404@paxarchia.galaxy.uni>

Hi Andreas and All,

On Fri, Aug 03, 2012 at 02:21:01PM -0700, Andreas Prlic wrote:
> Hi Jan,
> 
> There is no biosql ORM mapping for biojava 3 currently. If you need
> something like that you would need to use biojava 1 or patch biojava
> 3...

ok -- so is there any general suggestion / recommendation / best
practice for building applications that involve handling annotated
sequence data and a web UI?

Best regards, Jan


> Andreas
> 
> 
> 
> On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> > Dear All,
> >
> > is there a set of EJB 3 entities that correspond to BioSQL available?
> > I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
> > is that the recommended ORM solution?
> >
> > Personally, I'd prefer a set of classes, with the suitable annotations
> > from the javax.persistence package applied (@Entity, @Id etc.) to match
> > the BioSQL tables.
> >
> > Apparently there have been initiatives in this direction (e.g. [3]), has
> > any of these made it into mainstream BioJava? If not, why not?
> >
> > Best regards, Jan
> >
> > [1] http://biojava.org/wiki/BioJava:BioJavaXDocs
> > [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
> > [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
> > --
> >  +- Jan T. Kim -------------------------------------------------------+
> >  |             email: jttkim at gmail.com                                |
> >  |             WWW:   http://www.jtkim.dreamhosters.com/              |
> >  *-----=<  hierarchical systems are for files, not for humans  >=-----*
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*


From andreas at sdsc.edu  Wed Aug  8 03:08:35 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 7 Aug 2012 20:08:35 -0700
Subject: [Biojava-l] Are there EJB entities for BioSQL?
In-Reply-To: <20120806091003.GA3404@paxarchia.galaxy.uni>
References: <20120803124703.GB3415@paxarchia.galaxy.uni>
	<CALthepwCeEnot-RviEscZD4xLy4j--gDsf+ZmjhvmDYR+77GBw@mail.gmail.com>
	<20120806091003.GA3404@paxarchia.galaxy.uni>
Message-ID: <CALthepznaGXHsY4VRZ=JSeXqsGDrPZZbwwypdughPgBt_bWZcQ@mail.gmail.com>

Hi Jan,

that really depends on what you want to do. My first response based on
your comment would be to take a look at the Distributed Annotation
System and the various DAS clients. We can say more if you tell us a
bit more specific what your intention is.

Andreas


On Mon, Aug 6, 2012 at 2:10 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> Hi Andreas and All,
>
> On Fri, Aug 03, 2012 at 02:21:01PM -0700, Andreas Prlic wrote:
>> Hi Jan,
>>
>> There is no biosql ORM mapping for biojava 3 currently. If you need
>> something like that you would need to use biojava 1 or patch biojava
>> 3...
>
> ok -- so is there any general suggestion / recommendation / best
> practice for building applications that involve handling annotated
> sequence data and a web UI?
>
> Best regards, Jan
>
>
>> Andreas
>>
>>
>>
>> On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <jttkim at googlemail.com> wrote:
>> > Dear All,
>> >
>> > is there a set of EJB 3 entities that correspond to BioSQL available?
>> > I've noticed that there are is a Hibernate mapping in biojavax [1, 2] --
>> > is that the recommended ORM solution?
>> >
>> > Personally, I'd prefer a set of classes, with the suitable annotations
>> > from the javax.persistence package applied (@Entity, @Id etc.) to match
>> > the BioSQL tables.
>> >
>> > Apparently there have been initiatives in this direction (e.g. [3]), has
>> > any of these made it into mainstream BioJava? If not, why not?
>> >
>> > Best regards, Jan
>> >
>> > [1] http://biojava.org/wiki/BioJava:BioJavaXDocs
>> > [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM
>> > [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html
>> > --
>> >  +- Jan T. Kim -------------------------------------------------------+
>> >  |             email: jttkim at gmail.com                                |
>> >  |             WWW:   http://www.jtkim.dreamhosters.com/              |
>> >  *-----=<  hierarchical systems are for files, not for humans  >=-----*
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
>  +- Jan T. Kim -------------------------------------------------------+
>  |             email: jttkim at gmail.com                                |
>  |             WWW:   http://www.jtkim.dreamhosters.com/              |
>  *-----=<  hierarchical systems are for files, not for humans  >=-----*
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From sbliven at ucsd.edu  Wed Aug  8 08:03:26 2012
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 8 Aug 2012 01:03:26 -0700
Subject: [Biojava-l] should biojava svn be moved to github ?
In-Reply-To: <CA+P6ar=GUcPf9=Rm=0fSrXrykm2ObtvQjk2QBSNkLkw+sJnaew@mail.gmail.com>
References: <CALthepwubGmyu1wApqB=C9QytQKtk0-G3WwU0ZDYvdGnDRcqnw@mail.gmail.com>
	<CAPXi2mkRnxSDpxEFFt=GkEyz=+j7h+=4Cp5aUUXUKeW_twx7fg@mail.gmail.com>
	<18F721FE-ECF0-4D82-9A52-9983A06FC92D@gmail.com>
	<CAOjYwMy0xz8yDi1QfvrFoaSFOs-hFZnmTqDOv6JHmFZ2a7qRVw@mail.gmail.com>
	<CALthepzYwkCj3uCex-5EQ1ns3+c73BXZQGbr2fBNqjJfCWHmXA@mail.gmail.com>
	<CAOjYwMyR=Xu4F_QQbpXdqkRxUTSku7UDfKfeD4E0NaRUay-=dA@mail.gmail.com>
	<CA+P6ar=GUcPf9=Rm=0fSrXrykm2ObtvQjk2QBSNkLkw+sJnaew@mail.gmail.com>
Message-ID: <CA+P6arnDu81eYWTc_BT5T+0saZqArvXFcHjQ3FEXOZS0UCXHOw@mail.gmail.com>

I thought people here might be interested to know that Rosetta is currently
switching from SVN to GIT. They have a pretty complicated build
configuration, but GIT seems up to the challenge. They had an interesting
list of benefits drafted on the internal Baker
wiki<http://docu.bakerlab.org/doku.php?id=proposed_changes:switch_to_git>I
thought would be interesting to share:

End User ( You only use the binaries)

   - Your database version will always match the binary version ( so no
   more segfaults because your database is different)
   - You can switch to other people's patched databases easily!

 Infrequent Developers( A commit every so often )

   - Everything from End User applies
   - You can update every day *SAFELY*
   - You can work locally, and never actually commit your changes if you
   don't want to ( but still benefit from having version control, rollbacks,
   etc.)
   - You benefit from other people's uncommited changes( see below )
   - Committing your small change is much easier because you don't
*MERGE*with trunk, you
   *PATCH **ON TOP* of trunk
   - Workflow stays pretty much the same

 Frequent Developers

   - Everything from Infrequent Developers applies
   - You can create many local branches, one for each feature or bugfix
   - When you commit, you commit a whole branch at a time, which makes
      reading history very easy
       - You can update your local branch on *TOP* of the trunk
   - By applying your local branch as a series of patches, conflict
      resolution is MUCH easier (no enormous merge conflict resolutions)
       - Everyone's local branch is completely visible to you, allowing you
   to share uncommited changes very easily
   - Workflow changes quite a bit, but for the better

 Repository Manager

   - Other than setting up initial users, you don't have to do anything
   - Automated testing handles rejections of commits


Cheers,

Spencer



On Fri, Aug 3, 2012 at 8:54 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>
> I'm all for it, provided (as others have mentioned)
>
> Eclipse support is now good enough for day-to-day stuff (maybe falling
back to command line for complicated merges and branches)
> It integrates with Maven for releases
>
> I was also slightly concerned with the overhead of storing the full git
repository. Surprisingly, a git checkout doesn't have that much more
overhead than a SVN checkout, despite storing full histories for each file.
>
> Biojava trunk checkout
> Bare files: 29MB
> SVN checkout: 60MB (107% overhead)
> GIT checkout: 74MB (155% overhead)
>
> However, GIT did take substantially longer to download from github than
SVN took from the biojava server. Since server speeds likely differ
significantly, that's not apples-to-apples, but it might be realistic.
>
> SVN checkout: 1m9.333s
> GIT checkout: 4m50.871s
>
> Overall I'm in favor of making the switch.
>
> -Spencer
>
>
>
>
> On Fri, Aug 3, 2012 at 4:11 PM, Michael Heuer <heuermh at gmail.com> wrote:
>>
>> Thanks, Andreas, that is a good document.
>>
>> One problem we might face is that some of the repository operations
>> are performed by the maven release plugin itself and then we're at the
>> mercy of the implementers of that plugin to have done it correctly.
>>
>>    michael
>>
>>
>> On Fri, Aug 3, 2012 at 6:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > Hi Michael,
>> >
>> > About the question how to cut a release from a distributed repository:
>> > I found this article an interesting read:
>> >
>> > http://nvie.com/posts/a-successful-git-branching-model/
>> >
>> > Andreas
>> >
>> >
>> > On Fri, Aug 3, 2012 at 8:57 AM, Michael Heuer <heuermh at gmail.com>
wrote:
>> >> -0
>> >>
>> >> I use github for quite a few personal things and mercurial via Google
>> >> Code on a different project and while I think there are some benefits
>> >> to the distributed model I don't understand how it would work from the
>> >> point of view of a release manager.  Does anyone have any pointers to
>> >> documentation on how to manage and cut a release from a distributed
>> >> repository?
>> >>
>> >> With the current svn mirror on github, developers can already fork and
>> >> create pull requests, they just need to be applied back to the svn
>> >> repository.  Is there any advantage to moving the repository to
>> >> github?  Are there any people who will start contributing because the
>> >> repository is on github that are unwilling to do so with the current
>> >> model (send patches to the mailing list or issue tracker)?
>> >>
>> >> My current client just started a new project on Google Code and we had
>> >> a similar conversation:  subversion on Google Code vs. git/mercurial
>> >> on Google Code vs. git at github vs. subversion on Google Code + read
>> >> only git mirror at github vs. subversion on Google Code + read/write
>> >> git mirror at github.  In the end we went with subversion on Google
>> >> Code with possibility of git mirror later because we understand how
>> >> the Maven release process works with subversion and we liked the issue
>> >> tracker at Google Code a lot better than the one at github.
>> >>
>> >>    michael
>> >>
>> >>
>> >> On Thu, Aug 2, 2012 at 11:14 PM,  <daniel.quest at gmail.com> wrote:
>> >>> Github ==awesome.
>> >>> Go for it and let the social coding begin
>> >>>
>> >>> Dan
>> >>>
>> >>> Sent from my iPhone
>> >>>
>> >>> On Aug 2, 2012, at 10:11 PM, Hannes Brandst?tter-M?ller<
biojava at hannes.oib.com> wrote:
>> >>>
>> >>>> On Fri, Aug 3, 2012 at 1:52 AM, Andreas Prlic <andreas at sdsc.edu>
wrote:
>> >>>>> Hi,
>> >>>>>
>> >>>>> I was wondering how people feel about migrating the BioJava  svn
>> >>>>> repository and starting to use github for the trunk development?
>> >>>>> (Currently github is only a read-only copy of our developer svn).
>> >>>>>
>> >>>>> Any opinions?
>> >>>>>
>> >>>>> Andreas
>> >>>>
>> >>>> I'm in favor - git pull requests make submitting patches so much
easier, IMHO.
>> >>>>
>> >>>> Hannes
>> >>
>> >> _______________________________________________
>> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From andreas at sdsc.edu  Fri Aug 10 15:46:50 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 10 Aug 2012 08:46:50 -0700
Subject: [Biojava-l] new BioJava paper published
Message-ID: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>

Hi,

I am pleased to announce that the latest BioJava paper describing the
version 3 series has been published and is now available online.

Thanks to all developers for their contributions, it would not have
been possible without them!

Andreas


Abstract:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

PDF:

http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

Citation:

BioJava: an open-source framework for bioinformatics in 2012

Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis

Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494


From power3d at gmail.com  Fri Aug 10 16:47:27 2012
From: power3d at gmail.com (Tony Power)
Date: Fri, 10 Aug 2012 17:47:27 +0100
Subject: [Biojava-l] new BioJava paper published
In-Reply-To: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>
References: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>
Message-ID: <CAMNg4HjufdC6dXVZZVKcXWJqAOfZPR9r=e2YF0eNdBQvJE32OA@mail.gmail.com>

Congratulations.

Tony

On Fri, Aug 10, 2012 at 4:46 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> I am pleased to announce that the latest BioJava paper describing the
> version 3 series has been published and is now available online.
>
> Thanks to all developers for their contributions, it would not have
> been possible without them!
>
> Andreas
>
>
> Abstract:
>
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref
>
> PDF:
>
> http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref
>
> Citation:
>
> BioJava: an open-source framework for bioinformatics in 2012
>
> Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
> Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
> Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
> Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
>
> Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From jprocter at compbio.dundee.ac.uk  Mon Aug 13 07:34:19 2012
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Mon, 13 Aug 2012 08:34:19 +0100
Subject: [Biojava-l] [Biojava-dev]  new BioJava paper published
In-Reply-To: <CAMNg4HjufdC6dXVZZVKcXWJqAOfZPR9r=e2YF0eNdBQvJE32OA@mail.gmail.com>
References: <CALthepyG--cKLZHtZJNeHYSQorqxN8=M4bVAftvJy8DTiPEFEg@mail.gmail.com>
	<CAMNg4HjufdC6dXVZZVKcXWJqAOfZPR9r=e2YF0eNdBQvJE32OA@mail.gmail.com>
Message-ID: <5028ADFB.5010906@compbio.dundee.ac.uk>

Hi bj3 developers!

> On Fri, Aug 10, 2012 at 4:46 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi,
>>
>> I am pleased to announce that the latest BioJava paper describing the
>> version 3 series has been published and is now available online.
>>
>> Thanks to all developers for their contributions, it would not have
>> been possible without them!

And I must say, it is really nice to see v3 in print .. you should all 
be proud!

Jim.




From ralf at ark.in-berlin.de  Wed Aug 29 07:38:20 2012
From: ralf at ark.in-berlin.de (ralf at ark.in-berlin.de)
Date: Wed, 29 Aug 2012 09:38:20 +0200
Subject: [Biojava-l] issues with mailman
In-Reply-To: <20120824165821.GA3008@ark.in-berlin.de>
References: <20120824165821.GA3008@ark.in-berlin.de>
Message-ID: <20120829073820.GB2440@ark.in-berlin.de>

Hello,
it appears mailman won't send password reminders,
also Noscript complained about a "potential cross-site
scripting (XSS) attempt from http://biojava.org"...
When trying to subscribe it complains about invalid email,
and finally, two mails to this list have not appeared
in one of the moderator's mailbox.

So, there appears to be something wrong...

Thanks to Andreas for subscribing me manually.




From ralf at ark.in-berlin.de  Wed Aug 29 08:21:41 2012
From: ralf at ark.in-berlin.de (ralf at ark.in-berlin.de)
Date: Wed, 29 Aug 2012 10:21:41 +0200
Subject: [Biojava-l] issues with mailman
In-Reply-To: <CAKVJ-_6o+kfXtFyWfEnMvLbA40QyM87VbaB7UXjn4dcZidc_NA@mail.gmail.com>
References: <20120824165821.GA3008@ark.in-berlin.de>
	<20120829073820.GB2440@ark.in-berlin.de>
	<CAKVJ-_6o+kfXtFyWfEnMvLbA40QyM87VbaB7UXjn4dcZidc_NA@mail.gmail.com>
Message-ID: <20120829082141.GA2659@ark.in-berlin.de>

On Wed, Aug 29, 2012 at 09:00:00AM +0100, Peter Cock wrote:
> On Wednesday, August 29, 2012, wrote:
> > also Noscript complained about a "potential cross-site
> > scripting (XSS) attempt from http://biojava.org"...
> 
> Was that from an open-bio.org URL? It is actually
> the same server for BioJava.org so I can imagine
> how an apparent cross-site scripting attempt
> might happen.

The offending page: 
http://lists.open-bio.org/mailman/options/biojava-l

Details:
[NoScript XSS] Sanitized suspicious upload to
[http://lists.open-bio.org/mailman/options/biojava-l] from
[http://www.biojava.org/mailman/listinfo/biojava-l]: transformed into a
download-only GET request.

If this is a Noscript bug, give me a hint, I have no idea
about such things.


ralf



From p.j.a.cock at googlemail.com  Wed Aug 29 08:44:19 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Aug 2012 09:44:19 +0100
Subject: [Biojava-l] issues with mailman
In-Reply-To: <20120829082141.GA2659@ark.in-berlin.de>
References: <20120824165821.GA3008@ark.in-berlin.de>
	<20120829073820.GB2440@ark.in-berlin.de>
	<CAKVJ-_6o+kfXtFyWfEnMvLbA40QyM87VbaB7UXjn4dcZidc_NA@mail.gmail.com>
	<20120829082141.GA2659@ark.in-berlin.de>
Message-ID: <CAKVJ-_4R+=WXm3e79WTEAW38Ts3bvabj+vazt-nFZtZegcxa3w@mail.gmail.com>

On Wed, Aug 29, 2012 at 9:21 AM, ralf at ark.in-berlin.de
<ralf at ark.in-berlin.de> wrote:
> On Wed, Aug 29, 2012 at 09:00:00AM +0100, Peter Cock wrote:
>> On Wednesday, August 29, 2012, wrote:
>> > also Noscript complained about a "potential cross-site
>> > scripting (XSS) attempt from http://biojava.org"...
>>
>> Was that from an open-bio.org URL? It is actually
>> the same server for BioJava.org so I can imagine
>> how an apparent cross-site scripting attempt
>> might happen.
>
> The offending page:
> http://lists.open-bio.org/mailman/options/biojava-l
>
> Details:
> [NoScript XSS] Sanitized suspicious upload to
> [http://lists.open-bio.org/mailman/options/biojava-l] from
> [http://www.biojava.org/mailman/listinfo/biojava-l]: transformed into a
> download-only GET request.
>
> If this is a Noscript bug, give me a hint, I have no idea
> about such things.
>
> ralf

I think it is harmless, notice both these URLs work:
http://www.biojava.org/mailman/options/biojava-l
http://lists.open-bio.org/mailman/options/biojava-l
but they both submit the form to lists.open-bio.org.

So technically the Noscript warning is correct - if
you use the www.biojava.org address it is sending
the information to lists.open-bio.org (both are OBF
servers, although under different domain names).

Similarly you can send send to this mailing list as
biojava-l at lists.open-bio.org or biojava-l at biojava.org

Peter