[Biojava-dev] BioJava3 on Maven Central?

Tue May 10 08:34:37 UTC 2011

I have put 'biojava3-core-3.0' on central as a third party bundle

http://search.maven.org/#search|ga|1|biojava

I added a 'developers' element to the pom to make it clear that you were the originators, and that I had merely put it up as 3rd party (sonatype upload requires a developers element anyway...)  

I needed this single artifact available to allow me to publish our own Jensembl code which depends on core, and core itself has no further third party dependencies

I used the older 3.0 artifact so that there would be no conflict snafus if biojava decide to publish 3.1 to central

Trevor Paterson PhD
trevor.paterson at roslin.ed.ac.uk <mailto:trevor.paterson at roslin.ed.ac.uk> 

Bioinformatics 
The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
Midlothian
EH25 9RG
Scotland UK

phone +44 (0)131 651 9157

http://bioinformatics.roslin.ed.ac.uk/ <http://bioinformatics.roslin.ed.ac.uk/> 

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________________________________

From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: 10 May 2011 00:04
To: Michael Heuer
Cc: PATERSON Trevor; biojava-dev; LAW Andy
Subject: Re: [Biojava-dev] BioJava3 on Maven Central?

Hi Michael, 

you are probably one of the biggest Maven experts on the list, would you like to take on the project to get BioJava set up on Maven Central? I believe you already did it once for one of the 1.X versions...

That would be great help...

Andreas

On Sun, May 8, 2011 at 9:07 PM, Michael Heuer <heuermh at acm.org> wrote:

	I think we need to try (again) to push our external dependencies to
	publish to Maven Central so that we can in turn, or remove or replace
	those external dependencies if that is not possible.

	Sonatype will explicitly not allow option 1) below, see

	https://docs.sonatype.org/display/Repository/Sonatype+OSS+Maven+Repository+Usage+Guide#SonatypeOSSMavenRepositoryUsageGuide-6.CentralSyncRequirement

	and I can't imagine Apache would allow the rsync option from the biojava
	repository, as they aren't really supporting that any more.

	  michael

	On Thu, 5 May 2011, Andreas Prlic wrote:

	> Hi Trevor,
	>
	> I guess in principle we would like to have all of BioJava  in Maven
	> central, however as you already know there is the issue with the
	> external dependencies...
	>
	> Not all of the modules have external dependencies. However I am not
	> sure how helpful a partial upload of BioJava would be, containing only
	> a sub-set of the available libraries...
	>
	> Andreas
	>
	>
	>
	>
	> On Thu, May 5, 2011 at 7:08 AM, PATERSON Trevor
	> <trevor.paterson at roslin.ed.ac.uk> wrote:
	> > Hi guys
	> >
	> > We are keen to publish our JEnsembl artifacts on Maven Central, and our JEnsembl code depends on the biojava3-core artifact.
	> >
	> > (see http://jensembl.sourceforge.net/).
	> >
	> > Central now strongly discourage referring to external repositories (like biojava) because there is no guarantee of permanence.
	> >
	> > (see http://www.sonatype.com/people/2010/03/why-external-repos-are-being-phased-out-of-central/).
	> >
	> > I know that external dependencies were a snafu last time publishing biojava on Central was discussed - is that still the case?
	> >
	> > Unless you have considered again publishing to Central, if we do go ahead with publishing JEnsembl on Central we will have to either
	> >
	> > 1. ignore Central's recommendations and include the reference to the biojava repository (if they let us get away with that)
	> >
	> > or
	> >
	> > 2. upload biojava3-core to Central  ourselves, as an external dependency
	> >
	> > (see https://docs.sonatype.org/display/Repository/Uploading+3rd-party+Artifacts+to+Maven+Central).
	> >
	> > this would involve bundling up and signing the pom/binary/source and javdoc artifacts and uploading through Sonatype.
	> > (NB biojava yourself wouldn't be allowed to do this as you are not 3rd party!)
	> >
	> > My personal preference would be option 1, as option 2 seems a bit 'cheeky' aswell as redundant and smelly,
	> > and personally I have no concerns about the reliability of the biojava repo in the medium term.
	> >
	> > However Maven central documents seem to be really heavily against this....
	> >
	> > what are your thought on this?
	> >
	> > The Maven etiquette on uploading 3rd party dependencies suggests that the first step is confirming whether you have any plans to upload to Central....
	> >
	> > cheers
	> > trevor
	> >
	> >
	> >
	> > Trevor Paterson PhD
	> > trevor.paterson at roslin.ed.ac.uk<mailto:trevor.paterson at roslin.ed.ac.uk>
	> >
	> > Bioinformatics
	> > The Roslin Institute
	> > Royal (Dick) School of Veterinary Studies
	> > University of Edinburgh
	> > Easter Bush
	> > Midlothian
	> > EH25 9RG
	> > Scotland UK
	> >
	> > phone +44 (0)131 651 9157 <tel:%2B44%20%280%29131%20651%209157> 
	> >
	> > http://bioinformatics.roslin.ed.ac.uk/
	> >
	> > Please consider the environment before printing this e-mail
	> >
	> > The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336
	> > Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.
	> >
	> >
	> >
	> > The University of Edinburgh is a charitable body, registered in
	> > Scotland, with registration number SC005336.
	> >
	> > _______________________________________________
	> > biojava-dev mailing list
	> > biojava-dev at lists.open-bio.org
	> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
	> >
	> >
	>
	>
	>
	> --
	> -----------------------------------------------------------------------
	> Dr. Andreas Prlic
	> Senior Scientist, RCSB PDB Protein Data Bank
	> University of California, San Diego
	> (+1) 858.246.0526 <tel:%28%2B1%29%20858.246.0526> 
	> -----------------------------------------------------------------------
	>
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	>

-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.