[Biojava-dev] next steps

[Richard Holland]

I found when creating modules for the testbed biojava3 that it was
easier to do it by hand.

Only two things need to be done - first of all a list of modules needs
to be added to the parent pom.xml of the project, then each module has
its own pom.xml referencing the parent pom.xml.

Once created this way it only takes a project refresh in
Eclipse/NetBeans for the new module to show up.

See the example pom.xmls under the old biojava3 branch for details.

cheers,
Richard

On Wed, 2009-05-27 at 21:31 -0700, Andreas Prlic wrote:
> Hi Scooter,
> 
> quick update: There is also an eclipse plugin for JDepend, that
> provides a user interface to browse thought the dependencies.
> 
> As I already mentioned earlier, I had some quick progress with the
> maven plugin to convert the project to maven and create a first pom.
> At the moment I am testing how  best to create  sub-projects that
> should contain the modules.  The plugin does not seem to make it easy
> to create new modules, so I agree with your earlier suggestion that it
> is best to modularize first and the mavenize 2nd... Should we create a
> branch in svn and play around with refactoring there and once we are
> happy with it we can switch that branch to become the trunk?
> 
> Andreas
> 
> 
> 
> 
> On Mon, May 25, 2009 at 3:59 PM, Scooter Willis <HWillis at scripps.edu> wrote:
> > I attached the JDepend output for BioJava. This will help on the circular
> > dependencies where core classes should not have dependencies on other
> > packages and if they do it should be refactored into the core class.
> >
> > Scooter
> > ________________________________
> > From: mike.smoot at gmail.com on behalf of Mike Smoot
> > Sent: Mon 5/25/2009 1:07 PM
> > To: Scooter Willis
> > Cc: Andreas Prlic; biojava-dev at lists.open-bio.org
> > Subject: Re: [Biojava-dev] next steps
> >
> >
> >
> > On Mon, May 25, 2009 at 7:48 AM, Scooter Willis <HWillis at scripps.edu> wrote:
> >>
> >> I was looking at the biojava code yesterday to see how easy it would be to
> >> divide up into functionally grouped jars based on package hierarchy. I tried
> >> to find some refactoring tools that would give a network graph view of class
> >> relationships. It is simple enough to parse source for import statements and
> >> build some sort of graph relationship tool. It is also easy enough to start
> >> dragging packages around to different projects in netbeans and resolve
> >> compiler errors.
> >
> > JDepend is a nice tool for evaluating package dependencies.
> >
> > http://www.clarkware.com/software/JDepend.html
> >
> >
> > Mike
> >
> > --
> > ____________________________________________________________
> > Michael Smoot, Ph.D.               Bioengineering Department
> > tel: 858-822-4756         University of California San Diego
> >
> 
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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/