[Owl-devel] suggestions for updating the package structure in OWL

Jose M. Duarte jose.m.duarte at gmail.com
Fri Mar 19 10:07:43 EDT 2010

Well that sounds like a very reasonable plan. I especially like the idea of
having a core package and project packages, that will hopefully make things
a lot clearer.

And I would say it's better doing this soon rather than waiting to do it
when it might be too difficult.

One thing I'd add to that if we are going to rearrange things is to also use
the standard java layout with the DNS name as unique identifier. I've just
checked and (surprisingly!) the owl.org domain is not taken! So I'm
considering getting it. So basically we could name things org.owl.package
(which is still a nice short name). Well now that I see Dan's email it's
true that OWL is an acronym that is very likely to have been used a lot
(even in a dyslexic way ;-) ). As he points out it is already in use in the
bioinformatics context. Well I would say it is still ok, we knew that we had
chosen a very popular name anyway...

One important question to ask before rearranging things is which external
code do we want to keep up-to-date and linked to the latest development
version of the library and which one we can consider "frozen" so that
there's no need to update it (it will still be able to run with older
tags/branches but not with the trunk). For sure CMView should be kept
up-to-date. Any others?


On 19 March 2010 11:13, Henning Stehr <stehr at molgen.mpg.de> wrote:

> Dear developers,
> since we are currently rearranging some stuff in OWL which always
> makes it necessary to
> update imports and calls in other projects, maybe its a good time to
> think about the package
> structure in general to make OWL fit for the future.
> So here are some suggestions for changes to the package structure in OWL:
> Minor changes:
> - move all SomethingRunner classes from owl.proteinstructure and
> owl.sequence to owl.runners
> - create a subpackage owl.runners.blast and move all Blast related stuff
> there
> - move owl.tinker to owl.runners.tinker and create owl.runners.gromacs
> for gromacs stuff
> - create a subpackage proteinstructure.graphs and move all RIG and AIG
> related stuff there
> - maybe create proteinstructure.graphs.rigs and
> proteinstructure.graphs.aigs
> Major changes:
> - make a root package 'owl' and move everything there, i.e.
> owl.proteinstructure, owl.sequence, ...
>  this would be clearer and prevent name conflicts with other
> libraries which may also contain e.g. a 'sequence' package
> - currently there are two types of packages:
>  1. those containing collections of basic classes such as sequence,
> proteinstructure, features, connections, runners and
>  2. those containing essentially independent projects such as casp,
> deltaRank, embed, sadp.
>  Suggestion: Create a package owl.core and move all packages from 1.
> there. The basic idea would be that 'core' should
> be stuff that is used by many projects and 2. stuff that is more for a
> specific usecase
> - if we do the above, owl.proteinstructure.decoyScoring should be
> moved to owl.decoyScoring
> As you can see some of these are more long term plans but maybe it's
> less painfull to do it all together so that hopefully
> the package structure can remain stable for a while.
> For the moment, I won't do anything, but what do you think about these
> changes? We can dicuss later when would be
> a good time to actually do it.
> Henning
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