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

[Henning Stehr]

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