[Owl-devel] Major refactoring of the package structure of OWL

[Henning Stehr]

Dear Developers,

as announced in my previous email, we have done a major refactoring of
the OWL package structure.
Details about the changes are listed below. You will likely have to
update all projects with references
to OWL. If you encounter any problems, please report them to the list.
In the worst case, you can go back to the
tag owl-1.2.0 which has been created in SVN just before the refactoring.

Henning

----

The package structure before refactoring:

src
|-- actionTools
|-- casp
| |-- benchmarking
| |-- pipeline
| `-- tools
|-- connections
|-- deltaRank
|-- embed
| `-- contactmaps
|-- features
|-- graphAveraging
|-- litNet
|-- ppi
|-- proteinstructure
| `-- decoyScoring
|-- runners
|-- sadp
|-- sequence
|-- tests
| |-- proteinstructure
| | `-- data
| |-- sequence
| |-- tinker
| `-- tools
|-- tinker
`-- tools

----

The changes that have been made:

Major changes:

    * created a package 'owl' which is now the root of all other
packages, i.e. owl.casp
    * created a package 'owl.core' to contain all core packages,
           - i.e. those which are more general purpose and which will
likely be used by many projects
           - in contrast to those which can be considered special
purpose packages or separate projects, such as casp, decoyScoring,
etc.

Minor changes:

    * created a subpackage owl.runners.blast and moved all Blast
related stuff there (from sequence)
    * moved GTG related classes from sequence to owl.core.connections
    * moved owl.tinker to owl.runners.tinker and created
owl.runners.gromacs for gromacs stuff
    * created a subpackage proteinstructure.graphs and moved all RIG
and AIG related stuff there
    * moved owl.proteinstructure.decoyScoring to owl.decoyScoring
    * moved actionTools to util.actionTools
    * moved all SomethingRunner classes from owl.proteinstructure and
owl.sequence to owl.runners
    * moved connection type classes from owl.core.structure to
owl.core.connections
    * moved alignment related classes from owl.core.structure to new
packages owl.core.sequence.alignment and owl.core.structure.alignment
    * moved feature type classes from owl.core.structure (which are
not yet implemented using our feature system) to new package
owl.core.structure.features
    * moved general prupose classes from owl.core.structure to to owl.core.util
    * adapted package structure in tests to new package structure

Name changes:

    * renamed package 'proteinstructure' to 'structure'
    * renamed package 'tools' to 'util'
    * renamed several classes to make the name more self-explanatory,
e.g. Alignment -> MultipleSequenceAlignment

----

The new package structure after refactoring:

src
`-- owl
    |-- casp
    |   |-- benchmarking
    |   |-- pipeline
    |   `-- tools
    |-- core
    |   |-- connections
    |   |-- features
    |   |-- runners
    |   |   |-- blast
    |   |   |-- gromacs
    |   |   `-- tinker
    |   |-- sequence
    |   |   `-- alignment
    |   |-- structure
    |   |   |-- alignment
    |   |   |-- features
    |   |   `-- graphs
    |   `-- util
    |       `-- actionTools
    |-- decoyScoring
    |-- deltaRank
    |-- embed
    |   `-- contactmaps
    |-- graphAveraging
    |-- litNet
    |-- ppi
    |-- sadp
    `-- tests
        `-- core
            |-- runners
            |   |-- blast
            |   `-- tinker
            |-- structure
            |   `-- data
            `-- util