Issue-Ref: 3620
Issue-Url: https://af3-developer.fortiss.org/issues/3620



Signed-off-by: Simon Barner <barner@fortiss.org>

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* Adds a injector/binder analyzer that allows to query which phenotypes
  are affected by Genotype modifications.
* Create a Holder for Phenotypes that may be preserved.
* Add preserved phenotypes to the decoding cache before launching the
  actual decoding.
* Update Opt4J to enable tracking of modified genotypes.
* Correct the crossover and mutate module for the ProvidingPhenotype.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

Also move all opt4j libs in a separate folder.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* Otherwise, the genotypes of already evaluated Individuals are altered.
* Remove copy operations from crossover operators.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* The operator selection is now embedded in the Opt4J framework, so
  remove all code in this plugin related to that feature.
* The previous implementation was buggy such that multiple operators
  could be bound to one genotype, but only one of them was executed per
  exploration run (random selection).
* Fixing these issues in this plugin would have been a suboptimal
  solution since the required selection logic would need to be
  duplicated in each module binding multiple operators.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* Switch the ExplorationEvaluationService to not rely on eclipse
  extension points but use java registration methods. This service has
  now a close relation to the ExplorationFeatureService that holds all
  ExplorationModules.
  Additional information and logic required for evaluation is found in
  the ExplorationEvaluationService.
* Register the MappingEvaluatorObjective for DSML Expressions and the
  EvaluatorModules specific for the ParitionExploration.
* Add the @Provides annotation to each evaluation function such that
  their method parameters are automatically injected by Guice.
* Extract the parsing of IExpressions to parsers which are called from
  the corresponding IExplorationModules.
* Provisioning interception:
  * Generalize the DecodingInterceptor into a ProvisionInterceptor such
    that it can be used for the create phase as well. Along, make the
    update mechanism via sub-modules providing same types optional (used
    only in the decode phase).
  * Add an Interceptor module such that already created Genotypes can be
    provided to other create methods that depend upon them. This avoids
    launching the create method for the same time several times, causing
    inconsistencies between the Genotypes.
  * Add a @Creates annotation for method interception binding.
* Add additionally required @Provides annotation in the
  SystemModelAdaper.
* Create a TaskMapper that encapsulates the Task -> ITaskAdapter
  associations. It is used, for instance, in the evaluators where the
  ExplorationTargets are defined on AF3 elements whereas the DSE
  internally works on reduced elements.
* Remove the non-used cglib library.
* Add the ByteBuddy library (v1.8.17) to be able to generate code at
  runtime. It is used to generate Provider Classes (using @Provides
  methods) that are supplied to the injectors of follow up phases (e.g.,
  decode -> evaluate) such that previous results are available to these
  injectors.
* NOTE / IMPORTANT: This commit leaves several outdated and (now) unused
  classes in place. They will be removed in follow up commits.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* Update Guice to a self-compile version that allows overriding
  @Provides methods.
* Create an "@PluginDecoder" annotation along with a MethodInterceptor
  that intercepts such annotated decode methods. It launches all decode
  methods that provide the same phenotype prior to executing itself
  (sub-decoding). These sub-decoders are providing updates to the
  phenotype before the actual decoding is executed.
  NOTE: Sub-decoder methods must be annotated with the "@Named("XYZ")"
  key where XYZ is the class name of the decoder. This is required to
  avoid @Provides methods that would return the same type.
* Re-create the DecoderModules by the Guice Injector before passing them
  to the GuiceDecoder such that Method Interceptors can be installed
  before the GuiceDecoder is instantiated.
* Correct the integration of the PlatformCommunicationGraphEncoding.
* Add more required @Provides Methods to the SystemModelAdapter.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

Issue-Ref: 3478
Issue-Url: https://af3-developer.fortiss.org/issues/3478



Signed-off-by: Simon Barner <barner@fortiss.org>

- Remove private copy of JGraphT 0.9.0
- Use JGraph 1.2.0 copy exported by af3.exploration
- Port source code, e.g.
  - moved packages
  - DirectedGraph -> DefaultDirectedGraph
  - CycleFoundException -> IllegalArgumentException
  - DirectedSubgraph -> MaskSubgraph

Issue-Ref: 3478
Issue-Url: https://af3-developer.fortiss.org/issues/3478



Signed-off-by: Simon Barner <barner@fortiss.org>

* Self-build version that allows to embed the opt4j injector as a child
  injector.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* Enables to build provisioning modules that do not implement empty
  configuration() methods.
* Additional bug fixes.
* Also update Guava to version 25.1 due to deps from guice.

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

Signed-off-by: Alexander Diewald <diewald@fortiss.org>

* Exploration.alg:
  * Register the .alg plugin via an IStattup extension to avoid dependencies on this plugin.
  * Create a objective and a constraint evaluator that can handle DSML expressions.
  * Adjust the opt4j extensions.
  * Temporally introduce the MappingEncoding marker interface to support the DSML evaluators (--> allocation expressions).
  * Fix some minor bugs and warnings.
  * Move the porting utils to the alg plugin (previously in alg.ui).
  * Move the plot code to the alg plugin (previously in alg.ui) until the transition to the AF3 visualization framework is finished.
* Exploration.smt:
  * Create a backend implementation for the smt-based exploration.
  * Minor adjustments (I/O) to comply with the backend mechanism.
* Exploration:
  * Package renaming of the DSE backend mechanism.
  * Make the DSE backend mechanism independent of the eclipse extension mechanism.
  * Integrate the Exploration solution Classes in the EMF model.
  * Minor adjustments of the DSE backend API.
* Exploration.ui:
  * Add a combobox to select the DSE backend for the Deployment synthesis
  * Adjust the GUI backends to comply with the DSE backend interfaces.
refs 2939

Please fix your SVN configurations!

See https://af3-developer.fortiss.org/projects/autofocus3/wiki/Developer_Installation, Section "Initial Workspace Content Check-out", §6.