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CHANGELOG.md

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APE 1.1.12 - log4j version fix Latest

  • Changed log4j version dependency to 2.17.0, due to security issues.
  • Updated other mvn dependencies

APE 1.1.11 - DOI release

  • Fix needed to obtain the DOI

APE 1.1.9 - Export abstract and executable CWL

  • Export abstract and executable CWL
  • Improved synthesis execution flags

APE 1.1.8 - Improved Class structure and naming

Improved class structure and naming to support extensions with additional solving techniques. The new structure allows for easy extensions with other (non-SAT) solvers.

APE 1.1.7 - Adding synthesis execution flags

  • Added synthesis execution flag (class SATsolutionsList)
  • Improved SolutionWorkflow class by adding methods for PNG retrieval of the workflows (e.g., getDataflowGraphPNG(..))

APE 1.1.5 - Adding long predicate labels

  • Added method PredicateLabel.getLongLabel()
  • Improved ModuleNode.getNodeFullLabel() method and renamed to ModuleNode.getNodeLongLabel()

APE 1.1.4 - Improving SolutionWorkflowNode (updated)

  • Introduced method SolutionWorkflowNode.getNodeFullLabel()
  • Improved method descriptions

APE 1.1.3 - Improved synthesis run handling

Implemented:

  • Cleaning temp files used for synthesis encoding after each SAT run
  • Introduced "timeout(sec)" configuration field

APE 1.1.2 - Constraint parsing fix

Parsing of constraints got fixed. The error occurred in case of defining constraints over concrete operations that are not part of the ontology.

APE 1.1.1 - Strict taxonomy hiararchy

Improvements:

  • Implemented stricter tool annotations and added the corresponding core configuration field (strict_tool_annotations)
  • Removed message passing approach
  • Improved APE API (added new methods and improved documentation)

APE 1.0.3 - Interface improvements

  • Provided interface for building constraints from JSON objects
  • Tested new functionalities
  • Improved constraint descriptions (ConstraintTemplate in ConstraintFactory)
  • Improved constraint printouts in debug mode

APE 1.0.2 - constraint improvements

  • Improved constraint formatting
  • Refactored interface for auxiliary predicated
  • Improved documentation and testing

The first stable version of APE 1.0.1

APE is a command line tool and Java API for the automated exploration of possible computational pipelines (scientific workflows) from large collections of computational tools.

The first stable version of the software includes:

  • APE-1.0.1.jar (the library jar)
  • APE-1.0.1-executable.jar (command line executable jar, that includes all the dependencies)
  • APE-1.0.1-javadoc.jar
  • APE-1.0.1-sources.jar