CHANGELOG.md

APE 2.6.0 - Snakemake, Partial Workflows and Major Refactorings

• Maven Group change to org.workflomics
• Snakemake output support by @CGru21
• Added configuration for explicitly accepting or skipping partial outputs, i.e. outputs where the executed command is unknown by @eladrion
• Major refactoring
• Test resources improvements
• Markdown documentation updates (Releases, Maven Bundles, Security contacts, general contacts)

APE 2.5.3 - CWL Support Improvements, Bugfixes

• Introduce a new CWL parser and related classes to support APE semantic annotations embedded into the CWL files.
• Bugfixes in CNF handling output numbering
• Bump commons-lang3 to 3.19.0
• Documentation Updates

APE 2.4.0 - CLI Extensions, Template Enhancements

• CLI is extended. It now allows users to automatically convert tools from bioinformatics domain (specifically bio.tools), using methods: pull-a-tool, convert-tools and bio.tools (The previous interface only allowed workflow synthesis while we are now using the command synthesis).
• Included more constraint templates
• Migrate to Java 17

APE 2.3.0 - CWL Improvements and General Code Improvements

CWL Support Enhancements

• Removed full CWL implementation support within the annotation file due to maintainability challenges and insufficient examples.
• Introduced a cwl_reference field for direct linkage to CWL implementation files of tools, facilitating easier access and usability.

Code and Documentation Improvements

• Conducted a comprehensive refactor of the codebase, including improvements in naming conventions to enhance code clarity and quality.
• Updated the project's security guidelines to ensure compliance with current best practices.

Minor Fixes and Updates

• Implemented small fixes to address issues and improve overall functionality.
• Updated the releases list to keep users informed of new versions and available features.

APE 2.2.6 - General Enhancements

• Added SECURITY.md
• Build process updates
• Enhancements of Badges (e.g. fair-software)
• API methods improvements

APE 2.2.0 - Code refactor and Taverna style workflow outputs

• Fix CITATION.cff formatting and update the file
• Refactor code and implement the Taverna style workflow outputs
• Fix JavaDoc error
• Update README.md - remove a badge

APE 2.1.8 - Improved CWL generation and code refactor

• Create codeql.yml
• Update constraint formats and annotation labels
• Introduce constraints APERunConfig tag & refactor
• Update README.md
• Fix build badge
• CWL fixes and dependencies update
• Create CITATION.cff

APE 2.1.5 - Support executable CWL outputs

• Configuration files can be provided as URLs and can contain URLs
• CWL files are now executable
• CWL input file (.yml) is also provided
• Tests are improved
• Refactoring

APE 2.0.3 - Improved SLTLx Templates and direct encoding

• Added new NL templates for SLTLx
• Added encoding runtime message
• Fixed issue with cache of SLTLx specified constraints on synthesis re-run

APE 2.0.2 - New SLTLx Templates, added workflow output dependency

• Added new constraint templates
• Workflows no longer use provided inputs as outputs

APE 2.0.0 - Support for SLTLx

APE formalism is extended to support the SLTLx logic. The solving engine is still a SAT solver. The project is restructured and it includes a parser for the underlying logic. Problem constraints can now be specified using constraints as well as directly in SLTLx.

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