Bump to version 2.6

CHANGELOG.md

@@ -1,3 +1,92 @@
+### 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

CITATION.cff

@@ -7,8 +7,8 @@ type: software
 authors:
   - given-names: Vedran
     family-names: Kasalica
-    email: v.kasalica@esciencecenter.nl
-    affiliation: Netherlands eScience Center, Netherlands
+    email: vedran.kasalica@health-ri.nl
+    affiliation: Health-RI, Netherlands
     orcid: 'https://orcid.org/0000-0002-0097-1056'
   - given-names: Anna-Lena
     family-names: Lamprecht