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)

v2.5.3

Key changes

• Introduce a new CWL parser and related classes to support APE semantic annotations embedded into the CWL files.
• Bugfixes (#112 and #119)
• Bump commons-lang3 to 3.19.0

Summary

This release mainly refactors and extends the CWL support of APE. It includes improving error handling and allowing for the use of arbitrary CWL keys in input/output descriptions. Also, the tests and documentations were updated to reflect these changes.
Apart from this, minor improvements as small bugfixes and dependeny updates were part of this release.

v2.4.0

Key changes

• 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 (see documentation. The previous interface only allowed workflow synthesis (now using the command synthesis).
• Included more constraint templates
• Migrate to Java 17

Summary

This release refactors the bio.tools API, now accessible at the CLI level for generating APE annotations, and introduces two new constraint templates for workflow generation, used in the Workflomics project. The update also includes migrating the codebase to Java 17, improved APE documentation and GitHub templates for easier PR and Issue creation. Additionally, the constraint templates are now explicitly encoded in CNF, with future plans to incorporate logical constructs.

v2.3.0

Release Notes

Overview

This release introduces significant enhancements to our project's integration with the Common Workflow Language (CWL), aimed at improving usability and maintainability. Key updates include changes to CWL support, codebase refactor, security updates, and documentation improvements.

Changes

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.

PRs

• Update SECURITY.md by @vedran-kasalica in #102
• Small fixes by @vedran-kasalica in #103
• Improve CWL support + refactor by @vedran-kasalica in #108
• Update releases list by @vedran-kasalica in #105

Full Changelog: v2.2.6...v2.3.0

APE 2.2.6: Enhancements and Fixes by @vedran-kasalica

Summary

In the latest update (v2.2.6) of the APE repository, several changes were implemented by @vedran-kasalica. These include the creation of a SECURITY.md file (Pull Request #90), updates to the build process (Pull Request #91), and enhancements to badges (Pull Request #92). Additionally, a fair-software GitHub action was added, and badges were organized (Pull Request #93). The changes also involved fixing fair-software badge issues (Pull Request #96), improving workflow figures (Pull Request #97), enhancing API methods (Pull Request #99), refining figure styling (Pull Request #100), and addressing test-related issues (Pull Request #101). For a detailed overview, the full changelog is available here.

Full Changelog: v.2.2.0...v2.2.6

Code refactor and Taverna style workflow outputs

Summary

Code was refactored (new interfaces were added and the existing structure was improved), the library now supports generating workflows in a format similar to the Apache Taverna (workflow management) workflows and Citation.cff file formatting was fixed and updated.

For developers

While the interface has remained unchanged, structure of the code was improved, therefore, you might have to update the paths in your APE imports (e.g., package parser was renamed to parserSLTLx, sat_impl to minisat etc.).

What's Changed

• Fix citation.cff formatting by @vedran-kasalica in #85
• Refactor code and implement the Taverna style workflow outputs by @vedran-kasalica in #86
• Fix Javadoc error by @vedran-kasalica in #87
• Update CITATION.cff by @vedran-kasalica in #88
• Update README.md - remove a badge by @vedran-kasalica in #89

Full Changelog: v2.1.8...v.2.2.0

Improved CWL generation and code refactor

What's Changed

• Create codeql.yml by @vedran-kasalica in #71
• Update constraint formats and annotation labels by @vedran-kasalica in #72
• Introduce constraints APERunConfig tag & refactor by @vedran-kasalica in #73
• Update version by @vedran-kasalica in #74
• Update README.md by @vedran-kasalica in #76
• Fix build badge by @vedran-kasalica in #77
• CWL fixes and dependencies update by @vedran-kasalica in #78
• Create CITATION.cff by @vedran-kasalica in #81

Full Changelog: v2.1.5...v2.1.7

APE 2.1.5 - Support executable CWL outputs

The release introduces:

• 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

Improvements:

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