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Recent Releases of io.github.sanctuuary

io.github.sanctuuary - 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.

- Java
Published by vedran-kasalica over 1 year ago

io.github.sanctuuary - 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 https://github.com/sanctuuary/APE/pull/102
  • Small fixes by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/103
  • Improve CWL support + refactor by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/108
  • Update releases list by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/105

Full Changelog: https://github.com/sanctuuary/APE/compare/v2.2.6...v2.3.0

- Java
Published by vedran-kasalica about 2 years ago

io.github.sanctuuary - 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: https://github.com/sanctuuary/APE/compare/v.2.2.0...v2.2.6

- Java
Published by vedran-kasalica about 2 years ago

io.github.sanctuuary - 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 https://github.com/sanctuuary/APE/pull/85
  • Refactor code and implement the Taverna style workflow outputs by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/86
  • Fix Javadoc error by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/87
  • Update CITATION.cff by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/88
  • Update README.md - remove a badge by @vedran-kasalica in https://github.com/sanctuuary/APE/pull/89

Full Changelog: https://github.com/sanctuuary/APE/compare/v2.1.8...v.2.2.0

- Java
Published by vedran-kasalica over 2 years ago

io.github.sanctuuary - Improved CWL generation and code refactor

What's Changed

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

Full Changelog: https://github.com/sanctuuary/APE/compare/v2.1.5...v2.1.7

- Java
Published by vedran-kasalica over 2 years ago

io.github.sanctuuary - 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

- Java
Published by vedran-kasalica over 2 years ago

io.github.sanctuuary - 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

- Java
Published by vedran-kasalica over 3 years ago

io.github.sanctuuary - APE 2.0.2 - New SLTLx Templates, added workflow output dependency

Improvements: - Added new constraint templates - Workflows no longer use provided inputs as outputs

- Java
Published by vedran-kasalica over 3 years ago

io.github.sanctuuary - 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.

- Java
Published by vedran-kasalica almost 4 years ago

io.github.sanctuuary - APE 1.1.12 - log4j version fix

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

- Java
Published by vedran-kasalica about 4 years ago

io.github.sanctuuary - APE 1.1.11 - DOI release

Fix needed to obtain the DOI

- Java
Published by vedran-kasalica over 4 years ago

io.github.sanctuuary - APE 1.1.9 - Export abstract and executable CWL

Export abstract and executable CWL Improved synthesis execution flags

- Java
Published by vedran-kasalica over 4 years ago

io.github.sanctuuary - 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.

- Java
Published by vedran-kasalica over 4 years ago

io.github.sanctuuary - 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(..))

- Java
Published by vedran-kasalica about 5 years ago

io.github.sanctuuary - APE 1.1.5 - Adding long predicate labels

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

- Java
Published by vedran-kasalica about 5 years ago

io.github.sanctuuary - APE 1.1.4 - Improving SolutionWorkflowNode (updated)

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

- Java
Published by vedran-kasalica about 5 years ago

io.github.sanctuuary - 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

- Java
Published by vedran-kasalica about 5 years ago

io.github.sanctuuary - 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.

- Java
Published by vedran-kasalica about 5 years ago

io.github.sanctuuary - APE 1.1.1 - Strict taxonomy hiararchy

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

- Java
Published by vedran-kasalica over 5 years ago

io.github.sanctuuary - 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

- Java
Published by vedran-kasalica over 5 years ago

io.github.sanctuuary - APE 1.0.2 - constraint improvements

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

- Java
Published by vedran-kasalica over 5 years ago

io.github.sanctuuary - The first stable version of APE

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

- Java
Published by vedran-kasalica over 5 years ago