Workflow Optimizations and Benchmark Enhancements

Release notes

This release marks significant improvements and updates to the project, focusing on workflow optimizations, dependency updates, and benchmarking improvements. We've also addressed several issues to enhance the overall functionality and reliability of our tools.

What's Changed

Workflow and Dependency Updates

• Updated Maven configuration and GitHub actions to improve build processes and dependency management.
• Introduced fixes to Maven wrapper configuration for better project setup and reliability.
• Enhanced GitHub workflows to build and publish runnable images, making deployment and testing more efficient.
• Improved design-time benchmarks for more accurate performance analysis.
• Updated GitHub actions for better CI/CD practices and code quality checks.

Benchmarks and Documentation

• Implemented design-time benchmarks to measure and improve the performance of our tools.
• Added badges and GitHub action for software fairness, emphasizing our commitment to open and fair software practices.
• Introduced Taverna workflow design, expanding the project's capabilities and compatibility with different workflow standards.
• Updated project documentation and API to support SVG figures, enhancing the visual representation of data.

Fixes and Enhancements

• Addressed issues with SVG file handling and Docker image configurations, ensuring smoother operations and deployment.
• Fixed tool-level benchmark syntax and JSON object creation for benchmarks, improving the accuracy and readability of performance data.
• Made significant updates to design-time benchmarks, including syntax fixes, verification improvements, and JSON updates.
• Introduced a POST method for returning zipped CWL files, facilitating easier integration and use of CWL workflows.

Dependency Updates

• Several dependencies have been updated to their latest versions, addressing potential security vulnerabilities and ensuring compatibility with the latest technologies.

Acknowledgments

We're thrilled to acknowledge the contributions from our community members and the support from automated tools that help keep our project secure and up-to-date:

• A special shoutout to @csc-felipe for his valuable contributions, enhancing our Maven configuration and GitHub workflows.
• We are especially grateful to @kretep for his diligent review of PRs.
• Thanks to automated updates by Dependabot, our project's dependencies remain secure and current, ensuring the best possible foundation for our work.

We appreciate all contributions, whether they come from individuals or automated systems, as they collectively help improve and secure our project.

PRs

• Update maven.yml - fix dependency graph by @vedran-kasalica in #15
• Fix the maven wrapper configuration by @csc-felipe in #14
• Update maven.yml by @vedran-kasalica in #13
• Do not fail the action in case the dependency graph fails by @vedran-kasalica in #16
• Make github workflow build and publish a runnable restape image by @csc-felipe in #12
• Implement design-time benchmarks by @vedran-kasalica in #11
• Update Github actions by @vedran-kasalica in #24
• Bump snok/container-retention-policy from 2.1.1 to 2.1.2 by @dependabot in #23
• Bump docker/build-push-action from 4 to 5 by @dependabot in #22
• Bump actions/checkout from 3 to 4 by @dependabot in #21
• Bump docker/metadata-action from 4 to 5 by @dependabot in #20
• Bump docker/login-action from 2 to 3 by @dependabot in #19
• Benchmarks biotools oeb by @vedran-kasalica in #25
• Add badges and GH action for software fairness by @vedran-kasalica in #28
• Introduce the Taverna workflow design by @vedran-kasalica in #29
• Update APE version by @vedran-kasalica in #30
• Fix benchmarks by @vedran-kasalica in #31
• Fix tool level benchmark syntax by @vedran-kasalica in #32
• Create JSONObject for each mini benchmark by @vedran-kasalica in #34
• Install Arial to the docker image by @vedran-kasalica in #35
• Fix docker img by @vedran-kasalica in #36
• Support SVG figures and update the API by @vedran-kasalica in #37
• Fix the issue with svg files by @vedran-kasalica in #38
• Bump snok/container-retention-policy from 2.1.2 to 2.1.3 by @dependabot in #40
• Bump actions/setup-java from 3 to 4 by @dependabot in #39
• Create codeql.yml by @vedran-kasalica in #41
• Adhere to the best coding practices by @vedran-kasalica in #42
• Improve design-time benchmarks by @vedran-kasalica in #47
• Update the design-time benchmark json by @vedran-kasalica in #50
• Introduce a POST method that returns zipped CWL files by @vedran-kasalica in #51
• Fix the design time bench verification by @vedran-kasalica in #53
• Improve GH actions by @vedran-kasalica in #54
• Add a manual trigger to publish.yaml by @vedran-kasalica in #56
• Update RESTful APE: Version and Testing Enhancements by @vedran-kasalica in #55

New Contributors

• @csc-felipe made his first contribution in #14
• @dependabot made their first contribution in #23

Full Changelog: v0.2.4...v.0.3.1

RESTful APE Interface: Enhanced Interaction with APE Library

RESTful APE Interface v0.2.4 Release

We're excited to introduce the RESTful APE Interface v0.2.4, a powerful tool for seamless interaction with the APE library. This release empowers users to:

• Retrieve Domain Information: Access data types/formats, available tools, and constraints within the domain.
• Execute Workflow Synthesis: Streamline the process of workflow creation.
• Retrieve Figures/Images: Obtain resulting visual representations.
• Download Executable CWL Files: Easily access and utilize generated workflows.

Upgrade now and elevate your workflow synthesis experience!

What's Changed

• Synthesis execution by @vedran-kasalica in #2
• Reference APE mvn by @vedran-kasalica in #3
• Cwl input yml by @vedran-kasalica in #4

New Contributors

• @vedran-kasalica made their first contribution in #2

Full Changelog: https://github.com/sanctuuary/restape/commits/v0.2.4