Description

A big refactor that addresses many issues. Look at the commit history and related issues for more details.

Fixes

• Fixes Provide Filter and DataTransformer separately to WorkflowExecutor. #32
• Fixes Invert the dependency between WorkflowConfig and Workflow #36
• Fixes Remove ContextManager requirement of Workflow #38
• Fixes Move application guides to an "Apps" section of the docs #39
• Fixes Update terminology and component structures to match the paper #41

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Refactoring (internal implementation changes)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update (no changes to the code)
• CI change (changes to CI workflows, packages, templates, etc.)
• Version changes (changes to the package or dependency versions)

Testing

N/A

Pull Request Checklist

Please confirm the PR meets the following requirements.

• Relevant tags are added (breaking, bug, dependencies, documentation, enhancement, refactor).
• Code changes pass pre-commit (e.g., ruff, mypy, etc.).
• Tests have been added to show the fix is effective or that the new feature works.
• New and existing unit tests pass locally with the changes.
• Docs have been updated and reviewed if relevant.