error improvements

[mr-c]

• address some deprecations
• detect non-Workflow CWL documents and give a better error message

Description

When the use provides a path to a CWL document that is not class: Workflow or a $graph containing a class: Workflow, we need a better error message than Error: The workflow could not be found within the repository

Motivation and Context

Fixes #582

How Has This Been Tested?

I tested locally with the provided Git repository URL, branch, and path in the original issue.

Screenshots (if appropriate):

Types of changes

• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [ ] I have updated the documentation accordingly.
• [ ] I have added tests to cover my changes.
• [x] All new and existing tests passed.

[mr-c]

@kinow Could you add a test? I'm not familiar with the testing framework

[kinow]

@kinow Could you add a test? I'm not familiar with the testing framework

Sorry, saw this comment before approving. Let me take a look…

[kinow]

(Clicked on Update branch -- forgot to check if there was an option to rebase...)

[mr-c]

@kinow I rebased and fixed the conflicts