Add more TypedDict definitions

[GlassOfWhiskey]

This commit adds more TypedDict definitions for File, Dirent, and Directory objects. In addition, it adds the exitCode entry to the CWLRuntimeParameterContext, which was missing.

[mr-c]

Thanks for the PR. I think there are some Seven Bridges workflows that decorate input and output Files and Directories with additional fields and reference those fields from CWL Parameter Expressions.

See common-workflow-language/common-workflow-language#710 for some references to this.

So I don't think we can discard or throw an error on references to additional fields. An engine could optimize for the standard fields and use a slower path for extension fields, if that helps.

[GlassOfWhiskey]

Is that allowed by the standard? Shouldn't it be a ns:MyFile class object that extends File?

[GlassOfWhiskey]

@mr-c btw I think I fixed it. I also foud a slightly better way to check keys through TypeGuard functions. However, I am quite surprised there is no way to automatically access the Literal type of TypedDict keys from the TypedDict definition. I can obviously to TypedDict.__annotations__.keys() but this is not typed as Literal so it does not work.

[mr-c]

Is that allowed by the standard? Shouldn't it be a ns:MyFile class object that extends File?

Extra namespaced fields are allowed

[codecov]

Codecov Report

❌ Patch coverage is 86.11111% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 34.69%. Comparing base (b9de378) to head (af8b854).

Files with missing lines	Patch %	Lines
cwl_utils/sandboxjs.py	66.66%	1 Missing and 1 partial ⚠️
cwl_utils/types.py	92.00%	2 Missing ⚠️
cwl_utils/expression.py	66.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #393      +/-   ##
==========================================
+ Coverage   34.66%   34.69%   +0.02%     
==========================================
  Files          30       30              
  Lines       35412    35437      +25     
  Branches     9538     9541       +3     
==========================================
+ Hits        12275    12294      +19     
- Misses      20257    20261       +4     
- Partials     2880     2882       +2     

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