Codegen changes to support cwltool --fast-parse

[tetron]

Made via common-workflow-language/schema_salad#587

• PR for changes to CWL v1.2.1 proposed
• PR for CWL v1.1 schema refinements we will use a custom branch: https://github.com/common-workflow-language/common-workflow-language/tree/codegen
• PR for CWL v1.0 schema refinements https://github.com/common-workflow-language/cwl-v1.1/tree/codegen

[mr-c]

AttributeError: 'LoadingOptions' object has no attribute 'original_doc'

[lgtm-com]

This pull request introduces 1 alert when merging c889cf2 into 5a00d2c - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com]

This pull request introduces 1 alert when merging 346cbd5 into 5a00d2c - view on LGTM.com

new alerts:

• 1 for Unused import

[mr-c]

the outputSource refscope fix broke the expression refactoring tool

cwl_utils.errors.WorkflowException: param out1 not found in class: Workflow

[lgtm-com]

This pull request introduces 1 alert when merging 84c51ee into 5a00d2c - view on LGTM.com

new alerts:

• 1 for Unused import

[codecov]

Codecov Report

Merging #156 (a7641fd) into main (53a129b) will increase coverage by 0.59%.
The diff coverage is 50.00%.

❗ Current head a7641fd differs from pull request most recent head d028dff. Consider uploading reports for the commit d028dff to get more accurate results

@@            Coverage Diff             @@
##             main     #156      +/-   ##
==========================================
+ Coverage   29.53%   30.13%   +0.59%     
==========================================
  Files          28       28              
  Lines       20763    21541     +778     
  Branches     5775     5981     +206     
==========================================
+ Hits         6133     6491     +358     
- Misses      13301    13627     +326     
- Partials     1329     1423      +94     

Impacted Files	Coverage Δ
cwl_utils/cite_extract.py	53.33% <0.00%> (ø)
cwl_utils/docker_extract.py	50.00% <0.00%> (-7.15%)	⬇️
cwl_utils/parser/cwl_v1_0.py	30.45% <ø> (+1.08%)	⬆️
cwl_utils/parser/cwl_v1_1.py	27.44% <ø> (+1.10%)	⬆️
cwl_utils/parser/cwl_v1_2.py	29.58% <ø> (+0.82%)	⬆️
cwl_utils/cwl_v1_2_expression_refactor.py	33.19% <50.00%> (ø)
cwl_utils/expression_refactor.py	80.48% <100.00%> (ø)
cwl_utils/parser/__init__.py	71.13% <100.00%> (ø)
cwl_utils/image_puller.py	43.07% <0.00%> (-43.08%)	⬇️
... and 3 more

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[lgtm-com]

This pull request introduces 1 alert when merging a154797 into 5a00d2c - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com]

This pull request introduces 1 alert when merging 4d1b211 into 53a129b - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com]

This pull request introduces 1 alert when merging d028dff into 53a129b - view on LGTM.com

new alerts:

• 1 for Unused import