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Merged
mr-c merged 2 commits into from
Dec 16, 2025
Merged

Add more TypedDict definitions #393

mr-c merged 2 commits into from
Dec 16, 2025
+306 −149

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@GlassOfWhiskey GlassOfWhiskey commented Dec 12, 2025

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.

@GlassOfWhiskey GlassOfWhiskey force-pushed the more-on-types branch 3 times, most recently from e5420a6 to 8ae3b07 Compare December 13, 2025 08:05
@GlassOfWhiskey GlassOfWhiskey requested a review from mr-c December 13, 2025 08:29
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mr-c requested changes Dec 13, 2025
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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.

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GlassOfWhiskey commented Dec 13, 2025

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

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GlassOfWhiskey commented Dec 13, 2025

@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.

@GlassOfWhiskey GlassOfWhiskey requested a review from mr-c December 13, 2025 10:37
@GlassOfWhiskey GlassOfWhiskey mentioned this pull request Dec 13, 2025
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mr-c commented Dec 13, 2025

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

Extra namespaced fields are allowed

GlassOfWhiskey added a commit to common-workflow-language/cwltool that referenced this pull request Dec 13, 2025
@GlassOfWhiskey
Experiment with TypedDict in CWL types
e37b528 
This commit checks that the new `TypedDict` type aliases specified in
cwl-utils with PR common-workflow-language/cwl-utils#393 do not break
anything in the cwltool type system.
@GlassOfWhiskey GlassOfWhiskey force-pushed the more-on-types branch 2 times, most recently from 11526da to 7c8a166 Compare December 13, 2025 11:56
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codecov bot commented Dec 13, 2025 •
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Codecov Report

❌ Patch coverage is 81.48148% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 36.92%. Comparing base (c39b6e6) to head (4fa3716).
⚠️ Report is 5 commits behind head on main.

Files with missing lines Patch % Lines
cwl_utils/cwl_v1_0_expression_refactor.py 60.00% 2 Missing ⚠️
cwl_utils/cwl_v1_1_expression_refactor.py 60.00% 2 Missing ⚠️
cwl_utils/sandboxjs.py 66.66% 1 Missing and 1 partial ⚠️
cwl_utils/types.py 92.85% 2 Missing ⚠️
cwl_utils/cwl_v1_2_expression_refactor.py 66.66% 1 Missing ⚠️
cwl_utils/expression.py 66.66% 0 Missing and 1 partial ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #393      +/-   ##
==========================================
+ Coverage   34.66%   36.92%   +2.26%     
==========================================
  Files          30       47      +17     
  Lines       35412    36721    +1309     
  Branches     9538     9563      +25     
==========================================
+ Hits        12275    13561    +1286     
- Misses      20257    20273      +16     
- Partials     2880     2887       +7

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@GlassOfWhiskey GlassOfWhiskey force-pushed the more-on-types branch 5 times, most recently from 985b93e to af8b854 Compare December 14, 2025 21:55
mr-c pushed a commit to common-workflow-language/cwltool that referenced this pull request Dec 15, 2025
@GlassOfWhiskey @mr-c
Experiment with TypedDict in CWL types
b782752 
This commit checks that the new `TypedDict` type aliases specified in
cwl-utils with PR common-workflow-language/cwl-utils#393 do not break
anything in the cwltool type system.
@GlassOfWhiskey GlassOfWhiskey requested a review from mr-c December 15, 2025 21:39
mr-c pushed a commit to common-workflow-language/cwltool that referenced this pull request Dec 16, 2025
@GlassOfWhiskey @mr-c
Experiment with TypedDict in CWL types
852b080 
This commit checks that the new `TypedDict` type aliases specified in
cwl-utils with PR common-workflow-language/cwl-utils#393 do not break
anything in the cwltool type system.
@GlassOfWhiskey @mr-c
Add more TypedDict definitions
0be3d59 
for `File`, `Dirent`, and `Directory` objects. In addition, it adds the `exitCode` entry to the `CWLRuntimeParameterContext`, which was missing.
Use `TypeIs` instead of `TypeGuard`.
@mr-c mr-c enabled auto-merge (rebase) December 16, 2025 18:44
@mr-c mr-c merged commit e3e74b0 into main Dec 16, 2025
28 checks passed
@mr-c mr-c deleted the more-on-types branch December 16, 2025 18:48
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