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Typed CWL parsers #396

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Typed CWL parsers #396

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5066c40
Typed CWL parsers
GlassOfWhiskey Dec 18, 2025
fb00216
WIP expression_refactor type fixes
mr-c Dec 19, 2025
762dfda
Fix typing errors in utils
GlassOfWhiskey Dec 19, 2025
6feb025
Regenerate parsers with native ints
GlassOfWhiskey Dec 19, 2025
bf0cebb
ProcessGenerator schema improvement
mr-c Dec 20, 2025
2053090
finish type fixing cwl_v1_0_expression_refactor
mr-c Dec 20, 2025
f9f5ad9
finish type fixing cwl_v1_1_expression_refactor
mr-c Dec 20, 2025
4145441
finish type fixing cwl_v1_2_expression_refactor
mr-c Dec 20, 2025
9cc48d1
Regenerate parsers
GlassOfWhiskey Dec 20, 2025
c2f6056
expression-refactor: fix detection of non-string Sequences
mr-c Dec 21, 2025
7a34d2b
bandit: allow asserts
mr-c Dec 21, 2025
510ae16
inputs_schema_gen: type fixes
mr-c Dec 21, 2025
202802e
Using LoadContents in type alias
GlassOfWhiskey Dec 21, 2025
a73b6a8
WIP
mr-c Dec 21, 2025
a2853a0
Make `param_for_source_id` return any CWL parameter
GlassOfWhiskey Dec 26, 2025
ac5ef61
Regenerate prsers with fixed CWL versions
GlassOfWhiskey Dec 26, 2025
08e2578
Regenerate parsers without abstract classes
GlassOfWhiskey Apr 4, 2026
c47584f
Regenerate parsers with generic Loaders
GlassOfWhiskey Apr 5, 2026
9af07e7
Regenerate parsers with mypyc annotations
GlassOfWhiskey Apr 5, 2026
41f3078
Regenerate parsers with explicit Enum types
GlassOfWhiskey Apr 5, 2026
9fd4031
Simplify union types
GlassOfWhiskey Apr 5, 2026
dbe81b8
Moved out version-independent functions
GlassOfWhiskey Apr 7, 2026
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2 changes: 1 addition & 1 deletion cwl_utils/cite_extract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ def main() -> int:


def extract_software_reqs(
process: cwl.Process,
process: cwl.Process | cwl.WorkflowStep,
) -> Iterator[cwl.SoftwareRequirement]:
"""Return an iterator over any SoftwareRequirements found in the given process."""
if process.requirements:
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