Add typed parsers - #454
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Regenerate the v1.0, v1.1, and v1.2 CWL parsers using the latest Schema SALAD version, which adds type annotations to classes, loaders, and fields (`FieldType`, `EnumFieldType`, generic `Loader[FieldType]`, etc.). Adjust all downstream machinery to resolve the resulting type errors: - Update type aliases in `cwl_utils.parser` (`PrimitiveType`, `InputParameterType`, `OutputParameterType`, `CommandInputParameterType`, `CommandOutputParameterType`, `EnvironmentDef`, `CWLVersion`, `CWLTypeSchema`, `ParameterType`, `ParameterTypeOrArraySchema`) - Harden `cwl_utils.types` with `is_sequence()` and the `SrcSink` namedtuple - Fix expression refactorors, `inputs_schema_gen` (anonymous array schemas, `Sequence` doc values, `SchemaDefRequirement` cast), docker/cite extraction, and `cwl_utils.utils` - Adjust tests according to the new typing utilities
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Regenerate the v1.0, v1.1, and v1.2 CWL parsers using the latest Schema SALAD version, which adds type annotations to classes, loaders, and fields (
FieldType,EnumFieldType, genericLoader[FieldType], etc.).Adjust all downstream machinery to resolve the resulting type errors:
cwl_utils.parser(PrimitiveType,InputParameterType,OutputParameterType,CommandInputParameterType,CommandOutputParameterType,EnvironmentDef,CWLVersion,CWLTypeSchema,ParameterType,ParameterTypeOrArraySchema)cwl_utils.typeswithis_sequence()and theSrcSinknamedtupleinputs_schema_gen(anonymous array schemas,Sequencedoc values,SchemaDefRequirementcast), docker/cite extraction, andcwl_utils.utils