monarch-initiative / koza

Data transformation framework for LinkML data models
https://koza.monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
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Bump pyyaml to 6.0 #96

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Versions of pyyaml below 6.0 create a dependency conflict with prefixmaps. Bumping the version up to 6.0 appears to work for the most part, with the exception of a single test:

=================================== FAILURES ===================================
___________________________ test_valid_input[gene0] ____________________________

gene = {'category': ['biolink:NamedThing', 'biolink:Gene'], 'id': 'BOGUS:12345', 'name': 'Bogus Gene 12345'}

    @pytest.mark.parametrize("gene", [valid_gene])
    def test_valid_input(gene):
        validator = Validator(schema="tests/resources/biolink-model.yaml")
        v = validator.validate(obj=gene, target_class="NamedThing")
        result = v.validation_results[0]
>       assert result.valid == True
E       assert False == True
E        +  where False = ValidationResult(plugin_name='JsonSchemaValidationPlugin', valid=False, validation_messages=[ValidationMessage(severit..., field=None, value=None, message="Additional properties are not allowed ('category', 'id', 'name' were unexpected)")]).valid

tests/unit/test_validation.py:22: AssertionError
=========================== short test summary info ============================
FAILED tests/unit/test_validation.py::test_valid_input[gene0] - assert False ...
================== 1 failed, 103 passed in 318.04s (0:05:18) ===================

Any other reason that pyyaml is pinned to <6.0?

caufieldjh commented 2 years ago

No longer necessary - fixed by https://github.com/linkml/prefixmaps/pull/9