Update Python dependencies #14195
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Update Python dependencies #14195
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jmchilton
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Jun 27, 2022
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The new Markdown 3.4.0 package broke sphinx-markdown-tables, so we need either a new release of the latter containing ryanfox/sphinx-markdown-tables#37 or to pin the former to |
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Fix the following traceback when running
`pytest test/unit/tool_util/test_cwl.py`:
```
def test_boolean_defaults():
> proxy = workflow_proxy(_cwl_tool_path("v1.2/tests/conditionals/cond-wf-002_nojs.cwl"))
test/unit/tool_util/test_cwl.py:244:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/cwl/parser.py:760: in workflow_proxy
return _to_cwl_workflow_object(workflow_path, strict_cwl_validation=strict_cwl_validation)
lib/galaxy/tool_util/cwl/parser.py:851: in _to_cwl_workflow_object
cwl_workflow = _schema_loader(strict_cwl_validation).tool(path=workflow_path)
lib/galaxy/tool_util/cwl/schema.py:86: in tool
process_definition = self.process_definition(raw_process_reference)
lib/galaxy/tool_util/cwl/schema.py:68: in process_definition
loading_context, uri = resolve_and_validate_document(
.venv/lib/python3.8/site-packages/cwltool/load_tool.py:384: in resolve_and_validate_document
document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:965: in resolve_all
???
schema_salad/ref_resolver.py:1197: in validate_links
???
schema_salad/ref_resolver.py:1124: in validate_links
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E schema_salad.exceptions.ValidationException: test/functional/tools/cwl_tools/v1.2/tests/conditionals/cond-wf-002_nojs.cwl:2:1: Field `cwlVersion`
E contains undefined
E reference to
E `file:///usr/users/ga002/soranzon/software/nsoranzo_galaxy/test/functional/tools/cwl_tools/v1.2/tests/conditionals/v1.2`
schema_salad/ref_resolver.py:1062: ValidationException
```
Note that the unit test doesn't fail if run on its own with
`pytest test/unit/tool_util/test_cwl.py::test_boolean_defaults` .
nsoranzo
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Green at last! Can someone please merge? |
jdavcs
approved these changes
Jul 25, 2022
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Run
make update-dependencies.