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Fix: Fix OS

Fix: Fix OS #20

GitHub Actions / JUnit Test Report failed Nov 11, 2024 in 0s

30 tests run, 17 passed, 11 skipped, 2 failed.

Annotations

Check failure on line 22 in tests/test_vacuum_workflow.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_vacuum_workflow.test_ValidateVacuumSynthesis@group_vacuum

jsonschema.exceptions.ValidationError: '__no_default_value__' is not of type 'array'

Failed validating 'type' in schema:
    {'type': 'array', 'items': {'type': 'string'}}

On instance:
    '__no_default_value__'
Raw output
vacuum_working_directory = (PosixPath('/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/tmp/popen-gw0/test_ValidateVacuumSynthesis0/out'), PosixPath('/home/runner/work/synthesis-workflow/synthesis-workflow/tests/data/in_vacuum/out'))
data_dir = PosixPath('/home/runner/work/synthesis-workflow/synthesis-workflow/tests/data')

    @pytest.mark.xdist_group("group_vacuum")
    def test_ValidateVacuumSynthesis(vacuum_working_directory, data_dir):
        """Test the synthesis workflow in vacuum."""
        np.random.seed(0)
    
        # Run the workflow
>       assert luigi.build([ValidateVacuumSynthesis()], local_scheduler=True)

/home/runner/work/synthesis-workflow/synthesis-workflow/tests/test_vacuum_workflow.py:22: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/interface.py:239: in build
    luigi_run_result = _schedule_and_run(tasks, worker_scheduler_factory, override_defaults=env_params)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/interface.py:173: in _schedule_and_run
    success &= worker.run()
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:1229: in run
    self._handle_next_task()
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:1120: in _handle_next_task
    self._email_task_failure(task, expl)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:745: in _email_task_failure
    self._email_error(task, formatted_traceback,
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:751: in _email_error
    formatted_subject = subject.format(task=task, host=self.host)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/task.py:563: in __repr__
    param_values = self.get_param_values(params, [], self.param_kwargs)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/task.py:415: in get_param_values
    result[param_name] = params_dict[param_name].normalize(arg)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/parameter.py:376: in normalize
    return super().normalize(x)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/parameter.py:1300: in normalize
    jsonschema.validate(instance=unfrozen_value, schema=self.schema)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

instance = '__no_default_value__'
schema = {'items': {'type': 'string'}, 'type': 'array'}
cls = <class 'jsonschema.validators.Draft202012Validator'>, args = ()
kwargs = {}
validator = Draft202012Validator(schema={'items': {'type': 'string'}, 'type': 'array'}, format_checker=None)
error = <ValidationError: "'__no_default_value__' is not of type 'array'">

    def validate(instance, schema, cls=None, *args, **kwargs):  # noqa: D417
        """
        Validate an instance under the given schema.
    
            >>> validate([2, 3, 4], {"maxItems": 2})
            Traceback (most recent call last):
                ...
            ValidationError: [2, 3, 4] is too long
    
        :func:`~jsonschema.validators.validate` will first verify that the
        provided schema is itself valid, since not doing so can lead to less
        obvious error messages and fail in less obvious or consistent ways.
    
        If you know you have a valid schema already, especially
        if you intend to validate multiple instances with
        the same schema, you likely would prefer using the
        `jsonschema.protocols.Validator.validate` method directly on a
        specific validator (e.g. ``Draft202012Validator.validate``).
    
    
        Arguments:
    
            instance:
    
                The instance to validate
    
            schema:
    
                The schema to validate with
    
            cls (jsonschema.protocols.Validator):
    
                The class that will be used to validate the instance.
    
        If the ``cls`` argument is not provided, two things will happen
        in accordance with the specification. First, if the schema has a
        :kw:`$schema` keyword containing a known meta-schema [#]_ then the
        proper validator will be used. The specification recommends that
        all schemas contain :kw:`$schema` properties for this reason. If no
        :kw:`$schema` property is found, the default validator class is the
        latest released draft.
    
        Any other provided positional and keyword arguments will be passed
        on when instantiating the ``cls``.
    
        Raises:
    
            `jsonschema.exceptions.ValidationError`:
    
                if the instance is invalid
    
            `jsonschema.exceptions.SchemaError`:
    
                if the schema itself is invalid
    
        .. rubric:: Footnotes
        .. [#] known by a validator registered with
            `jsonschema.validators.validates`
    
        """
        if cls is None:
            cls = validator_for(schema)
    
        cls.check_schema(schema)
        validator = cls(schema, *args, **kwargs)
        error = exceptions.best_match(validator.iter_errors(instance))
        if error is not None:
>           raise error
E           jsonschema.exceptions.ValidationError: '__no_default_value__' is not of type 'array'
E           
E           Failed validating 'type' in schema:
E               {'type': 'array', 'items': {'type': 'string'}}
E           
E           On instance:
E               '__no_default_value__'

/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/jsonschema/validators.py:1332: ValidationError

Check failure on line 17 in tests/test_O1_workflow.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_O1_workflow.test_ValidateSynthesis@group_O1

jsonschema.exceptions.ValidationError: '__no_default_value__' is not of type 'array'

Failed validating 'type' in schema:
    {'type': 'array', 'items': {'type': 'string'}}

On instance:
    '__no_default_value__'
Raw output
small_O1_working_directory = (PosixPath('/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/tmp/popen-gw2/test_ValidateSynth...e/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/tmp/popen-gw2/test_ValidateSynthesis0/small_O1'))
data_dir = PosixPath('/home/runner/work/synthesis-workflow/synthesis-workflow/tests/data')

    @pytest.mark.xdist_group("group_O1")
    def test_ValidateSynthesis(small_O1_working_directory, data_dir):
        """Test the synthesis workflow in simple atlas."""
        np.random.seed(0)
    
        # Run the workflow
>       assert luigi.build([ValidateSynthesis()], local_scheduler=True)

/home/runner/work/synthesis-workflow/synthesis-workflow/tests/test_O1_workflow.py:17: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/interface.py:239: in build
    luigi_run_result = _schedule_and_run(tasks, worker_scheduler_factory, override_defaults=env_params)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/interface.py:173: in _schedule_and_run
    success &= worker.run()
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:1229: in run
    self._handle_next_task()
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:1120: in _handle_next_task
    self._email_task_failure(task, expl)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:745: in _email_task_failure
    self._email_error(task, formatted_traceback,
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/worker.py:751: in _email_error
    formatted_subject = subject.format(task=task, host=self.host)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/task.py:563: in __repr__
    param_values = self.get_param_values(params, [], self.param_kwargs)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/task.py:415: in get_param_values
    result[param_name] = params_dict[param_name].normalize(arg)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/parameter.py:376: in normalize
    return super().normalize(x)
/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/luigi/parameter.py:1300: in normalize
    jsonschema.validate(instance=unfrozen_value, schema=self.schema)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

instance = '__no_default_value__'
schema = {'items': {'type': 'string'}, 'type': 'array'}
cls = <class 'jsonschema.validators.Draft202012Validator'>, args = ()
kwargs = {}
validator = Draft202012Validator(schema={'items': {'type': 'string'}, 'type': 'array'}, format_checker=None)
error = <ValidationError: "'__no_default_value__' is not of type 'array'">

    def validate(instance, schema, cls=None, *args, **kwargs):  # noqa: D417
        """
        Validate an instance under the given schema.
    
            >>> validate([2, 3, 4], {"maxItems": 2})
            Traceback (most recent call last):
                ...
            ValidationError: [2, 3, 4] is too long
    
        :func:`~jsonschema.validators.validate` will first verify that the
        provided schema is itself valid, since not doing so can lead to less
        obvious error messages and fail in less obvious or consistent ways.
    
        If you know you have a valid schema already, especially
        if you intend to validate multiple instances with
        the same schema, you likely would prefer using the
        `jsonschema.protocols.Validator.validate` method directly on a
        specific validator (e.g. ``Draft202012Validator.validate``).
    
    
        Arguments:
    
            instance:
    
                The instance to validate
    
            schema:
    
                The schema to validate with
    
            cls (jsonschema.protocols.Validator):
    
                The class that will be used to validate the instance.
    
        If the ``cls`` argument is not provided, two things will happen
        in accordance with the specification. First, if the schema has a
        :kw:`$schema` keyword containing a known meta-schema [#]_ then the
        proper validator will be used. The specification recommends that
        all schemas contain :kw:`$schema` properties for this reason. If no
        :kw:`$schema` property is found, the default validator class is the
        latest released draft.
    
        Any other provided positional and keyword arguments will be passed
        on when instantiating the ``cls``.
    
        Raises:
    
            `jsonschema.exceptions.ValidationError`:
    
                if the instance is invalid
    
            `jsonschema.exceptions.SchemaError`:
    
                if the schema itself is invalid
    
        .. rubric:: Footnotes
        .. [#] known by a validator registered with
            `jsonschema.validators.validates`
    
        """
        if cls is None:
            cls = validator_for(schema)
    
        cls.check_schema(schema)
        validator = cls(schema, *args, **kwargs)
        error = exceptions.best_match(validator.iter_errors(instance))
        if error is not None:
>           raise error
E           jsonschema.exceptions.ValidationError: '__no_default_value__' is not of type 'array'
E           
E           Failed validating 'type' in schema:
E               {'type': 'array', 'items': {'type': 'string'}}
E           
E           On instance:
E               '__no_default_value__'

/home/runner/work/synthesis-workflow/synthesis-workflow/.tox/min_versions/lib/python3.9/site-packages/jsonschema/validators.py:1332: ValidationError