def test_union_select_spearman(key, value):
config = workflow_config.MisfitConfig(
workflow={"clustering": {
"fcluster": {
key: value
}
}})
assert config.workflow.type == "custom_scale"
def test_union_select_auto_scale():
config = workflow_config.MisfitConfig(
workflow={"clustering": {
"fcluster": {
"depth": 1
}
}})
assert config.workflow.type == "auto_scale"
def test_workflow_custom(key, value):
config_data = {
"type": "custom_scale",
"clustering": {
"fcluster": {
key: value
}
},
}
workflow_config.MisfitConfig(workflow=config_data)
def test_config_workflow():
config_data = {
"observations": ["WWPR"],
"workflow": {
"type": "custom_scale",
"clustering": {
"linkage": {"method": "complete", "metric": "jensenshannon"}
},
"pca": {"threshold": 0.98},
},
}
config = workflow_config.MisfitConfig(**config_data)
assert config.workflow.type == "custom_scale"
def test_default_clustering_method():
config = workflow_config.MisfitConfig()
assert config.workflow.type == "auto_scale"
def test_default_scaling_threshold():
config = workflow_config.MisfitConfig()
assert config.workflow.pca.threshold == 0.95
def test_invalid_scaling_threshold(threshold, workflow, expected_error):
config_data = {"workflow": {"type": workflow, "pca": {"threshold": threshold}}}
with pytest.raises(pydantic.ValidationError, match=expected_error):
workflow_config.MisfitConfig(**config_data)
def test_config_workflow_valid(workflow):
config_data = {"workflow": {"type": workflow}}
config = workflow_config.MisfitConfig(**config_data)
assert config.workflow.type == workflow
def test_auto_scale_invalid_fcluster(key, expected_error):
config_data = {"type": "auto_scale", "clustering": {"fcluster": {key: 0.1}}}
with pytest.raises(pydantic.ValidationError, match=expected_error):
workflow_config.MisfitConfig(workflow=config_data)
def test_valid_scaling_threshold(threshold, workflow):
config_data = {"workflow": {"type": workflow, "pca": {"threshold": threshold}}}
config = workflow_config.MisfitConfig(**config_data)
assert config.workflow.pca.threshold == threshold