Merge pull request #65 from pepkit/issue20_output_schema

Align Pipestat output schema with looper output schema

codecov.yml

@@ -5,6 +5,10 @@ coverage:
         target: 80%    # the required coverage value
         threshold: 1%  # the leniency in hitting the target
         informational: true
+    patch:
+      default:
+        target: 80%
+        informational: true
 ignore:
   - "*/argparser.py"
   - "*/cli.py"

pipestat/parsed_schema.py

@@ -91,9 +91,11 @@ def __init__(self, data: Union[Dict[str, Any], Path, str]) -> None:
         self._status_data = _safe_pop_one_mapping(key="status", data=data, info_name="status")
 
         if data:
-            raise SchemaError(
-                f"Extra top-level key(s) in given schema data: {', '.join(data.keys())}"
+            _LOGGER.info(
+                "Top-Level arguments found in output schema. They will be assigned to project-level."
             )
+            extra_project_data = _recursively_replace_custom_types(data)
+            self._project_level_data.update(extra_project_data)
 
         # Check that no reserved keywords were used as data items.
         resv_kwds = {"id", SAMPLE_NAME}

tests/test_parsed_schema.py

@@ -203,13 +203,6 @@ def test_parsed_schema__has_correct_data_and_print(
             f"Could not find valid pipeline identifier (key '{SCHEMA_PIPELINE_NAME_KEY}') in given schema data",
         )
         for data in SCHEMA_DATA_TUPLES_WITHOUT_PIPELINE_NAME
-    ]
-    + [
-        (
-            dict(data + [(SCHEMA_PIPELINE_NAME_KEY, "test_pipe"), ("extra_key", "placeholder")]),
-            "Extra top-level key(s) in given schema data: extra_key",
-        )
-        for data in SCHEMA_DATA_TUPLES_WITHOUT_PIPELINE_NAME
     ],
 )
 def test_insufficient_schema__raises_expected_error_and_message(schema_data, expected_message):