Merge pull request #200 from biggraph/darabos-griffe

Fix Griffe warnings, requirements.txt, and an improved error message

examples/requirements.txt

@@ -1,6 +1,3 @@
 # Example of a requirements.txt file. LynxKite will automatically install anything you put here.
 faker
 matplotlib
-chembl_webresource_client
-rcsb-api
-itertools

lynxkite-core/src/lynxkite/core/ops.py

@@ -247,7 +247,7 @@ def op(
     """Decorator for defining an operation."""
 
     def decorator(func):
-        doc = parse_doc(func.__doc__)
+        doc = parse_doc(func)
         sig = inspect.signature(func)
         _view = view
         if view == "matplotlib":
@@ -444,16 +444,45 @@ def run_user_script(script_path: pathlib.Path):
 
 
 @functools.cache
-def parse_doc(doc):
-    """Griffe is an optional dependency. When available, we returned the parsed docstring."""
+def parse_doc(func):
+    """Griffe is an optional dependency. When available, we return the parsed docstring."""
+    doc = func.__doc__
     try:
         import griffe
     except ImportError:
         return doc
     if doc is None:
         return None
+    ds = griffe.Docstring(doc, parent=_get_griffe_function(func))
     if "----" in doc:
-        doc = griffe.Docstring(doc).parse("numpy")
+        ds = ds.parse("numpy")
     else:
-        doc = griffe.Docstring(doc).parse("google")
-    return json.loads(json.dumps(doc, cls=griffe.JSONEncoder))
+        ds = ds.parse("google")
+    return json.loads(json.dumps(ds, cls=griffe.JSONEncoder))
+
+
+def _get_griffe_function(func):
+    """Returns a griffe.Function object based on the signature of the function."""
+    import griffe
+
+    sig = inspect.signature(func)
+    parameters = []
+    for name, param in sig.parameters.items():
+        if param.annotation is inspect.Parameter.empty:
+            annotation = None
+        else:
+            annotation = param.annotation.__name__
+        parameters.append(
+            griffe.Parameter(
+                name,
+                annotation=annotation,
+                kind=griffe.ParameterKind.keyword_only
+                if param.kind == inspect.Parameter.KEYWORD_ONLY
+                else griffe.ParameterKind.positional_or_keyword,
+            )
+        )
+    return griffe.Function(
+        func.__name__,
+        parameters=griffe.Parameters(*parameters),
+        returns=str(sig.return_annotation),
+    )

lynxkite-graph-analytics/src/lynxkite_graph_analytics/core.py

@@ -224,12 +224,16 @@ async def _execute_node(
                     missing.append(p.name)
                 continue
             x = input_map[p.name]
-            if p.type == nx.Graph and isinstance(x, Bundle):
-                x = x.to_nx()
-            elif p.type == Bundle and isinstance(x, nx.Graph):
-                x = Bundle.from_nx(x)
-            elif p.type == Bundle and isinstance(x, pd.DataFrame):
-                x = Bundle.from_df(x)
+            if p.type == nx.Graph:
+                if isinstance(x, Bundle):
+                    x = x.to_nx()
+                assert isinstance(x, nx.Graph), "Input must be a graph."
+            elif p.type == Bundle:
+                if isinstance(x, nx.Graph):
+                    x = Bundle.from_nx(x)
+                elif isinstance(x, pd.DataFrame):
+                    x = Bundle.from_df(x)
+                assert isinstance(x, Bundle), "Input must be a graph or dataframe."
             inputs.append(x)
     except Exception as e:
         if not os.environ.get("LYNXKITE_SUPPRESS_OP_ERRORS"):

lynxkite-graph-analytics/src/lynxkite_graph_analytics/lynxkite_ops.py

@@ -303,7 +303,7 @@ def create_graph(bundle: core.Bundle, *, relations: str = None) -> core.Bundle:
         relations (str, optional): Set of relations to set for the bundle. The parameter
             should be a JSON object where the keys are relation names and the values are
             a dictionary representation of a `RelationDefinition`.
-        Defaults to None.
+            Defaults to None.
 
     Returns:
         Bundle: The input bundle with the new relations set.