Merge branch 'main' into switch-ror

Author: cthoyt

pyproject.toml

@@ -90,7 +90,7 @@ dependencies = [
     "typing_extensions",
     "rdflib",
     "obographs>=0.0.8",
-    "sssom_pydantic>=0.1.1",
+    "sssom_pydantic>=0.2.0",
     "pytz",
 ]
 
@@ -101,11 +101,11 @@ tests = [
     "coverage[toml]",
 ]
 docs = [
-    "sphinx>=8",
+    "sphinx>=8,<9",
     "sphinx-rtd-theme>=3.0",
     "sphinx-click", 
     "sphinx_automodapi",
-    "sphinx_toolbox",
+    "sphinx_toolbox<=4.0.0",
 ]
 lint = [
     "ruff",

src/pyobo/api/xrefs.py

@@ -124,7 +124,11 @@ def get_semantic_mappings(
     )
     if converter is None:
         converter = get_converter()
-    return [row_to_semantic_mapping(row, converter=converter) for _, row in df.iterrows()]
+    return [
+        # TODO upstream this into sssom-pydantic?
+        row_to_semantic_mapping({k: v for k, v in row.items() if pd.notna(v)}, converter=converter)
+        for _, row in df.iterrows()
+    ]
 
 
 def get_mappings_df(