Resolve conflict in poetry lock

Knowledge-Graph-Hub · Aug 2, 2023 · 03bafc4 · 03bafc4
2 parents 1cf7ea0 + 66e310a
commit 03bafc4
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Showing 4 changed files with 1,007 additions and 1,494 deletions.
diff --git a/kg_covid_19/make_holdouts.py b/kg_covid_19/make_holdouts.py
@@ -203,7 +203,8 @@ def _generate_negative_edges(
             warnings.warn(
                 "Couldn't generate %i negative edges - only %i edges left "
                 "after removing positives and reflexives"
-                % (edges_df.shape[0], negative_edges.shape[0])
+                % (edges_df.shape[0], negative_edges.shape[0]),
+                stacklevel=2
             )
             negative_edges = negative_edges.head(negative_edges.shape[0])
         else:

diff --git a/kg_covid_19/transform_utils/intact/intact.py b/kg_covid_19/transform_utils/intact/intact.py
@@ -99,7 +99,6 @@ def run(self, data_file: Optional[str] = None):
         os.makedirs(self.output_dir, exist_ok=True)
 
         with open(output_node_file, "w") as node, open(output_edge_file, "w") as edge:
-
             # write node.tsv header
             node.write("\t".join(self.node_header) + "\n")
             edge.write("\t".join(self.edge_header) + "\n")
@@ -170,7 +169,7 @@ def interaction_to_edge(
             interaction_type_str = (
                 interaction_type[0]
                 .getElementsByTagName("shortLabel")[0]
-                .firstChild._data
+                .firstChild._data  # type: ignore
             )
 
             participants = interaction.getElementsByTagName("participant")
@@ -353,7 +352,11 @@ def parse_experiment_info(self, xmldoc: minidom.Document) -> Dict[int, str]:
             # interaction detection method
             try:
                 method = experiment.getElementsByTagName("interactionDetectionMethod")
-                label = method[0].getElementsByTagName("shortLabel")[0].firstChild.data
+                label = (
+                    method[0]
+                    .getElementsByTagName("shortLabel")[0]
+                    .firstChild.data  # type: ignore
+                )
                 exp_dict[exp_id]["detection_method"] = label
             except (KeyError, IndexError, AttributeError):
                 pass