ci: fix python lint env and resolve ontology clippy regressions

Author: AlexMikhalev

.github/workflows/python-bindings.yml

@@ -42,9 +42,6 @@ jobs:
         with:
           enable-cache: true
 
-      - name: Install dependencies
-        run: uv pip install --system black ruff mypy
-
       - name: Setup virtual environment
         working-directory: crates/terraphim_automata_py
         run: |
@@ -55,6 +52,7 @@ jobs:
           else
             source .venv/bin/activate
           fi
+          uv pip install black ruff mypy
 
       - name: Fix Black formatting
         working-directory: crates/terraphim_automata_py
@@ -64,16 +62,28 @@ jobs:
           else
             source .venv/bin/activate
           fi
-          uv run black python/
+          black python/
         continue-on-error: false
 
       - name: Lint with Ruff
         working-directory: crates/terraphim_automata_py
-        run: ruff check python/
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            source .venv/Scripts/activate
+          else
+            source .venv/bin/activate
+          fi
+          ruff check python/
 
       - name: Type check with mypy
         working-directory: crates/terraphim_automata_py
-        run: mypy python/terraphim_automata/ --ignore-missing-imports
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            source .venv/Scripts/activate
+          else
+            source .venv/bin/activate
+          fi
+          mypy python/terraphim_automata/ --ignore-missing-imports
         continue-on-error: true
 
   test:

crates/terraphim_multi_agent/src/agents/ontology_agents.rs

@@ -182,10 +182,8 @@ If no match found, respond with:
   "normalized_prov": null,
   "normalized_score": null,
   "normalized_method": null
-}}"#,
-                ontology_list,
-                entity.raw_value,
-                format!("{:?}", entity.entity_type)
+            }}"#,
+                ontology_list, entity.raw_value, entity.entity_type
             );
 
             let request = LlmRequest::new(vec![
@@ -276,7 +274,7 @@ impl ReviewAgent {
     /// Review and improve low-confidence normalizations
     pub async fn review(
         &self,
-        entities: &mut Vec<ExtractedEntity>,
+        entities: &mut [ExtractedEntity],
     ) -> MultiAgentResult<Vec<ExtractedEntity>> {
         let client = self.llm_client.write().await;
 
@@ -292,7 +290,7 @@ impl ReviewAgent {
             .collect();
 
         if low_confidence.is_empty() {
-            return Ok(entities.clone());
+            return Ok(entities.to_vec());
         }
 
         let review_prompt = format!(
@@ -373,7 +371,7 @@ Respond with ONLY valid JSON array:
 
         info!("Review complete for {} entities", entities.len());
 
-        Ok(entities.clone())
+        Ok(entities.to_vec())
     }
 }
 

crates/terraphim_multi_agent/src/workflows/ontology_workflow.rs

@@ -144,16 +144,15 @@ impl OntologyWorkflow {
     pub async fn execute(&self, text: &str) -> MultiAgentResult<OntologyWorkflowResult> {
         let start_time = std::time::Instant::now();
         let total_tokens = 0u64;
-        let extraction_iterations;
-        let mut normalization_iterations;
+        let extraction_iterations = 1;
+        let mut normalization_iterations = 1;
         let mut review_triggered = false;
 
         // Step 1: Lead agent routes to Extraction Agent
         log::info!("Starting Dynamic Ontology workflow with LeadWithSpecialists pattern");
 
         // Step 2: Extraction Agent extracts entities and relationships
         let schema_signal = self.extract_entities(text).await?;
-        extraction_iterations = 1;
         log::info!(
             "Extracted {} entities and {} relationships",
             schema_signal.entities.len(),
@@ -164,7 +163,6 @@ impl OntologyWorkflow {
         let mut grounded_entities = self
             .normalize_entities(schema_signal.entities.clone())
             .await?;
-        normalization_iterations = 1;
         log::info!("Normalized {} entities", grounded_entities.len());
 
         // Step 4: Coverage Agent checks ontology coverage
@@ -309,10 +307,8 @@ If no match found, respond with:
   "normalized_prov": null,
   "normalized_score": null,
   "normalized_method": null
-}}"#,
-                ontology_list,
-                entity.raw_value,
-                format!("{:?}", entity.entity_type)
+            }}"#,
+                ontology_list, entity.raw_value, entity.entity_type
             );
 
             let request = LlmRequest::new(vec![
@@ -367,7 +363,7 @@ If no match found, respond with:
     /// Review Agent: Review and improve low coverage
     async fn review_and_improve(
         &self,
-        entities: &mut Vec<ExtractedEntity>,
+        entities: &mut [ExtractedEntity],
         _coverage: &CoverageSignal,
     ) -> MultiAgentResult<Vec<ExtractedEntity>> {
         let mut client = self.llm_client.write().await;
@@ -453,7 +449,7 @@ Respond with ONLY valid JSON array:
             }
         }
 
-        Ok(entities.clone())
+        Ok(entities.to_vec())
     }
 }
 

crates/terraphim_multi_agent/tests/ontology_integration_test.rs

@@ -71,10 +71,7 @@ mod tests {
 mod tests {
     // Stub tests when hgnc feature is not enabled
     #[test]
-    fn test_hgnc_stub() {
-        // HGNC tests require the hgnc feature
-        assert!(true);
-    }
+    fn test_hgnc_stub() {}
 }
 
 #[cfg(test)]
@@ -84,7 +81,7 @@ mod generic_tests {
     /// Test coverage signal calculation
     #[test]
     fn test_coverage_signal_calculation() {
-        let entities = vec![
+        let entities = [
             ExtractedEntity {
                 entity_type: "cancer_diagnosis".to_string(),
                 raw_value: "lung carcinoma".to_string(),
@@ -135,7 +132,7 @@ mod generic_tests {
     /// Test coverage above threshold
     #[test]
     fn test_coverage_above_threshold() {
-        let entities = vec![
+        let entities = [
             ExtractedEntity {
                 entity_type: "cancer_diagnosis".to_string(),
                 raw_value: "lung carcinoma".to_string(),