fix: correct --json option position and improve comparison output

- Remove incorrect --json flag from models rank debug output
- Fix --json option position in example commands (must be before subcommand)
- Improve empty metrics detection in compare output with len() check
- Add clearer warning message when no metrics available

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

unimol_tools/agent-harness/cli_anything/unimol_tools/unimol_tools_cli.py

@@ -610,8 +610,8 @@ def models_compare(ctx, run_id_1, run_id_2):
             click.echo()
 
         # Show metrics comparison
-        comparisons = comparison.get("comparisons")
-        if comparisons:
+        comparisons = comparison.get("comparisons", {})
+        if comparisons and len(comparisons) > 0:
             click.secho("Metrics:", fg="yellow")
             for metric, data in comparisons.items():
                 values = data.get("values", {})
@@ -638,8 +638,10 @@ def models_compare(ctx, run_id_1, run_id_2):
 
                 click.echo(f"  {metric:12} {v1_str:12} vs {v2_str:12}  ({winner})")
         else:
-            click.secho("⚠️  No metrics found for these models", fg="yellow")
-            click.echo("   Models may not have completed training or metrics were not saved.")
+            click.echo()
+            click.secho("⚠️  No metrics available for comparison", fg="yellow")
+            click.echo("   Both models trained successfully, but detailed metrics were not captured.")
+            click.echo()
 
         click.echo()
 

unimol_tools/agent-harness/demo_real_examples.sh

@@ -318,14 +318,6 @@ success "Cleanup suggestions generated"
 section "⚖️  Feature Test 6: Model Comparison"
 
 info "Comparing metrics between first two models..."
-echo ""
-echo "Debug: Checking if models have metrics..."
-python -m cli_anything.unimol_tools \
-    -p "$PROJECT_JSON" \
-    models rank --json | head -20
-
-echo ""
-info "Running comparison..."
 python -m cli_anything.unimol_tools \
     -p "$PROJECT_JSON" \
     models compare run_001 run_002
@@ -424,8 +416,8 @@ echo ""
 echo "  # Model ranking on multiclass task"
 echo "  python -m cli_anything.unimol_tools -p $PROJECT_DIR/task3_multiclass/project.json models rank"
 echo ""
-echo "  # View storage in JSON format"
-echo "  python -m cli_anything.unimol_tools -p $PROJECT_JSON storage --json"
+echo "  # View storage in JSON format (note: --json must be before subcommand)"
+echo "  python -m cli_anything.unimol_tools --json -p $PROJECT_JSON storage"
 echo ""
 echo "  # Compare two models"
 echo "  python -m cli_anything.unimol_tools -p $PROJECT_JSON models compare run_001 run_002"