Fix: replace removed gr.update() with component constructors for Gradio 5.x

gr.update() was removed in Gradio 5.x, causing "No API found" error
on HuggingFace Spaces when clicking SCOPE or Custom database options.

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

docs/LEARNINGS.md

@@ -194,8 +194,9 @@ except ImportError:
     create_structure_with_heatmap = None
 ```
 
-### Gradio 4.x Breaking Changes
+### Gradio 4.x/5.x Breaking Changes
 - `gr.Dataframe(height=...)` removed - don't use height parameter
+- `gr.update()` removed in Gradio 5.x - use component constructors instead (e.g. `gr.File(visible=False)` not `gr.update(visible=False)`). Causes "No API found" error on HF Spaces.
 - Use `gr.themes.Soft()` instead of custom CSS where possible
 - Test locally with same Gradio version as HF Spaces
 

protein_conformal/backend/gradio_interface.py

@@ -1256,22 +1256,22 @@ MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPL
                 return (
                     DEFAULT_LOOKUP_EMBEDDING,
                     DEFAULT_LOOKUP_METADATA,
-                    gr.update(value=None, visible=False),
-                    gr.update(value=None, visible=False),
+                    gr.File(value=None, visible=False),
+                    gr.File(value=None, visible=False),
                 )
             if db_choice == "SCOPE":
                 return (
                     DEFAULT_SCOPE_EMBEDDING,
                     DEFAULT_SCOPE_METADATA,
-                    gr.update(value=None, visible=False),
-                    gr.update(value=None, visible=False),
+                    gr.File(value=None, visible=False),
+                    gr.File(value=None, visible=False),
                 )
             # Custom database
             return (
                 CUSTOM_UPLOAD_EMBEDDING,
                 CUSTOM_UPLOAD_METADATA,
-                gr.update(visible=True),
-                gr.update(visible=True),
+                gr.File(visible=True),
+                gr.File(visible=True),
             )
 
         db_type.change(