Fix: Add real-time log updates with yield statements

app.py

@@ -23,21 +23,35 @@ def build_reagent_index(progress=gr.Progress()):
     """Main function to build the reagent index."""
     
     if not HF_TOKEN:
-        return "❌ Error: HF_TOKEN not found! Please add it to Space secrets.", "", 0
+        yield "❌ Error: HF_TOKEN not found! Please add it to Space secrets.", [], 0
     
     try:
+        log_messages = []
+        
         progress(0, desc="Authenticating...")
+        log_messages.append("[*] Authenticating with Hugging Face...")
+        yield "\n".join(log_messages), [], 0.0
         
         # 1. Authentication
         login(token=HF_TOKEN)
         progress(0.05, desc="Authenticated successfully")
+        log_messages.append("[OK] Authenticated successfully\n")
+        yield "\n".join(log_messages), [], 0.05
         
         # 2. Load dataset
         progress(0.1, desc="Loading dataset...")
+        log_messages.append("[*] Loading dataset in streaming mode...")
+        yield "\n".join(log_messages), [], 0.1
+        
         ds = load_dataset(ORIGINAL_DATASET, split='train', streaming=True)
+        log_messages.append("[OK] Dataset loaded\n")
+        yield "\n".join(log_messages), [], 0.1
         
         # 3. Process reactions
         progress(0.15, desc="Processing reactions...")
+        log_messages.append("[*] Processing 2.7M reactions...")
+        log_messages.append("This will take 10-20 minutes, please be patient...\n")
+        yield "\n".join(log_messages), [], 0.15
         
         smiles_to_reactions = defaultdict(list)
         name_to_reactions = defaultdict(list)
@@ -46,11 +60,15 @@ def build_reagent_index(progress=gr.Progress()):
         try:
             import pubchempy as pcp
             PUBCHEM_AVAILABLE = True
+            log_messages.append("[OK] PubChem available for chemical name lookup\n")
         except ImportError:
             PUBCHEM_AVAILABLE = False
+            log_messages.append("[⚠] PubChem not available - using SMILES only\n")
+        
+        yield "\n".join(log_messages), [], 0.15
         
         processed = 0
-        logs = ["[*] Starting reagent index creation...\n"]
+        last_logged = 0
         
         for reaction in ds:
             processed += 1
@@ -58,11 +76,13 @@ def build_reagent_index(progress=gr.Progress()):
             if SAMPLE_SIZE and processed > SAMPLE_SIZE:
                 break
             
-            # Update progress every 500 reactions
-            if processed % 500 == 0:
+            # Update progress every 10,000 reactions (less frequent for better performance)
+            if processed - last_logged >= 10000:
                 pct = min(0.6, (processed / 2700000) * 0.5 + 0.15)
                 progress(pct, desc=f"Processing: {processed:,} reactions...")
-                logs.append(f"[{processed:,}] Processed {processed:,} reactions...")
+                log_messages.append(f"[{processed:,}] Processed {processed:,} reactions...")
+                yield "\n".join(log_messages), [], pct
+                last_logged = processed
             
             reaction_id = reaction.get('reaction_id', 'unknown')
             
@@ -104,8 +124,10 @@ def build_reagent_index(progress=gr.Progress()):
                             except:
                                 pass
         
-        logs.append(f"\n[OK] Processed {processed:,} reactions\n")
+        log_messages.append(f"\n[OK] Processed {processed:,} reactions\n")
         progress(0.65, desc="Building index...")
+        log_messages.append("[*] Building index entries...")
+        yield "\n".join(log_messages), [], 0.65
         
         # 4. Build index
         index_entries = []
@@ -132,29 +154,27 @@ def build_reagent_index(progress=gr.Progress()):
                 'common_name': name
             })
         
-        logs.append(f"[OK] Created {len(index_entries):,} index entries")
-        logs.append(f"    - SMILES: {len(smiles_to_reactions):,}")
-        logs.append(f"    - Names: {len(name_to_reactions):,}\n")
-        
+        log_messages.append(f"[OK] Created {len(index_entries):,} index entries")
+        log_messages.append(f"    - SMILES: {len(smiles_to_reactions):,}")
+        log_messages.append(f"    - Names: {len(name_to_reactions):,}\n")
         progress(0.8, desc="Uploading to Hugging Face...")
+        log_messages.append("[*] Uploading to Hugging Face...")
+        yield "\n".join(log_messages), [], 0.8
         
         # 5. Upload to HF
         index_dataset = Dataset.from_list(index_entries)
         index_dataset.push_to_hub(HF_DATASET_NAME, private=False, token=HF_TOKEN)
         
-        logs.append("[OK] Upload complete!\n")
-        logs.append("="*70)
-        logs.append("SUCCESS! Reagent index created and uploaded!")
-        logs.append("="*70)
-        logs.append(f"Dataset URL: https://huggingface.co/datasets/{HF_DATASET_NAME}")
-        logs.append(f"Total entries: {len(index_entries):,}")
-        logs.append(f"Total reactions: {processed:,}")
+        log_messages.append("[OK] Upload complete!\n")
+        log_messages.append("="*70)
+        log_messages.append("SUCCESS! Reagent index created and uploaded!")
+        log_messages.append("="*70)
+        log_messages.append(f"Dataset URL: https://huggingface.co/datasets/{HF_DATASET_NAME}")
+        log_messages.append(f"Total entries: {len(index_entries):,}")
+        log_messages.append(f"Total reactions: {processed:,}")
         
         progress(1.0, desc="Complete!")
         
-        # Format output
-        log_text = "\n".join(logs)
-        
         # Create sample table
         sample_data = []
         for i, entry in enumerate(index_entries[:10]):
@@ -164,13 +184,13 @@ def build_reagent_index(progress=gr.Progress()):
                 entry['count']
             ])
         
-        return log_text, sample_data, 1.0
+        yield "\n".join(log_messages), sample_data, 1.0
         
     except Exception as e:
         error_msg = f"❌ Error: {str(e)}\n\n{type(e).__name__}"
         import traceback
         error_msg += f"\n\n{traceback.format_exc()}"
-        return error_msg, [], 0.0
+        yield error_msg, [], 0.0
 
 
 # Create Gradio interface