Update app.py

app.py

@@ -173,7 +173,6 @@ with tab2:
 # TAB 3: Pipetting Command Generator
 # --------------------------------------------------
 
-
 with tab3:
     st.header("🧪 Pipetting Command Generator")
     st.markdown("""
@@ -181,6 +180,7 @@ with tab3:
     The app will:
     - Auto-detect or create `Sample`, `Position#`, `Total edited`, and `Volume per "1"` columns  
     - Generate pipetting commands dynamically for any number of positions  
+    - Use one source well per source index and reroute to the next source if a well is full  
     - Display and allow CSV download for both commands and source volume summaries  
     """)
 
@@ -212,7 +212,6 @@ with tab3:
             # --- Detect Position columns ---
             position_cols = [c for c in df.columns if re.match(r"(?i)^position\s*\d+", c)]
             if not position_cols:
-                # If not found, auto-generate for numeric-like columns
                 non_pos_cols = {"sample", "total edited", 'volume per "1"', "volume per 1"}
                 candidate_cols = [c for c in df.columns if c.lower() not in non_pos_cols]
                 if not candidate_cols:
@@ -239,7 +238,6 @@ with tab3:
             # --- Constants ---
             ROWS_96 = ["A", "B", "C", "D", "E", "F", "G", "H"]
             COLS_96 = list(range(1, 13))
-            GROUP_START_COLS = [1, 5, 9]
             num_positions = len(position_cols)
 
             def well_name(row_letter, col_number):
@@ -252,19 +250,13 @@ with tab3:
                 col_idx = within_plate % 12
                 return plate_num, well_name(ROWS_96[row_idx], COLS_96[col_idx])
 
-            def source_index_to_group_coords(source_idx):
-                group_idx = source_idx - 1
-                plate_num = 1 + (group_idx // 24)
-                within_plate_group = group_idx % 24
-                row_idx = within_plate_group // 3
-                group_in_row = within_plate_group % 3
-                row_letter = ROWS_96[row_idx]
-                start_col = GROUP_START_COLS[group_in_row]
-                return plate_num, row_letter, start_col
-
-            def source_index_to_wells(source_idx):
-                plate_num, row_letter, start_col = source_index_to_group_coords(source_idx)
-                return [(plate_num, well_name(row_letter, start_col + offset)) for offset in range(4)]
+            # one well per source index
+            def source_index_to_well(source_idx):
+                plate_num = ((source_idx - 1) // 96) + 1
+                within_plate = (source_idx - 1) % 96
+                row_idx = within_plate // 12
+                col_idx = within_plate % 12
+                return plate_num, well_name(ROWS_96[row_idx], COLS_96[col_idx])
 
             def pick_tool(volume_ul):
                 return "TS_10" if volume_ul <= 10.0 else "TS_50"
@@ -272,8 +264,7 @@ with tab3:
             # --- Core logic ---
             commands = []
             source_volume_totals = {}
-            per_source_well_cum = {i: [0.0, 0.0, 0.0, 0.0] for i in range(1, num_positions + 1)}
-            per_source_wells = {i: source_index_to_wells(i) for i in range(1, num_positions + 1)}
+            per_source_vol = {i: 0.0 for i in range(1, num_positions + 1)}
 
             for _, row in df.iterrows():
                 sample_id = int(row["Sample"])
@@ -292,23 +283,38 @@ with tab3:
                     if not is_one:
                         continue
 
-                    wells_list = per_source_wells[pos_idx]
-                    cum_list = per_source_well_cum[pos_idx]
-
-                    chosen = None
-                    for w_i, ((plate_num, well_str), current_vol) in enumerate(zip(wells_list, cum_list)):
-                        if current_vol + vol_per_one <= max_per_well_ul:
-                            chosen = (w_i, plate_num, well_str)
-                            break
-                    if chosen is None:
-                        st.error(f"Source {pos_idx} has all 4 wells full. Cannot add {vol_per_one} µL.")
-                        st.stop()
-
-                    w_i, src_plate, src_well = chosen
-                    cum_list[w_i] += vol_per_one
-                    per_source_well_cum[pos_idx] = cum_list
+                    src_plate, src_well = source_index_to_well(pos_idx)
+                    current_vol = per_source_vol[pos_idx]
+
+                    # reroute if source full
+                    if current_vol + vol_per_one > max_per_well_ul:
+                        rerouted = False
+                        for next_src in range(pos_idx + 1, num_positions + 1):
+                            next_plate, next_well = source_index_to_well(next_src)
+                            if per_source_vol[next_src] + vol_per_one <= max_per_well_ul:
+                                st.warning(f"⚠️ Source {pos_idx} full → rerouted {vol_per_one:.2f} µL to Source {next_src}.")
+                                per_source_vol[next_src] += vol_per_one
+                                source_volume_totals[(next_plate, next_well)] = source_volume_totals.get((next_plate, next_well), 0.0) + vol_per_one
+                                commands.append({
+                                    "SourceIdx": f"{pos_idx}→{next_src}",
+                                    "Source plate": next_plate,
+                                    "Source well": next_well,
+                                    "Destination plate": dest_plate,
+                                    "Destination well": dest_well,
+                                    "Volume": round(vol_per_one, 2),
+                                    "Tool": tool,
+                                    "Note": "Rerouted due to full source"
+                                })
+                                rerouted = True
+                                break
+                        if not rerouted:
+                            st.error(f"❌ All sources from {pos_idx} onward full. Cannot add {vol_per_one} µL for Sample {sample_id}.")
+                            st.stop()
+                        continue  # skip normal addition
+
+                    # normal case
+                    per_source_vol[pos_idx] += vol_per_one
                     source_volume_totals[(src_plate, src_well)] = source_volume_totals.get((src_plate, src_well), 0.0) + vol_per_one
-
                     commands.append({
                         "SourceIdx": pos_idx,
                         "Source plate": src_plate,
@@ -322,22 +328,28 @@ with tab3:
             # --- Compile results ---
             commands_df = pd.DataFrame(commands)
             commands_df = commands_df.sort_values(
-                by=["SourceIdx", "Source plate", "Source well", "Destination plate", "Destination well"],
+                by=["Source plate", "Source well", "Destination plate", "Destination well"],
                 kind="stable"
             )
-            commands_df = commands_df[["Source plate", "Source well", "Destination plate", "Destination well", "Volume", "Tool"]]
+
+            if "Note" in commands_df.columns:
+                commands_df = commands_df[["SourceIdx", "Source plate", "Source well",
+                                            "Destination plate", "Destination well", "Volume", "Tool", "Note"]]
+            else:
+                commands_df = commands_df[["SourceIdx", "Source plate", "Source well",
+                                            "Destination plate", "Destination well", "Volume", "Tool"]]
 
             # --- Source summary ---
             summary_rows = []
             for src_idx in range(1, num_positions + 1):
-                for plate_num, well_str in per_source_wells[src_idx]:
-                    total = source_volume_totals.get((plate_num, well_str), 0.0)
-                    summary_rows.append({
-                        "Source": src_idx,
-                        "Source plate": plate_num,
-                        "Source well": well_str,
-                        "Total volume taken (µL)": round(total, 2)
-                    })
+                src_plate, src_well = source_index_to_well(src_idx)
+                total = source_volume_totals.get((src_plate, src_well), 0.0)
+                summary_rows.append({
+                    "Source": src_idx,
+                    "Source plate": src_plate,
+                    "Source well": src_well,
+                    "Total volume taken (µL)": round(total, 2)
+                })
             summary_df = pd.DataFrame(summary_rows)
 
             st.success(f"✅ Generated {len(commands_df)} commands across {num_positions} positions.")
@@ -363,4 +375,4 @@ with tab3:
         except Exception as e:
             st.error(f"❌ Error processing file: {e}")
     else:
-        st.info("👆 Upload an Excel/CSV/TXT file to start generating pipetting commands.")
+        st.info("👆 Upload an Excel/CSV/TXT file to start generating pipetting commands.")