fix: pass full residue set to knapsack

app.py

@@ -68,12 +68,11 @@ Path(log_file).touch()
 
 logger = logging.getLogger("instanovo")
 logger.setLevel(logging.INFO)
-if not logger.handlers:
-    file_handler = logging.FileHandler(log_file)
-    file_handler.setLevel(logging.INFO)
-    stream_handler = logging.StreamHandler()
-    stream_handler.setLevel(logging.INFO)
-    logger.addHandler(stream_handler)
+file_handler = logging.FileHandler(log_file)
+file_handler.setLevel(logging.INFO)
+formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
+file_handler.setFormatter(formatter)
+logger.addHandler(file_handler)
 
 
 def load_models_and_knapsack():
@@ -147,33 +146,29 @@ def load_models_and_knapsack():
         if not knapsack_exists:
             logger.info("Knapsack not found or failed to load. Generating knapsack...")
             try:
-                residue_masses_knapsack = dict(RESIDUE_SET.residue_masses.copy())
+                residue_masses_for_calc = dict(RESIDUE_SET.residue_masses.copy())
                 special_and_nonpositive = list(RESIDUE_SET.special_tokens) + [
-                    k for k, v in residue_masses_knapsack.items() if v <= 0
+                    k for k, v in residue_masses_for_calc.items() if v <= 0
                 ]
                 if special_and_nonpositive:
-                     logger.info(f"Excluding special/non-positive mass residues from knapsack: {special_and_nonpositive}")
-                     for res in set(special_and_nonpositive):
-                         if res in residue_masses_knapsack:
-                             del residue_masses_knapsack[res]
-
-                valid_residue_indices = {
-                    res: idx
-                    for res, idx in RESIDUE_SET.residue_to_index.items()
-                    if res in residue_masses_knapsack
-                }
-
-                if not residue_masses_knapsack:
+                        logger.info(f"Excluding special/non-positive mass residues from knapsack: {special_and_nonpositive}")
+                        for res in set(special_and_nonpositive):
+                            if res in residue_masses_for_calc:
+                                del residue_masses_for_calc[res]
+
+                full_residue_indices = RESIDUE_SET.residue_to_index
+
+                if not residue_masses_for_calc: # Check if any residues are left for calculation
                     raise ValueError("No valid residues with positive mass found for knapsack generation.")
 
+                logger.info("Generating knapsack. This will take a few minutes, please be patient.")
                 KNAPSACK = Knapsack.construct_knapsack(
-                    residue_masses=residue_masses_knapsack,
-                    residue_indices=valid_residue_indices,
+                    residue_masses=residue_masses_for_calc,
+                    residue_indices=full_residue_indices,
                     max_mass=MAX_MASS,
                     mass_scale=MASS_SCALE,
                 )
                 logger.info(f"Knapsack generated. Saving to {KNAPSACK_DIR}...")
-                KNAPSACK_DIR.mkdir(parents=True, exist_ok=True)
                 KNAPSACK.save(str(KNAPSACK_DIR))
                 logger.info("Knapsack saved.")
             except Exception as e:
@@ -717,6 +712,10 @@ with gr.Blocks(
              *   **Knapsack Beam Search:** use this for the best results and highest peptide recall, but is about 10x slower than Greedy Search.
          *   `delta_mass_ppm` shows the lowest absolute precursor mass error (ppm) across isotopes 0-1 for the final sequence.
          *   Check logs for progress, especially for large files or slower methods.
+
+         **Links:**
+        * [InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments](https://www.nature.com/articles/s42256-025-01019-5), Eloff, Kalogeropoulos et al. 2025, Nature Machine Intelligence.
+        * [GitHub Repository for InstaNovo](https://github.com/instadeepai/instanovo)
          """,
          elem_classes="feedback"
     )