minor fixes

Author: florian-huber

ms2query/database/ann_index.py

@@ -5,8 +5,7 @@
 import numpy as np
 import pandas as pd
 from matchms import Spectrum
-from ms2deepscore.models import load_model
-from ms2deepscore import compute_embedding_array
+from ms2deepscore.models import compute_embedding_array, load_model
 import faiss
 
 from .spectra_merging import ensure_merged_tables  # schema with precursor_mz + metadata fields

ms2query/database/compound_database.py

@@ -324,6 +324,7 @@ def get_fingerprint(self, comp_id: str) -> Optional[Tuple[np.ndarray, np.ndarray
     # ---------- batch getters ----------
 
     def get_compounds(self, comp_ids: List[str]) -> pd.DataFrame:
+        # TODO: Allow returning duplicates? And handle arrays.
         """
         Return metadata for many compounds (no fingerprint blobs), order preserved as in comp_ids.
         Missing comp_ids are omitted from the result.
@@ -349,12 +350,16 @@ def get_compounds(self, comp_ids: List[str]) -> pd.DataFrame:
         return df
 
     def get_fingerprints(self, comp_ids: List[str]) -> List[Optional[Tuple[np.ndarray, np.ndarray]]]:
+        # TODO: Allow returning duplicates? And handle arrays.
         """
         Return a list of fingerprints aligned with comp_ids.
         Each item is (bits, counts) or None if not found/empty.
         """
         if not comp_ids:
             return []
+        
+        if isinstance(comp_ids, np.ndarray):
+            comp_ids = [x for x in comp_ids]
 
         placeholders = ",".join("?" for _ in comp_ids)
         rows = self._conn.execute(f"""

setup.py

@@ -43,7 +43,7 @@
         "matplotlib",
         "skl2onnx",
         #"onnx<1.16.2",
-        #"onnxruntime<1.16", # 1.16 breaks the code due to the issue https://github.com/iomega/ms2query/issues/208
+        "onnxruntime>1.16", # 1.16 breaks the code due to the issue https://github.com/iomega/ms2query/issues/208
     ],
     extras_require={"dev": ["bump2version",
                             "isort>=5.1.0",