import linting

Author: florian-huber

tests/test_ann_index.py

@@ -2,14 +2,13 @@
 import json
 import sqlite3
 from typing import List, Tuple
-
 import numpy as np
 import pytest
 from matchms import Spectrum
-
 from ms2query.database import ANNIndex
 from ms2query.database.spectra_merging import ensure_merged_tables
 
+
 # --- small helpers for array <-> BLOB used in tests (mirrors the production helpers) ---
 
 def _ndarray_to_blob(arr: np.ndarray) -> bytes:

tests/test_compound_database.py

@@ -4,17 +4,16 @@
 import numpy as np
 import pandas as pd
 import pytest
-
-# >>> adjust to your package/module path
 from ms2query.database.compound_database import (
     CompoundDatabase,
     SpecToCompoundMap,
-    map_from_spectraldb_metadata,
+    compute_fingerprints,  # returns List[Optional[(bits, counts)]]
     get_unique_compounds_from_spectraldb,
-    compute_fingerprints,              # returns List[Optional[(bits, counts)]]
     inchikey14_from_full,
+    map_from_spectraldb_metadata,
 )
 
+
 # -------------------------
 # Helpers
 # -------------------------

tests/test_fingerprint_computation.py

@@ -1,16 +1,16 @@
 import numpy as np
 import pytest
-
 from ms2query.fingerprint_computation import (
     FingerprintGenerator,
     SparseFingerprintGenerator,
-    get_mol_from_smiles,
-    prepare_sparse_vector,
     compute_fingerprints_from_smiles,
-    count_fingerprint_keys,
     compute_idf,
+    count_fingerprint_keys,
+    get_mol_from_smiles,
+    prepare_sparse_vector,
 )
 
+
 # -----------------------
 # Test doubles / fakes
 # -----------------------

tests/test_merging_utils.py

@@ -1,15 +1,14 @@
 # test_merge_spectra.py
 import numpy as np
 import pytest
-from numpy.testing import assert_allclose
 from matchms import Spectrum
-
-# Adjust if your module name is different:
 from ms2query.spectral_processing.merging_utils import (
-    normalize_spectrum_sum,
     _merge_cluster_to_consensus,
     get_merged_spectra,
+    normalize_spectrum_sum,
 )
+from numpy.testing import assert_allclose
+
 
 # ---------- helpers ----------
 

tests/test_spectral_database.py

@@ -3,7 +3,6 @@
 import pandas as pd
 import pytest
 from matchms import Spectrum
-
 from ms2query.database.spectral_database import SpectralDatabase