ruff

Author: niekdejonge

ms2query/benchmarking/EvaluateMethods.py

@@ -1,11 +1,8 @@
 import random
-
+from typing import Callable, List, Tuple
 import numpy as np
-from typing import Callable, Tuple, List
-
 from matchms.similarity.vector_similarity_functions import jaccard_similarity_matrix
 from tqdm import tqdm
-
 from ms2query.benchmarking.SpectrumDataSet import SpectraWithFingerprints, SpectrumSetBase
 
 

ms2query/benchmarking/SpectrumDataSet.py

@@ -1,12 +1,10 @@
 import copy
 from collections import Counter
-from typing import List, Dict, Iterable
-
+from typing import Dict, Iterable, List
 import numpy as np
 from matchms import Spectrum
 from matchms.filtering.metadata_processing.add_fingerprint import _derive_fingerprint_from_inchi
-
-from ms2deepscore.models import compute_embedding_array, SiameseSpectralModel
+from ms2deepscore.models import SiameseSpectralModel, compute_embedding_array
 from tqdm import tqdm
 
 

ms2query/benchmarking/reference_methods/PredictMS2DeepScoreSimilarity.py

@@ -1,7 +1,5 @@
 from typing import Tuple
-
 import numpy as np
-
 from ms2deepscore.vector_operations import cosine_similarity_matrix
 from tqdm import tqdm
 

ms2query/benchmarking/reference_methods/predict_best_possible_match.py

@@ -1,8 +1,6 @@
 from typing import Dict
-
 import numpy as np
 from matchms.similarity.vector_similarity_functions import jaccard_similarity_matrix
-
 from ms2query.benchmarking.SpectrumDataSet import SpectraWithFingerprints
 
 

ms2query/benchmarking/reference_methods/predict_highest_cosine.py

@@ -1,5 +1,4 @@
-from typing import Tuple, List
-
+from typing import List, Tuple
 from matchms import Scores
 from matchms.similarity.CosineGreedy import CosineGreedy
 from matchms.similarity.PrecursorMzMatch import PrecursorMzMatch

ms2query/benchmarking/reference_methods/predict_highest_ms2deepscore.py

@@ -1,5 +1,4 @@
-from typing import Tuple, List
-
+from typing import List, Tuple
 from ms2query.benchmarking.reference_methods.PredictMS2DeepScoreSimilarity import predict_top_ms2deepscores
 from ms2query.benchmarking.SpectrumDataSet import SpectraWithMS2DeepScoreEmbeddings
 

ms2query/benchmarking/reference_methods/predict_using_closest_tanimoto.py

@@ -1,11 +1,10 @@
+from typing import List, Tuple
 import numpy as np
 from ms2deepscore.vector_operations import cosine_similarity_matrix
-from typing import Tuple, List
-
-from ms2query.benchmarking.SpectrumDataSet import SpectraWithMS2DeepScoreEmbeddings, SpectraWithFingerprints
+from tqdm import tqdm
+from ms2query.benchmarking.SpectrumDataSet import SpectraWithFingerprints, SpectraWithMS2DeepScoreEmbeddings
 from ms2query.metrics import generalized_tanimoto_similarity_matrix
 
-from tqdm import tqdm
 
 def predict_using_closest_tanimoto(
     library_spectra: SpectraWithMS2DeepScoreEmbeddings, query_spectra: SpectraWithMS2DeepScoreEmbeddings,

ms2query/benchmarking/reference_methods/predict_with_integrated_similarity_flow.py

@@ -1,8 +1,7 @@
-from typing import Tuple, List
-from tqdm import tqdm
+from typing import List, Tuple
 import numpy as np
 from matchms.similarity.vector_similarity_functions import jaccard_similarity_matrix
-
+from tqdm import tqdm
 from ms2query.benchmarking.reference_methods.PredictMS2DeepScoreSimilarity import predict_top_ms2deepscores
 from ms2query.benchmarking.SpectrumDataSet import SpectraWithMS2DeepScoreEmbeddings
 

tests/conftest.py

@@ -1,6 +1,5 @@
 import os
 from pathlib import Path
-
 import numpy as np
 from matchms.Spectrum import Spectrum
 from ms2deepscore.models import load_model

tests/testPredictMS2DeepScoreSimilarity.py

@@ -1,11 +1,10 @@
 import numpy as np
 import pytest
-
 from ms2query.benchmarking.reference_methods.PredictMS2DeepScoreSimilarity import (
     predict_top_ms2deepscores,
 )
-from tests.conftest import create_test_spectra, ms2deepscore_model
 from ms2query.benchmarking.SpectrumDataSet import SpectraWithMS2DeepScoreEmbeddings
+from tests.conftest import create_test_spectra, ms2deepscore_model
 
 
 @pytest.mark.parametrize(