prospector

.github/workflows/CI_build.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Run test with coverage
         run: pytest --cov --cov-report term --cov-report xml -m "not integration"
       - name: Check style against standards using prospector
-        run: prospector -o grouped -o pylint:pylint-report.txt
+        run: prospector -o grouped -o pylint:pylint-report.txt --ignore-paths notebooks
       - name: Check whether import statements are used consistently
         run: isort --check-only --diff .
       - name: SonarCloud Scan

ms2query/benchmarking/collect_test_data_results.py

@@ -13,7 +13,6 @@
 from matchms.calculate_scores import calculate_scores
 from matchms.similarity.CosineGreedy import CosineGreedy
 from matchms.similarity.ModifiedCosine import ModifiedCosine
-from ms2deepscore import MS2DeepScore
 from ms2deepscore.models import SiameseSpectralModel, compute_embedding_array
 from spec2vec.vector_operations import cosine_similarity_matrix
 from tqdm import tqdm

ms2query/ms2library.py

@@ -250,8 +250,6 @@ def _get_all_ms2ds_scores(self, query_spectrum: Spectrum
             Spectrum for which similarity scores should be calculated for all
             spectra in the ms2ds embeddings file.
         """
-        ms2ds = MS2DeepScore(self.ms2ds_model, progress_bar=False)
-
         query_embeddings = compute_embedding_array(self.ms2ds_model, [query_spectrum])
 
         library_ms2ds_embeddings_numpy = self.ms2ds_embeddings.to_numpy()