Update ms2library to use new ms2deepscore methods

ms2query/ms2library.py

@@ -5,7 +5,7 @@
 from gensim.models import Word2Vec
 from matchms.Spectrum import Spectrum
 from ms2deepscore import MS2DeepScore
-from ms2deepscore.models import load_model as load_ms2ds_model
+from ms2deepscore.models import load_model as load_ms2ds_model, compute_embedding_array
 from onnxruntime import InferenceSession
 from spec2vec.vector_operations import calc_vector, cosine_similarity_matrix
 from tqdm import tqdm
@@ -82,7 +82,7 @@ def __init__(self,
         self.s2v_embeddings: pd.DataFrame = load_df_from_parquet_file(s2v_embeddings_file_name)
         self.ms2ds_embeddings: pd.DataFrame = load_df_from_parquet_file(ms2ds_embeddings_file_name)
 
-        assert self.ms2ds_model.base.output_shape[1] == self.ms2ds_embeddings.shape[1], \
+        assert self.ms2ds_model.model_settings.embedding_dim == self.ms2ds_embeddings.shape[1], \
             "Dimension of pre-computed MS2DeepScore embeddings does not fit given model."
 
         # load precursor mz's
@@ -251,7 +251,9 @@ def _get_all_ms2ds_scores(self, query_spectrum: Spectrum
             spectra in the ms2ds embeddings file.
         """
         ms2ds = MS2DeepScore(self.ms2ds_model, progress_bar=False)
-        query_embeddings = ms2ds.calculate_vectors([query_spectrum])
+
+        query_embeddings = compute_embedding_array(self.ms2ds_model, [query_spectrum])
+
         library_ms2ds_embeddings_numpy = self.ms2ds_embeddings.to_numpy()
         ms2ds_scores = cosine_similarity_matrix(library_ms2ds_embeddings_numpy,
                                                 query_embeddings)
@@ -397,7 +399,7 @@ def get_ms2query_model_prediction_single_spectrum(
 def select_files_for_ms2query(file_names: List[str], files_to_select=None):
     """Selects the files needed for MS2Library based on their file extensions. """
     dict_with_file_extensions = \
-        {"sqlite": ".sqlite", "s2v_model": ".model", "ms2ds_model": ".hdf5",
+        {"sqlite": ".sqlite", "s2v_model": ".model", "ms2ds_model": ".pt",
          "ms2query_model": ".onnx", "s2v_embeddings": "s2v_embeddings.parquet",
          "ms2ds_embeddings": "ms2ds_embeddings.parquet"}
     if files_to_select is not None: