Remove pickled embeddings from tests and update select_files_for_ms2q…

…uery
iomega · Nov 26, 2023 · 9d1fd33 · 9d1fd33
1 parent 39f9273
commit 9d1fd33
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Showing 5 changed files with 1 addition and 42 deletions.
diff --git a/ms2query/ms2library.py b/ms2query/ms2library.py
@@ -386,8 +386,7 @@ 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",
-         "ms2query_model": ".onnx", "s2v_embeddings": "s2v_embeddings.pickle",
-         "ms2ds_embeddings": "ms2ds_embeddings.pickle"}
+         "ms2query_model": ".onnx"}
     if files_to_select is not None:
         dict_with_file_extensions = {key: value for key, value in dict_with_file_extensions.items()
                                      if key in files_to_select}

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -112,19 +112,3 @@ def hundred_test_spectra(path_to_general_test_files):
 def expected_tanimoto_scores_df(path_to_general_test_files):
     return pd.read_csv(os.path.join(path_to_general_test_files,
                                     "tanimoto_scores_100_test_spectra.csv"), index_col=0)
-
-
-@pytest.fixture(scope="package")
-def expected_ms2ds_embeddings(path_to_general_test_files):
-    expected_embeddings = load_pickled_file(os.path.join(
-        path_to_general_test_files,
-        "100_test_spectra_ms2ds_embeddings.pickle"))
-    return expected_embeddings
-
-
-@pytest.fixture(scope="package")
-def expected_s2v_embeddings(path_to_general_test_files):
-    expected_embeddings = load_pickled_file(os.path.join(
-        path_to_general_test_files,
-        "100_test_spectra_s2v_embeddings.pickle"))
-    return expected_embeddings
diff --git a/tests/test_files/100_test_spectra_ms2ds_embeddings.pickle b/tests/test_files/100_test_spectra_ms2ds_embeddings.pickle
diff --git a/tests/test_files/100_test_spectra_s2v_embeddings.pickle b/tests/test_files/100_test_spectra_s2v_embeddings.pickle
diff --git a/tests/test_library_files_creator.py b/tests/test_library_files_creator.py
@@ -22,30 +22,6 @@ def test_give_already_used_file_name(tmp_path, path_to_general_test_files, hundr
         LibraryFilesCreator(hundred_test_spectra, tmp_path)
 
 
-def test_create_ms2ds_embeddings(tmp_path, path_to_general_test_files,
-                                 hundred_test_spectra,
-                                 expected_ms2ds_embeddings,
-                                 ms2deepscore_model_file_name):
-    """Tests store_ms2ds_embeddings"""
-    library_spectra = [normalize_and_filter_peaks(s) for s in hundred_test_spectra if s is not None]
-    embeddings = create_ms2ds_embeddings(ms2ds_model=load_ms2ds_model(ms2deepscore_model_file_name),
-                                         list_of_spectra=library_spectra)
-    pd.testing.assert_frame_equal(embeddings, expected_ms2ds_embeddings,
-                                  check_exact=False,
-                                  atol=1e-5)
-
-
-def test_create_s2v_embeddings(tmp_path, path_to_general_test_files, hundred_test_spectra,
-                              expected_s2v_embeddings,
-                               spec2vec_model_file_name):
-    """Tests store_ms2ds_embeddings"""
-    library_spectra = [normalize_and_filter_peaks(s) for s in hundred_test_spectra if s is not None]
-
-    embeddings = create_s2v_embeddings(Word2Vec.load(spec2vec_model_file_name), library_spectra)
-    pd.testing.assert_frame_equal(embeddings, expected_s2v_embeddings,
-                                  check_exact=False,
-                                  atol=1e-5)
-
 def check_sqlite_files_are_equal(new_sqlite_file_name, reference_sqlite_file, check_metadata=True):
     """Raises an error if the two sqlite files are not equal"""
     # Test if file is made