isort

ms2query/create_new_library/library_files_creator.py

@@ -5,7 +5,7 @@
 
 import os
 from pathlib import Path
-from typing import List, Union, Dict
+from typing import Dict, List, Union
 import matchms.filtering as msfilters
 import numpy as np
 import pandas as pd
@@ -17,9 +17,11 @@
 from spec2vec.vector_operations import calc_vector
 from tqdm import tqdm
 from ms2query.clean_and_filter_spectra import create_spectrum_documents
-from ms2query.create_new_library.add_classifire_classifications import select_compound_classes
-from ms2query.create_new_library.create_sqlite_database import initialize_tables, fill_spectrum_data_table, \
-    fill_inchikeys_table, add_dataframe_to_sqlite
+from ms2query.create_new_library.add_classifire_classifications import \
+    select_compound_classes
+from ms2query.create_new_library.create_sqlite_database import (
+    add_dataframe_to_sqlite, fill_inchikeys_table, fill_spectrum_data_table,
+    initialize_tables)
 from ms2query.utils import return_non_existing_file_name
 
 

tests/test_library_files_creator.py

@@ -1,16 +1,16 @@
 import os
 import sqlite3
-
 import numpy as np
 import pandas as pd
 import pytest
 from gensim.models import Word2Vec
 from ms2deepscore.models import load_model as load_ms2ds_model
-
-from ms2query.clean_and_filter_spectra import normalize_and_filter_peaks_multiple_spectra, normalize_and_filter_peaks
-from ms2query.create_new_library.add_classifire_classifications import _convert_to_dataframe
-from ms2query.create_new_library.library_files_creator import LibraryFilesCreator, create_ms2ds_embeddings, \
-    create_s2v_embeddings
+from ms2query.clean_and_filter_spectra import (
+    normalize_and_filter_peaks, normalize_and_filter_peaks_multiple_spectra)
+from ms2query.create_new_library.add_classifire_classifications import \
+    _convert_to_dataframe
+from ms2query.create_new_library.library_files_creator import (
+    LibraryFilesCreator, create_ms2ds_embeddings, create_s2v_embeddings)
 
 
 def test_give_already_used_file_name(tmp_path, path_to_general_test_files, hundred_test_spectra):

tests/test_ms2library.py

@@ -4,7 +4,8 @@
 import pandas as pd
 from ms2query.ms2library import MS2Library, create_library_object_from_one_dir
 from ms2query.utils import SettingsRunMS2Query, column_names_for_output
-from tests.test_utils import check_correct_results_csv_file, check_expected_headers
+from tests.test_utils import (check_correct_results_csv_file,
+                              check_expected_headers)
 
 
 def test_get_all_ms2ds_scores(ms2library, test_spectra):

tests/test_run_ms2query.py

@@ -8,7 +8,8 @@
                                    zenodo_dois)
 from ms2query.utils import SettingsRunMS2Query
 from tests.test_ms2library import MS2Library
-from tests.test_utils import check_correct_results_csv_file, check_expected_headers
+from tests.test_utils import (check_correct_results_csv_file,
+                              check_expected_headers)
 
 
 if sys.version_info < (3, 8):