undo isort

notebooks/GNPS_15_12_2021/benchmarking/benchmark_speed_ms2query.py

@@ -6,10 +6,10 @@
 
 import os
 import time
-
 from ms2query.ms2library import MS2Library
 from ms2query.run_ms2query import run_complete_folder
 
+
 start_time = time.time()
 
 path_root = os.path.dirname(os.getcwd())

notebooks/GNPS_15_12_2021/data_processing_and_training_models/5_train_ms2deepscore_model.py

@@ -1,6 +1,5 @@
 import os
 import pickle
-
 import numpy as np
 import tensorflow as tf
 from ms2deepscore import SpectrumBinner
@@ -10,6 +9,7 @@
     EarlyStopping, ModelCheckpoint)
 from tensorflow.keras.optimizers import Adam  # pylint: disable=import-error
 
+
 path_data = "C:\\HSD\\OneDrive - Hochschule Düsseldorf\\Data\\ms2query"
 
 outfile = os.path.join(path_data, "GNPS_15_12_2021_pos_train.pickle")

notebooks/GNPS_15_12_2021/data_processing_and_training_models/6_train_spec2vec_model.py

@@ -1,12 +1,10 @@
 import os
-
 from matchms.filtering import (add_losses, add_precursor_mz, default_filters,
                                normalize_intensities,
                                reduce_to_number_of_peaks,
                                require_minimum_number_of_peaks, select_by_mz)
 from spec2vec import SpectrumDocument
 from spec2vec.model_building import train_new_word2vec_model
-
 from ms2query.utils import load_pickled_file
 
 

notebooks/GNPS_15_12_2021/data_processing_and_training_models/negative_mode/5_neg_train_ms2deepscore_model.py

@@ -1,6 +1,5 @@
 import os
 import pickle
-
 import numpy as np
 import tensorflow as tf
 from ms2deepscore import SpectrumBinner
@@ -10,6 +9,7 @@
     EarlyStopping, ModelCheckpoint)
 from tensorflow.keras.optimizers import Adam  # pylint: disable=import-error
 
+
 path_root = os.path.dirname(os.getcwd())
 
 path_data = os.path.join(path_root, "../../../data/libraries_and_models/gnps_15_12_2021/in_between_files")

notebooks/GNPS_15_12_2021/data_processing_and_training_models/negative_mode/6_neg_train_spec2vec_model.py

@@ -1,12 +1,10 @@
 import os
-
 from matchms.filtering import (add_losses, add_precursor_mz, default_filters,
                                normalize_intensities,
                                reduce_to_number_of_peaks,
                                require_minimum_number_of_peaks, select_by_mz)
 from spec2vec import SpectrumDocument
 from spec2vec.model_building import train_new_word2vec_model
-
 from ms2query.utils import load_pickled_file
 
 

setup.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 import os
-
 from setuptools import find_packages, setup
 
+
 here = os.path.abspath(os.path.dirname(__file__))
 
 version = {}