diff --git a/alphadia/calibration/models.py b/alphadia/calibration/models.py
index c508f7c8..a25ac3bb 100644
--- a/alphadia/calibration/models.py
+++ b/alphadia/calibration/models.py
@@ -1,7 +1,6 @@
 import numpy as np
-
-from sklearn.preprocessing import PolynomialFeatures
 from sklearn.base import BaseEstimator, RegressorMixin
+from sklearn.preprocessing import PolynomialFeatures
 
 
 class LOESSRegression(BaseEstimator, RegressorMixin):
diff --git a/alphadia/calibration/property.py b/alphadia/calibration/property.py
index 1391651f..0463c427 100644
--- a/alphadia/calibration/property.py
+++ b/alphadia/calibration/property.py
@@ -2,19 +2,20 @@
 import logging
 import pickle
 
-# alphadia imports
-from alphadia.plotting.utils import density_scatter
-from alphadia.calibration.models import LOESSRegression
+import numpy as np
 
 # third party imports
 import pandas as pd
-import numpy as np
-from matplotlib import pyplot as plt
-
 import sklearn.base
+from matplotlib import pyplot as plt
 from sklearn.linear_model import LinearRegression
-from sklearn.preprocessing import PolynomialFeatures
 from sklearn.pipeline import Pipeline
+from sklearn.preprocessing import PolynomialFeatures
+
+from alphadia.calibration.models import LOESSRegression
+
+# alphadia imports
+from alphadia.plotting.utils import density_scatter
 
 
 class Calibration:
diff --git a/alphadia/cli.py b/alphadia/cli.py
index 074a046d..4b78126c 100644
--- a/alphadia/cli.py
+++ b/alphadia/cli.py
@@ -1,25 +1,21 @@
 #!python
 
 # native imports
+# alpha family imports
+# third party imports
+import argparse
+import json
 import logging
+import os
+import re
 import sys
 
 import yaml
-import os
-import re
-import json
 
 # alphadia imports
 import alphadia
-from alphadia.workflow import reporting
 from alphadia import utils
-
-
-# alpha family imports
-
-# third party imports
-import argparse
-
+from alphadia.workflow import reporting
 
 logger = logging.getLogger()
 
diff --git a/alphadia/consensus/utils.py b/alphadia/consensus/utils.py
index 084ded8d..0e2ee794 100644
--- a/alphadia/consensus/utils.py
+++ b/alphadia/consensus/utils.py
@@ -1,5 +1,6 @@
 import logging
 import os
+
 import pandas as pd
 
 logger = logging.getLogger()
diff --git a/alphadia/data/alpharaw.py b/alphadia/data/alpharaw.py
index 299275c1..ca8edc49 100644
--- a/alphadia/data/alpharaw.py
+++ b/alphadia/data/alpharaw.py
@@ -1,24 +1,26 @@
 # native imports
+import logging
 import math
 import os
-import logging
 
-# alphadia imports
-from alphadia import utils
+import numba as nb
 
-from alphadia.data.stats import log_stats
+# third party imports
+import numpy as np
+import pandas as pd
+from alpharaw import mzml as alpharawmzml
+
+# TODO fix: "import resolves to its containing file"
+from alpharaw import sciex as alpharawsciex
 
 # alpha family imports
 from alpharaw import (
     thermo as alpharawthermo,
-)  # TODO fix: "import resolves to its containing file"
-from alpharaw import sciex as alpharawsciex
-from alpharaw import mzml as alpharawmzml
+)
 
-# third party imports
-import numpy as np
-import numba as nb
-import pandas as pd
+# alphadia imports
+from alphadia import utils
+from alphadia.data.stats import log_stats
 
 logger = logging.getLogger()
 
diff --git a/alphadia/data/bruker.py b/alphadia/data/bruker.py
index 5f04a053..8bdff4ba 100644
--- a/alphadia/data/bruker.py
+++ b/alphadia/data/bruker.py
@@ -1,23 +1,24 @@
 # native imports
+import logging
 import math
 import os
-import logging
 
-# alphadia imports
-from alphadia import utils
-from alphadia.data.stats import log_stats
+import alphatims.bruker
+import alphatims.tempmmap as tm
 
 # alpha family imports
 import alphatims.utils
-import alphatims.bruker
-import alphatims.tempmmap as tm
+import numba as nb
 
 # third party imports
 import numpy as np
-import numba as nb
 from numba.core import types
 from numba.experimental import jitclass
 
+# alphadia imports
+from alphadia import utils
+from alphadia.data.stats import log_stats
+
 logger = logging.getLogger()
 
 
diff --git a/alphadia/data/stats.py b/alphadia/data/stats.py
index 55c9dcc8..94a2f885 100644
--- a/alphadia/data/stats.py
+++ b/alphadia/data/stats.py
@@ -1,6 +1,7 @@
-import numpy as np
 import logging
 
+import numpy as np
+
 logger = logging.getLogger()
 
 
diff --git a/alphadia/fdr.py b/alphadia/fdr.py
index a365f467..5c9911cb 100644
--- a/alphadia/fdr.py
+++ b/alphadia/fdr.py
@@ -1,19 +1,18 @@
 # native imports
-import os
 import logging
+import os
 
-# alphadia imports
-
-# alpha family imports
-from alphadia import fragcomp
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
 
 # third party imports
 import pandas as pd
-import numpy as np
-import matplotlib.pyplot as plt
-import matplotlib as mpl
 import sklearn
 
+# alphadia imports
+# alpha family imports
+from alphadia import fragcomp
 
 logger = logging.getLogger()
 
diff --git a/alphadia/fdrexperimental.py b/alphadia/fdrexperimental.py
index 733c6d9b..21c28892 100644
--- a/alphadia/fdrexperimental.py
+++ b/alphadia/fdrexperimental.py
@@ -1,20 +1,18 @@
 # native imports
-from abc import ABC, abstractmethod
 import warnings
+from abc import ABC, abstractmethod
 from copy import deepcopy
 
 # alphadia imports
-
 # alpha family imports
-
 # third party imports
 import numpy as np
 import torch
 import torch.nn as nn
 import torch.optim as optim
 from sklearn import model_selection
-from tqdm import tqdm
 from torchmetrics.classification import BinaryAUROC
+from tqdm import tqdm
 
 
 class Classifier(ABC):
diff --git a/alphadia/fdrx/base.py b/alphadia/fdrx/base.py
index cd051759..f98161aa 100644
--- a/alphadia/fdrx/base.py
+++ b/alphadia/fdrx/base.py
@@ -2,18 +2,19 @@
 It is flexible with regards to the features, type of classifier and type of identifications (precursors, peptides, proteins).
 """
 
-import sklearn.base
-import pandas as pd
+import logging
+
 import numpy as np
-from alphadia.fragcomp import FragmentCompetition
-from alphadia.fdrx.stats import get_pep, add_q_values, keep_best
+import pandas as pd
+import sklearn.base
+
 from alphadia.fdrx.plotting import (
     _plot_fdr_curve,
     _plot_roc_curve,
     _plot_score_distribution,
 )
-
-import logging
+from alphadia.fdrx.stats import add_q_values, get_pep, keep_best
+from alphadia.fragcomp import FragmentCompetition
 
 logger = logging.getLogger()
 
diff --git a/alphadia/fdrx/plotting.py b/alphadia/fdrx/plotting.py
index 050fcb0b..efb8920f 100644
--- a/alphadia/fdrx/plotting.py
+++ b/alphadia/fdrx/plotting.py
@@ -1,5 +1,5 @@
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 import sklearn.metrics
 
 
diff --git a/alphadia/features.py b/alphadia/features.py
index ceb35132..14d2a60d 100644
--- a/alphadia/features.py
+++ b/alphadia/features.py
@@ -1,14 +1,14 @@
 # native imports
 
 # alphadia imports
-from alphadia import utils
-from alphadia.numba import numeric
+import numba as nb
 
 # alpha family imports
-
 # third party imports
 import numpy as np
-import numba as nb
+
+from alphadia import utils
+from alphadia.numba import numeric
 
 
 @nb.njit
diff --git a/alphadia/fragcomp.py b/alphadia/fragcomp.py
index 4245682d..bc7fc712 100644
--- a/alphadia/fragcomp.py
+++ b/alphadia/fragcomp.py
@@ -1,10 +1,11 @@
-from alphadia import utils
-from alphatims import utils as timsutils
 import logging
+
+import numba as nb
 import numpy as np
 import pandas as pd
+from alphatims import utils as timsutils
 
-import numba as nb
+from alphadia import utils
 
 logger = logging.getLogger(__name__)
 
diff --git a/alphadia/grouping.py b/alphadia/grouping.py
index 68f89a2f..0069cbf8 100644
--- a/alphadia/grouping.py
+++ b/alphadia/grouping.py
@@ -5,9 +5,10 @@
 # alpha family imports
 
 # third party imports
+from typing import Any
+
 import numpy as np
 import pandas as pd
-from typing import Any
 from numpy.typing import NDArray
 
 
diff --git a/alphadia/libtransform.py b/alphadia/libtransform.py
index 64390db8..03e78584 100644
--- a/alphadia/libtransform.py
+++ b/alphadia/libtransform.py
@@ -1,29 +1,27 @@
 # native imports
-from pathlib import Path
 import logging
-
 import os
 import typing
+from pathlib import Path
 
-# alphadia imports
-from alphadia import utils, validate
+# third party imports
+import numpy as np
+import pandas as pd
 
 # alpha family imports
 from alphabase.peptide import fragment
+from alphabase.peptide.fragment import get_charged_frag_types
 from alphabase.protein import fasta
-from alphabase.spectral_library.flat import SpecLibFlat
+from alphabase.protein.fasta import protease_dict
 from alphabase.spectral_library.base import SpecLibBase
-from alphabase.spectral_library.reader import LibraryReaderBase
 from alphabase.spectral_library.decoy import decoy_lib_provider
-from alphabase.peptide.fragment import get_charged_frag_types
-from alphabase.protein.fasta import protease_dict
-
-from peptdeep.protein.fasta import PredictSpecLibFasta
+from alphabase.spectral_library.flat import SpecLibFlat
+from alphabase.spectral_library.reader import LibraryReaderBase
 from peptdeep.pretrained_models import ModelManager
+from peptdeep.protein.fasta import PredictSpecLibFasta
 
-# third party imports
-import numpy as np
-import pandas as pd
+# alphadia imports
+from alphadia import utils, validate
 
 logger = logging.getLogger()
 
diff --git a/alphadia/numba/config.py b/alphadia/numba/config.py
index e416ed70..a38777d8 100644
--- a/alphadia/numba/config.py
+++ b/alphadia/numba/config.py
@@ -1,13 +1,12 @@
 # native imports
 
 # alphadia imports
-from alphadia.workflow import reporting
-
 # alpha family imports
-
 # third party imports
 import numpy as np
 
+from alphadia.workflow import reporting
+
 
 class JITConfig:
     """
diff --git a/alphadia/numba/fft.py b/alphadia/numba/fft.py
index 6f039c5d..8c93b57e 100644
--- a/alphadia/numba/fft.py
+++ b/alphadia/numba/fft.py
@@ -1,16 +1,15 @@
-import numpy as np
 import numba as nb
+import numpy as np
+from numba.extending import overload
+from rocket_fft import pocketfft
 from rocket_fft.overloads import (
-    ndshape_and_axes,
-    zeropad_or_crop,
-    increase_shape,
-    get_fct,
     decrease_shape,
+    get_fct,
+    increase_shape,
+    ndshape_and_axes,
     resize,
+    zeropad_or_crop,
 )
-from rocket_fft import pocketfft
-
-from numba.extending import overload
 
 
 class NumbaContextOnly(Exception):
diff --git a/alphadia/numba/fragments.py b/alphadia/numba/fragments.py
index f220e535..89c9e986 100644
--- a/alphadia/numba/fragments.py
+++ b/alphadia/numba/fragments.py
@@ -6,8 +6,8 @@
 
 # third party imports
 import numba as nb
-from numba.extending import overload_method
 import numpy as np
+from numba.extending import overload_method
 
 
 @nb.experimental.jitclass()
diff --git a/alphadia/numba/numeric.py b/alphadia/numba/numeric.py
index 629426c4..e6189c19 100644
--- a/alphadia/numba/numeric.py
+++ b/alphadia/numba/numeric.py
@@ -5,8 +5,8 @@
 # alpha family imports
 
 # third party imports
-import numpy as np
 import numba as nb
+import numpy as np
 
 
 @nb.njit(parallel=False, fastmath=True)
diff --git a/alphadia/outputaccumulator.py b/alphadia/outputaccumulator.py
index 1d40f706..9bfad363 100644
--- a/alphadia/outputaccumulator.py
+++ b/alphadia/outputaccumulator.py
@@ -22,19 +22,17 @@
 
 """
 
-import numba as nb
-import pandas as pd
-import numpy as np
-import os
+import logging
 import multiprocessing
+import os
 import threading
-from tqdm import tqdm
 
+import numba as nb
+import numpy as np
+import pandas as pd
 from alphabase.spectral_library import base
 from alphabase.spectral_library.flat import SpecLibFlat
-
-
-import logging
+from tqdm import tqdm
 
 logger = logging.getLogger()
 
diff --git a/alphadia/outputtransform.py b/alphadia/outputtransform.py
index 2a78e745..5dd2773f 100644
--- a/alphadia/outputtransform.py
+++ b/alphadia/outputtransform.py
@@ -1,36 +1,29 @@
 # native imports
 import logging
 import os
+from collections.abc import Iterator
 
+import directlfq.config as lfqconfig
+import directlfq.normalization as lfqnorm
+import directlfq.protein_intensity_estimation as lfqprot_estimation
+import directlfq.utils as lfqutils
+import numpy as np
+import pandas as pd
+from alphabase.peptide import precursor
+from alphabase.spectral_library import base
+from alphabase.spectral_library.base import SpecLibBase
+from sklearn.model_selection import train_test_split
+from sklearn.neural_network import MLPClassifier
+from sklearn.preprocessing import StandardScaler
 
-from alphadia import grouping, libtransform, utils
-from alphadia import fdr
+from alphadia import fdr, grouping, libtransform, utils
+from alphadia.consensus.utils import read_df, write_df
 from alphadia.outputaccumulator import (
-    TransferLearningAccumulator,
     AccumulationBroadcaster,
+    TransferLearningAccumulator,
 )
-from alphadia.consensus.utils import read_df, write_df
 from alphadia.transferlearning.train import FinetuneManager
 
-import pandas as pd
-import numpy as np
-from sklearn.preprocessing import StandardScaler
-from sklearn.model_selection import train_test_split
-from sklearn.neural_network import MLPClassifier
-
-
-from collections.abc import Iterator
-from alphabase.spectral_library import base
-from alphabase.spectral_library.base import SpecLibBase
-from alphabase.peptide import precursor
-
-
-import directlfq.utils as lfqutils
-import directlfq.normalization as lfqnorm
-import directlfq.protein_intensity_estimation as lfqprot_estimation
-import directlfq.config as lfqconfig
-
-
 logger = logging.getLogger()
 
 
diff --git a/alphadia/peakgroup/kernel.py b/alphadia/peakgroup/kernel.py
index 4b64b4e3..8cd37e28 100644
--- a/alphadia/peakgroup/kernel.py
+++ b/alphadia/peakgroup/kernel.py
@@ -1,16 +1,14 @@
 # native imports
 import logging
 
-
-# alphadia imports
-from alphadia.data import bruker, alpharaw
+import numba as nb
 
 # alpha family imports
-
 # third party imports
 import numpy as np
-import numba as nb
 
+# alphadia imports
+from alphadia.data import alpharaw, bruker
 
 logger = logging.getLogger()
 
diff --git a/alphadia/peakgroup/search.py b/alphadia/peakgroup/search.py
index 3a0ec6bb..8497c6c4 100644
--- a/alphadia/peakgroup/search.py
+++ b/alphadia/peakgroup/search.py
@@ -1,15 +1,7 @@
 # native imports
 import logging
-
 import os
 
-# alphadia imports
-from alphadia import utils
-from alphadia.numba import fragments, numeric, config, fft
-from alphadia import validate
-from alphadia.peakgroup.kernel import GaussianKernel
-from alphadia.peakgroup.utils import assemble_isotope_mz
-
 # alpha family imports
 import alphatims
 
@@ -18,6 +10,11 @@
 import numpy as np
 import pandas as pd
 
+# alphadia imports
+from alphadia import utils, validate
+from alphadia.numba import config, fft, fragments, numeric
+from alphadia.peakgroup.kernel import GaussianKernel
+from alphadia.peakgroup.utils import assemble_isotope_mz
 
 logger = logging.getLogger()
 
diff --git a/alphadia/peakgroup/utils.py b/alphadia/peakgroup/utils.py
index 192b7410..788c8f7e 100644
--- a/alphadia/peakgroup/utils.py
+++ b/alphadia/peakgroup/utils.py
@@ -1,8 +1,9 @@
-import numpy as np
 import numba as nb
-from alphadia.numba.fft import NumbaContextOnly
+import numpy as np
 from numba.extending import overload
 
+from alphadia.numba.fft import NumbaContextOnly
+
 
 def assemble_isotope_mz(mono_mz, charge, isotope_intensity):
     """
diff --git a/alphadia/planning.py b/alphadia/planning.py
index dc7fd485..cc04cd88 100644
--- a/alphadia/planning.py
+++ b/alphadia/planning.py
@@ -1,31 +1,30 @@
 # native imports
 import logging
-
-import socket
-from pathlib import Path
 import os
+import socket
 from datetime import datetime
+from pathlib import Path
 
-# alphadia imports
-from alphadia import libtransform, outputtransform
-from alphadia.workflow import peptidecentric, reporting
-from alphadia.workflow.config import Config
-import alphadia
-import alpharaw
 import alphabase
-import peptdeep
+import alpharaw
 import alphatims
 import directlfq
-
-# alpha family imports
-from alphabase.spectral_library.flat import SpecLibFlat
-from alphabase.spectral_library.base import SpecLibBase
+import peptdeep
 
 # third party imports
 import torch
-
 from alphabase.constants import modification
+from alphabase.spectral_library.base import SpecLibBase
+
+# alpha family imports
+from alphabase.spectral_library.flat import SpecLibFlat
+
+import alphadia
 
+# alphadia imports
+from alphadia import libtransform, outputtransform
+from alphadia.workflow import peptidecentric, reporting
+from alphadia.workflow.config import Config
 
 logger = logging.getLogger()
 
diff --git a/alphadia/plexscoring.py b/alphadia/plexscoring.py
index 2521f746..92731ab3 100644
--- a/alphadia/plexscoring.py
+++ b/alphadia/plexscoring.py
@@ -1,30 +1,26 @@
 # native imports
 import logging
 
+# alpha family imports
+import alphatims.utils
+import numba as nb
+import numpy as np
+
+# third party imports
+import pandas as pd
 
 # alphadia imports
-from alphadia import validate, utils, features, quadrupole
-from alphadia.numba import fragments
-from alphadia.data import bruker, alpharaw
+from alphadia import features, quadrupole, utils, validate
+from alphadia.data import alpharaw, bruker
+from alphadia.numba import config, fragments
 from alphadia.plotting.cycle import plot_cycle
 from alphadia.plotting.debug import (
     plot_fragment_profile,
-    plot_precursor,
     plot_fragments,
+    plot_precursor,
     plot_template,
 )
 
-# alpha family imports
-import alphatims.utils
-
-# third party imports
-import pandas as pd
-import numpy as np
-import numba as nb
-
-
-from alphadia.numba import config
-
 logger = logging.getLogger()
 
 NUM_FEATURES = 46
diff --git a/alphadia/plotting/cycle.py b/alphadia/plotting/cycle.py
index fef58695..dadaf692 100644
--- a/alphadia/plotting/cycle.py
+++ b/alphadia/plotting/cycle.py
@@ -1,14 +1,13 @@
 # native imports
 import os
 
-# alphadia imports
+import matplotlib.pyplot as plt
+import numpy as np
 
+# alphadia imports
 # alpha family imports
-
 # third party imports
 from matplotlib import patches
-import numpy as np
-import matplotlib.pyplot as plt
 
 
 def _generate_patch_collection_nomobility(
diff --git a/alphadia/plotting/debug.py b/alphadia/plotting/debug.py
index c1c8aa9d..d2d5ec86 100644
--- a/alphadia/plotting/debug.py
+++ b/alphadia/plotting/debug.py
@@ -1,15 +1,14 @@
 # native imports
 
 # alphadia imports
-from alphadia.plotting import utils
-from alphadia import quadrupole
-
 # alpha family imports
-
 # third party imports
 import matplotlib.pyplot as plt
 import numpy as np
 
+from alphadia import quadrupole
+from alphadia.plotting import utils
+
 
 def plot_fragment_profile(
     template,
diff --git a/alphadia/plotting/utils.py b/alphadia/plotting/utils.py
index 228d2093..526d0b03 100644
--- a/alphadia/plotting/utils.py
+++ b/alphadia/plotting/utils.py
@@ -5,10 +5,10 @@
 # alpha family imports
 
 # third party imports
-from scipy.stats import gaussian_kde
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+from scipy.stats import gaussian_kde
 
 
 def lighten_color(color, amount=0.5):
@@ -29,9 +29,10 @@ def lighten_color(color, amount=0.5):
     tuple
         lightened color
     """
-    import matplotlib.colors as mc
     import colorsys
 
+    import matplotlib.colors as mc
+
     try:
         c = mc.cnames[color]
     except KeyError:
diff --git a/alphadia/quadrupole.py b/alphadia/quadrupole.py
index 9505ea75..8917ecdc 100644
--- a/alphadia/quadrupole.py
+++ b/alphadia/quadrupole.py
@@ -1,17 +1,17 @@
 # native imports
 
 # alphadia imports
-from alphadia import utils
-
 # alpha family imports
 import alphatims.utils
 
 # third party imports
 import numba as nb
-from numba.experimental import jitclass
 import numpy as np
+from numba.experimental import jitclass
 from scipy.optimize import curve_fit
 
+from alphadia import utils
+
 
 @alphatims.utils.njit
 def logistic(x: np.array, mu: float, sigma: float):
diff --git a/alphadia/test_data_downloader.py b/alphadia/test_data_downloader.py
index 2e43037d..66e8b740 100644
--- a/alphadia/test_data_downloader.py
+++ b/alphadia/test_data_downloader.py
@@ -1,13 +1,13 @@
 """Download files from sharing links."""
 
-import os
 import base64
-import traceback
-from abc import ABC, abstractmethod
-from urllib.request import urlopen
-from urllib.request import urlretrieve
 import cgi
+import os
+import traceback
 import zipfile
+from abc import ABC, abstractmethod
+from urllib.request import urlopen, urlretrieve
+
 import progressbar
 
 
diff --git a/alphadia/transferlearning/metrics.py b/alphadia/transferlearning/metrics.py
index e05b1338..c10e7454 100644
--- a/alphadia/transferlearning/metrics.py
+++ b/alphadia/transferlearning/metrics.py
@@ -1,7 +1,7 @@
 import numpy as np
 import pandas as pd
-from peptdeep.utils import linear_regression
 from peptdeep.model.ms2 import calc_ms2_similarity
+from peptdeep.utils import linear_regression
 
 
 class TestMetricBase:
diff --git a/alphadia/transferlearning/train.py b/alphadia/transferlearning/train.py
index 30cbf07d..b72509cd 100644
--- a/alphadia/transferlearning/train.py
+++ b/alphadia/transferlearning/train.py
@@ -1,28 +1,27 @@
-import torch
-import pandas as pd
+import logging
+
 import numpy as np
-from tqdm import tqdm
-from torch.optim.lr_scheduler import LambdaLR
+import pandas as pd
+import torch
 from alphabase.peptide.fragment import remove_unused_fragments
+from peptdeep.model.charge import ChargeModelForModAASeq
+from peptdeep.model.model_interface import CallbackHandler, LR_SchedulerInterface
+from peptdeep.pretrained_models import ModelManager
+from peptdeep.settings import global_settings
+from torch.optim.lr_scheduler import LambdaLR
+from tqdm import tqdm
 
 from alphadia.transferlearning.metrics import (
-    MetricManager,
-    L1LossTestMetric,
-    LinearRegressionTestMetric,
     AbsErrorPercentileTestMetric,
-    CELossTestMetric,
     AccuracyTestMetric,
-    PrecisionRecallTestMetric,
+    CELossTestMetric,
+    L1LossTestMetric,
+    LinearRegressionTestMetric,
+    MetricManager,
     Ms2SimilarityTestMetric,
+    PrecisionRecallTestMetric,
 )
 
-from peptdeep.settings import global_settings
-from peptdeep.pretrained_models import ModelManager
-from peptdeep.model.model_interface import LR_SchedulerInterface, CallbackHandler
-from peptdeep.model.charge import ChargeModelForModAASeq
-import logging
-
-
 logger = logging.getLogger()
 
 settings = {
diff --git a/alphadia/utils.py b/alphadia/utils.py
index 0a64aa0b..8408b584 100644
--- a/alphadia/utils.py
+++ b/alphadia/utils.py
@@ -1,22 +1,20 @@
 # native imports
 import logging
-from ctypes import Structure, c_double
-import re
 import platform
-import torch
-
+import re
+from ctypes import Structure, c_double
 
 # alphadia imports
-
 # alpha family imports
 import alphatims.bruker
 import alphatims.utils
+import matplotlib.patches as patches
+import numba as nb
+import numpy as np
 
 # third party imports
 import pandas as pd
-import numpy as np
-import numba as nb
-import matplotlib.patches as patches
+import torch
 
 logger = logging.getLogger()
 
diff --git a/alphadia/validate.py b/alphadia/validate.py
index d5cb51b0..a8007d5f 100644
--- a/alphadia/validate.py
+++ b/alphadia/validate.py
@@ -1,13 +1,12 @@
 # native imports
 import logging
 
-# alphadia imports
+import numpy as np
 
+# alphadia imports
 # alpha family imports
-
 # third party imports
 import pandas as pd
-import numpy as np
 
 logger = logging.getLogger()
 
diff --git a/alphadia/workflow/base.py b/alphadia/workflow/base.py
index c0bacd1e..b06fc5d7 100644
--- a/alphadia/workflow/base.py
+++ b/alphadia/workflow/base.py
@@ -1,15 +1,14 @@
 # native imports
-import os
 import logging
+import os
 
+# alpha family imports
+from alphabase.spectral_library.base import SpecLibBase
 
 # alphadia imports
-from alphadia.data import bruker, alpharaw
+from alphadia.data import alpharaw, bruker
 from alphadia.workflow import manager, reporting
 
-# alpha family imports
-from alphabase.spectral_library.base import SpecLibBase
-
 # third party imports
 
 logger = logging.getLogger()
diff --git a/alphadia/workflow/config.py b/alphadia/workflow/config.py
index df3de56d..4af78454 100644
--- a/alphadia/workflow/config.py
+++ b/alphadia/workflow/config.py
@@ -22,13 +22,14 @@
 - But we still define the source of the update to be the first experiment that triggered the change.
 """
 
-import yaml
-from typing import Any
 import copy
 import json
-import pandas as pd
-import numpy as np
 import logging
+from typing import Any
+
+import numpy as np
+import pandas as pd
+import yaml
 
 logger = logging.getLogger()
 
diff --git a/alphadia/workflow/manager.py b/alphadia/workflow/manager.py
index fe3fa199..109280f9 100644
--- a/alphadia/workflow/manager.py
+++ b/alphadia/workflow/manager.py
@@ -1,24 +1,23 @@
 # native imports
+import logging
 import os
-import typing
 import pickle
+import typing
 from copy import deepcopy
-import logging
 
-# alphadia imports
-import alphadia
-from alphadia.calibration.property import calibration_model_provider, Calibration
-from alphadia import fdr
-from alphadia.workflow import reporting
+import numpy as np
 
 # alpha family imports
-
 # third party imports
 import pandas as pd
-import numpy as np
+import torch
 import xxhash
 
-import torch
+# alphadia imports
+import alphadia
+from alphadia import fdr
+from alphadia.calibration.property import Calibration, calibration_model_provider
+from alphadia.workflow import reporting
 
 logger = logging.getLogger()
 
diff --git a/alphadia/workflow/peptidecentric.py b/alphadia/workflow/peptidecentric.py
index a9c6f7b9..582f6e7c 100644
--- a/alphadia/workflow/peptidecentric.py
+++ b/alphadia/workflow/peptidecentric.py
@@ -1,22 +1,22 @@
 # native imports
 import logging
 
-
-# alphadia imports
-from alphadia import plexscoring, utils, fragcomp
-from alphadia import fdrexperimental as fdrx
-from alphadia.peakgroup import search
-from alphadia.workflow import manager, base
+# third party imports
+import numpy as np
+import pandas as pd
+import seaborn as sns
+from alphabase.peptide.fragment import get_charged_frag_types
 
 # alpha family imports
 from alphabase.spectral_library.base import SpecLibBase
 from alphabase.spectral_library.flat import SpecLibFlat
-from alphabase.peptide.fragment import get_charged_frag_types
 
-# third party imports
-import numpy as np
-import pandas as pd
-import seaborn as sns
+from alphadia import fdrexperimental as fdrx
+
+# alphadia imports
+from alphadia import fragcomp, plexscoring, utils
+from alphadia.peakgroup import search
+from alphadia.workflow import base, manager
 
 logger = logging.getLogger()
 
diff --git a/alphadia/workflow/reporting.py b/alphadia/workflow/reporting.py
index 1f53ae75..d08ec45d 100644
--- a/alphadia/workflow/reporting.py
+++ b/alphadia/workflow/reporting.py
@@ -1,23 +1,21 @@
 # native imports
-import traceback
+import base64
+import json
 import logging
 import os
 import time
-from datetime import datetime, timedelta
+import traceback
 import typing
 import warnings
-import json
-import base64
+from datetime import datetime, timedelta
 from io import BytesIO
 
 # alphadia imports
-
 # alpha family imports
-
 # third party imports
 import matplotlib
-from matplotlib.figure import Figure
 import numpy as np
+from matplotlib.figure import Figure
 
 # global variable which tracks if any logger has been initiated
 # As soon as its instantiated the default logger will be configured with a path to save the log file
diff --git a/pyproject.toml b/pyproject.toml
index ede85129..666bdd92 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,18 +72,10 @@ select =  [
     "B",
     # flake8-simplify
     "SIM",
+    # isort
+    "I",
 ]
 
-#    # Pyflakes
-#    "F",
-#    # pyupgrade
-#    "UP",
-#    # flake8-bugbear
-#    "B",
-#    # flake8-simplify
-#    "SIM",
-#    # isort
-#    "I",
 ignore = [
     "E501",  # Line too long  (ruff wraps code, but not docstrings)
     "B028",  #  No explicit `stacklevel` keyword argument found (for warnings)
diff --git a/release/pyinstaller/cli_hook.py b/release/pyinstaller/cli_hook.py
index c5836304..c412fa6c 100644
--- a/release/pyinstaller/cli_hook.py
+++ b/release/pyinstaller/cli_hook.py
@@ -1,10 +1,10 @@
 import sys
 
-
 if __name__ == "__main__":
-    from alphadia import cli
     import multiprocessing
 
+    from alphadia import cli
+
     # catch pyinstaller bug
     # subprocess.CalledProcessError: Command '['/Applications/alphaDIA.app/Contents/Frameworks/alphadia', '-sS', '-c', 'import platform; print(platform.mac_ver()[0])']' returned non-zero exit status 2.
     # [36481] Failed to execute script 'cli_hook' due to unhandled exception!
diff --git a/tests/e2e_tests/calc_metrics.py b/tests/e2e_tests/calc_metrics.py
index e0434d68..11e5b64d 100644
--- a/tests/e2e_tests/calc_metrics.py
+++ b/tests/e2e_tests/calc_metrics.py
@@ -6,15 +6,14 @@
 import os
 import sys
 from abc import ABC, abstractmethod
+from datetime import datetime
 from typing import Any
 
-import pandas as pd
-import neptune
-
 import matplotlib.pyplot as plt
-from datetime import datetime
+import neptune
+import pandas as pd
 
-from tests.e2e_tests.prepare_test_data import get_test_case, OUTPUT_DIR_NAME
+from tests.e2e_tests.prepare_test_data import OUTPUT_DIR_NAME, get_test_case
 
 NEPTUNE_PROJECT_NAME = os.environ.get("NEPTUNE_PROJECT_NAME")
 
diff --git a/tests/performance_tests/1_brunner_2022_1ng_all.py b/tests/performance_tests/1_brunner_2022_1ng_all.py
index c27529a3..6bd9f948 100644
--- a/tests/performance_tests/1_brunner_2022_1ng_all.py
+++ b/tests/performance_tests/1_brunner_2022_1ng_all.py
@@ -1,13 +1,11 @@
 import logging
-
-
 import os
 
 import matplotlib
+from alphabase.spectral_library.base import SpecLibBase
 
 from alphadia.extraction.planning import Plan
 from alphadia.test_data_downloader import DataShareDownloader
-from alphabase.spectral_library.base import SpecLibBase
 
 logging.basicConfig(
     format="%(asctime)s %(levelname)s: %(message)s", datefmt="%Y-%m-%d %H:%M:%S"
diff --git a/tests/performance_tests/diann_psm_extraction.py b/tests/performance_tests/diann_psm_extraction.py
index 38dc4392..29118a7d 100644
--- a/tests/performance_tests/diann_psm_extraction.py
+++ b/tests/performance_tests/diann_psm_extraction.py
@@ -1,23 +1,20 @@
 import logging
-
-from alphadia.test_data_downloader import DataShareDownloader
-
 import os
-import neptune.new as neptune
 import pathlib
 import socket
 
+import neptune.new as neptune
 
-from alphadia.extraction.planning import Plan
 from alphadia.extraction.calibration import RunCalibration
+from alphadia.extraction.candidateselection import MS1CentricCandidateSelection
 from alphadia.extraction.data import TimsTOFDIA
+from alphadia.extraction.planning import Plan
 from alphadia.extraction.scoring import (
+    MS2ExtractionWorkflow,
     fdr_correction,
     unpack_fragment_info,
-    MS2ExtractionWorkflow,
 )
-from alphadia.extraction.candidateselection import MS1CentricCandidateSelection
-
+from alphadia.test_data_downloader import DataShareDownloader
 
 logging.basicConfig(
     format="%(asctime)s %(levelname)s: %(message)s", datefmt="%Y-%m-%d %H:%M:%S"
diff --git a/tests/performance_tests/fdr_test.py b/tests/performance_tests/fdr_test.py
index 609862ce..e717e440 100644
--- a/tests/performance_tests/fdr_test.py
+++ b/tests/performance_tests/fdr_test.py
@@ -1,14 +1,15 @@
 # setup basic argpasrse comand line script to run the fdr test
 # with the options --threads and --size between 0 and 100%
 
-import matplotlib
 import argparse
 import tempfile
-import pandas as pd
-import torch
-import numpy as np
 import time
+
+import matplotlib
 import neptune
+import numpy as np
+import pandas as pd
+import torch
 
 import alphadia
 from alphadia import fdr, fdrexperimental
diff --git a/tests/unit_tests/conftest.py b/tests/unit_tests/conftest.py
index f4097b3f..17201d33 100644
--- a/tests/unit_tests/conftest.py
+++ b/tests/unit_tests/conftest.py
@@ -1,11 +1,12 @@
-import pytest
 import os
 import re
-import pandas as pd
-import numpy as np
-import matplotlib
 import tempfile
 
+import matplotlib
+import numpy as np
+import pandas as pd
+import pytest
+
 matplotlib.use("Agg")
 from matplotlib import pyplot as plt
 
diff --git a/tests/unit_tests/test_calibration_models.py b/tests/unit_tests/test_calibration_models.py
index cf5ffea8..12a83eb9 100644
--- a/tests/unit_tests/test_calibration_models.py
+++ b/tests/unit_tests/test_calibration_models.py
@@ -1,5 +1,6 @@
-import pytest
 import numpy as np
+import pytest
+
 from alphadia.calibration.models import LOESSRegression
 
 
diff --git a/tests/unit_tests/test_calibration_property.py b/tests/unit_tests/test_calibration_property.py
index 8291edb6..cadee274 100644
--- a/tests/unit_tests/test_calibration_property.py
+++ b/tests/unit_tests/test_calibration_property.py
@@ -1,14 +1,13 @@
-from alphadia.calibration.property import Calibration
-from sklearn.linear_model import LinearRegression
-from alphadia.calibration.models import LOESSRegression
+import os
+import tempfile
 
 import numpy as np
 import pandas as pd
-
 import pytest
+from sklearn.linear_model import LinearRegression
 
-import tempfile
-import os
+from alphadia.calibration.models import LOESSRegression
+from alphadia.calibration.property import Calibration
 
 
 def test_uninitialized_calibration():
diff --git a/tests/unit_tests/test_config_updater.py b/tests/unit_tests/test_config_updater.py
index 9f783c43..61696e0a 100644
--- a/tests/unit_tests/test_config_updater.py
+++ b/tests/unit_tests/test_config_updater.py
@@ -1,6 +1,7 @@
-import yaml
 from io import StringIO
+
 import pandas as pd
+import yaml
 
 from alphadia.workflow.config import Config, get_update_table
 
diff --git a/tests/unit_tests/test_consensus.py b/tests/unit_tests/test_consensus.py
index 65aa5b19..10558525 100644
--- a/tests/unit_tests/test_consensus.py
+++ b/tests/unit_tests/test_consensus.py
@@ -1,7 +1,9 @@
-import pytest
-import pandas as pd
 import os
+
+import pandas as pd
+import pytest
 from conftest import random_tempfolder
+
 from alphadia.consensus.utils import read_df, write_df
 
 
diff --git a/tests/unit_tests/test_data.py b/tests/unit_tests/test_data.py
index 57509738..d2fa02d5 100644
--- a/tests/unit_tests/test_data.py
+++ b/tests/unit_tests/test_data.py
@@ -1,7 +1,7 @@
-from alphadia.data import bruker, alpharaw
-
-import pytest
 import numpy as np
+import pytest
+
+from alphadia.data import alpharaw, bruker
 
 
 def test_transpose():
diff --git a/tests/unit_tests/test_fdr.py b/tests/unit_tests/test_fdr.py
index 8246b43f..8042ce7d 100644
--- a/tests/unit_tests/test_fdr.py
+++ b/tests/unit_tests/test_fdr.py
@@ -1,19 +1,17 @@
 import os
+import tempfile
 import warnings
+
+import matplotlib
 import numpy as np
 import pandas as pd
 import pytest
-import tempfile
+import torch
 
 from alphadia import fdr
 from alphadia import fdrexperimental as fdrx
 from alphadia.workflow import manager
 
-
-import torch
-
-import matplotlib
-
 feature_columns = [
     "base_width_mobility",
     "base_width_rt",
diff --git a/tests/unit_tests/test_fdrx_base.py b/tests/unit_tests/test_fdrx_base.py
index 1a918bb9..75694a7f 100644
--- a/tests/unit_tests/test_fdrx_base.py
+++ b/tests/unit_tests/test_fdrx_base.py
@@ -1,9 +1,11 @@
+from unittest.mock import patch
+
 import numpy as np
 import pandas as pd
-from unittest.mock import patch
-from alphadia.fdrx.base import TargetDecoyFDR
 from sklearn.linear_model import LogisticRegression
 
+from alphadia.fdrx.base import TargetDecoyFDR
+
 
 @patch("matplotlib.pyplot.show")
 def test_target_decoy_fdr(mock_show):
diff --git a/tests/unit_tests/test_fdrx_plotting.py b/tests/unit_tests/test_fdrx_plotting.py
index f2211ca7..1e1ee39e 100644
--- a/tests/unit_tests/test_fdrx_plotting.py
+++ b/tests/unit_tests/test_fdrx_plotting.py
@@ -1,10 +1,12 @@
-import numpy as np
-import matplotlib.pyplot as plt
 from unittest.mock import patch
+
+import matplotlib.pyplot as plt
+import numpy as np
+
 from alphadia.fdrx.plotting import (
-    _plot_score_distribution,
-    _plot_roc_curve,
     _plot_fdr_curve,
+    _plot_roc_curve,
+    _plot_score_distribution,
 )
 
 
diff --git a/tests/unit_tests/test_fdrx_stats.py b/tests/unit_tests/test_fdrx_stats.py
index b51c4d48..929b52f1 100644
--- a/tests/unit_tests/test_fdrx_stats.py
+++ b/tests/unit_tests/test_fdrx_stats.py
@@ -1,6 +1,7 @@
-from alphadia.fdrx.stats import keep_best, get_pep, add_q_values, fdr_to_q_values
-import pandas as pd
 import numpy as np
+import pandas as pd
+
+from alphadia.fdrx.stats import add_q_values, fdr_to_q_values, get_pep, keep_best
 
 
 def test_keep_best():
diff --git a/tests/unit_tests/test_finetunemetrics.py b/tests/unit_tests/test_finetunemetrics.py
index 5c03e52f..b2af071b 100644
--- a/tests/unit_tests/test_finetunemetrics.py
+++ b/tests/unit_tests/test_finetunemetrics.py
@@ -2,19 +2,21 @@
 Test the metrics module.
 """
 
+from math import isclose
+
 import numpy as np
+from scipy import linalg, stats
+from sklearn.metrics import accuracy_score, log_loss, precision_score, recall_score
+
 from alphadia.transferlearning.metrics import (
-    LinearRegressionTestMetric,
     AbsErrorPercentileTestMetric,
-    L1LossTestMetric,
-    CELossTestMetric,
     AccuracyTestMetric,
-    PrecisionRecallTestMetric,
+    CELossTestMetric,
+    L1LossTestMetric,
+    LinearRegressionTestMetric,
     MetricManager,
+    PrecisionRecallTestMetric,
 )
-from scipy import stats, linalg
-from math import isclose
-from sklearn.metrics import log_loss, accuracy_score, precision_score, recall_score
 
 
 def get_regression_test_input():
diff --git a/tests/unit_tests/test_fragcomp.py b/tests/unit_tests/test_fragcomp.py
index 64a874bf..ce8d24cb 100644
--- a/tests/unit_tests/test_fragcomp.py
+++ b/tests/unit_tests/test_fragcomp.py
@@ -1,7 +1,8 @@
-from alphadia import fragcomp
 import numpy as np
 import pandas as pd
 
+from alphadia import fragcomp
+
 
 def test_fragment_overlap():
     frag_mz_1 = np.array([100, 200, 300, 400, 500, 600, 700, 800, 900, 1000])
diff --git a/tests/unit_tests/test_grouping.py b/tests/unit_tests/test_grouping.py
index 57fda6c5..2b5acf02 100644
--- a/tests/unit_tests/test_grouping.py
+++ b/tests/unit_tests/test_grouping.py
@@ -1,6 +1,7 @@
-import pytest
 import numpy as np
 import pandas as pd
+import pytest
+
 from alphadia import grouping
 
 
diff --git a/tests/unit_tests/test_libtransform.py b/tests/unit_tests/test_libtransform.py
index 426de399..7326171c 100644
--- a/tests/unit_tests/test_libtransform.py
+++ b/tests/unit_tests/test_libtransform.py
@@ -1,4 +1,5 @@
 import tempfile
+
 import numpy as np
 
 from alphadia import libtransform
diff --git a/tests/unit_tests/test_numba.py b/tests/unit_tests/test_numba.py
index 9ad30275..c9c40f02 100644
--- a/tests/unit_tests/test_numba.py
+++ b/tests/unit_tests/test_numba.py
@@ -2,16 +2,14 @@
 
 # local
 from alphadia import utils
-from alphadia.numba.fragments import get_ion_group_mapping
-
 from alphadia.numba.fft import convolve_fourier
-
+from alphadia.numba.fragments import get_ion_group_mapping
 from alphadia.numba.numeric import (
-    symetric_limits_1d,
-    symetric_limits_2d,
-    save_corrcoeff,
     fragment_correlation,
     fragment_correlation_different,
+    save_corrcoeff,
+    symetric_limits_1d,
+    symetric_limits_2d,
 )
 
 
diff --git a/tests/unit_tests/test_numba_fft.py b/tests/unit_tests/test_numba_fft.py
index 20065e34..acfd4241 100644
--- a/tests/unit_tests/test_numba_fft.py
+++ b/tests/unit_tests/test_numba_fft.py
@@ -1,8 +1,8 @@
-import pytest
-import numpy as np
 import numba as nb
+import numpy as np
+import pytest
 
-from alphadia.numba.fft import rfft2, irfft2, convolve_fourier
+from alphadia.numba.fft import convolve_fourier, irfft2, rfft2
 
 
 @pytest.mark.parametrize("shape", [(100, 2), (2, 100), (100, 100)])
diff --git a/tests/unit_tests/test_numba_numeric.py b/tests/unit_tests/test_numba_numeric.py
index ea7ee94b..c6510897 100644
--- a/tests/unit_tests/test_numba_numeric.py
+++ b/tests/unit_tests/test_numba_numeric.py
@@ -1,4 +1,5 @@
 import numpy as np
+
 from alphadia.numba.numeric import search_sorted_left
 
 
diff --git a/tests/unit_tests/test_outputaccumulator.py b/tests/unit_tests/test_outputaccumulator.py
index 063687d0..5e51d99f 100644
--- a/tests/unit_tests/test_outputaccumulator.py
+++ b/tests/unit_tests/test_outputaccumulator.py
@@ -1,11 +1,13 @@
 import os
+import shutil
 import tempfile
+
 import numpy as np
 import pandas as pd
-from conftest import mock_precursor_df, mock_fragment_df
-from alphadia import outputtransform
 from alphabase.spectral_library.base import SpecLibBase
-import shutil
+from conftest import mock_fragment_df, mock_precursor_df
+
+from alphadia import outputtransform
 
 
 def prepare_input_data():
diff --git a/tests/unit_tests/test_outputtransform.py b/tests/unit_tests/test_outputtransform.py
index bc492f11..350432e9 100644
--- a/tests/unit_tests/test_outputtransform.py
+++ b/tests/unit_tests/test_outputtransform.py
@@ -1,10 +1,12 @@
-import tempfile
-from alphadia import outputtransform
-import pandas as pd
-import numpy as np
 import os
 import shutil
-from conftest import mock_precursor_df, mock_fragment_df
+import tempfile
+
+import numpy as np
+import pandas as pd
+from conftest import mock_fragment_df, mock_precursor_df
+
+from alphadia import outputtransform
 
 
 def test_output_transform():
diff --git a/tests/unit_tests/test_peakgroup_kernel.py b/tests/unit_tests/test_peakgroup_kernel.py
index a60a6ea3..d37c8d45 100644
--- a/tests/unit_tests/test_peakgroup_kernel.py
+++ b/tests/unit_tests/test_peakgroup_kernel.py
@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 from alphadia.peakgroup.kernel import GaussianKernel, multivariate_normal
 
 
diff --git a/tests/unit_tests/test_peakgroup_utils.py b/tests/unit_tests/test_peakgroup_utils.py
index 5387e00a..28878880 100644
--- a/tests/unit_tests/test_peakgroup_utils.py
+++ b/tests/unit_tests/test_peakgroup_utils.py
@@ -1,8 +1,9 @@
-from alphadia.peakgroup.utils import assemble_isotope_mz
 import numba as nb
 import numpy as np
 import pytest
 
+from alphadia.peakgroup.utils import assemble_isotope_mz
+
 
 @nb.njit
 def wrap_assemble_isotope_mz(mz, charge, intensities):
diff --git a/tests/unit_tests/test_planning.py b/tests/unit_tests/test_planning.py
index 8b8c5cd9..b8bb38c8 100644
--- a/tests/unit_tests/test_planning.py
+++ b/tests/unit_tests/test_planning.py
@@ -1,9 +1,11 @@
+import os
 import tempfile
+
 import pytest
-import os
+from alphabase.constants import _const
+
 from alphadia import planning
 from alphadia.test_data_downloader import DataShareDownloader
-from alphabase.constants import _const
 
 
 @pytest.mark.slow
diff --git a/tests/unit_tests/test_plotting.py b/tests/unit_tests/test_plotting.py
index c1b78552..87a7c308 100644
--- a/tests/unit_tests/test_plotting.py
+++ b/tests/unit_tests/test_plotting.py
@@ -1,9 +1,8 @@
 import matplotlib
 import numpy as np
 
-from alphadia.plotting.utils import lighten_color
-
 from alphadia.plotting.cycle import plot_cycle
+from alphadia.plotting.utils import lighten_color
 
 
 def test_lighten_color():
diff --git a/tests/unit_tests/test_quadrupole.py b/tests/unit_tests/test_quadrupole.py
index c8876338..b3a13bb0 100644
--- a/tests/unit_tests/test_quadrupole.py
+++ b/tests/unit_tests/test_quadrupole.py
@@ -1,13 +1,13 @@
+# global
+import numpy as np
+import pytest
+
 from alphadia.quadrupole import (
     SimpleQuadrupole,
     logistic_rectangle,
     quadrupole_transfer_function_single,
 )
 
-# global
-import numpy as np
-import pytest
-
 
 @pytest.fixture()
 def get_fake_quadrupole():
diff --git a/tests/unit_tests/test_reporting.py b/tests/unit_tests/test_reporting.py
index 8af88641..a6e1aba2 100644
--- a/tests/unit_tests/test_reporting.py
+++ b/tests/unit_tests/test_reporting.py
@@ -1,12 +1,12 @@
-from matplotlib import pyplot as plt
-import numpy as np
-import os
 import logging
-import time
+import os
 import sys
-import pytest
+import time
 
+import numpy as np
+import pytest
 from conftest import random_tempfolder
+from matplotlib import pyplot as plt
 
 from alphadia.workflow import reporting
 
diff --git a/tests/unit_tests/test_utils.py b/tests/unit_tests/test_utils.py
index 64bce9a3..bc10da03 100644
--- a/tests/unit_tests/test_utils.py
+++ b/tests/unit_tests/test_utils.py
@@ -4,23 +4,22 @@
 # builtin
 
 # local
+# global
+import numpy as np
+import pandas as pd
+import pytest
+
 from alphadia.utils import (
     amean0,
     amean1,
     calculate_score_groups,
-    wsl_to_windows,
-    windows_to_wsl,
-    merge_missing_columns,
     get_torch_device,
+    merge_missing_columns,
+    windows_to_wsl,
+    wsl_to_windows,
 )
 
 
-# global
-import numpy as np
-import pandas as pd
-import pytest
-
-
 @pytest.mark.parametrize("use_gpu", [True, False])
 def test_get_torch_device(use_gpu):
     # given
diff --git a/tests/unit_tests/test_workflow.py b/tests/unit_tests/test_workflow.py
index be8de860..0a3362d4 100644
--- a/tests/unit_tests/test_workflow.py
+++ b/tests/unit_tests/test_workflow.py
@@ -1,16 +1,17 @@
-import tempfile
 import os
 import shutil
+import tempfile
+from pathlib import Path
+
 import numpy as np
 import pandas as pd
-import yaml
 import pytest
-from pathlib import Path
-
-from alphadia.calibration.property import Calibration
+import yaml
 from sklearn.linear_model import LinearRegression
+
 from alphadia.calibration.models import LOESSRegression
-from alphadia.workflow import manager, base
+from alphadia.calibration.property import Calibration
+from alphadia.workflow import base, manager
 
 
 def test_base_manager():