diff --git a/pyproject.toml b/pyproject.toml
index 048b438df..a64cb9736 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,24 +1,24 @@
 [build-system]
 requires = [
-  'setuptools>=40.6.0',
-  'wheel'
+  "setuptools>=40.6.0",
+  "wheel"
 ]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 88
-python-version = ['py36']
-include = '\.pyi?$'
-exclude = '''
+target-version = ["py38"]
+include = "\\.pyi?$"
+exclude = """
 
 (
   /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
+      \\.eggs         # exclude a few common directories in the
+    | \\.git          # root of the project
+    | \\.hg
+    | \\.mypy_cache
+    | \\.tox
+    | \\.venv
     | _build
     | buck-out
     | build
@@ -27,4 +27,4 @@ exclude = '''
     | benchmarks
   )/
 )
-'''
+"""
diff --git a/src/cobra/core/configuration.py b/src/cobra/core/configuration.py
index 43512261c..576fcf6ec 100644
--- a/src/cobra/core/configuration.py
+++ b/src/cobra/core/configuration.py
@@ -1,6 +1,5 @@
 """Provide a global configuration object."""
 
-
 import logging
 import pathlib
 import types
diff --git a/src/cobra/core/species.py b/src/cobra/core/species.py
index 39749fcd0..486ea23a9 100644
--- a/src/cobra/core/species.py
+++ b/src/cobra/core/species.py
@@ -1,6 +1,5 @@
 """Define the Species class, used as a base for Gene and Metabolite."""
 
-
 from copy import deepcopy
 from typing import TYPE_CHECKING, FrozenSet, Optional
 
diff --git a/src/cobra/exceptions.py b/src/cobra/exceptions.py
index 6736b1e72..95cf1155a 100644
--- a/src/cobra/exceptions.py
+++ b/src/cobra/exceptions.py
@@ -1,4 +1,5 @@
 """Module for shared exceptions in the Cobra package."""
+
 import optlang.interface
 
 
diff --git a/src/cobra/flux_analysis/gapfilling.py b/src/cobra/flux_analysis/gapfilling.py
index 0347f3925..0f572bf75 100644
--- a/src/cobra/flux_analysis/gapfilling.py
+++ b/src/cobra/flux_analysis/gapfilling.py
@@ -1,6 +1,5 @@
 """Provide the base class and utility function for gap filling."""
 
-
 import logging
 from typing import TYPE_CHECKING, Dict, List, Optional, Union
 
diff --git a/src/cobra/flux_analysis/loopless.py b/src/cobra/flux_analysis/loopless.py
index e218f53ac..ca09b862c 100644
--- a/src/cobra/flux_analysis/loopless.py
+++ b/src/cobra/flux_analysis/loopless.py
@@ -1,6 +1,5 @@
 """Provide functions to remove thermodynamically infeasible loops."""
 
-
 from typing import TYPE_CHECKING, Dict, Optional, Union
 
 import numpy as np
diff --git a/src/cobra/flux_analysis/variability.py b/src/cobra/flux_analysis/variability.py
index 4b1066f2b..38cd937f4 100644
--- a/src/cobra/flux_analysis/variability.py
+++ b/src/cobra/flux_analysis/variability.py
@@ -1,6 +1,5 @@
 """Provide variability based methods such as flux variability or gene essentiality."""
 
-
 import logging
 from typing import TYPE_CHECKING, List, Optional, Set, Tuple, Union
 from warnings import warn
diff --git a/src/cobra/io/__init__.py b/src/cobra/io/__init__.py
index 66d8a1b92..f81680c1c 100644
--- a/src/cobra/io/__init__.py
+++ b/src/cobra/io/__init__.py
@@ -1,6 +1,5 @@
 """Provide functions for loading and saving metabolic models."""
 
-
 from cobra.io.dict import model_from_dict, model_to_dict
 from cobra.io.json import from_json, load_json_model, save_json_model, to_json
 from cobra.io.mat import load_matlab_model, save_matlab_model
diff --git a/src/cobra/io/json.py b/src/cobra/io/json.py
index f6bded5bc..6ffbebcf7 100644
--- a/src/cobra/io/json.py
+++ b/src/cobra/io/json.py
@@ -1,4 +1,5 @@
 """Provide functions for I/O in JSON format."""
+
 from pathlib import Path
 from typing import IO, TYPE_CHECKING, Any, Union
 
@@ -72,7 +73,7 @@ def save_json_model(
     filename: Union[str, Path, IO],
     sort: bool = False,
     pretty: bool = False,
-    **kwargs: Any
+    **kwargs: Any,
 ) -> None:
     """Write the cobra model to a file in JSON format.
 
diff --git a/src/cobra/io/mat.py b/src/cobra/io/mat.py
index e37f7cf5d..c3a7be0bd 100644
--- a/src/cobra/io/mat.py
+++ b/src/cobra/io/mat.py
@@ -213,19 +213,23 @@ def _cell_to_str_list(
     """
     if str_prefix and pattern_split:
         return [
-            [
-                str_prefix + str_found if str_prefix not in str_found else str_found
-                for str_found in pattern_split.findall(str(each_cell[0][0]))
-            ]
-            if np.size(each_cell[0])
-            else empty_value
+            (
+                [
+                    str_prefix + str_found if str_prefix not in str_found else str_found
+                    for str_found in pattern_split.findall(str(each_cell[0][0]))
+                ]
+                if np.size(each_cell[0])
+                else empty_value
+            )
             for each_cell in m_cell
         ]
     elif pattern_split:
         return [
-            pattern_split.findall(str(each_cell[0][0]))
-            if np.size(each_cell[0])
-            else empty_value
+            (
+                pattern_split.findall(str(each_cell[0][0]))
+                if np.size(each_cell[0])
+                else empty_value
+            )
             for each_cell in m_cell
         ]
     else:
@@ -481,9 +485,11 @@ def mat_parse_notes(
             # things like PMC or OMIM, but those are placed as string in notes.
             _notes = _cell_to_str_list(mat_struct[caseunfold[mat_key]][0, 0])
             notes[name] = [
-                _pubmed_re.sub("", x).strip()
-                if x and len(_pubmed_re.sub("", x).strip())
-                else None
+                (
+                    _pubmed_re.sub("", x).strip()
+                    if x and len(_pubmed_re.sub("", x).strip())
+                    else None
+                )
                 for x in _notes
             ]
         elif mat_key == "rxnConfidenceScores".casefold():
diff --git a/src/cobra/io/sbml.py b/src/cobra/io/sbml.py
index 4d07f9326..5445ce951 100644
--- a/src/cobra/io/sbml.py
+++ b/src/cobra/io/sbml.py
@@ -614,9 +614,9 @@ def _sbml_to_model(
                 {
                     "familyName": c.getFamilyName() if c.isSetFamilyName() else None,
                     "givenName": c.getGivenName() if c.isSetGivenName() else None,
-                    "organisation": c.getOrganisation()
-                    if c.isSetOrganisation()
-                    else None,
+                    "organisation": (
+                        c.getOrganisation() if c.isSetOrganisation() else None
+                    ),
                     "email": c.getEmail() if c.isSetEmail() else None,
                 }
             )
diff --git a/src/cobra/io/web/__init__.py b/src/cobra/io/web/__init__.py
index 2d4625a2e..d55a41985 100644
--- a/src/cobra/io/web/__init__.py
+++ b/src/cobra/io/web/__init__.py
@@ -1,6 +1,5 @@
 """Provide functionality to access remote model repositories."""
 
-
 from .abstract_model_repository import AbstractModelRepository
 from .bigg_models_repository import BiGGModels
 from .biomodels_repository import BioModels
diff --git a/src/cobra/io/web/abstract_model_repository.py b/src/cobra/io/web/abstract_model_repository.py
index fa547cf1a..9db3cefc4 100644
--- a/src/cobra/io/web/abstract_model_repository.py
+++ b/src/cobra/io/web/abstract_model_repository.py
@@ -1,6 +1,5 @@
 """Provide an abstract base class that describes a remote model repository."""
 
-
 from abc import ABC, abstractmethod
 from typing import Union
 
diff --git a/src/cobra/io/web/bigg_models_repository.py b/src/cobra/io/web/bigg_models_repository.py
index e961734a1..23e6fd660 100644
--- a/src/cobra/io/web/bigg_models_repository.py
+++ b/src/cobra/io/web/bigg_models_repository.py
@@ -1,6 +1,5 @@
 """Provide a concrete implementation of the BioModels repository interface."""
 
-
 from io import BytesIO
 
 import httpx
diff --git a/src/cobra/io/web/biomodels_repository.py b/src/cobra/io/web/biomodels_repository.py
index fa53cf4c1..77bbffe06 100644
--- a/src/cobra/io/web/biomodels_repository.py
+++ b/src/cobra/io/web/biomodels_repository.py
@@ -1,6 +1,5 @@
 """Provide functions for loading metabolic models over the wire."""
 
-
 import gzip
 from io import BytesIO
 from typing import List
diff --git a/src/cobra/io/web/cobrapy_repository.py b/src/cobra/io/web/cobrapy_repository.py
index 9a1d225f1..969bbd5cf 100644
--- a/src/cobra/io/web/cobrapy_repository.py
+++ b/src/cobra/io/web/cobrapy_repository.py
@@ -1,6 +1,5 @@
 """Provide functions for loading metabolic models from local package data."""
 
-
 import importlib_resources
 
 import cobra.data
diff --git a/src/cobra/io/web/load.py b/src/cobra/io/web/load.py
index 5244904ac..21bd619a7 100644
--- a/src/cobra/io/web/load.py
+++ b/src/cobra/io/web/load.py
@@ -1,6 +1,5 @@
 """Provide a function ``load_model`` to access remote model repositories."""
 
-
 import gzip
 import logging
 from typing import TYPE_CHECKING, Iterable
diff --git a/src/cobra/manipulation/delete.py b/src/cobra/manipulation/delete.py
index 1fe8c0a4d..0ef6454f5 100644
--- a/src/cobra/manipulation/delete.py
+++ b/src/cobra/manipulation/delete.py
@@ -1,4 +1,5 @@
 """Provide functions for pruning reactions, metabolites and genes."""
+
 import logging
 from ast import And, BoolOp, Name, NodeTransformer
 from functools import partial
diff --git a/src/cobra/sampling/achr.py b/src/cobra/sampling/achr.py
index e3d3e842e..7d56ee558 100644
--- a/src/cobra/sampling/achr.py
+++ b/src/cobra/sampling/achr.py
@@ -94,7 +94,7 @@ def __init__(
         thinning: int = 100,
         nproj: Optional[int] = None,
         seed: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         """Initialize a new ACHRSampler."""
         super().__init__(model, thinning, nproj=nproj, seed=seed, **kwargs)
diff --git a/src/cobra/sampling/optgp.py b/src/cobra/sampling/optgp.py
index fad9ee4f7..97231c8e2 100644
--- a/src/cobra/sampling/optgp.py
+++ b/src/cobra/sampling/optgp.py
@@ -1,6 +1,5 @@
 """Provide the OptGP sampler class and helper functions."""
 
-
 from typing import TYPE_CHECKING, Dict, Optional, Tuple
 
 import numpy as np
@@ -110,10 +109,10 @@ def __init__(
         processes: Optional[int] = None,
         nproj: Optional[int] = None,
         seed: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         """Initialize a new OptGPSampler."""
-        super().__init__(model, thinning, nproj=nproj, seed=seed, *kwargs)
+        super().__init__(model, thinning, nproj=nproj, seed=seed, **kwargs)
         self.generate_fva_warmup()
 
         if processes is None:
diff --git a/src/cobra/summary/metabolite_summary.py b/src/cobra/summary/metabolite_summary.py
index f9fdef4ac..3dbb03de8 100644
--- a/src/cobra/summary/metabolite_summary.py
+++ b/src/cobra/summary/metabolite_summary.py
@@ -1,6 +1,5 @@
 """Provide the metabolite summary class."""
 
-
 import logging
 from operator import attrgetter
 from textwrap import shorten
diff --git a/src/cobra/summary/model_summary.py b/src/cobra/summary/model_summary.py
index 832fe6f15..7ee3ecc1c 100644
--- a/src/cobra/summary/model_summary.py
+++ b/src/cobra/summary/model_summary.py
@@ -1,6 +1,5 @@
 """Provide the model summary class."""
 
-
 import logging
 from operator import attrgetter
 from typing import TYPE_CHECKING, Dict, List, Optional, Union
diff --git a/src/cobra/summary/reaction_summary.py b/src/cobra/summary/reaction_summary.py
index a8e7f20ba..0d98b5bc5 100644
--- a/src/cobra/summary/reaction_summary.py
+++ b/src/cobra/summary/reaction_summary.py
@@ -1,6 +1,5 @@
 """Provide the reaction summary class."""
 
-
 import logging
 from textwrap import dedent, shorten
 from typing import TYPE_CHECKING, Optional, Union
diff --git a/src/cobra/summary/summary.py b/src/cobra/summary/summary.py
index e7403b051..70bb55d40 100644
--- a/src/cobra/summary/summary.py
+++ b/src/cobra/summary/summary.py
@@ -1,6 +1,5 @@
 """Provide the abstract base summary class."""
 
-
 import logging
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING, Optional, Union
diff --git a/src/cobra/util/process_pool.py b/src/cobra/util/process_pool.py
index 6b255427c..e977e3ce5 100644
--- a/src/cobra/util/process_pool.py
+++ b/src/cobra/util/process_pool.py
@@ -1,6 +1,5 @@
 """Provide a process pool with enhanced performance on Windows."""
 
-
 import multiprocessing
 import os
 import pickle
@@ -30,7 +29,7 @@ def __init__(
         initializer: Optional[Callable] = None,
         initargs: Tuple = (),
         maxtasksperchild: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         """
         Initialize a process pool.
diff --git a/tests/test_core/test_gene.py b/tests/test_core/test_gene.py
index c79e25d84..39ff74e2d 100644
--- a/tests/test_core/test_gene.py
+++ b/tests/test_core/test_gene.py
@@ -1,6 +1,5 @@
 """Test functions of gene.py ."""
 
-
 from cobra.core import Model
 
 
diff --git a/tests/test_core/test_group.py b/tests/test_core/test_group.py
index 9768ca82f..a5ed210e1 100644
--- a/tests/test_core/test_group.py
+++ b/tests/test_core/test_group.py
@@ -1,6 +1,5 @@
 """Test functions of group via model.py."""
 
-
 import pytest
 
 from cobra import Model
diff --git a/tests/test_flux_analysis/test_deletion.py b/tests/test_flux_analysis/test_deletion.py
index fb462845a..11b8a9e8b 100644
--- a/tests/test_flux_analysis/test_deletion.py
+++ b/tests/test_flux_analysis/test_deletion.py
@@ -1,6 +1,5 @@
 """Test functionalities of reaction and gene deletions."""
 
-
 import math
 import os
 from typing import Callable, List
diff --git a/tests/test_medium/test_boundary_types.py b/tests/test_medium/test_boundary_types.py
index 792a71513..2299d5165 100644
--- a/tests/test_medium/test_boundary_types.py
+++ b/tests/test_medium/test_boundary_types.py
@@ -1,6 +1,5 @@
 """Test functionalities of boundary type detection functions."""
 
-
 import pytest
 
 from cobra.core import Metabolite, Model, Reaction
diff --git a/tests/test_summary/test_metabolite_summary.py b/tests/test_summary/test_metabolite_summary.py
index 1f543bfd0..7339228fc 100644
--- a/tests/test_summary/test_metabolite_summary.py
+++ b/tests/test_summary/test_metabolite_summary.py
@@ -1,6 +1,5 @@
 """Unit test the MetaboliteSummary class."""
 
-
 import pytest
 
 from cobra.flux_analysis import flux_variability_analysis, pfba
diff --git a/tests/test_summary/test_model_summary.py b/tests/test_summary/test_model_summary.py
index c05e8ab00..479581fe6 100644
--- a/tests/test_summary/test_model_summary.py
+++ b/tests/test_summary/test_model_summary.py
@@ -1,6 +1,5 @@
 """Unit test the model summary."""
 
-
 import pytest
 
 from cobra.flux_analysis import flux_variability_analysis, pfba
diff --git a/tests/test_summary/test_reaction_summary.py b/tests/test_summary/test_reaction_summary.py
index 8926285a2..8542301dc 100644
--- a/tests/test_summary/test_reaction_summary.py
+++ b/tests/test_summary/test_reaction_summary.py
@@ -1,6 +1,5 @@
 """Unit test the ReactionSummary class."""
 
-
 import pytest
 
 from cobra.flux_analysis import flux_variability_analysis, pfba
diff --git a/tests/test_util/test_process_pool.py b/tests/test_util/test_process_pool.py
index 3c60a7570..40f174960 100644
--- a/tests/test_util/test_process_pool.py
+++ b/tests/test_util/test_process_pool.py
@@ -1,6 +1,5 @@
 """Test the behaviour of the ProcessPool class."""
 
-
 import os
 from typing import Iterable, Tuple