diff --git a/release-notes/0.9.0.md b/release-notes/0.9.0.md
index ed7bd5f9..edb546df 100644
--- a/release-notes/0.9.0.md
+++ b/release-notes/0.9.0.md
@@ -6,9 +6,11 @@ following changes:
 
 # Features
 - bump `pymetadata>=0.4.0` to switch to OLS4
-- python 3.12 support
-- dropping python 3.9
+- python 3.12 support (dropping python 3.9)
 - pydantic fixes
 - bugfixes
+- updated sbml4humans
+- libsbml-4.20.4
+- improved ODE generation
 
 Your sbmlutils team
diff --git a/src/sbmlutils/__init__.py b/src/sbmlutils/__init__.py
index ede484d9..242e4afb 100644
--- a/src/sbmlutils/__init__.py
+++ b/src/sbmlutils/__init__.py
@@ -1,4 +1,5 @@
 """sbmlutils - Python utilities for SBML."""
+
 from pathlib import Path
 
 __author__ = "Matthias König"
diff --git a/src/sbmlutils/biomodels.py b/src/sbmlutils/biomodels.py
index 1b1b4462..36d04e1c 100644
--- a/src/sbmlutils/biomodels.py
+++ b/src/sbmlutils/biomodels.py
@@ -1,4 +1,5 @@
 """Utilities for downloading biomodel models."""
+
 import shutil
 import tempfile
 from pathlib import Path
diff --git a/src/sbmlutils/comp/__init__.py b/src/sbmlutils/comp/__init__.py
index 331ca695..d5279bf2 100644
--- a/src/sbmlutils/comp/__init__.py
+++ b/src/sbmlutils/comp/__init__.py
@@ -1,4 +1,5 @@
 """Package for SBML comp."""
+
 from .comp import (
     # Port,
     create_ExternalModelDefinition,
diff --git a/src/sbmlutils/comp/flatten.py b/src/sbmlutils/comp/flatten.py
index db1a7f80..b5f21dcb 100644
--- a/src/sbmlutils/comp/flatten.py
+++ b/src/sbmlutils/comp/flatten.py
@@ -1,4 +1,5 @@
 """Helpers for model flattening."""
+
 import os
 import time
 from pathlib import Path
diff --git a/src/sbmlutils/console.py b/src/sbmlutils/console.py
index 3a03c22a..6f7da271 100644
--- a/src/sbmlutils/console.py
+++ b/src/sbmlutils/console.py
@@ -1,4 +1,5 @@
 """Rich console for logging."""
+
 from rich import pretty
 from rich.console import Console
 from rich.theme import Theme
diff --git a/src/sbmlutils/converters/copasi.py b/src/sbmlutils/converters/copasi.py
index 803ad699..29e3dfc0 100644
--- a/src/sbmlutils/converters/copasi.py
+++ b/src/sbmlutils/converters/copasi.py
@@ -1,4 +1,5 @@
 """Helpers to work with COPASI files."""
+
 from pathlib import Path
 
 import libsbml
diff --git a/src/sbmlutils/converters/mathml.py b/src/sbmlutils/converters/mathml.py
index addcec09..c41ce97f 100644
--- a/src/sbmlutils/converters/mathml.py
+++ b/src/sbmlutils/converters/mathml.py
@@ -6,6 +6,7 @@
     *, /, +, -
     and, or, not
 """
+
 from math import *
 from typing import Any, Dict, Optional, Tuple
 
diff --git a/src/sbmlutils/converters/odefac_example/odefac_example.py b/src/sbmlutils/converters/odefac_example/odefac_example.py
index 5ad92c19..de7aab47 100644
--- a/src/sbmlutils/converters/odefac_example/odefac_example.py
+++ b/src/sbmlutils/converters/odefac_example/odefac_example.py
@@ -1,4 +1,5 @@
 """Example of creating markdown and python code."""
+
 from pathlib import Path
 
 from sbmlutils.console import console
diff --git a/src/sbmlutils/converters/xpp_examples.py b/src/sbmlutils/converters/xpp_examples.py
index 82ee21af..0906aeb4 100644
--- a/src/sbmlutils/converters/xpp_examples.py
+++ b/src/sbmlutils/converters/xpp_examples.py
@@ -5,6 +5,7 @@
 pip install libroadrunner
 ```
 """
+
 from pathlib import Path
 
 import roadrunner
diff --git a/src/sbmlutils/cytoscape.py b/src/sbmlutils/cytoscape.py
index 30cf9995..b026ae3f 100644
--- a/src/sbmlutils/cytoscape.py
+++ b/src/sbmlutils/cytoscape.py
@@ -1,17 +1,20 @@
 """Module for visualiation in Cytoscape."""
+
 import os
 import tempfile
+
+
 os.environ["PY4CYTOSCAPE_DETAIL_LOGGER_DIR"] = str(tempfile.gettempdir())
 
-from pathlib import Path
-from typing import Any, Union
+from pathlib import Path  # noqa: E402
+from typing import Any, Union  # noqa: E402
 
-import py4cytoscape as p4c
-from requests.exceptions import RequestException
+import py4cytoscape as p4c  # type: ignore  # noqa: E402
+from requests.exceptions import RequestException  # noqa: E402
 
-from sbmlutils import log
-from sbmlutils.console import console
-from sbmlutils.parser import antimony_to_sbml
+from sbmlutils import log  # noqa: E402
+from sbmlutils.console import console  # noqa: E402
+from sbmlutils.parser import antimony_to_sbml  # noqa: E402
 
 
 logger = log.get_logger(__name__)
diff --git a/src/sbmlutils/data/interpolation.py b/src/sbmlutils/data/interpolation.py
index 82aa0c2e..383bb59e 100644
--- a/src/sbmlutils/data/interpolation.py
+++ b/src/sbmlutils/data/interpolation.py
@@ -8,6 +8,7 @@
 The functionality is very useful, but only if this can be applied to existing
 models in a simple manner.
 """
+
 from __future__ import annotations
 
 from pathlib import Path
diff --git a/src/sbmlutils/data/interpolation_example.py b/src/sbmlutils/data/interpolation_example.py
index 37a7bacd..21379de7 100644
--- a/src/sbmlutils/data/interpolation_example.py
+++ b/src/sbmlutils/data/interpolation_example.py
@@ -1,4 +1,5 @@
 """Example demonstrating the interpolation of data."""
+
 import tempfile
 from pathlib import Path
 
diff --git a/src/sbmlutils/data/interpolation_pancreas.py b/src/sbmlutils/data/interpolation_pancreas.py
index f7226887..f1356158 100644
--- a/src/sbmlutils/data/interpolation_pancreas.py
+++ b/src/sbmlutils/data/interpolation_pancreas.py
@@ -1,4 +1,5 @@
 """Example demonstrating the interpolation of data."""
+
 import tempfile
 from pathlib import Path
 from typing import Optional
diff --git a/src/sbmlutils/distrib/distrib_examples.py b/src/sbmlutils/distrib/distrib_examples.py
index 6a17dd4d..816cfab5 100644
--- a/src/sbmlutils/distrib/distrib_examples.py
+++ b/src/sbmlutils/distrib/distrib_examples.py
@@ -1,4 +1,5 @@
 """Code for working with the libsbml distrib package."""
+
 import tempfile
 
 import libsbml
diff --git a/src/sbmlutils/distrib/distrib_packages.py b/src/sbmlutils/distrib/distrib_packages.py
index d120bd8e..fc18bfed 100644
--- a/src/sbmlutils/distrib/distrib_packages.py
+++ b/src/sbmlutils/distrib/distrib_packages.py
@@ -1,4 +1,5 @@
 """Example testing uncertainty with libsbml packages."""
+
 import tempfile
 from pathlib import Path
 
diff --git a/src/sbmlutils/examples/__init__.py b/src/sbmlutils/examples/__init__.py
index 2669e1b4..bde95d8a 100644
--- a/src/sbmlutils/examples/__init__.py
+++ b/src/sbmlutils/examples/__init__.py
@@ -1,4 +1,5 @@
 """Examples for model creation."""
+
 from pathlib import Path
 from sbmlutils.examples.dallaman import dallaman
 from sbmlutils.examples.demo import demo
diff --git a/src/sbmlutils/examples/algebraic_rule.py b/src/sbmlutils/examples/algebraic_rule.py
index 5ea70e57..e33c6806 100644
--- a/src/sbmlutils/examples/algebraic_rule.py
+++ b/src/sbmlutils/examples/algebraic_rule.py
@@ -1,4 +1,5 @@
 """AlgebraicRule example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.resources import EXAMPLES_DIR
diff --git a/src/sbmlutils/examples/annotation.py b/src/sbmlutils/examples/annotation.py
index b96217ed..cfa8687a 100644
--- a/src/sbmlutils/examples/annotation.py
+++ b/src/sbmlutils/examples/annotation.py
@@ -3,6 +3,7 @@
 Model demonstrates how to annotate model objects with SBOTerms and Terms from
 other ontologies. Annotations use the functionality from `pymetadata`.
 """
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *
diff --git a/src/sbmlutils/examples/assignment.py b/src/sbmlutils/examples/assignment.py
index 5c1b7c24..d1b141fa 100644
--- a/src/sbmlutils/examples/assignment.py
+++ b/src/sbmlutils/examples/assignment.py
@@ -1,4 +1,5 @@
 """AssignmentRule and InitialAssignment example."""
+
 from sbmlutils.console import console
 from sbmlutils.converters import odefac
 from sbmlutils.examples import templates
diff --git a/src/sbmlutils/examples/combine_archive/omex_models.py b/src/sbmlutils/examples/combine_archive/omex_models.py
index 9948f00b..d6f14b92 100644
--- a/src/sbmlutils/examples/combine_archive/omex_models.py
+++ b/src/sbmlutils/examples/combine_archive/omex_models.py
@@ -2,6 +2,7 @@
 
 This demonstrates just the very core SBML functionality.
 """
+
 from pathlib import Path
 from typing import Optional
 
@@ -69,7 +70,7 @@
 for k in range(n_cells - 1):
     _m.reactions.append(  # type: ignore
         Reaction(
-            sid=f"J{k}", equation=f"S{k} <-> S{k+1}", formula=f"D * (S{k}-S{k+1})"
+            sid=f"J{k}", equation=f"S{k} <-> S{k + 1}", formula=f"D * (S{k} - S{k + 1})"
         ),
     )
 
diff --git a/src/sbmlutils/examples/compartment_species_reaction.py b/src/sbmlutils/examples/compartment_species_reaction.py
index 50aa2626..c2f17132 100644
--- a/src/sbmlutils/examples/compartment_species_reaction.py
+++ b/src/sbmlutils/examples/compartment_species_reaction.py
@@ -1,4 +1,5 @@
 """Compartment, Species, Reaction example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *
diff --git a/src/sbmlutils/examples/dallaman/__init__.py b/src/sbmlutils/examples/dallaman/__init__.py
new file mode 100644
index 00000000..6dce3e99
--- /dev/null
+++ b/src/sbmlutils/examples/dallaman/__init__.py
@@ -0,0 +1 @@
+"""Module for DallaMan Meal model."""
diff --git a/src/sbmlutils/examples/demo/demo.py b/src/sbmlutils/examples/demo/demo.py
index fd347d39..fa32ce9b 100644
--- a/src/sbmlutils/examples/demo/demo.py
+++ b/src/sbmlutils/examples/demo/demo.py
@@ -1,4 +1,5 @@
 """Demo kinetic network."""
+
 from pathlib import Path
 
 from sbmlutils.examples import templates
diff --git a/src/sbmlutils/examples/distrib/distrib_comp.py b/src/sbmlutils/examples/distrib/distrib_comp.py
index 1ac86509..02a1d8f0 100644
--- a/src/sbmlutils/examples/distrib/distrib_comp.py
+++ b/src/sbmlutils/examples/distrib/distrib_comp.py
@@ -1,4 +1,5 @@
 """Distrib and comp example to check flattening."""
+
 import shutil
 from pathlib import Path
 
diff --git a/src/sbmlutils/examples/distrib/distrib_distributions.py b/src/sbmlutils/examples/distrib/distrib_distributions.py
index 610200fe..c358f731 100644
--- a/src/sbmlutils/examples/distrib/distrib_distributions.py
+++ b/src/sbmlutils/examples/distrib/distrib_distributions.py
@@ -1,4 +1,5 @@
 """Distrib example demonstrating distributions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.validation import ValidationOptions
diff --git a/src/sbmlutils/examples/distrib/distrib_uncertainties.py b/src/sbmlutils/examples/distrib/distrib_uncertainties.py
index 62ca34d8..356e3a97 100644
--- a/src/sbmlutils/examples/distrib/distrib_uncertainties.py
+++ b/src/sbmlutils/examples/distrib/distrib_uncertainties.py
@@ -1,4 +1,5 @@
 """Uncertainty example."""
+
 import libsbml
 
 from sbmlutils.examples import templates
diff --git a/src/sbmlutils/examples/fbc/fbc_key_value_pair.py b/src/sbmlutils/examples/fbc/fbc_key_value_pair.py
index e3e07c09..71482d4b 100644
--- a/src/sbmlutils/examples/fbc/fbc_key_value_pair.py
+++ b/src/sbmlutils/examples/fbc/fbc_key_value_pair.py
@@ -1,4 +1,5 @@
 """FBC example for KeyValuePairs."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *
diff --git a/src/sbmlutils/examples/fbc/fbc_mass_charge.py b/src/sbmlutils/examples/fbc/fbc_mass_charge.py
index 6c1c0c9e..05056de1 100644
--- a/src/sbmlutils/examples/fbc/fbc_mass_charge.py
+++ b/src/sbmlutils/examples/fbc/fbc_mass_charge.py
@@ -1,4 +1,5 @@
 """FBC mass and charge example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *
diff --git a/src/sbmlutils/examples/fbc/fbc_userdefinedconstraints.py b/src/sbmlutils/examples/fbc/fbc_userdefinedconstraints.py
index 70686d33..647639e9 100644
--- a/src/sbmlutils/examples/fbc/fbc_userdefinedconstraints.py
+++ b/src/sbmlutils/examples/fbc/fbc_userdefinedconstraints.py
@@ -1,4 +1,5 @@
 """FBA example with UserDefinedConstraints."""
+
 import numpy as np
 
 from sbmlutils.examples import templates
diff --git a/src/sbmlutils/examples/fbc/fbc_v2.py b/src/sbmlutils/examples/fbc/fbc_v2.py
index 09e8493f..de7f94ce 100644
--- a/src/sbmlutils/examples/fbc/fbc_v2.py
+++ b/src/sbmlutils/examples/fbc/fbc_v2.py
@@ -1,4 +1,5 @@
 """FBA example with exchange reactions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *
diff --git a/src/sbmlutils/examples/fbc/fbc_v3.py b/src/sbmlutils/examples/fbc/fbc_v3.py
index 5403f20e..7df9416b 100644
--- a/src/sbmlutils/examples/fbc/fbc_v3.py
+++ b/src/sbmlutils/examples/fbc/fbc_v3.py
@@ -1,4 +1,5 @@
 """FBA example with exchange reactions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *
diff --git a/src/sbmlutils/examples/fbc/fbc_version3.py b/src/sbmlutils/examples/fbc/fbc_version3.py
index 5ade1ae8..ae0ed085 100644
--- a/src/sbmlutils/examples/fbc/fbc_version3.py
+++ b/src/sbmlutils/examples/fbc/fbc_version3.py
@@ -3,6 +3,7 @@
 For latest SBML fbc v3 specification see
 https://github.com/bgoli/sbml-fbc-spec/blob/main/sf_svn/spec/main.pdf
 """
+
 from logging import getLogger
 from pathlib import Path
 
diff --git a/src/sbmlutils/examples/icg/__init__.py b/src/sbmlutils/examples/icg/__init__.py
index 83b60dab..ca6005d2 100644
--- a/src/sbmlutils/examples/icg/__init__.py
+++ b/src/sbmlutils/examples/icg/__init__.py
@@ -1,4 +1,5 @@
 """ICG examples."""
+
 from pathlib import Path
 
 ICG_PATH = Path(__file__).parent
diff --git a/src/sbmlutils/examples/icg/factory.py b/src/sbmlutils/examples/icg/factory.py
index 0e78512f..3e1f4f7e 100644
--- a/src/sbmlutils/examples/icg/factory.py
+++ b/src/sbmlutils/examples/icg/factory.py
@@ -1,4 +1,5 @@
 """ICG model factory."""
+
 from pathlib import Path
 from typing import Any, Dict
 
diff --git a/src/sbmlutils/examples/icg/model_body.py b/src/sbmlutils/examples/icg/model_body.py
index 7b031014..fa0aa0a7 100644
--- a/src/sbmlutils/examples/icg/model_body.py
+++ b/src/sbmlutils/examples/icg/model_body.py
@@ -1,4 +1,5 @@
 """PKPD model for whole-body icg metabolism."""
+
 import os
 
 import numpy as np
diff --git a/src/sbmlutils/examples/icg/model_liver.py b/src/sbmlutils/examples/icg/model_liver.py
index 61ac1515..e8b08ce1 100644
--- a/src/sbmlutils/examples/icg/model_liver.py
+++ b/src/sbmlutils/examples/icg/model_liver.py
@@ -1,4 +1,5 @@
 """ICG liver model."""
+
 from pathlib import Path
 
 from sbmlutils.cytoscape import visualize_sbml
diff --git a/src/sbmlutils/examples/model.py b/src/sbmlutils/examples/model.py
index f6ffe840..c581cb2e 100644
--- a/src/sbmlutils/examples/model.py
+++ b/src/sbmlutils/examples/model.py
@@ -2,6 +2,7 @@
 
 This demonstrates just the very core SBML functionality.
 """
+
 from pathlib import Path
 
 import libsbml
diff --git a/src/sbmlutils/examples/model_definitions.py b/src/sbmlutils/examples/model_definitions.py
index e73b70e6..1a56276b 100644
--- a/src/sbmlutils/examples/model_definitions.py
+++ b/src/sbmlutils/examples/model_definitions.py
@@ -1,4 +1,5 @@
 """Multiple model definitions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 
diff --git a/src/sbmlutils/examples/multiple_substance_units.py b/src/sbmlutils/examples/multiple_substance_units.py
index b45c8742..fef54ed5 100644
--- a/src/sbmlutils/examples/multiple_substance_units.py
+++ b/src/sbmlutils/examples/multiple_substance_units.py
@@ -1,4 +1,5 @@
 """Example for substance units."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *
diff --git a/src/sbmlutils/examples/notes.py b/src/sbmlutils/examples/notes.py
index 8a46ccbe..88c4ff70 100644
--- a/src/sbmlutils/examples/notes.py
+++ b/src/sbmlutils/examples/notes.py
@@ -1,4 +1,5 @@
 """Example model with notes."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 
diff --git a/src/sbmlutils/examples/parameter.py b/src/sbmlutils/examples/parameter.py
index 475413ee..859d406a 100644
--- a/src/sbmlutils/examples/parameter.py
+++ b/src/sbmlutils/examples/parameter.py
@@ -1,4 +1,5 @@
 """Parameter example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *
diff --git a/src/sbmlutils/examples/reaction.py b/src/sbmlutils/examples/reaction.py
index 98b44ede..bbbae1d4 100644
--- a/src/sbmlutils/examples/reaction.py
+++ b/src/sbmlutils/examples/reaction.py
@@ -1,4 +1,5 @@
 """Create reaction example."""
+
 import numpy as np
 
 from sbmlutils.examples import templates
diff --git a/src/sbmlutils/examples/templates.py b/src/sbmlutils/examples/templates.py
index 73a58632..e2fccebe 100644
--- a/src/sbmlutils/examples/templates.py
+++ b/src/sbmlutils/examples/templates.py
@@ -1,4 +1,5 @@
 """Template information for the model creation."""
+
 from datetime import datetime
 
 from sbmlutils.factory import Creator
diff --git a/src/sbmlutils/examples/tiny/simulation.py b/src/sbmlutils/examples/tiny/simulation.py
index 6349c371..afbc5114 100644
--- a/src/sbmlutils/examples/tiny/simulation.py
+++ b/src/sbmlutils/examples/tiny/simulation.py
@@ -10,6 +10,7 @@
 ```
 
 """
+
 from pathlib import Path
 
 import pandas as pd
diff --git a/src/sbmlutils/examples/tiny/tiny.py b/src/sbmlutils/examples/tiny/tiny.py
index 97900ce9..b4c7a123 100644
--- a/src/sbmlutils/examples/tiny/tiny.py
+++ b/src/sbmlutils/examples/tiny/tiny.py
@@ -1,4 +1,5 @@
 """Tiny model example."""
+
 from math import inf
 from pathlib import Path
 
diff --git a/src/sbmlutils/examples/tutorial/linear_chain.py b/src/sbmlutils/examples/tutorial/linear_chain.py
index 9815be47..c26e68d5 100644
--- a/src/sbmlutils/examples/tutorial/linear_chain.py
+++ b/src/sbmlutils/examples/tutorial/linear_chain.py
@@ -4,6 +4,7 @@
 `sbmlutils` allows to generate patterns of objects by combining loops in combination
 with string patterns. In this example we create a kinetic model of a linear chain.
 """
+
 from sbmlutils.converters import odefac
 from sbmlutils.cytoscape import visualize_sbml
 from sbmlutils.examples import templates
@@ -34,15 +35,17 @@
             sid=f"S{k + 2}",
             initialConcentration=0.0,
             compartment="cell",
-            name=f"Species {k +2}",
+            name=f"Species {k + 2}",
         ),
     )
     model.parameters.append(
-        Parameter(sid=f"k{k+1}", value=0.1, name=f"rate constant {k+1}"),
+        Parameter(sid=f"k{k + 1}", value=0.1, name=f"rate constant {k + 1}"),
     )
     model.reactions.append(
         Reaction(
-            sid=f"J{k+1}", equation=f"S{k+1} -> S{k+2}", formula=f"k{k+1} * S{k+1}"
+            sid=f"J{k + 1}",
+            equation=f"S{k + 1} -> S{k + 2}",
+            formula=f"k{k + 1} * S{k + 1}",
         ),
     )
 
diff --git a/src/sbmlutils/examples/tutorial/minimal_model.py b/src/sbmlutils/examples/tutorial/minimal_model.py
index 98f6be8d..285f7eb9 100644
--- a/src/sbmlutils/examples/tutorial/minimal_model.py
+++ b/src/sbmlutils/examples/tutorial/minimal_model.py
@@ -2,6 +2,7 @@
 
 This demonstrates just the very core SBML functionality.
 """
+
 from sbmlutils.cytoscape import visualize_sbml
 from sbmlutils.factory import *
 from sbmlutils.metadata import *
diff --git a/src/sbmlutils/examples/tutorial/minimal_model_annotations.py b/src/sbmlutils/examples/tutorial/minimal_model_annotations.py
index cac31226..9b61532e 100644
--- a/src/sbmlutils/examples/tutorial/minimal_model_annotations.py
+++ b/src/sbmlutils/examples/tutorial/minimal_model_annotations.py
@@ -1,4 +1,5 @@
 """Annotate an existing model."""
+
 from pathlib import Path
 
 from sbmlutils.cytoscape import visualize_sbml
diff --git a/src/sbmlutils/examples/tutorial/minimal_model_comp.py b/src/sbmlutils/examples/tutorial/minimal_model_comp.py
index bb9b1076..090fa25c 100644
--- a/src/sbmlutils/examples/tutorial/minimal_model_comp.py
+++ b/src/sbmlutils/examples/tutorial/minimal_model_comp.py
@@ -1,4 +1,5 @@
 """Example creating composite model."""
+
 from pathlib import Path
 
 from sbmlutils.comp import flatten_sbml
@@ -40,7 +41,7 @@
 for k in range(n_cells - 1):
     model.reactions.append(
         Reaction(
-            sid=f"J{k}", equation=f"S{k} <-> S{k+1}", formula=f"D * (S{k}-S{k+1})"
+            sid=f"J{k}", equation=f"S{k} <-> S{k + 1}", formula=f"D * (S{k} - S{k + 1})"
         ),
     )
 
diff --git a/src/sbmlutils/examples/tutorial/model_composition.py b/src/sbmlutils/examples/tutorial/model_composition.py
index 7171b198..5896ab8f 100644
--- a/src/sbmlutils/examples/tutorial/model_composition.py
+++ b/src/sbmlutils/examples/tutorial/model_composition.py
@@ -1,4 +1,5 @@
 """Example for model composition via multiple models."""
+
 from pathlib import Path
 
 from sbmlutils.cytoscape import visualize_sbml
diff --git a/src/sbmlutils/examples/tutorial/random_network.py b/src/sbmlutils/examples/tutorial/random_network.py
index 7e6f5431..d13a1133 100644
--- a/src/sbmlutils/examples/tutorial/random_network.py
+++ b/src/sbmlutils/examples/tutorial/random_network.py
@@ -1,4 +1,5 @@
 """Example creating random network."""
+
 import random
 
 from sbmlutils.cytoscape import visualize_sbml
@@ -34,7 +35,7 @@
 
     model.reactions.append(
         Reaction(
-            sid=f"J{k+1}",
+            sid=f"J{k + 1}",
             equation=f"S{k_source} -> S{k_target}",
             formula=f"k * S{k_source}",
         ),
diff --git a/src/sbmlutils/examples/unit_definitions.py b/src/sbmlutils/examples/unit_definitions.py
index 5b812f00..16d7c161 100644
--- a/src/sbmlutils/examples/unit_definitions.py
+++ b/src/sbmlutils/examples/unit_definitions.py
@@ -1,4 +1,5 @@
 """Example model with UnitDefinitions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *
diff --git a/src/sbmlutils/examples/units_namespace.py b/src/sbmlutils/examples/units_namespace.py
index 64fc176f..528c8da9 100644
--- a/src/sbmlutils/examples/units_namespace.py
+++ b/src/sbmlutils/examples/units_namespace.py
@@ -2,6 +2,7 @@
 
 Model used for testing units namespacing.
 """
+
 from pathlib import Path
 
 from sbmlutils.examples import templates
diff --git a/src/sbmlutils/factory.py b/src/sbmlutils/factory.py
index f4dfb9a7..45659e16 100644
--- a/src/sbmlutils/factory.py
+++ b/src/sbmlutils/factory.py
@@ -15,6 +15,7 @@
 To create complete models one should use the modelcreator functionality,
 which takes care of the order of object creation.
 """
+
 from __future__ import annotations
 
 import datetime
diff --git a/src/sbmlutils/fbc/cobra.py b/src/sbmlutils/fbc/cobra.py
index 44cb60e1..c4a40eeb 100644
--- a/src/sbmlutils/fbc/cobra.py
+++ b/src/sbmlutils/fbc/cobra.py
@@ -1,4 +1,5 @@
 """cobrapy based helper methods."""
+
 from pathlib import Path
 from typing import Dict
 
diff --git a/src/sbmlutils/fbc/fbc.py b/src/sbmlutils/fbc/fbc.py
index 8e2e44aa..56e52eab 100644
--- a/src/sbmlutils/fbc/fbc.py
+++ b/src/sbmlutils/fbc/fbc.py
@@ -1,4 +1,5 @@
 """Helper functions for working with FBC and cobrapy models."""
+
 import warnings
 
 import libsbml
diff --git a/src/sbmlutils/io/__init__.py b/src/sbmlutils/io/__init__.py
index 199bbc7c..50cde2fe 100644
--- a/src/sbmlutils/io/__init__.py
+++ b/src/sbmlutils/io/__init__.py
@@ -1,2 +1,3 @@
 """Helper functions for input/output (IO)."""
+
 from .sbml import read_sbml, validate_sbml, write_sbml
diff --git a/src/sbmlutils/io/sbml.py b/src/sbmlutils/io/sbml.py
index deed204f..931dc748 100644
--- a/src/sbmlutils/io/sbml.py
+++ b/src/sbmlutils/io/sbml.py
@@ -1,4 +1,5 @@
 """Utility functions for reading, writing and validating SBML."""
+
 from pathlib import Path
 from typing import Optional, Union
 
diff --git a/src/sbmlutils/layout/__init__.py b/src/sbmlutils/layout/__init__.py
index f5fa8f63..f4fa6264 100644
--- a/src/sbmlutils/layout/__init__.py
+++ b/src/sbmlutils/layout/__init__.py
@@ -1,2 +1,3 @@
 """Package for SBML layout."""
+
 from .layout import *
diff --git a/src/sbmlutils/layout/layout.py b/src/sbmlutils/layout/layout.py
index 43e305d9..468bfb67 100644
--- a/src/sbmlutils/layout/layout.py
+++ b/src/sbmlutils/layout/layout.py
@@ -1,4 +1,5 @@
 """Utilities for the creation and work with layout models."""
+
 from typing import Dict, List, Optional
 
 import libsbml
diff --git a/src/sbmlutils/log.py b/src/sbmlutils/log.py
index e675d8d5..7b266ad0 100644
--- a/src/sbmlutils/log.py
+++ b/src/sbmlutils/log.py
@@ -2,6 +2,7 @@
 
 Using rich for output formating.
 """
+
 import logging
 from typing import List
 
diff --git a/src/sbmlutils/manipulation/merge.py b/src/sbmlutils/manipulation/merge.py
index 9a77c2f7..b4584479 100644
--- a/src/sbmlutils/manipulation/merge.py
+++ b/src/sbmlutils/manipulation/merge.py
@@ -3,6 +3,7 @@
 The following is a helper function for merging multiple SBML models into
 a single model.
 """
+
 import os
 from pathlib import Path
 from typing import Dict, Optional
diff --git a/src/sbmlutils/metadata/__init__.py b/src/sbmlutils/metadata/__init__.py
index 035ed887..34cd1232 100644
--- a/src/sbmlutils/metadata/__init__.py
+++ b/src/sbmlutils/metadata/__init__.py
@@ -2,5 +2,6 @@
 
 Most metadata functionality is part pf `pymetadata`.
 """
+
 from .miriam import *
 from .sbo import *
diff --git a/src/sbmlutils/metadata/annotator.py b/src/sbmlutils/metadata/annotator.py
index 4d4ed09a..d4712b46 100644
--- a/src/sbmlutils/metadata/annotator.py
+++ b/src/sbmlutils/metadata/annotator.py
@@ -10,6 +10,7 @@
 A standard workflow is looking up the components for instance in things like OLS
 ontology lookup service.
 """
+
 import os
 import re
 from pathlib import Path
diff --git a/src/sbmlutils/notes.py b/src/sbmlutils/notes.py
index f5690ad2..e157c703 100644
--- a/src/sbmlutils/notes.py
+++ b/src/sbmlutils/notes.py
@@ -4,6 +4,7 @@
 Markdown -> HTML conversion is performed using `markdown-it-py` for the conversion.
 No styles for the display are inserted here.
 """
+
 import textwrap
 from enum import Enum
 
diff --git a/src/sbmlutils/parser.py b/src/sbmlutils/parser.py
index 023cb334..81c3a126 100644
--- a/src/sbmlutils/parser.py
+++ b/src/sbmlutils/parser.py
@@ -4,6 +4,7 @@
 FIXME: no support for modelHistory
 
 """
+
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Union
 
@@ -168,9 +169,9 @@ def parse_sbase_kwargs(sbase: libsbml.SBase) -> Dict[str, Any]:
             Compartment(
                 value=c.getSize() if c.isSetSize() else NaN,
                 constant=c.getConstant() if c.isSetConstant() else True,
-                spatialDimensions=c.getSpatialDimensions()
-                if c.isSetSpatialDimensions()
-                else None,
+                spatialDimensions=(
+                    c.getSpatialDimensions() if c.isSetSpatialDimensions() else None
+                ),
                 # unit=p.getUnits(),
                 **parse_sbase_kwargs(c),
             )
@@ -182,16 +183,20 @@ def parse_sbase_kwargs(sbase: libsbml.SBase) -> Dict[str, Any]:
             Species(
                 compartment=s.getCompartment() if s.isSetCompartment() else None,
                 initialAmount=s.getInitialAmount() if s.isSetInitialAmount() else None,
-                initialConcentration=s.getInitialConcentration()
-                if s.isSetInitialConcentration()
-                else None,
+                initialConcentration=(
+                    s.getInitialConcentration()
+                    if s.isSetInitialConcentration()
+                    else None
+                ),
                 constant=s.getConstant() if s.isSetConstant() else None,
-                hasOnlySubstanceUnits=s.getHasOnlySubstanceUnits()
-                if s.isSetHasOnlySubstanceUnits()
-                else None,
-                boundaryCondition=s.getBoundaryCondition()
-                if s.isSetBoundaryCondition()
-                else None,
+                hasOnlySubstanceUnits=(
+                    s.getHasOnlySubstanceUnits()
+                    if s.isSetHasOnlySubstanceUnits()
+                    else None
+                ),
+                boundaryCondition=(
+                    s.getBoundaryCondition() if s.isSetBoundaryCondition() else None
+                ),
                 # unit=p.getUnits(),
                 **parse_sbase_kwargs(s),
             )
@@ -212,12 +217,14 @@ def parse_sbase_kwargs(sbase: libsbml.SBase) -> Dict[str, Any]:
             equation.reactants.append(
                 EquationPart(
                     species=reactant.getSpecies() if reactant.isSetSpecies() else None,
-                    stoichiometry=reactant.getStoichiometry()
-                    if reactant.isSetStoichiometry()
-                    else None,
-                    constant=reactant.getConstant()
-                    if reactant.isSetConstant()
-                    else True,
+                    stoichiometry=(
+                        reactant.getStoichiometry()
+                        if reactant.isSetStoichiometry()
+                        else None
+                    ),
+                    constant=(
+                        reactant.getConstant() if reactant.isSetConstant() else True
+                    ),
                     **parse_sbase_kwargs(reactant),
                 )
             )
@@ -226,9 +233,11 @@ def parse_sbase_kwargs(sbase: libsbml.SBase) -> Dict[str, Any]:
             equation.products.append(
                 EquationPart(
                     species=product.getSpecies() if product.isSetSpecies() else None,
-                    stoichiometry=product.getStoichiometry()
-                    if product.isSetStoichiometry()
-                    else None,
+                    stoichiometry=(
+                        product.getStoichiometry()
+                        if product.isSetStoichiometry()
+                        else None
+                    ),
                     constant=product.getConstant() if product.isSetConstant() else True,
                     **parse_sbase_kwargs(product),
                 )
diff --git a/src/sbmlutils/reaction_equation.py b/src/sbmlutils/reaction_equation.py
index 0a65c7e3..5095927d 100644
--- a/src/sbmlutils/reaction_equation.py
+++ b/src/sbmlutils/reaction_equation.py
@@ -39,6 +39,7 @@
     'f * acoa =>',
 
 """
+
 from __future__ import annotations
 
 import re
diff --git a/src/sbmlutils/report/api.py b/src/sbmlutils/report/api.py
index 4209be21..b65fd2cb 100644
--- a/src/sbmlutils/report/api.py
+++ b/src/sbmlutils/report/api.py
@@ -3,6 +3,7 @@
 This provides basic functionality of
 parsing the model and returning the JSON representation based on fastAPI.
 """
+
 import tempfile
 import time
 import traceback
diff --git a/src/sbmlutils/report/api_examples.py b/src/sbmlutils/report/api_examples.py
index 5a4d8bbb..484c1df8 100644
--- a/src/sbmlutils/report/api_examples.py
+++ b/src/sbmlutils/report/api_examples.py
@@ -1,4 +1,5 @@
 """Example models for the sbml4humans API."""
+
 from pathlib import Path
 from typing import List, Optional
 
diff --git a/src/sbmlutils/report/mathml.py b/src/sbmlutils/report/mathml.py
index 3d63b2fc..9743c74c 100644
--- a/src/sbmlutils/report/mathml.py
+++ b/src/sbmlutils/report/mathml.py
@@ -167,7 +167,7 @@ def _fix_mathit_symbols(tex_str: str) -> str:
     # replace greek symbols
     for symbol in greek_symbols:
         tex_str = tex_str.replace(
-            r"\mathit{" + symbol + "}", r"\mathit{" + f"\{symbol}" + "}"  # noqa: W605
+            r"\mathit{" + symbol + "}", r"\mathit{" + f"\\{symbol}" + "}"  # noqa: W605
         )
 
     return tex_str
diff --git a/src/sbmlutils/report/sbmlinfo.py b/src/sbmlutils/report/sbmlinfo.py
index 5202de5c..24a09c72 100644
--- a/src/sbmlutils/report/sbmlinfo.py
+++ b/src/sbmlutils/report/sbmlinfo.py
@@ -3,6 +3,7 @@
 The model dictionary can be used for rendering the HTML report.
 The information can be serialized to JSON for later rendering in web app.
 """
+
 from __future__ import annotations
 
 import hashlib
@@ -386,12 +387,16 @@ def sbase_dict(cls, sbase: libsbml.SBase) -> Dict[str, Any]:
                         "value": upar.getValue() if upar.isSetValue() else None,
                         "units": upar.getUnits() if upar.isSetUnits() else None,
                         "type": upar.getTypeAsString() if upar.isSetType() else None,
-                        "definitionURL": upar.getDefinitionURL()
-                        if upar.isSetDefinitionURL()
-                        else None,
-                        "math": astnode_to_latex(upar.getMath())
-                        if upar.isSetMath()
-                        else None,
+                        "definitionURL": (
+                            upar.getDefinitionURL()
+                            if upar.isSetDefinitionURL()
+                            else None
+                        ),
+                        "math": (
+                            astnode_to_latex(upar.getMath())
+                            if upar.isSetMath()
+                            else None
+                        ),
                     }
 
                     u_dict["uncertaintyParameters"].append(param_dict)
@@ -486,9 +491,9 @@ def model_history(cls, sbase: libsbml.SBase) -> Optional[Dict]:
                 {
                     "givenName": c.getGivenName() if c.isSetGivenName() else None,
                     "familyName": c.getFamilyName() if c.isSetFamilyName() else None,
-                    "organization": c.getOrganization()
-                    if c.isSetOrganization()
-                    else None,
+                    "organization": (
+                        c.getOrganization() if c.isSetOrganization() else None
+                    ),
                     "email": c.getEmail() if c.isSetEmail() else None,
                 }
             )
@@ -691,12 +696,16 @@ def species(
             sfbc = s.getPlugin("fbc")
             d["fbc"] = (
                 {
-                    "formula": sfbc.getChemicalFormula()
-                    if sfbc.isSetChemicalFormula()
-                    else None,
-                    "charge": sfbc.getCharge()
-                    if (sfbc.isSetCharge() and sfbc.getCharge() != 0)
-                    else None,
+                    "formula": (
+                        sfbc.getChemicalFormula()
+                        if sfbc.isSetChemicalFormula()
+                        else None
+                    ),
+                    "charge": (
+                        sfbc.getCharge()
+                        if (sfbc.isSetCharge() and sfbc.getCharge() != 0)
+                        else None
+                    ),
                 }
                 if sfbc
                 else None
@@ -901,9 +910,9 @@ def _species_reference(species: libsbml.SpeciesReference) -> Dict[str, Any]:
         """Resolve species reference."""
         return {
             "species": species.getSpecies() if species.isSetSpecies() else None,
-            "stoichiometry": species.getStoichiometry()
-            if species.isSetStoichiometry()
-            else 1.0,
+            "stoichiometry": (
+                species.getStoichiometry() if species.isSetStoichiometry() else 1.0
+            ),
             "constant": species.getConstant() if species.isSetConstant() else None,
         }
 
@@ -1065,9 +1074,11 @@ def events(self, model: libsbml.Model) -> List[Dict[str, Any]]:
             )
             if trigger:
                 d["trigger"] = {
-                    "math": astnode_to_latex(trigger.getMath())
-                    if trigger.isSetMath()
-                    else None,
+                    "math": (
+                        astnode_to_latex(trigger.getMath())
+                        if trigger.isSetMath()
+                        else None
+                    ),
                     "initialValue": trigger.initial_value,
                     "persistent": trigger.persistent,
                 }
@@ -1095,9 +1106,9 @@ def events(self, model: libsbml.Model) -> List[Dict[str, Any]]:
                 assignments.append(
                     {
                         "variable": eva.getVariable() if eva.isSetVariable() else None,
-                        "math": astnode_to_latex(eva.getMath())
-                        if eva.isSetMath()
-                        else None,
+                        "math": (
+                            astnode_to_latex(eva.getMath()) if eva.isSetMath() else None
+                        ),
                     }
                 )
             d["listOfEventAssignments"] = assignments
@@ -1235,9 +1246,9 @@ def objectives(self, model: libsbml.Model) -> List[Dict[str, Any]]:
                     part = {
                         "sign": sign,
                         "coefficient": abs(coefficient),
-                        "reaction": f_obj.getReaction()
-                        if f_obj.isSetReaction()
-                        else None,
+                        "reaction": (
+                            f_obj.getReaction() if f_obj.isSetReaction() else None
+                        ),
                     }
                     flux_objectives.append(part)
                 d["fluxObjectives"] = flux_objectives
diff --git a/src/sbmlutils/report/units.py b/src/sbmlutils/report/units.py
index d3a3db2e..3cf8db19 100644
--- a/src/sbmlutils/report/units.py
+++ b/src/sbmlutils/report/units.py
@@ -1,4 +1,5 @@
 """Helper functions for formating and rendering units."""
+
 from typing import Optional, Union
 
 import libsbml
diff --git a/src/sbmlutils/resources/__init__.py b/src/sbmlutils/resources/__init__.py
index d161bec0..ab90ca6f 100644
--- a/src/sbmlutils/resources/__init__.py
+++ b/src/sbmlutils/resources/__init__.py
@@ -1,4 +1,5 @@
 """Resources for testing."""
+
 from pathlib import Path
 from typing import List
 
@@ -162,7 +163,6 @@ def all_distrib_paths() -> List[Path]:
     COMP_SPT_KIDNEY,
     COMP_SPT_BODY_FLAT,
     COMP_SPT_BODY,
-
     DISTRIB_DISTRIBUTIONS_SBML,
     DISTRIB_UNCERTAINTIES_SBML,
     FBC_ECOLI_CORE_SBML,
diff --git a/src/sbmlutils/resources/converters/odefac_template.pytemp b/src/sbmlutils/resources/converters/odefac_template.pytemp
index 99978245..4d8d2e5a 100644
--- a/src/sbmlutils/resources/converters/odefac_template.pytemp
+++ b/src/sbmlutils/resources/converters/odefac_template.pytemp
@@ -10,11 +10,12 @@ volume: [{{model_units["volume"]}}]
 area: [{{model_units["area"]}}]
 length: [{{model_units["length"]}}]
 """
+from typing import Any
 import numpy as np
 import pandas as pd
 
 
-def piecewise(*kwargs):
+def piecewise(*kwargs: Any) -> Any:
     """Piecewise function.
 
     piecewise      | x1, y1, [x2, y2,] [...] [z] | A piecewise function: if (y1), x1.  Otherwise, if (y2), x2, etc.  Otherwise, z.
@@ -90,7 +91,7 @@ def f_y(x: np.ndarray, t: float, p: np.ndarray) -> np.ndarray:
     return y
 
 
-def f_z(X, T, p):
+def f_z(X: np.ndarray, T: np.ndarray, p: np.ndarray) -> np.ndarray:
     """ DataFrame of full timecourse of solution. """
     (Nt, Nx) = X.shape
     Ny = len(yids)
diff --git a/src/sbmlutils/resources/examples/linear_chain.py b/src/sbmlutils/resources/examples/linear_chain.py
index c7b37e94..db1462ad 100644
--- a/src/sbmlutils/resources/examples/linear_chain.py
+++ b/src/sbmlutils/resources/examples/linear_chain.py
@@ -10,17 +10,20 @@
 area: [-]
 length: [-]
 """
+
+from typing import Any
+
 import numpy as np
 import pandas as pd
 
 
-def piecewise(*kwargs):
+def piecewise(*kwargs: Any) -> Any:
     """Piecewise function.
 
     piecewise      | x1, y1, [x2, y2,] [...] [z] | A piecewise function: if (y1), x1.  Otherwise, if (y2), x2, etc.  Otherwise, z.
     """
-    for k in np.floor(len(kwargs)/2.0):
-        if kwargs[k+1]:
+    for k in np.floor(len(kwargs) / 2.0):
+        if kwargs[k + 1]:
             return kwargs[k]
     if len(kwargs) % 2 == 1:
         return kwargs[-1]
@@ -29,112 +32,183 @@ def piecewise(*kwargs):
 # -------------------
 # ids
 # -------------------
-xids = ["S1", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S2", "S20", "S21", "S3", "S4", "S5", "S6", "S7", "S8", "S9", ]
-pids = ["cell", "k1", "k10", "k11", "k12", "k13", "k14", "k15", "k16", "k17", "k18", "k19", "k2", "k20", "k3", "k4", "k5", "k6", "k7", "k8", "k9", ]
-yids = ["J1", "J10", "J11", "J12", "J13", "J14", "J15", "J16", "J17", "J18", "J19", "J2", "J20", "J3", "J4", "J5", "J6", "J7", "J8", "J9", ]
+xids = [
+    "S1",
+    "S10",
+    "S11",
+    "S12",
+    "S13",
+    "S14",
+    "S15",
+    "S16",
+    "S17",
+    "S18",
+    "S19",
+    "S2",
+    "S20",
+    "S21",
+    "S3",
+    "S4",
+    "S5",
+    "S6",
+    "S7",
+    "S8",
+    "S9",
+]
+pids = [
+    "cell",
+    "k1",
+    "k10",
+    "k11",
+    "k12",
+    "k13",
+    "k14",
+    "k15",
+    "k16",
+    "k17",
+    "k18",
+    "k19",
+    "k2",
+    "k20",
+    "k3",
+    "k4",
+    "k5",
+    "k6",
+    "k7",
+    "k8",
+    "k9",
+]
+yids = [
+    "J1",
+    "J10",
+    "J11",
+    "J12",
+    "J13",
+    "J14",
+    "J15",
+    "J16",
+    "J17",
+    "J18",
+    "J19",
+    "J2",
+    "J20",
+    "J3",
+    "J4",
+    "J5",
+    "J6",
+    "J7",
+    "J8",
+    "J9",
+]
 
 # -------------------
 # initial conditions
 # -------------------
-x0 = np.array([
-    10.0,     # [0] S1 [-/-]  in cell
-    0.0,     # [1] S10 [-/-] Species 10 in cell
-    0.0,     # [2] S11 [-/-] Species 11 in cell
-    0.0,     # [3] S12 [-/-] Species 12 in cell
-    0.0,     # [4] S13 [-/-] Species 13 in cell
-    0.0,     # [5] S14 [-/-] Species 14 in cell
-    0.0,     # [6] S15 [-/-] Species 15 in cell
-    0.0,     # [7] S16 [-/-] Species 16 in cell
-    0.0,     # [8] S17 [-/-] Species 17 in cell
-    0.0,     # [9] S18 [-/-] Species 18 in cell
-    0.0,     # [10] S19 [-/-] Species 19 in cell
-    0.0,     # [11] S2 [-/-] Species 2 in cell
-    0.0,     # [12] S20 [-/-] Species 20 in cell
-    0.0,     # [13] S21 [-/-] Species 21 in cell
-    0.0,     # [14] S3 [-/-] Species 3 in cell
-    0.0,     # [15] S4 [-/-] Species 4 in cell
-    0.0,     # [16] S5 [-/-] Species 5 in cell
-    0.0,     # [17] S6 [-/-] Species 6 in cell
-    0.0,     # [18] S7 [-/-] Species 7 in cell
-    0.0,     # [19] S8 [-/-] Species 8 in cell
-    0.0,     # [20] S9 [-/-] Species 9 in cell
-])
+x0 = np.array(
+    [
+        10.0,  # [0] S1 [-/-]  in cell
+        0.0,  # [1] S10 [-/-] Species 10 in cell
+        0.0,  # [2] S11 [-/-] Species 11 in cell
+        0.0,  # [3] S12 [-/-] Species 12 in cell
+        0.0,  # [4] S13 [-/-] Species 13 in cell
+        0.0,  # [5] S14 [-/-] Species 14 in cell
+        0.0,  # [6] S15 [-/-] Species 15 in cell
+        0.0,  # [7] S16 [-/-] Species 16 in cell
+        0.0,  # [8] S17 [-/-] Species 17 in cell
+        0.0,  # [9] S18 [-/-] Species 18 in cell
+        0.0,  # [10] S19 [-/-] Species 19 in cell
+        0.0,  # [11] S2 [-/-] Species 2 in cell
+        0.0,  # [12] S20 [-/-] Species 20 in cell
+        0.0,  # [13] S21 [-/-] Species 21 in cell
+        0.0,  # [14] S3 [-/-] Species 3 in cell
+        0.0,  # [15] S4 [-/-] Species 4 in cell
+        0.0,  # [16] S5 [-/-] Species 5 in cell
+        0.0,  # [17] S6 [-/-] Species 6 in cell
+        0.0,  # [18] S7 [-/-] Species 7 in cell
+        0.0,  # [19] S8 [-/-] Species 8 in cell
+        0.0,  # [20] S9 [-/-] Species 9 in cell
+    ]
+)
 
 # -------------------
 # parameters
 # -------------------
-p = np.array([
-    1.0,     # [0] cell [-] 
-    0.1,     # [1] k1 [-] rate constant 1
-    0.1,     # [2] k10 [-] rate constant 10
-    0.1,     # [3] k11 [-] rate constant 11
-    0.1,     # [4] k12 [-] rate constant 12
-    0.1,     # [5] k13 [-] rate constant 13
-    0.1,     # [6] k14 [-] rate constant 14
-    0.1,     # [7] k15 [-] rate constant 15
-    0.1,     # [8] k16 [-] rate constant 16
-    0.1,     # [9] k17 [-] rate constant 17
-    0.1,     # [10] k18 [-] rate constant 18
-    0.1,     # [11] k19 [-] rate constant 19
-    0.1,     # [12] k2 [-] rate constant 2
-    0.1,     # [13] k20 [-] rate constant 20
-    0.1,     # [14] k3 [-] rate constant 3
-    0.1,     # [15] k4 [-] rate constant 4
-    0.1,     # [16] k5 [-] rate constant 5
-    0.1,     # [17] k6 [-] rate constant 6
-    0.1,     # [18] k7 [-] rate constant 7
-    0.1,     # [19] k8 [-] rate constant 8
-    0.1,     # [20] k9 [-] rate constant 9
-])
+p = np.array(
+    [
+        1.0,  # [0] cell [-]
+        0.1,  # [1] k1 [-] rate constant 1
+        0.1,  # [2] k10 [-] rate constant 10
+        0.1,  # [3] k11 [-] rate constant 11
+        0.1,  # [4] k12 [-] rate constant 12
+        0.1,  # [5] k13 [-] rate constant 13
+        0.1,  # [6] k14 [-] rate constant 14
+        0.1,  # [7] k15 [-] rate constant 15
+        0.1,  # [8] k16 [-] rate constant 16
+        0.1,  # [9] k17 [-] rate constant 17
+        0.1,  # [10] k18 [-] rate constant 18
+        0.1,  # [11] k19 [-] rate constant 19
+        0.1,  # [12] k2 [-] rate constant 2
+        0.1,  # [13] k20 [-] rate constant 20
+        0.1,  # [14] k3 [-] rate constant 3
+        0.1,  # [15] k4 [-] rate constant 4
+        0.1,  # [16] k5 [-] rate constant 5
+        0.1,  # [17] k6 [-] rate constant 6
+        0.1,  # [18] k7 [-] rate constant 7
+        0.1,  # [19] k8 [-] rate constant 8
+        0.1,  # [20] k9 [-] rate constant 9
+    ]
+)
 
 
 def f_dxdt(x: np.ndarray, t: float, p: np.ndarray) -> np.ndarray:
     """ODE system."""
-    J1 = p[1] * x[0]  # [0] J1 [-/-] 
-    J10 = p[2] * x[1]  # [1] J10 [-/-] 
-    J11 = p[3] * x[2]  # [2] J11 [-/-] 
-    J12 = p[4] * x[3]  # [3] J12 [-/-] 
-    J13 = p[5] * x[4]  # [4] J13 [-/-] 
-    J14 = p[6] * x[5]  # [5] J14 [-/-] 
-    J15 = p[7] * x[6]  # [6] J15 [-/-] 
-    J16 = p[8] * x[7]  # [7] J16 [-/-] 
-    J17 = p[9] * x[8]  # [8] J17 [-/-] 
-    J18 = p[10] * x[9]  # [9] J18 [-/-] 
-    J19 = p[11] * x[10]  # [10] J19 [-/-] 
-    J2 = p[12] * x[11]  # [11] J2 [-/-] 
-    J20 = p[13] * x[12]  # [12] J20 [-/-] 
-    J3 = p[14] * x[14]  # [13] J3 [-/-] 
-    J4 = p[15] * x[15]  # [14] J4 [-/-] 
-    J5 = p[16] * x[16]  # [15] J5 [-/-] 
-    J6 = p[17] * x[17]  # [16] J6 [-/-] 
-    J7 = p[18] * x[18]  # [17] J7 [-/-] 
-    J8 = p[19] * x[19]  # [18] J8 [-/-] 
-    J9 = p[20] * x[20]  # [19] J9 [-/-] 
+    J1 = p[1] * x[0]  # [0] J1 [-/-]
+    J10 = p[2] * x[1]  # [1] J10 [-/-]
+    J11 = p[3] * x[2]  # [2] J11 [-/-]
+    J12 = p[4] * x[3]  # [3] J12 [-/-]
+    J13 = p[5] * x[4]  # [4] J13 [-/-]
+    J14 = p[6] * x[5]  # [5] J14 [-/-]
+    J15 = p[7] * x[6]  # [6] J15 [-/-]
+    J16 = p[8] * x[7]  # [7] J16 [-/-]
+    J17 = p[9] * x[8]  # [8] J17 [-/-]
+    J18 = p[10] * x[9]  # [9] J18 [-/-]
+    J19 = p[11] * x[10]  # [10] J19 [-/-]
+    J2 = p[12] * x[11]  # [11] J2 [-/-]
+    J20 = p[13] * x[12]  # [12] J20 [-/-]
+    J3 = p[14] * x[14]  # [13] J3 [-/-]
+    J4 = p[15] * x[15]  # [14] J4 [-/-]
+    J5 = p[16] * x[16]  # [15] J5 [-/-]
+    J6 = p[17] * x[17]  # [16] J6 [-/-]
+    J7 = p[18] * x[18]  # [17] J7 [-/-]
+    J8 = p[19] * x[19]  # [18] J8 [-/-]
+    J9 = p[20] * x[20]  # [19] J9 [-/-]
 
     # ode
-    return np.ndarray([
-        -J1 / p[0],  # [0] S1 [-/-] 
-        J9 / p[0] - J10 / p[0],  # [1] S10 [-/-] Species 10
-        J10 / p[0] - J11 / p[0],  # [2] S11 [-/-] Species 11
-        J11 / p[0] - J12 / p[0],  # [3] S12 [-/-] Species 12
-        J12 / p[0] - J13 / p[0],  # [4] S13 [-/-] Species 13
-        J13 / p[0] - J14 / p[0],  # [5] S14 [-/-] Species 14
-        J14 / p[0] - J15 / p[0],  # [6] S15 [-/-] Species 15
-        J15 / p[0] - J16 / p[0],  # [7] S16 [-/-] Species 16
-        J16 / p[0] - J17 / p[0],  # [8] S17 [-/-] Species 17
-        J17 / p[0] - J18 / p[0],  # [9] S18 [-/-] Species 18
-        J18 / p[0] - J19 / p[0],  # [10] S19 [-/-] Species 19
-        J1 / p[0] - J2 / p[0],  # [11] S2 [-/-] Species 2
-        J19 / p[0] - J20 / p[0],  # [12] S20 [-/-] Species 20
-        J20 / p[0],  # [13] S21 [-/-] Species 21
-        J2 / p[0] - J3 / p[0],  # [14] S3 [-/-] Species 3
-        J3 / p[0] - J4 / p[0],  # [15] S4 [-/-] Species 4
-        J4 / p[0] - J5 / p[0],  # [16] S5 [-/-] Species 5
-        J5 / p[0] - J6 / p[0],  # [17] S6 [-/-] Species 6
-        J6 / p[0] - J7 / p[0],  # [18] S7 [-/-] Species 7
-        J7 / p[0] - J8 / p[0],  # [19] S8 [-/-] Species 8
-        J8 / p[0] - J9 / p[0],  # [20] S9 [-/-] Species 9
-    ])
+    return np.ndarray(
+        [
+            -J1 / p[0],  # [0] S1 [-/-]
+            J9 / p[0] - J10 / p[0],  # [1] S10 [-/-] Species 10
+            J10 / p[0] - J11 / p[0],  # [2] S11 [-/-] Species 11
+            J11 / p[0] - J12 / p[0],  # [3] S12 [-/-] Species 12
+            J12 / p[0] - J13 / p[0],  # [4] S13 [-/-] Species 13
+            J13 / p[0] - J14 / p[0],  # [5] S14 [-/-] Species 14
+            J14 / p[0] - J15 / p[0],  # [6] S15 [-/-] Species 15
+            J15 / p[0] - J16 / p[0],  # [7] S16 [-/-] Species 16
+            J16 / p[0] - J17 / p[0],  # [8] S17 [-/-] Species 17
+            J17 / p[0] - J18 / p[0],  # [9] S18 [-/-] Species 18
+            J18 / p[0] - J19 / p[0],  # [10] S19 [-/-] Species 19
+            J1 / p[0] - J2 / p[0],  # [11] S2 [-/-] Species 2
+            J19 / p[0] - J20 / p[0],  # [12] S20 [-/-] Species 20
+            J20 / p[0],  # [13] S21 [-/-] Species 21
+            J2 / p[0] - J3 / p[0],  # [14] S3 [-/-] Species 3
+            J3 / p[0] - J4 / p[0],  # [15] S4 [-/-] Species 4
+            J4 / p[0] - J5 / p[0],  # [16] S5 [-/-] Species 5
+            J5 / p[0] - J6 / p[0],  # [17] S6 [-/-] Species 6
+            J6 / p[0] - J7 / p[0],  # [18] S7 [-/-] Species 7
+            J7 / p[0] - J8 / p[0],  # [19] S8 [-/-] Species 8
+            J8 / p[0] - J9 / p[0],  # [20] S9 [-/-] Species 9
+        ]
+    )
 
 
 def f_y(x: np.ndarray, t: float, p: np.ndarray) -> np.ndarray:
@@ -146,66 +220,66 @@ def f_y(x: np.ndarray, t: float, p: np.ndarray) -> np.ndarray:
     :return:
     """
 
-    J1 = p[1] * x[0]  # [0] J1  [-/-] 
-    J10 = p[2] * x[1]  # [1] J10  [-/-] 
-    J11 = p[3] * x[2]  # [2] J11  [-/-] 
-    J12 = p[4] * x[3]  # [3] J12  [-/-] 
-    J13 = p[5] * x[4]  # [4] J13  [-/-] 
-    J14 = p[6] * x[5]  # [5] J14  [-/-] 
-    J15 = p[7] * x[6]  # [6] J15  [-/-] 
-    J16 = p[8] * x[7]  # [7] J16  [-/-] 
-    J17 = p[9] * x[8]  # [8] J17  [-/-] 
-    J18 = p[10] * x[9]  # [9] J18  [-/-] 
-    J19 = p[11] * x[10]  # [10] J19  [-/-] 
-    J2 = p[12] * x[11]  # [11] J2  [-/-] 
-    J20 = p[13] * x[12]  # [12] J20  [-/-] 
-    J3 = p[14] * x[14]  # [13] J3  [-/-] 
-    J4 = p[15] * x[15]  # [14] J4  [-/-] 
-    J5 = p[16] * x[16]  # [15] J5  [-/-] 
-    J6 = p[17] * x[17]  # [16] J6  [-/-] 
-    J7 = p[18] * x[18]  # [17] J7  [-/-] 
-    J8 = p[19] * x[19]  # [18] J8  [-/-] 
-    J9 = p[20] * x[20]  # [19] J9  [-/-] 
+    J1 = p[1] * x[0]  # [0] J1  [-/-]
+    J10 = p[2] * x[1]  # [1] J10  [-/-]
+    J11 = p[3] * x[2]  # [2] J11  [-/-]
+    J12 = p[4] * x[3]  # [3] J12  [-/-]
+    J13 = p[5] * x[4]  # [4] J13  [-/-]
+    J14 = p[6] * x[5]  # [5] J14  [-/-]
+    J15 = p[7] * x[6]  # [6] J15  [-/-]
+    J16 = p[8] * x[7]  # [7] J16  [-/-]
+    J17 = p[9] * x[8]  # [8] J17  [-/-]
+    J18 = p[10] * x[9]  # [9] J18  [-/-]
+    J19 = p[11] * x[10]  # [10] J19  [-/-]
+    J2 = p[12] * x[11]  # [11] J2  [-/-]
+    J20 = p[13] * x[12]  # [12] J20  [-/-]
+    J3 = p[14] * x[14]  # [13] J3  [-/-]
+    J4 = p[15] * x[15]  # [14] J4  [-/-]
+    J5 = p[16] * x[16]  # [15] J5  [-/-]
+    J6 = p[17] * x[17]  # [16] J6  [-/-]
+    J7 = p[18] * x[18]  # [17] J7  [-/-]
+    J8 = p[19] * x[19]  # [18] J8  [-/-]
+    J9 = p[20] * x[20]  # [19] J9  [-/-]
 
     # --------------------------------------
 
     y = np.empty(shape=(20))
-    y[0] = J1  # [0] J1  [-/-] 
-    y[1] = J10  # [1] J10  [-/-] 
-    y[2] = J11  # [2] J11  [-/-] 
-    y[3] = J12  # [3] J12  [-/-] 
-    y[4] = J13  # [4] J13  [-/-] 
-    y[5] = J14  # [5] J14  [-/-] 
-    y[6] = J15  # [6] J15  [-/-] 
-    y[7] = J16  # [7] J16  [-/-] 
-    y[8] = J17  # [8] J17  [-/-] 
-    y[9] = J18  # [9] J18  [-/-] 
-    y[10] = J19  # [10] J19  [-/-] 
-    y[11] = J2  # [11] J2  [-/-] 
-    y[12] = J20  # [12] J20  [-/-] 
-    y[13] = J3  # [13] J3  [-/-] 
-    y[14] = J4  # [14] J4  [-/-] 
-    y[15] = J5  # [15] J5  [-/-] 
-    y[16] = J6  # [16] J6  [-/-] 
-    y[17] = J7  # [17] J7  [-/-] 
-    y[18] = J8  # [18] J8  [-/-] 
-    y[19] = J9  # [19] J9  [-/-] 
+    y[0] = J1  # [0] J1  [-/-]
+    y[1] = J10  # [1] J10  [-/-]
+    y[2] = J11  # [2] J11  [-/-]
+    y[3] = J12  # [3] J12  [-/-]
+    y[4] = J13  # [4] J13  [-/-]
+    y[5] = J14  # [5] J14  [-/-]
+    y[6] = J15  # [6] J15  [-/-]
+    y[7] = J16  # [7] J16  [-/-]
+    y[8] = J17  # [8] J17  [-/-]
+    y[9] = J18  # [9] J18  [-/-]
+    y[10] = J19  # [10] J19  [-/-]
+    y[11] = J2  # [11] J2  [-/-]
+    y[12] = J20  # [12] J20  [-/-]
+    y[13] = J3  # [13] J3  [-/-]
+    y[14] = J4  # [14] J4  [-/-]
+    y[15] = J5  # [15] J5  [-/-]
+    y[16] = J6  # [16] J6  [-/-]
+    y[17] = J7  # [17] J7  [-/-]
+    y[18] = J8  # [18] J8  [-/-]
+    y[19] = J9  # [19] J9  [-/-]
 
     return y
 
 
-def f_z(X, T, p):
-    """ DataFrame of full timecourse of solution. """
+def f_z(X: np.ndarray, T: np.ndarray, p: np.ndarray) -> np.ndarray:
+    """DataFrame of full timecourse of solution."""
     (Nt, Nx) = X.shape
     Ny = len(yids)
     Nz = 1 + Nx + Ny
     columns = ["time"] + xids + yids
     Z = np.empty(shape=(Nt, Nz))
     Z[:, 0] = T
-    Z[:, 1:(Nx+1)] = X
+    Z[:, 1 : (Nx + 1)] = X
     for kt in range(Nt):
         y = f_y(x=X[kt, :], t=T[kt], p=p)
-        Z[kt, (Nx+1):] = y
+        Z[kt, (Nx + 1) :] = y
 
     Z = pd.DataFrame(Z, columns=columns)
-    return Z
\ No newline at end of file
+    return Z
diff --git a/src/sbmlutils/utils.py b/src/sbmlutils/utils.py
index d8f37766..49407e78 100644
--- a/src/sbmlutils/utils.py
+++ b/src/sbmlutils/utils.py
@@ -1,4 +1,5 @@
 """Utility functions."""
+
 import functools
 import hashlib
 import time
diff --git a/src/sbmlutils/validation.py b/src/sbmlutils/validation.py
index 92d41bee..ed742448 100644
--- a/src/sbmlutils/validation.py
+++ b/src/sbmlutils/validation.py
@@ -1,4 +1,5 @@
 """Helpers for validation and checking of SBML and libsbml operations."""
+
 import time
 from dataclasses import dataclass
 from typing import Iterable, List, Optional
diff --git a/tests/converters/test_copasi.py b/tests/converters/test_copasi.py
index 82b5ca90..3e3be026 100644
--- a/tests/converters/test_copasi.py
+++ b/tests/converters/test_copasi.py
@@ -1,4 +1,5 @@
 """Testing COPASI functionality."""
+
 from pathlib import Path
 
 from sbmlutils.converters import copasi
diff --git a/tests/converters/test_odefac.py b/tests/converters/test_odefac.py
index 90d1ba67..d6683c80 100644
--- a/tests/converters/test_odefac.py
+++ b/tests/converters/test_odefac.py
@@ -1,4 +1,5 @@
 """Testing ODE factory."""
+
 from pathlib import Path
 
 import libsbml
diff --git a/tests/converters/test_xpp.py b/tests/converters/test_xpp.py
index d90bb27f..7ca3988d 100644
--- a/tests/converters/test_xpp.py
+++ b/tests/converters/test_xpp.py
@@ -1,4 +1,5 @@
 """Test XPP generation."""
+
 from pathlib import Path
 
 from sbmlutils.converters import xpp
diff --git a/tests/examples/test_examples.py b/tests/examples/test_examples.py
index 1a7ebeb7..9c07ae80 100644
--- a/tests/examples/test_examples.py
+++ b/tests/examples/test_examples.py
@@ -1,4 +1,5 @@
 """Example model creation."""
+
 from pathlib import Path
 from typing import Any
 
diff --git a/tests/examples/test_galactose.py b/tests/examples/test_galactose.py
index 0a7eb772..b6b67fa4 100644
--- a/tests/examples/test_galactose.py
+++ b/tests/examples/test_galactose.py
@@ -1,4 +1,5 @@
 """Test the galactose model."""
+
 from sbmlutils.io.sbml import validate_sbml
 from sbmlutils.resources import GALACTOSE_SINGLECELL_SBML
 
diff --git a/tests/fbc/test_cobra.py b/tests/fbc/test_cobra.py
index 651dcba0..d9a9482f 100644
--- a/tests/fbc/test_cobra.py
+++ b/tests/fbc/test_cobra.py
@@ -1,4 +1,5 @@
 """Testing cobra and fbc functionality."""
+
 from pathlib import Path
 
 import pytest
diff --git a/tests/interpolation/test_interpolation.py b/tests/interpolation/test_interpolation.py
index 5806e608..f02d593c 100644
--- a/tests/interpolation/test_interpolation.py
+++ b/tests/interpolation/test_interpolation.py
@@ -1,4 +1,5 @@
 """Test interpolation."""
+
 from pathlib import Path
 
 import pandas as pd
diff --git a/tests/io/test_sbml.py b/tests/io/test_sbml.py
index cd40b4a1..24358f6b 100644
--- a/tests/io/test_sbml.py
+++ b/tests/io/test_sbml.py
@@ -1,4 +1,5 @@
 """Test SBML reading and writing."""
+
 from pathlib import Path
 
 import libsbml
diff --git a/tests/manipulation/test_merge.py b/tests/manipulation/test_merge.py
index c61c0b6d..7e478538 100644
--- a/tests/manipulation/test_merge.py
+++ b/tests/manipulation/test_merge.py
@@ -1,4 +1,5 @@
 """Test model merging functionality."""
+
 from pathlib import Path
 
 from sbmlutils import comp, validation
diff --git a/tests/metadata/test_annotator.py b/tests/metadata/test_annotator.py
index 49ae0e39..9eb3b69f 100644
--- a/tests/metadata/test_annotator.py
+++ b/tests/metadata/test_annotator.py
@@ -1,4 +1,5 @@
 """Test annotation functions and annotating of SBML models."""
+
 import re
 from pathlib import Path
 from typing import Iterable
diff --git a/tests/report/test_api.py b/tests/report/test_api.py
index 77ba749c..4c5f7c5e 100644
--- a/tests/report/test_api.py
+++ b/tests/report/test_api.py
@@ -1,4 +1,5 @@
 """Test SBML report."""
+
 from pathlib import Path
 
 import pytest
diff --git a/tests/report/test_mathml.py b/tests/report/test_mathml.py
index 285f7c08..5b3133da 100644
--- a/tests/report/test_mathml.py
+++ b/tests/report/test_mathml.py
@@ -1,4 +1,5 @@
 """Test MathML functionality."""
+
 import libsbml
 import pytest
 
diff --git a/tests/test_biomodels.py b/tests/test_biomodels.py
index 31916bca..614ad6e8 100644
--- a/tests/test_biomodels.py
+++ b/tests/test_biomodels.py
@@ -1,4 +1,5 @@
 """Testing the biomodels module."""
+
 from pathlib import Path
 
 import pytest
diff --git a/tests/test_comp.py b/tests/test_comp.py
index cc7d4157..bc9f43cd 100644
--- a/tests/test_comp.py
+++ b/tests/test_comp.py
@@ -1,4 +1,5 @@
 """Tests for the comp package."""
+
 import libsbml
 
 from sbmlutils import comp
diff --git a/tests/test_distrib.py b/tests/test_distrib.py
index a35073d4..b2a0ffaf 100644
--- a/tests/test_distrib.py
+++ b/tests/test_distrib.py
@@ -1,4 +1,5 @@
 """Test distrib functionality."""
+
 import libsbml
 
 from sbmlutils.distrib import distrib_examples, distrib_packages
diff --git a/tests/test_factory.py b/tests/test_factory.py
index 1553058d..92adbf1a 100644
--- a/tests/test_factory.py
+++ b/tests/test_factory.py
@@ -1,4 +1,5 @@
 """Testing the factory methods."""
+
 from pathlib import Path
 from typing import Any, Dict
 
diff --git a/tests/test_history.py b/tests/test_history.py
index 1a639a54..177f14c5 100644
--- a/tests/test_history.py
+++ b/tests/test_history.py
@@ -1,4 +1,5 @@
 """Test history on SBML models."""
+
 import libsbml
 
 from sbmlutils.factory import Creator, date_now, set_model_history
diff --git a/tests/test_model.py b/tests/test_model.py
index 75c98b24..fc5cd974 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -1,4 +1,5 @@
 """Test model functionality."""
+
 import pytest
 
 from sbmlutils.factory import *
diff --git a/tests/test_model_creator.py b/tests/test_model_creator.py
index 008327d1..bb0b8ec0 100644
--- a/tests/test_model_creator.py
+++ b/tests/test_model_creator.py
@@ -1,4 +1,5 @@
 """Test the creator module."""
+
 from pathlib import Path
 
 import pytest
diff --git a/tests/test_notes.py b/tests/test_notes.py
index 594b0b44..33105ec4 100644
--- a/tests/test_notes.py
+++ b/tests/test_notes.py
@@ -1,4 +1,5 @@
 """Testing notes."""
+
 import re
 
 import libsbml
diff --git a/tests/test_parser.py b/tests/test_parser.py
index bb730d4c..3ebf6744 100644
--- a/tests/test_parser.py
+++ b/tests/test_parser.py
@@ -1,4 +1,5 @@
 """Test parsing of SBML."""
+
 from pathlib import Path
 from typing import List
 
diff --git a/tests/test_reaction_equation.py b/tests/test_reaction_equation.py
index 9f97e11d..136a1441 100644
--- a/tests/test_reaction_equation.py
+++ b/tests/test_reaction_equation.py
@@ -1,4 +1,5 @@
 """Test equations."""
+
 import pytest
 
 from sbmlutils.reaction_equation import (
diff --git a/tests/test_sbml_testsuite.py b/tests/test_sbml_testsuite.py
index 93e3706a..1aa19d0d 100644
--- a/tests/test_sbml_testsuite.py
+++ b/tests/test_sbml_testsuite.py
@@ -1,4 +1,5 @@
 """Testing the biomodels module."""
+
 from pathlib import Path
 
 import pytest
diff --git a/tests/test_udef_to_str.py b/tests/test_udef_to_str.py
index 0e7b1d1d..ea70c25e 100644
--- a/tests/test_udef_to_str.py
+++ b/tests/test_udef_to_str.py
@@ -1,4 +1,5 @@
 """Test UnitDefinition to string functions."""
+
 import libsbml
 import pytest
 
@@ -38,7 +39,7 @@ def test_unit_definition_str(uid: str, definition: str, expected: str) -> None:
     ("m3", "meter^3", "m^3"),
     ("m3", "meter^3/second", "\\frac{m^3}{s}"),
     ("mM", "mmole/liter", "\\frac{mmol}{l}"),
-    ("ml_per_s_kg", "ml/s/kg", "\\frac{ml}{s \cdot kg}"),  # noqa: W605
+    ("ml_per_s_kg", "ml/s/kg", "\\frac{ml}{s \\cdot kg}"),  # noqa: W605
     ("dimensionless", "dimensionless", "-"),
     ("item", "item", "item"),
 ]
diff --git a/tests/test_validation.py b/tests/test_validation.py
index c017bc86..d67733f5 100644
--- a/tests/test_validation.py
+++ b/tests/test_validation.py
@@ -1,4 +1,5 @@
 """Test SBML validation."""
+
 from pathlib import Path
 
 import pytest
diff --git a/tox.ini b/tox.ini
index 3fa450ce..ed01f3fd 100644
--- a/tox.ini
+++ b/tox.ini
@@ -136,10 +136,6 @@ follow_imports = silent
 disallow_untyped_defs = True
 disallow_incomplete_defs = True
 
-
-[py2cytoscape.data.cyrest_client]
-ignore_missing_imports = True
-
 [mypy-libsbml.*]
 ignore_missing_imports = True