From 2baa7a10f4149307ae7b3adbfbd0a466a843fdcd Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-munich.de>
Date: Mon, 22 Apr 2024 14:16:31 +0200
Subject: [PATCH] pyupgrade, pre-commit autoupdate

---
 .pre-commit-config.yaml                       |  9 ++-
 python/sdist/amici/__init__.py                |  7 ++-
 python/sdist/amici/_codegen/cxx_functions.py  |  1 +
 python/sdist/amici/_codegen/model_class.py    |  1 +
 python/sdist/amici/_codegen/template.py       |  6 +-
 python/sdist/amici/antimony_import.py         |  6 +-
 python/sdist/amici/bngl_import.py             |  1 -
 python/sdist/amici/compile.py                 | 10 ++--
 .../amici/conserved_quantities_demartino.py   |  7 +--
 .../sdist/amici/conserved_quantities_rref.py  |  4 +-
 python/sdist/amici/cxxcodeprinter.py          | 14 ++---
 python/sdist/amici/de_export.py               | 49 +++++++--------
 python/sdist/amici/de_model.py                |  4 +-
 python/sdist/amici/de_model_components.py     | 28 ++++-----
 python/sdist/amici/debugging/__init__.py      |  1 +
 python/sdist/amici/gradient_check.py          | 19 +++---
 python/sdist/amici/import_utils.py            | 28 ++++-----
 python/sdist/amici/logging.py                 | 16 ++---
 python/sdist/amici/numpy.py                   | 12 ++--
 python/sdist/amici/pandas.py                  | 20 +++----
 python/sdist/amici/petab/conditions.py        | 13 ++--
 python/sdist/amici/petab/import_helpers.py    | 12 ++--
 python/sdist/amici/petab/petab_import.py      |  3 +-
 python/sdist/amici/petab/petab_problem.py     | 19 +++---
 python/sdist/amici/petab/pysb_import.py       |  7 +--
 python/sdist/amici/petab/sbml_import.py       | 18 +++---
 python/sdist/amici/petab/simulations.py       | 15 ++---
 python/sdist/amici/petab/simulator.py         |  2 +-
 python/sdist/amici/petab/util.py              |  7 ++-
 python/sdist/amici/petab_import.py            |  1 +
 python/sdist/amici/petab_import_pysb.py       |  1 +
 python/sdist/amici/plotting.py                | 14 ++---
 python/sdist/amici/pysb_import.py             | 29 +++++----
 python/sdist/amici/sbml_import.py             | 60 +++++++++----------
 python/sdist/amici/setup.template.py          |  1 +
 python/sdist/amici/splines.py                 |  3 +-
 python/sdist/amici/swig.py                    |  1 +
 python/sdist/amici/swig_wrappers.py           | 11 ++--
 python/sdist/amici/sympy_utils.py             | 10 ++--
 python/sdist/amici/testing.py                 |  1 +
 python/sdist/pyproject.toml                   |  4 +-
 python/sdist/setup.py                         |  1 +
 python/tests/conftest.py                      |  1 +
 .../bngwiki_egfr_simple_deletemolecules.py    |  1 -
 python/tests/splines_utils.py                 | 22 +++----
 .../test_conserved_quantities_demartino.py    |  1 +
 python/tests/test_edata.py                    |  1 +
 python/tests/test_events.py                   |  1 +
 python/tests/test_heavisides.py               |  1 +
 python/tests/test_petab_simulate.py           |  1 +
 python/tests/test_rdata.py                    |  1 +
 python/tests/test_sbml_import.py              |  1 +
 python/tests/util.py                          |  1 +
 tests/benchmark-models/evaluate_benchmark.py  |  1 +
 .../benchmark-models/test_petab_benchmark.py  |  1 +
 tests/benchmark-models/test_petab_model.py    |  1 +
 56 files changed, 268 insertions(+), 243 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a2d00e00c1..449f94ca79 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: check-added-large-files
   - id: check-merge-conflict
@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.11
+  rev: v0.4.1
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,10 +28,9 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
     -   id: pyupgrade
-        args: ["--py39-plus"]
-        additional_dependencies: [pyupgrade==3.15.0]
+        args: ["--py310-plus"]
 
 exclude: '^(ThirdParty|models)/'
diff --git a/python/sdist/amici/__init__.py b/python/sdist/amici/__init__.py
index 76369eda37..942b669fa2 100644
--- a/python/sdist/amici/__init__.py
+++ b/python/sdist/amici/__init__.py
@@ -13,7 +13,8 @@
 import sys
 from pathlib import Path
 from types import ModuleType as ModelModule
-from typing import Any, Callable, Union
+from typing import Any
+from collections.abc import Callable
 
 
 def _get_amici_path():
@@ -138,7 +139,7 @@ def get_model(self) -> amici.Model:
 class add_path:
     """Context manager for temporarily changing PYTHONPATH"""
 
-    def __init__(self, path: Union[str, Path]):
+    def __init__(self, path: str | Path):
         self.path: str = str(path)
 
     def __enter__(self):
@@ -151,7 +152,7 @@ def __exit__(self, exc_type, exc_value, traceback):
 
 
 def import_model_module(
-    module_name: str, module_path: Union[Path, str]
+    module_name: str, module_path: Path | str
 ) -> ModelModule:
     """
     Import Python module of an AMICI model
diff --git a/python/sdist/amici/_codegen/cxx_functions.py b/python/sdist/amici/_codegen/cxx_functions.py
index 7831ed97c2..5fd5ead94a 100644
--- a/python/sdist/amici/_codegen/cxx_functions.py
+++ b/python/sdist/amici/_codegen/cxx_functions.py
@@ -1,4 +1,5 @@
 """Info about C++ functions in the generated model code."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass
diff --git a/python/sdist/amici/_codegen/model_class.py b/python/sdist/amici/_codegen/model_class.py
index e6366c1dfd..d24884ca89 100644
--- a/python/sdist/amici/_codegen/model_class.py
+++ b/python/sdist/amici/_codegen/model_class.py
@@ -1,4 +1,5 @@
 """Function for generating the ``amici::Model`` subclass for an amici model."""
+
 from __future__ import annotations
 
 from .cxx_functions import functions, multiobs_functions
diff --git a/python/sdist/amici/_codegen/template.py b/python/sdist/amici/_codegen/template.py
index 34f3391ed6..2a099ba907 100644
--- a/python/sdist/amici/_codegen/template.py
+++ b/python/sdist/amici/_codegen/template.py
@@ -1,7 +1,7 @@
 """Functions to apply template substitution to files."""
+
 from pathlib import Path
 from string import Template
-from typing import Union
 
 
 class TemplateAmici(Template):
@@ -17,8 +17,8 @@ class TemplateAmici(Template):
 
 
 def apply_template(
-    source_file: Union[str, Path],
-    target_file: Union[str, Path],
+    source_file: str | Path,
+    target_file: str | Path,
     template_data: dict[str, str],
 ) -> None:
     """
diff --git a/python/sdist/amici/antimony_import.py b/python/sdist/amici/antimony_import.py
index 545a2654bd..ad269f11fe 100644
--- a/python/sdist/amici/antimony_import.py
+++ b/python/sdist/amici/antimony_import.py
@@ -3,11 +3,11 @@
 https://antimony.sourceforge.net/
 https://tellurium.readthedocs.io/en/latest/antimony.html
 """
+
 from pathlib import Path
-from typing import Union
 
 
-def antimony2sbml(ant_model: Union[str, Path]) -> str:
+def antimony2sbml(ant_model: str | Path) -> str:
     """Convert Antimony model to SBML.
 
     :param ant_model: Antimony model as string or path to file
@@ -46,7 +46,7 @@ def antimony2sbml(ant_model: Union[str, Path]) -> str:
     return sbml_str
 
 
-def antimony2amici(ant_model: Union[str, Path], *args, **kwargs):
+def antimony2amici(ant_model: str | Path, *args, **kwargs):
     """Convert Antimony model to AMICI model.
 
     Converts the Antimony model provided as string of file to SBML and then imports it into AMICI.
diff --git a/python/sdist/amici/bngl_import.py b/python/sdist/amici/bngl_import.py
index 960413dbe6..8624ca15f1 100644
--- a/python/sdist/amici/bngl_import.py
+++ b/python/sdist/amici/bngl_import.py
@@ -5,7 +5,6 @@
 in the :term:`BNGL` format.
 """
 
-
 from pysb.importers.bngl import model_from_bngl
 
 from .pysb_import import pysb2amici
diff --git a/python/sdist/amici/compile.py b/python/sdist/amici/compile.py
index 6c4a336afc..eb3668bfbb 100644
--- a/python/sdist/amici/compile.py
+++ b/python/sdist/amici/compile.py
@@ -2,18 +2,18 @@
 Functionality for building the C++ extensions of an amici-created model
 package.
 """
+
 import subprocess
 import sys
-from typing import Optional, Union
 from pathlib import Path
 import os
 
 
 def build_model_extension(
-    package_dir: Union[str, Path],
-    verbose: Optional[Union[bool, int]] = False,
-    compiler: Optional[str] = None,
-    extra_msg: Optional[str] = None,
+    package_dir: str | Path,
+    verbose: bool | int | None = False,
+    compiler: str | None = None,
+    extra_msg: str | None = None,
 ) -> None:
     """
     Compile the model extension of an amici-created model package.
diff --git a/python/sdist/amici/conserved_quantities_demartino.py b/python/sdist/amici/conserved_quantities_demartino.py
index 4f2d326b54..43c84fdf5a 100644
--- a/python/sdist/amici/conserved_quantities_demartino.py
+++ b/python/sdist/amici/conserved_quantities_demartino.py
@@ -2,7 +2,6 @@
 import math
 import random
 import sys
-from typing import Optional, Union
 from collections.abc import MutableSequence, Sequence
 
 from .logging import get_logger
@@ -21,8 +20,8 @@ def compute_moiety_conservation_laws(
     num_species: int,
     num_reactions: int,
     max_num_monte_carlo: int = 20,
-    rng_seed: Union[None, bool, int] = False,
-    species_names: Optional[Sequence[str]] = None,
+    rng_seed: None | bool | int = False,
+    species_names: Sequence[str] | None = None,
 ) -> tuple[list[list[int]], list[list[float]]]:
     """Compute moiety conservation laws.
 
@@ -116,7 +115,7 @@ def _output(
     int_matched: list[int],
     species_indices: list[list[int]],
     species_coefficients: list[list[float]],
-    species_names: Optional[Sequence[str]] = None,
+    species_names: Sequence[str] | None = None,
     verbose: bool = False,
     log_level: int = logging.DEBUG,
 ):
diff --git a/python/sdist/amici/conserved_quantities_rref.py b/python/sdist/amici/conserved_quantities_rref.py
index b16053ab08..85dbd2b9b1 100644
--- a/python/sdist/amici/conserved_quantities_rref.py
+++ b/python/sdist/amici/conserved_quantities_rref.py
@@ -1,12 +1,12 @@
 """Find conserved quantities deterministically"""
 
-from typing import Literal, Optional, Union
+from typing import Literal
 
 import numpy as np
 
 
 def rref(
-    mat: np.array, round_ndigits: Optional[Union[Literal[False], int]] = None
+    mat: np.array, round_ndigits: Literal[False] | int | None = None
 ) -> np.array:
     """
     Bring matrix ``mat`` to reduced row echelon form
diff --git a/python/sdist/amici/cxxcodeprinter.py b/python/sdist/amici/cxxcodeprinter.py
index fb98b0aca0..d9de0ca8f8 100644
--- a/python/sdist/amici/cxxcodeprinter.py
+++ b/python/sdist/amici/cxxcodeprinter.py
@@ -1,8 +1,8 @@
 """C++ code generation"""
+
 import itertools
 import os
 import re
-from typing import Optional
 from collections.abc import Sequence
 from collections.abc import Iterable
 
@@ -49,7 +49,7 @@ def __init__(self):
         else:
             self._fpoptimizer = None
 
-    def doprint(self, expr: sp.Expr, assign_to: Optional[str] = None) -> str:
+    def doprint(self, expr: sp.Expr, assign_to: str | None = None) -> str:
         if self._fpoptimizer:
             if isinstance(expr, list):
                 expr = list(map(self._fpoptimizer, expr))
@@ -124,7 +124,7 @@ def _get_sym_lines_symbols(
         equations: sp.Matrix,
         variable: str,
         indent_level: int,
-        indices: Optional[Sequence[int]] = None,
+        indices: Sequence[int] | None = None,
     ) -> list[str]:
         """
         Generate C++ code for where array elements are directly replaced with
@@ -230,8 +230,8 @@ def print_bool(expr) -> str:
 def get_switch_statement(
     condition: str,
     cases: dict[int, list[str]],
-    indentation_level: Optional[int] = 0,
-    indentation_step: Optional[str] = " " * 4,
+    indentation_level: int | None = 0,
+    indentation_step: str | None = " " * 4,
 ):
     """
     Generate code for a C++ switch statement.
@@ -296,8 +296,8 @@ def csc_matrix(
     matrix: sp.Matrix,
     rownames: list[sp.Symbol],
     colnames: list[sp.Symbol],
-    identifier: Optional[int] = 0,
-    pattern_only: Optional[bool] = False,
+    identifier: int | None = 0,
+    pattern_only: bool | None = False,
 ) -> tuple[list[int], list[int], sp.Matrix, list[str], sp.Matrix]:
     """
     Generates the sparse symbolic identifiers, symbolic identifiers,
diff --git a/python/sdist/amici/de_export.py b/python/sdist/amici/de_export.py
index fea9325ab2..147ae3d381 100644
--- a/python/sdist/amici/de_export.py
+++ b/python/sdist/amici/de_export.py
@@ -9,6 +9,7 @@
 :py:func:`amici.sbml_import.SbmlImporter.sbml2amici` and
 :py:func:`amici.petab_import.import_model`.
 """
+
 from __future__ import annotations
 import copy
 import logging
@@ -1140,36 +1141,36 @@ def _write_model_header_cpp(self) -> None:
                         ] = impl
                 continue
 
-            tpl_data[
-                f"{func_name.upper()}_DEF"
-            ] = get_function_extern_declaration(
-                func_name, self.model_name, self.model.is_ode()
+            tpl_data[f"{func_name.upper()}_DEF"] = (
+                get_function_extern_declaration(
+                    func_name, self.model_name, self.model.is_ode()
+                )
             )
-            tpl_data[
-                f"{func_name.upper()}_IMPL"
-            ] = get_model_override_implementation(
-                func_name, self.model_name, self.model.is_ode()
+            tpl_data[f"{func_name.upper()}_IMPL"] = (
+                get_model_override_implementation(
+                    func_name, self.model_name, self.model.is_ode()
+                )
             )
             if func_name in sparse_functions:
-                tpl_data[
-                    f"{func_name.upper()}_COLPTRS_DEF"
-                ] = get_sunindex_extern_declaration(
-                    func_name, self.model_name, "colptrs"
+                tpl_data[f"{func_name.upper()}_COLPTRS_DEF"] = (
+                    get_sunindex_extern_declaration(
+                        func_name, self.model_name, "colptrs"
+                    )
                 )
-                tpl_data[
-                    f"{func_name.upper()}_COLPTRS_IMPL"
-                ] = get_sunindex_override_implementation(
-                    func_name, self.model_name, "colptrs"
+                tpl_data[f"{func_name.upper()}_COLPTRS_IMPL"] = (
+                    get_sunindex_override_implementation(
+                        func_name, self.model_name, "colptrs"
+                    )
                 )
-                tpl_data[
-                    f"{func_name.upper()}_ROWVALS_DEF"
-                ] = get_sunindex_extern_declaration(
-                    func_name, self.model_name, "rowvals"
+                tpl_data[f"{func_name.upper()}_ROWVALS_DEF"] = (
+                    get_sunindex_extern_declaration(
+                        func_name, self.model_name, "rowvals"
+                    )
                 )
-                tpl_data[
-                    f"{func_name.upper()}_ROWVALS_IMPL"
-                ] = get_sunindex_override_implementation(
-                    func_name, self.model_name, "rowvals"
+                tpl_data[f"{func_name.upper()}_ROWVALS_IMPL"] = (
+                    get_sunindex_override_implementation(
+                        func_name, self.model_name, "rowvals"
+                    )
                 )
 
         if self.model.num_states_solver() == self.model.num_states_rdata():
diff --git a/python/sdist/amici/de_model.py b/python/sdist/amici/de_model.py
index ea2807df52..f0b9c6cbb0 100644
--- a/python/sdist/amici/de_model.py
+++ b/python/sdist/amici/de_model.py
@@ -1,4 +1,5 @@
 """Symbolic differential equation model."""
+
 from __future__ import annotations
 
 import contextlib
@@ -6,7 +7,8 @@
 import itertools
 import re
 from itertools import chain
-from typing import Callable, TYPE_CHECKING
+from typing import TYPE_CHECKING
+from collections.abc import Callable
 from collections.abc import Sequence
 
 import numpy as np
diff --git a/python/sdist/amici/de_model_components.py b/python/sdist/amici/de_model_components.py
index eeeabb35db..bc93f44b87 100644
--- a/python/sdist/amici/de_model_components.py
+++ b/python/sdist/amici/de_model_components.py
@@ -1,7 +1,8 @@
 """Objects for AMICI's internal differential equation model representation"""
+
 import abc
 import numbers
-from typing import Optional, SupportsFloat, Union
+from typing import SupportsFloat
 
 import sympy as sp
 
@@ -45,7 +46,7 @@ def __init__(
         self,
         identifier: sp.Symbol,
         name: str,
-        value: Union[SupportsFloat, numbers.Number, sp.Expr],
+        value: SupportsFloat | numbers.Number | sp.Expr,
     ):
         """
         Create a new ModelQuantity instance.
@@ -165,7 +166,7 @@ def __init__(
         self._ncoeff: sp.Expr = coefficients[state_id]
         super().__init__(identifier, name, value)
 
-    def get_ncoeff(self, state_id) -> Union[sp.Expr, int, float]:
+    def get_ncoeff(self, state_id) -> sp.Expr | int | float:
         """
         Computes the normalized coefficient a_i/a_j where i is the index of
         the provided state_id and j is the index of the state that is
@@ -216,7 +217,7 @@ class State(ModelQuantity):
     Base class for differential and algebraic model states
     """
 
-    _conservation_law: Optional[ConservationLaw] = None
+    _conservation_law: ConservationLaw | None = None
 
     def get_x_rdata(self):
         """
@@ -323,7 +324,7 @@ def __init__(
         """
         super().__init__(identifier, name, init)
         self._dt = cast_to_sym(dt, "dt")
-        self._conservation_law: Union[ConservationLaw, None] = None
+        self._conservation_law: ConservationLaw | None = None
 
     def set_conservation_law(self, law: ConservationLaw) -> None:
         """
@@ -394,17 +395,16 @@ class Observable(ModelQuantity):
         function or residuals
     """
 
-    _measurement_symbol: Union[sp.Symbol, None] = None
+    _measurement_symbol: sp.Symbol | None = None
 
     def __init__(
         self,
         identifier: sp.Symbol,
         name: str,
         value: sp.Expr,
-        measurement_symbol: Optional[sp.Symbol] = None,
-        transformation: Optional[
-            ObservableTransformation
-        ] = ObservableTransformation.LIN,
+        measurement_symbol: sp.Symbol | None = None,
+        transformation: None
+        | (ObservableTransformation) = ObservableTransformation.LIN,
     ):
         """
         Create a new Observable instance.
@@ -459,8 +459,8 @@ def __init__(
         name: str,
         value: sp.Expr,
         event: sp.Symbol,
-        measurement_symbol: Optional[sp.Symbol] = None,
-        transformation: Optional[ObservableTransformation] = "lin",
+        measurement_symbol: sp.Symbol | None = None,
+        transformation: ObservableTransformation | None = "lin",
     ):
         """
         Create a new EventObservable instance.
@@ -668,8 +668,8 @@ def __init__(
         identifier: sp.Symbol,
         name: str,
         value: sp.Expr,
-        state_update: Union[sp.Expr, None],
-        initial_value: Optional[bool] = True,
+        state_update: sp.Expr | None,
+        initial_value: bool | None = True,
     ):
         """
         Create a new Event instance.
diff --git a/python/sdist/amici/debugging/__init__.py b/python/sdist/amici/debugging/__init__.py
index 81663d17b9..55b24e7b18 100644
--- a/python/sdist/amici/debugging/__init__.py
+++ b/python/sdist/amici/debugging/__init__.py
@@ -1,4 +1,5 @@
 """Functions for debugging AMICI simulation failures."""
+
 import amici
 import numpy as np
 
diff --git a/python/sdist/amici/gradient_check.py b/python/sdist/amici/gradient_check.py
index c5ddb03749..019f091e86 100644
--- a/python/sdist/amici/gradient_check.py
+++ b/python/sdist/amici/gradient_check.py
@@ -6,7 +6,6 @@
 """
 
 import copy
-from typing import Optional
 from collections.abc import Sequence
 
 import numpy as np
@@ -31,9 +30,9 @@ def check_finite_difference(
     edata: ExpData,
     ip: int,
     fields: list[str],
-    atol: Optional[float] = 1e-4,
-    rtol: Optional[float] = 1e-4,
-    epsilon: Optional[float] = 1e-3,
+    atol: float | None = 1e-4,
+    rtol: float | None = 1e-4,
+    epsilon: float | None = 1e-3,
 ) -> None:
     """
     Checks the computed sensitivity based derivatives against a finite
@@ -138,10 +137,10 @@ def check_finite_difference(
 def check_derivatives(
     model: Model,
     solver: Solver,
-    edata: Optional[ExpData] = None,
-    atol: Optional[float] = 1e-4,
-    rtol: Optional[float] = 1e-4,
-    epsilon: Optional[float] = 1e-3,
+    edata: ExpData | None = None,
+    atol: float | None = 1e-4,
+    rtol: float | None = 1e-4,
+    epsilon: float | None = 1e-3,
     check_least_squares: bool = True,
     skip_zero_pars: bool = False,
 ) -> None:
@@ -249,8 +248,8 @@ def _check_close(
     atol: float,
     rtol: float,
     field: str,
-    ip: Optional[int] = None,
-    verbose: Optional[bool] = True,
+    ip: int | None = None,
+    verbose: bool | None = True,
 ) -> None:
     """
     Compares computed values against expected values and provides rich
diff --git a/python/sdist/amici/import_utils.py b/python/sdist/amici/import_utils.py
index 029c2cc6de..1a0dc782db 100644
--- a/python/sdist/amici/import_utils.py
+++ b/python/sdist/amici/import_utils.py
@@ -1,16 +1,16 @@
 """Miscellaneous functions related to model import, independent of any specific
- model format"""
+model format"""
+
 import enum
 import itertools as itt
 import numbers
 import sys
 from typing import (
     Any,
-    Callable,
-    Optional,
     SupportsFloat,
     Union,
 )
+from collections.abc import Callable
 from collections.abc import Iterable, Sequence
 
 import sympy as sp
@@ -69,7 +69,7 @@ class ObservableTransformation(str, enum.Enum):
 
 
 def noise_distribution_to_observable_transformation(
-    noise_distribution: Union[str, Callable],
+    noise_distribution: str | Callable,
 ) -> ObservableTransformation:
     """
     Parse noise distribution string and extract observable transformation
@@ -90,7 +90,7 @@ def noise_distribution_to_observable_transformation(
 
 
 def noise_distribution_to_cost_function(
-    noise_distribution: Union[str, Callable],
+    noise_distribution: str | Callable,
 ) -> Callable[[str], str]:
     """
     Parse noise distribution string to a cost function definition amici can
@@ -258,7 +258,7 @@ def _get_str_symbol_identifiers(str_symbol: str) -> tuple:
 def smart_subs_dict(
     sym: sp.Expr,
     subs: SymbolDef,
-    field: Optional[str] = None,
+    field: str | None = None,
     reverse: bool = True,
 ) -> sp.Expr:
     """
@@ -315,7 +315,7 @@ def smart_subs(element: sp.Expr, old: sp.Symbol, new: sp.Expr) -> sp.Expr:
 
 
 def toposort_symbols(
-    symbols: SymbolDef, field: Optional[str] = None
+    symbols: SymbolDef, field: str | None = None
 ) -> SymbolDef:
     """
     Topologically sort symbol definitions according to their interdependency
@@ -420,8 +420,8 @@ def _parse_special_functions(sym: sp.Expr, toplevel: bool = True) -> sp.Expr:
 
 
 def _denest_piecewise(
-    args: Sequence[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]],
-) -> tuple[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]]:
+    args: Sequence[sp.Expr | sp.logic.boolalg.Boolean | bool],
+) -> tuple[sp.Expr | sp.logic.boolalg.Boolean | bool]:
     """
     Denest piecewise functions that contain piecewise as condition
 
@@ -567,7 +567,7 @@ def grouper(
 
 
 def _check_unsupported_functions(
-    sym: sp.Expr, expression_type: str, full_sym: Optional[sp.Expr] = None
+    sym: sp.Expr, expression_type: str, full_sym: sp.Expr | None = None
 ):
     """
     Recursively checks the symbolic expression for unsupported symbolic
@@ -619,7 +619,7 @@ def _check_unsupported_functions(
 
 
 def cast_to_sym(
-    value: Union[SupportsFloat, sp.Expr, BooleanAtom], input_name: str
+    value: SupportsFloat | sp.Expr | BooleanAtom, input_name: str
 ) -> sp.Expr:
     """
     Typecasts the value to :py:class:`sympy.Float` if possible, and ensures the
@@ -647,7 +647,7 @@ def cast_to_sym(
     return value
 
 
-def generate_measurement_symbol(observable_id: Union[str, sp.Symbol]):
+def generate_measurement_symbol(observable_id: str | sp.Symbol):
     """
     Generates the appropriate measurement symbol for the provided observable
 
@@ -662,7 +662,7 @@ def generate_measurement_symbol(observable_id: Union[str, sp.Symbol]):
     return symbol_with_assumptions(f"m{observable_id}")
 
 
-def generate_regularization_symbol(observable_id: Union[str, sp.Symbol]):
+def generate_regularization_symbol(observable_id: str | sp.Symbol):
     """
     Generates the appropriate regularization symbol for the provided observable
 
@@ -678,7 +678,7 @@ def generate_regularization_symbol(observable_id: Union[str, sp.Symbol]):
 
 
 def generate_flux_symbol(
-    reaction_index: int, name: Optional[str] = None
+    reaction_index: int, name: str | None = None
 ) -> sp.Symbol:
     """
     Generate identifier symbol for a reaction flux.
diff --git a/python/sdist/amici/logging.py b/python/sdist/amici/logging.py
index df39c4a219..0a345ee0a7 100644
--- a/python/sdist/amici/logging.py
+++ b/python/sdist/amici/logging.py
@@ -27,14 +27,14 @@
     "CRITICAL": logging.CRITICAL,
 }
 
-from typing import Callable, Optional, Union
+from collections.abc import Callable
 
 
 def _setup_logger(
-    level: Optional[int] = logging.WARNING,
-    console_output: Optional[bool] = True,
-    file_output: Optional[bool] = False,
-    capture_warnings: Optional[bool] = False,
+    level: int | None = logging.WARNING,
+    console_output: bool | None = True,
+    file_output: bool | None = False,
+    capture_warnings: bool | None = False,
 ) -> logging.Logger:
     """
     Set up a new :class:`logging.Logger` for AMICI logging.
@@ -118,7 +118,7 @@ def _setup_logger(
     return log
 
 
-def set_log_level(logger: logging.Logger, log_level: Union[int, bool]) -> None:
+def set_log_level(logger: logging.Logger, log_level: int | bool) -> None:
     if log_level is not None and log_level is not False:
         if isinstance(log_level, bool):
             log_level = logging.DEBUG
@@ -134,8 +134,8 @@ def set_log_level(logger: logging.Logger, log_level: Union[int, bool]) -> None:
 
 
 def get_logger(
-    logger_name: Optional[str] = BASE_LOGGER_NAME,
-    log_level: Optional[int] = None,
+    logger_name: str | None = BASE_LOGGER_NAME,
+    log_level: int | None = None,
     **kwargs,
 ) -> logging.Logger:
     """
diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index f40d0f4c6e..9aa03fc2dd 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -37,7 +37,7 @@ class is memory efficient as copies of the underlying C++ objects is
     _field_names: list[str] = []
     _field_dimensions: dict[str, list[int]] = dict()
 
-    def __getitem__(self, item: str) -> Union[np.ndarray, float]:
+    def __getitem__(self, item: str) -> np.ndarray | float:
         """
         Access to field names, copies data from C++ object into numpy
         array, reshapes according to field dimensions and stores values in
@@ -76,7 +76,7 @@ def __missing__(self, key: str) -> None:
         """
         raise KeyError(f"Unknown field name {key}.")
 
-    def __getattr__(self, item) -> Union[np.ndarray, float]:
+    def __getattr__(self, item) -> np.ndarray | float:
         """
         Attribute accessor for field names
 
@@ -245,7 +245,7 @@ class ReturnDataView(SwigPtrView):
         "t_last",
     ]
 
-    def __init__(self, rdata: Union[ReturnDataPtr, ReturnData]):
+    def __init__(self, rdata: ReturnDataPtr | ReturnData):
         """
         Constructor
 
@@ -309,7 +309,7 @@ def __init__(self, rdata: Union[ReturnDataPtr, ReturnData]):
 
     def __getitem__(
         self, item: str
-    ) -> Union[np.ndarray, ReturnDataPtr, ReturnData, float]:
+    ) -> np.ndarray | ReturnDataPtr | ReturnData | float:
         """
         Access fields by name.s
 
@@ -391,7 +391,7 @@ class ExpDataView(SwigPtrView):
         "fixedParametersPresimulation",
     ]
 
-    def __init__(self, edata: Union[ExpDataPtr, ExpData]):
+    def __init__(self, edata: ExpDataPtr | ExpData):
         """
         Constructor
 
@@ -429,7 +429,7 @@ def __init__(self, edata: Union[ExpDataPtr, ExpData]):
 
 def _field_as_numpy(
     field_dimensions: dict[str, list[int]], field: str, data: SwigPtrView
-) -> Union[np.ndarray, float, None]:
+) -> np.ndarray | float | None:
     """
     Convert data object field to numpy array with dimensions according to
     specified field dimensions
diff --git a/python/sdist/amici/pandas.py b/python/sdist/amici/pandas.py
index b776d2d5ef..b61cfa0c79 100644
--- a/python/sdist/amici/pandas.py
+++ b/python/sdist/amici/pandas.py
@@ -7,7 +7,7 @@
 
 import copy
 import math
-from typing import Optional, SupportsFloat, Union
+from typing import SupportsFloat, Union
 
 import amici
 import numpy as np
@@ -70,7 +70,7 @@ def _process_rdata_list(rdata_list: ReturnDatas) -> list[amici.ReturnDataView]:
 
 
 def getDataObservablesAsDataFrame(
-    model: AmiciModel, edata_list: ExpDatas, by_id: Optional[bool] = False
+    model: AmiciModel, edata_list: ExpDatas, by_id: bool | None = False
 ) -> pd.DataFrame:
     """
     Write Observables from experimental data as DataFrame.
@@ -123,7 +123,7 @@ def getSimulationObservablesAsDataFrame(
     model: amici.Model,
     edata_list: ExpDatas,
     rdata_list: ReturnDatas,
-    by_id: Optional[bool] = False,
+    by_id: bool | None = False,
 ) -> pd.DataFrame:
     """
     Write Observables from simulation results as DataFrame.
@@ -181,7 +181,7 @@ def getSimulationStatesAsDataFrame(
     model: amici.Model,
     edata_list: ExpDatas,
     rdata_list: ReturnDatas,
-    by_id: Optional[bool] = False,
+    by_id: bool | None = False,
 ) -> pd.DataFrame:
     """
     Get model state according to lists of ReturnData and ExpData.
@@ -237,7 +237,7 @@ def get_expressions_as_dataframe(
     model: amici.Model,
     edata_list: ExpDatas,
     rdata_list: ReturnDatas,
-    by_id: Optional[bool] = False,
+    by_id: bool | None = False,
 ) -> pd.DataFrame:
     """
     Get values of model expressions from lists of ReturnData as DataFrame.
@@ -293,7 +293,7 @@ def getResidualsAsDataFrame(
     model: amici.Model,
     edata_list: ExpDatas,
     rdata_list: ReturnDatas,
-    by_id: Optional[bool] = False,
+    by_id: bool | None = False,
 ) -> pd.DataFrame:
     """
     Convert a list of ReturnData and ExpData to pandas DataFrame with
@@ -626,8 +626,8 @@ def _get_names_or_ids(
 
 def _get_specialized_fixed_parameters(
     model: AmiciModel,
-    condition: Union[dict[str, SupportsFloat], pd.Series],
-    overwrite: Union[dict[str, SupportsFloat], pd.Series],
+    condition: dict[str, SupportsFloat] | pd.Series,
+    overwrite: dict[str, SupportsFloat] | pd.Series,
     by_id: bool,
 ) -> list[float]:
     """
@@ -661,7 +661,7 @@ def constructEdataFromDataFrame(
     df: pd.DataFrame,
     model: AmiciModel,
     condition: pd.Series,
-    by_id: Optional[bool] = False,
+    by_id: bool | None = False,
 ) -> amici.amici.ExpData:
     """
     Constructs an ExpData instance according to the provided Model
@@ -778,7 +778,7 @@ def constructEdataFromDataFrame(
 
 
 def getEdataFromDataFrame(
-    model: AmiciModel, df: pd.DataFrame, by_id: Optional[bool] = False
+    model: AmiciModel, df: pd.DataFrame, by_id: bool | None = False
 ) -> list[amici.amici.ExpData]:
     """
     Constructs a ExpData instances according to the provided Model and
diff --git a/python/sdist/amici/petab/conditions.py b/python/sdist/amici/petab/conditions.py
index 34dd44cbcb..61b8679765 100644
--- a/python/sdist/amici/petab/conditions.py
+++ b/python/sdist/amici/petab/conditions.py
@@ -1,4 +1,5 @@
 """PEtab conditions to AMICI ExpDatas."""
+
 import logging
 import numbers
 import warnings
@@ -218,7 +219,7 @@ def create_parameterized_edatas(
     problem_parameters: dict[str, numbers.Number],
     scaled_parameters: bool = False,
     parameter_mapping: ParameterMapping = None,
-    simulation_conditions: Union[pd.DataFrame, dict] = None,
+    simulation_conditions: pd.DataFrame | dict = None,
 ) -> list[amici.ExpData]:
     """Create list of :class:amici.ExpData objects with parameters filled in.
 
@@ -284,7 +285,7 @@ def create_parameterized_edatas(
 
 
 def create_edata_for_condition(
-    condition: Union[dict, pd.Series],
+    condition: dict | pd.Series,
     measurement_df: pd.DataFrame,
     amici_model: AmiciModel,
     petab_problem: petab.Problem,
@@ -369,7 +370,7 @@ def create_edata_for_condition(
 def create_edatas(
     amici_model: AmiciModel,
     petab_problem: petab.Problem,
-    simulation_conditions: Union[pd.DataFrame, dict] = None,
+    simulation_conditions: pd.DataFrame | dict = None,
 ) -> list[amici.ExpData]:
     """Create list of :class:`amici.amici.ExpData` objects for PEtab problem.
 
@@ -515,7 +516,7 @@ def _get_measurements_and_sigmas(
             if isinstance(
                 measurement.get(NOISE_PARAMETERS, None), numbers.Number
             ):
-                sigma_y[
-                    time_ix_for_obs_ix[observable_ix], observable_ix
-                ] = measurement[NOISE_PARAMETERS]
+                sigma_y[time_ix_for_obs_ix[observable_ix], observable_ix] = (
+                    measurement[NOISE_PARAMETERS]
+                )
     return y, sigma_y
diff --git a/python/sdist/amici/petab/import_helpers.py b/python/sdist/amici/petab/import_helpers.py
index 3caf951ace..29cbff07e6 100644
--- a/python/sdist/amici/petab/import_helpers.py
+++ b/python/sdist/amici/petab/import_helpers.py
@@ -2,12 +2,12 @@
 
 Functions for PEtab import that are independent of the model format.
 """
+
 import importlib
 import logging
 import os
 import re
 from pathlib import Path
-from typing import Union
 
 import amici
 import pandas as pd
@@ -30,9 +30,7 @@
 
 def get_observation_model(
     observable_df: pd.DataFrame,
-) -> tuple[
-    dict[str, dict[str, str]], dict[str, str], dict[str, Union[str, float]]
-]:
+) -> tuple[dict[str, dict[str, str]], dict[str, str], dict[str, str | float]]:
     """
     Get observables, sigmas, and noise distributions from PEtab observation
     table in a format suitable for
@@ -128,7 +126,7 @@ def petab_scale_to_amici_scale(scale_str: str) -> int:
     raise ValueError(f"Invalid parameter scale {scale_str}")
 
 
-def _create_model_name(folder: Union[str, Path]) -> str:
+def _create_model_name(folder: str | Path) -> str:
     """
     Create a name for the model.
     Just re-use the last part of the folder.
@@ -136,9 +134,7 @@ def _create_model_name(folder: Union[str, Path]) -> str:
     return os.path.split(os.path.normpath(folder))[-1]
 
 
-def _can_import_model(
-    model_name: str, model_output_dir: Union[str, Path]
-) -> bool:
+def _can_import_model(model_name: str, model_output_dir: str | Path) -> bool:
     """
     Check whether a module of that name can already be imported.
     """
diff --git a/python/sdist/amici/petab/petab_import.py b/python/sdist/amici/petab/petab_import.py
index cb896b39e3..0e63496d75 100644
--- a/python/sdist/amici/petab/petab_import.py
+++ b/python/sdist/amici/petab/petab_import.py
@@ -9,7 +9,6 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Union
 from warnings import warn
 
 import amici
@@ -34,7 +33,7 @@
 
 def import_petab_problem(
     petab_problem: petab.Problem,
-    model_output_dir: Union[str, Path, None] = None,
+    model_output_dir: str | Path | None = None,
     model_name: str = None,
     compile_: bool = None,
     non_estimated_parameters_as_constants=True,
diff --git a/python/sdist/amici/petab/petab_problem.py b/python/sdist/amici/petab/petab_problem.py
index 8ea177ad03..618b8b5247 100644
--- a/python/sdist/amici/petab/petab_problem.py
+++ b/python/sdist/amici/petab/petab_problem.py
@@ -1,6 +1,6 @@
 """PEtab-problem based simulations."""
+
 import copy
-from typing import Optional, Union
 
 import amici
 import pandas as pd
@@ -36,10 +36,10 @@ class PetabProblem:
     def __init__(
         self,
         petab_problem: petab.Problem,
-        amici_model: Optional[amici.Model] = None,
-        problem_parameters: Optional[dict[str, float]] = None,
+        amici_model: amici.Model | None = None,
+        problem_parameters: dict[str, float] | None = None,
         scaled_parameters: bool = False,
-        simulation_conditions: Union[pd.DataFrame, list[dict]] = None,
+        simulation_conditions: pd.DataFrame | list[dict] = None,
         store_edatas: bool = True,
     ):
         self._petab_problem = copy.deepcopy(petab_problem)
@@ -63,9 +63,9 @@ def __init__(
         if (
             preeq_id := PREEQUILIBRATION_CONDITION_ID
         ) in self._simulation_conditions:
-            self._simulation_conditions[
-                preeq_id
-            ] = self._simulation_conditions[preeq_id].fillna("")
+            self._simulation_conditions[preeq_id] = (
+                self._simulation_conditions[preeq_id].fillna("")
+            )
 
         if problem_parameters is None:
             # Use PEtab nominal values as default
@@ -102,7 +102,10 @@ def set_parameters(
         :param scaled_parameters: Whether the provided parameters are on PEtab
             `parameterScale` or not.
         """
-        if scaled_parameters != self._scaled_parameters and self._parameter_mapping is not None:
+        if (
+            scaled_parameters != self._scaled_parameters
+            and self._parameter_mapping is not None
+        ):
             # redo parameter mapping if scale changed
             self._parameter_mapping = create_parameter_mapping(
                 petab_problem=self._petab_problem,
diff --git a/python/sdist/amici/petab/pysb_import.py b/python/sdist/amici/petab/pysb_import.py
index 8c67bb0785..b770603935 100644
--- a/python/sdist/amici/petab/pysb_import.py
+++ b/python/sdist/amici/petab/pysb_import.py
@@ -8,7 +8,6 @@
 import logging
 import re
 from pathlib import Path
-from typing import Optional, Union
 
 import petab
 import pysb
@@ -165,9 +164,9 @@ def _add_initialization_variables(
 @log_execution_time("Importing PEtab model", logger)
 def import_model_pysb(
     petab_problem: petab.Problem,
-    model_output_dir: Optional[Union[str, Path]] = None,
-    verbose: Optional[Union[bool, int]] = True,
-    model_name: Optional[str] = None,
+    model_output_dir: str | Path | None = None,
+    verbose: bool | int | None = True,
+    model_name: str | None = None,
     **kwargs,
 ) -> None:
     """
diff --git a/python/sdist/amici/petab/sbml_import.py b/python/sdist/amici/petab/sbml_import.py
index 2484d57a7a..2c43c3adc4 100644
--- a/python/sdist/amici/petab/sbml_import.py
+++ b/python/sdist/amici/petab/sbml_import.py
@@ -4,7 +4,7 @@
 import tempfile
 from itertools import chain
 from pathlib import Path
-from typing import Optional, Union
+from typing import Union
 from warnings import warn
 
 import amici
@@ -31,17 +31,17 @@
 @log_execution_time("Importing PEtab model", logger)
 def import_model_sbml(
     sbml_model: Union[str, Path, "libsbml.Model"] = None,
-    condition_table: Optional[Union[str, Path, pd.DataFrame]] = None,
-    observable_table: Optional[Union[str, Path, pd.DataFrame]] = None,
-    measurement_table: Optional[Union[str, Path, pd.DataFrame]] = None,
+    condition_table: str | Path | pd.DataFrame | None = None,
+    observable_table: str | Path | pd.DataFrame | None = None,
+    measurement_table: str | Path | pd.DataFrame | None = None,
     petab_problem: petab.Problem = None,
-    model_name: Optional[str] = None,
-    model_output_dir: Optional[Union[str, Path]] = None,
-    verbose: Optional[Union[bool, int]] = True,
+    model_name: str | None = None,
+    model_output_dir: str | Path | None = None,
+    verbose: bool | int | None = True,
     allow_reinit_fixpar_initcond: bool = True,
     validate: bool = True,
     non_estimated_parameters_as_constants=True,
-    output_parameter_defaults: Optional[dict[str, float]] = None,
+    output_parameter_defaults: dict[str, float] | None = None,
     discard_sbml_annotations: bool = False,
     **kwargs,
 ) -> amici.SbmlImporter:
@@ -545,7 +545,7 @@ def _get_fixed_parameters_sbml(
 
 
 def _create_model_output_dir_name(
-    sbml_model: "libsbml.Model", model_name: Optional[str] = None
+    sbml_model: "libsbml.Model", model_name: str | None = None
 ) -> Path:
     """
     Find a folder for storing the compiled amici model.
diff --git a/python/sdist/amici/petab/simulations.py b/python/sdist/amici/petab/simulations.py
index 0f9aae3bfd..77f14ccb35 100644
--- a/python/sdist/amici/petab/simulations.py
+++ b/python/sdist/amici/petab/simulations.py
@@ -3,9 +3,10 @@
 Functionality related to running simulations or evaluating the objective
 function as defined by a PEtab problem.
 """
+
 import copy
 import logging
-from typing import Any, Optional, Union
+from typing import Any
 from collections.abc import Sequence
 
 import amici
@@ -72,12 +73,12 @@
 def simulate_petab(
     petab_problem: petab.Problem,
     amici_model: AmiciModel,
-    solver: Optional[amici.Solver] = None,
-    problem_parameters: Optional[dict[str, float]] = None,
-    simulation_conditions: Union[pd.DataFrame, dict] = None,
+    solver: amici.Solver | None = None,
+    problem_parameters: dict[str, float] | None = None,
+    simulation_conditions: pd.DataFrame | dict = None,
     edatas: list[AmiciExpData] = None,
     parameter_mapping: ParameterMapping = None,
-    scaled_parameters: Optional[bool] = False,
+    scaled_parameters: bool | None = False,
     log_level: int = logging.WARNING,
     num_threads: int = 1,
     failfast: bool = True,
@@ -262,11 +263,11 @@ def simulate_petab(
 def aggregate_sllh(
     amici_model: AmiciModel,
     rdatas: Sequence[amici.ReturnDataView],
-    parameter_mapping: Optional[ParameterMapping],
+    parameter_mapping: ParameterMapping | None,
     edatas: list[AmiciExpData],
     petab_scale: bool = True,
     petab_problem: petab.Problem = None,
-) -> Union[None, dict[str, float]]:
+) -> None | dict[str, float]:
     """
     Aggregate likelihood gradient for all conditions, according to PEtab
     parameter mapping.
diff --git a/python/sdist/amici/petab/simulator.py b/python/sdist/amici/petab/simulator.py
index a5f50112cc..9c655b1483 100644
--- a/python/sdist/amici/petab/simulator.py
+++ b/python/sdist/amici/petab/simulator.py
@@ -11,7 +11,7 @@
 
 import inspect
 import sys
-from typing import Callable
+from collections.abc import Callable
 
 import pandas as pd
 import petab
diff --git a/python/sdist/amici/petab/util.py b/python/sdist/amici/petab/util.py
index 742f7bdfe3..e30b829a04 100644
--- a/python/sdist/amici/petab/util.py
+++ b/python/sdist/amici/petab/util.py
@@ -1,6 +1,7 @@
 """Various helper functions for working with PEtab problems."""
+
 import re
-from typing import TYPE_CHECKING, Union
+from typing import TYPE_CHECKING
 
 import libsbml
 import pandas as pd
@@ -15,9 +16,9 @@
 
 def get_states_in_condition_table(
     petab_problem: petab.Problem,
-    condition: Union[dict, pd.Series] = None,
+    condition: dict | pd.Series = None,
     return_patterns: bool = False,
-) -> dict[str, tuple[Union[float, str, None], Union[float, str, None]]]:
+) -> dict[str, tuple[float | str | None, float | str | None]]:
     """Get states and their initial condition as specified in the condition table.
 
     Returns: Dictionary: ``stateId -> (initial condition simulation, initial condition preequilibration)``
diff --git a/python/sdist/amici/petab_import.py b/python/sdist/amici/petab_import.py
index d5c67753ac..b81484c1cc 100644
--- a/python/sdist/amici/petab_import.py
+++ b/python/sdist/amici/petab_import.py
@@ -7,6 +7,7 @@
 .. deprecated:: 0.21.0
     Use :mod:`amici.petab` instead.
 """
+
 import warnings
 
 warnings.warn(
diff --git a/python/sdist/amici/petab_import_pysb.py b/python/sdist/amici/petab_import_pysb.py
index 595018f208..a1597d53b5 100644
--- a/python/sdist/amici/petab_import_pysb.py
+++ b/python/sdist/amici/petab_import_pysb.py
@@ -4,6 +4,7 @@
 .. deprecated:: 0.21.0
     Use :mod:`amici.petab.pysb_import` instead.
 """
+
 import warnings
 
 from .petab.pysb_import import *  # noqa: F401, F403
diff --git a/python/sdist/amici/plotting.py b/python/sdist/amici/plotting.py
index 19dbe05f89..651ba0e23e 100644
--- a/python/sdist/amici/plotting.py
+++ b/python/sdist/amici/plotting.py
@@ -3,7 +3,7 @@
 --------
 Plotting related functions
 """
-from typing import Optional, Union
+
 from collections.abc import Iterable, Sequence
 
 import matplotlib.pyplot as plt
@@ -19,8 +19,8 @@
 
 def plot_state_trajectories(
     rdata: ReturnDataView,
-    state_indices: Optional[Sequence[int]] = None,
-    ax: Optional[Axes] = None,
+    state_indices: Sequence[int] | None = None,
+    ax: Axes | None = None,
     model: Model = None,
     prefer_names: bool = True,
     marker=None,
@@ -76,12 +76,12 @@ def plot_state_trajectories(
 
 def plot_observable_trajectories(
     rdata: ReturnDataView,
-    observable_indices: Optional[Iterable[int]] = None,
-    ax: Optional[Axes] = None,
+    observable_indices: Iterable[int] | None = None,
+    ax: Axes | None = None,
     model: Model = None,
     prefer_names: bool = True,
     marker=None,
-    edata: Union[amici.ExpData, amici.ExpDataView] = None,
+    edata: amici.ExpData | amici.ExpDataView = None,
 ) -> None:
     """
     Plot observable trajectories.
@@ -175,7 +175,7 @@ def plot_jacobian(rdata: ReturnDataView):
 
 
 def plot_expressions(
-    exprs: Union[Sequence[StrOrExpr], StrOrExpr], rdata: ReturnDataView
+    exprs: Sequence[StrOrExpr] | StrOrExpr, rdata: ReturnDataView
 ) -> None:
     """Plot the given expressions evaluated on the given simulation outputs.
 
diff --git a/python/sdist/amici/pysb_import.py b/python/sdist/amici/pysb_import.py
index 94aad595d9..46476a753d 100644
--- a/python/sdist/amici/pysb_import.py
+++ b/python/sdist/amici/pysb_import.py
@@ -12,10 +12,9 @@
 from pathlib import Path
 from typing import (
     Any,
-    Callable,
-    Optional,
     Union,
 )
+from collections.abc import Callable
 from collections.abc import Iterable
 
 import numpy as np
@@ -53,12 +52,12 @@
 
 def pysb2amici(
     model: pysb.Model,
-    output_dir: Optional[Union[str, Path]] = None,
+    output_dir: str | Path | None = None,
     observables: list[str] = None,
     constant_parameters: list[str] = None,
     sigmas: dict[str, str] = None,
-    noise_distributions: Optional[dict[str, Union[str, Callable]]] = None,
-    verbose: Union[int, bool] = False,
+    noise_distributions: dict[str, str | Callable] | None = None,
+    verbose: int | bool = False,
     assume_pow_positivity: bool = False,
     compiler: str = None,
     compute_conservation_laws: bool = True,
@@ -68,7 +67,7 @@ def pysb2amici(
     # See https://github.com/AMICI-dev/AMICI/pull/1672
     cache_simplify: bool = False,
     generate_sensitivity_code: bool = True,
-    model_name: Optional[str] = None,
+    model_name: str | None = None,
 ):
     r"""
     Generate AMICI C++ files for the provided model.
@@ -194,13 +193,13 @@ def ode_model_from_pysb_importer(
     constant_parameters: list[str] = None,
     observables: list[str] = None,
     sigmas: dict[str, str] = None,
-    noise_distributions: Optional[dict[str, Union[str, Callable]]] = None,
+    noise_distributions: dict[str, str | Callable] | None = None,
     compute_conservation_laws: bool = True,
     simplify: Callable = sp.powsimp,
     # Do not enable by default without testing.
     # See https://github.com/AMICI-dev/AMICI/pull/1672
     cache_simplify: bool = False,
-    verbose: Union[int, bool] = False,
+    verbose: int | bool = False,
 ) -> DEModel:
     """
     Creates an :class:`amici.DEModel` instance from a :class:`pysb.Model`
@@ -441,7 +440,7 @@ def _process_pysb_expressions(
     ode_model: DEModel,
     observables: list[str],
     sigmas: dict[str, str],
-    noise_distributions: Optional[dict[str, Union[str, Callable]]] = None,
+    noise_distributions: dict[str, str | Callable] | None = None,
 ) -> None:
     r"""
     Converts pysb expressions/observables into Observables (with
@@ -506,7 +505,7 @@ def _add_expression(
     ode_model: DEModel,
     observables: list[str],
     sigmas: dict[str, str],
-    noise_distributions: Optional[dict[str, Union[str, Callable]]] = None,
+    noise_distributions: dict[str, str | Callable] | None = None,
 ):
     """
     Adds expressions to the ODE model given and adds observables/sigmas if
@@ -621,7 +620,7 @@ def _process_pysb_observables(
     ode_model: DEModel,
     observables: list[str],
     sigmas: dict[str, str],
-    noise_distributions: Optional[dict[str, Union[str, Callable]]] = None,
+    noise_distributions: dict[str, str | Callable] | None = None,
 ) -> None:
     """
     Converts :class:`pysb.core.Observable` into
@@ -1349,7 +1348,7 @@ def has_fixed_parameter_ic(
 
 
 def extract_monomers(
-    complex_patterns: Union[pysb.ComplexPattern, list[pysb.ComplexPattern]],
+    complex_patterns: pysb.ComplexPattern | list[pysb.ComplexPattern],
 ) -> list[str]:
     """
     Constructs a list of monomer names contained in complex patterns.
@@ -1415,8 +1414,8 @@ def _get_unconserved_monomers(
 
 
 def _get_changed_stoichiometries(
-    reactants: Union[pysb.ComplexPattern, list[pysb.ComplexPattern]],
-    products: Union[pysb.ComplexPattern, list[pysb.ComplexPattern]],
+    reactants: pysb.ComplexPattern | list[pysb.ComplexPattern],
+    products: pysb.ComplexPattern | list[pysb.ComplexPattern],
 ) -> set[str]:
     """
     Constructs the set of monomer names which have different
@@ -1444,7 +1443,7 @@ def _get_changed_stoichiometries(
     return changed_stoichiometries
 
 
-def pysb_model_from_path(pysb_model_file: Union[str, Path]) -> pysb.Model:
+def pysb_model_from_path(pysb_model_file: str | Path) -> pysb.Model:
     """Load a pysb model module and return the :class:`pysb.Model` instance
 
     :param pysb_model_file: Full or relative path to the PySB model module
diff --git a/python/sdist/amici/sbml_import.py b/python/sdist/amici/sbml_import.py
index 8f7f67b02f..40c4881a09 100644
--- a/python/sdist/amici/sbml_import.py
+++ b/python/sdist/amici/sbml_import.py
@@ -4,6 +4,7 @@
 This module provides all necessary functionality to import a model specified
 in the `Systems Biology Markup Language (SBML) <http://sbml.org/Main_Page>`_.
 """
+
 import copy
 import itertools as itt
 import logging
@@ -15,10 +16,9 @@
 from pathlib import Path
 from typing import (
     Any,
-    Callable,
-    Optional,
     Union,
 )
+from collections.abc import Callable
 from collections.abc import Iterable, Sequence
 
 import libsbml as sbml
@@ -134,7 +134,7 @@ class SbmlImporter:
 
     def __init__(
         self,
-        sbml_source: Union[str, Path, sbml.Model],
+        sbml_source: str | Path | sbml.Model,
         show_sbml_warnings: bool = False,
         from_file: bool = True,
         discard_annotations: bool = False,
@@ -177,7 +177,7 @@ def __init__(
         # Long and short names for model components
         self.symbols: dict[SymbolId, dict[sp.Symbol, dict[str, Any]]] = {}
 
-        self._local_symbols: dict[str, Union[sp.Expr, sp.Function]] = {}
+        self._local_symbols: dict[str, sp.Expr | sp.Function] = {}
         self.compartments: SymbolicFormula = {}
         self.compartment_assignment_rules: SymbolicFormula = {}
         self.species_assignment_rules: SymbolicFormula = {}
@@ -269,21 +269,21 @@ def _reset_symbols(self) -> None:
     def sbml2amici(
         self,
         model_name: str,
-        output_dir: Union[str, Path] = None,
+        output_dir: str | Path = None,
         observables: dict[str, dict[str, str]] = None,
         event_observables: dict[str, dict[str, str]] = None,
         constant_parameters: Iterable[str] = None,
-        sigmas: dict[str, Union[str, float]] = None,
-        event_sigmas: dict[str, Union[str, float]] = None,
-        noise_distributions: dict[str, Union[str, Callable]] = None,
-        event_noise_distributions: dict[str, Union[str, Callable]] = None,
-        verbose: Union[int, bool] = logging.ERROR,
+        sigmas: dict[str, str | float] = None,
+        event_sigmas: dict[str, str | float] = None,
+        noise_distributions: dict[str, str | Callable] = None,
+        event_noise_distributions: dict[str, str | Callable] = None,
+        verbose: int | bool = logging.ERROR,
         assume_pow_positivity: bool = False,
         compiler: str = None,
         allow_reinit_fixpar_initcond: bool = True,
         compile: bool = True,
         compute_conservation_laws: bool = True,
-        simplify: Optional[Callable] = _default_simplify,
+        simplify: Callable | None = _default_simplify,
         cache_simplify: bool = False,
         log_as_log10: bool = True,
         generate_sensitivity_code: bool = True,
@@ -451,13 +451,13 @@ def _build_ode_model(
         observables: dict[str, dict[str, str]] = None,
         event_observables: dict[str, dict[str, str]] = None,
         constant_parameters: Iterable[str] = None,
-        sigmas: dict[str, Union[str, float]] = None,
-        event_sigmas: dict[str, Union[str, float]] = None,
-        noise_distributions: dict[str, Union[str, Callable]] = None,
-        event_noise_distributions: dict[str, Union[str, Callable]] = None,
-        verbose: Union[int, bool] = logging.ERROR,
+        sigmas: dict[str, str | float] = None,
+        event_sigmas: dict[str, str | float] = None,
+        noise_distributions: dict[str, str | Callable] = None,
+        event_noise_distributions: dict[str, str | Callable] = None,
+        verbose: int | bool = logging.ERROR,
         compute_conservation_laws: bool = True,
-        simplify: Optional[Callable] = _default_simplify,
+        simplify: Callable | None = _default_simplify,
         cache_simplify: bool = False,
         log_as_log10: bool = True,
         hardcode_symbols: Sequence[str] = None,
@@ -1043,7 +1043,7 @@ def add_d_dt(
         self,
         d_dt: sp.Expr,
         variable: sp.Symbol,
-        variable0: Union[float, sp.Expr],
+        variable0: float | sp.Expr,
         name: str,
     ) -> None:
         """
@@ -1701,8 +1701,8 @@ def get_empty_bolus_value() -> sp.Float:
     @log_execution_time("processing SBML observables", logger)
     def _process_observables(
         self,
-        observables: Union[dict[str, dict[str, str]], None],
-        sigmas: dict[str, Union[str, float]],
+        observables: dict[str, dict[str, str]] | None,
+        sigmas: dict[str, str | float],
         noise_distributions: dict[str, str],
     ) -> None:
         """
@@ -1768,7 +1768,7 @@ def _process_observables(
     def _process_event_observables(
         self,
         event_observables: dict[str, dict[str, str]],
-        event_sigmas: dict[str, Union[str, float]],
+        event_sigmas: dict[str, str | float],
         event_noise_distributions: dict[str, str],
     ) -> None:
         """
@@ -1884,7 +1884,7 @@ def _generate_default_observables(self):
 
     def _process_log_likelihood(
         self,
-        sigmas: dict[str, Union[str, float]],
+        sigmas: dict[str, str | float],
         noise_distributions: dict[str, str],
         events: bool = False,
         event_reg: bool = False,
@@ -2036,8 +2036,8 @@ def _process_species_references(self):
             )
 
     def _make_initial(
-        self, sym_math: Union[sp.Expr, None, float]
-    ) -> Union[sp.Expr, None, float]:
+        self, sym_math: sp.Expr | None | float
+    ) -> sp.Expr | None | float:
         """
         Transforms an expression to its value at the initial time point by
         replacing species by their initial values.
@@ -2488,7 +2488,7 @@ def _clean_reserved_symbols(self) -> None:
 
     def _sympy_from_sbml_math(
         self, var_or_math: [sbml.SBase, str]
-    ) -> Union[sp.Expr, float, None]:
+    ) -> sp.Expr | float | None:
         """
         Sympify Math of SBML variables with all sanity checks and
         transformations
@@ -2541,7 +2541,7 @@ def _sympy_from_sbml_math(
 
     def _get_element_initial_assignment(
         self, element_id: str
-    ) -> Union[sp.Expr, None]:
+    ) -> sp.Expr | None:
         """
         Extract value of sbml variable according to its initial assignment
 
@@ -2926,7 +2926,7 @@ def _get_list_of_species_references(
     ]
 
 
-def replace_logx(math_str: Union[str, float, None]) -> Union[str, float, None]:
+def replace_logx(math_str: str | float | None) -> str | float | None:
     """
     Replace logX(.) by log(., X) since sympy cannot parse the former
 
@@ -2961,7 +2961,7 @@ def _collect_event_assignment_parameter_targets(
 
 
 def _check_unsupported_functions_sbml(
-    sym: sp.Expr, expression_type: str, full_sym: Optional[sp.Expr] = None
+    sym: sp.Expr, expression_type: str, full_sym: sp.Expr | None = None
 ):
     try:
         _check_unsupported_functions(sym, expression_type, full_sym)
@@ -2979,8 +2979,8 @@ def _parse_special_functions_sbml(
 
 
 def _validate_observables(
-    observables: Union[dict[str, dict[str, str]], None],
-    sigmas: dict[str, Union[str, float]],
+    observables: dict[str, dict[str, str]] | None,
+    sigmas: dict[str, str | float],
     noise_distributions: dict[str, str],
     events: bool = False,
 ) -> None:
diff --git a/python/sdist/amici/setup.template.py b/python/sdist/amici/setup.template.py
index 11589564e0..1f2d099110 100644
--- a/python/sdist/amici/setup.template.py
+++ b/python/sdist/amici/setup.template.py
@@ -1,4 +1,5 @@
 """AMICI model package setup"""
+
 import os
 import sys
 from pathlib import Path
diff --git a/python/sdist/amici/splines.py b/python/sdist/amici/splines.py
index ea0cd0e06d..cd500a4570 100644
--- a/python/sdist/amici/splines.py
+++ b/python/sdist/amici/splines.py
@@ -5,6 +5,7 @@
 annotations from/to SBML files and for adding such splines to the AMICI C++
 code.
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
@@ -13,9 +14,9 @@
     from numbers import Real
     from typing import (
         Any,
-        Callable,
         Union,
     )
+    from collections.abc import Callable
     from collections.abc import Sequence
 
     from . import sbml_import
diff --git a/python/sdist/amici/swig.py b/python/sdist/amici/swig.py
index 5ba8017005..e0c518957f 100644
--- a/python/sdist/amici/swig.py
+++ b/python/sdist/amici/swig.py
@@ -1,4 +1,5 @@
 """Functions related to SWIG or SWIG-generated code"""
+
 from __future__ import annotations
 import ast
 import contextlib
diff --git a/python/sdist/amici/swig_wrappers.py b/python/sdist/amici/swig_wrappers.py
index b6023b2c34..3c4df44809 100644
--- a/python/sdist/amici/swig_wrappers.py
+++ b/python/sdist/amici/swig_wrappers.py
@@ -1,9 +1,10 @@
 """Convenience wrappers for the swig interface"""
+
 import logging
 import sys
 import warnings
 from contextlib import contextmanager, suppress
-from typing import Any, Optional, Union
+from typing import Any
 
 import amici
 import amici.amici as amici_swig
@@ -49,7 +50,7 @@ def _capture_cstdout():
 def runAmiciSimulation(
     model: AmiciModel,
     solver: AmiciSolver,
-    edata: Optional[AmiciExpData] = None,
+    edata: AmiciExpData | None = None,
 ) -> "numpy.ReturnDataView":
     """
     Convenience wrapper around :py:func:`amici.amici.runAmiciSimulation`
@@ -139,7 +140,7 @@ def runAmiciSimulations(
 
 
 def readSolverSettingsFromHDF5(
-    file: str, solver: AmiciSolver, location: Optional[str] = "solverSettings"
+    file: str, solver: AmiciSolver, location: str | None = "solverSettings"
 ) -> None:
     """
     Convenience wrapper for :py:func:`amici.readSolverSettingsFromHDF5`
@@ -153,8 +154,8 @@ def readSolverSettingsFromHDF5(
 
 def writeSolverSettingsToHDF5(
     solver: AmiciSolver,
-    file: Union[str, object],
-    location: Optional[str] = "solverSettings",
+    file: str | object,
+    location: str | None = "solverSettings",
 ) -> None:
     """
     Convenience wrapper for :py:func:`amici.amici.writeSolverSettingsToHDF5`
diff --git a/python/sdist/amici/sympy_utils.py b/python/sdist/amici/sympy_utils.py
index bc20c49dc4..2c8599ba7e 100644
--- a/python/sdist/amici/sympy_utils.py
+++ b/python/sdist/amici/sympy_utils.py
@@ -1,7 +1,9 @@
 """Functionality for working with sympy objects."""
+
 import os
 from itertools import starmap
-from typing import Union, Any, Callable
+from typing import Any
+from collections.abc import Callable
 import contextlib
 import sympy as sp
 import logging
@@ -111,9 +113,9 @@ def smart_jacobian(
 
 @log_execution_time("running smart_multiply", logger)
 def smart_multiply(
-    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix],
+    x: sp.MutableDenseMatrix | sp.MutableSparseMatrix,
     y: sp.MutableDenseMatrix,
-) -> Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix]:
+) -> sp.MutableDenseMatrix | sp.MutableSparseMatrix:
     """
     Wrapper around symbolic multiplication with some additional checks that
     reduce computation time for large matrices
@@ -136,7 +138,7 @@ def smart_multiply(
 
 
 def smart_is_zero_matrix(
-    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix],
+    x: sp.MutableDenseMatrix | sp.MutableSparseMatrix,
 ) -> bool:
     """A faster implementation of sympy's is_zero_matrix
 
diff --git a/python/sdist/amici/testing.py b/python/sdist/amici/testing.py
index 8d4a73fbe1..40b791d0d8 100644
--- a/python/sdist/amici/testing.py
+++ b/python/sdist/amici/testing.py
@@ -1,4 +1,5 @@
 """Test support functions"""
+
 import os
 import sys
 from tempfile import TemporaryDirectory
diff --git a/python/sdist/pyproject.toml b/python/sdist/pyproject.toml
index 6b427e2d16..58d39d4ea7 100644
--- a/python/sdist/pyproject.toml
+++ b/python/sdist/pyproject.toml
@@ -127,5 +127,7 @@ line-length = 79
 
 [tool.ruff]
 line-length = 79
-ignore = ["E402", "F403", "F405", "E741"]
 extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
+ignore = ["E402", "F403", "F405", "E741"]
diff --git a/python/sdist/setup.py b/python/sdist/setup.py
index cfc474ebe8..83bf33237a 100755
--- a/python/sdist/setup.py
+++ b/python/sdist/setup.py
@@ -9,6 +9,7 @@
 - swig>=3.0
 - Optional: hdf5 libraries and headers
 """
+
 import os
 import sys
 from pathlib import Path
diff --git a/python/tests/conftest.py b/python/tests/conftest.py
index 1da7cb31b3..d8d882fcfd 100644
--- a/python/tests/conftest.py
+++ b/python/tests/conftest.py
@@ -1,4 +1,5 @@
 """pytest configuration file"""
+
 import copy
 import importlib
 import os
diff --git a/python/tests/pysb_test_models/bngwiki_egfr_simple_deletemolecules.py b/python/tests/pysb_test_models/bngwiki_egfr_simple_deletemolecules.py
index 1a39d4a846..4c40f7e815 100644
--- a/python/tests/pysb_test_models/bngwiki_egfr_simple_deletemolecules.py
+++ b/python/tests/pysb_test_models/bngwiki_egfr_simple_deletemolecules.py
@@ -3,7 +3,6 @@
 http://bionetgen.org/index.php/Egfr_simple
 """
 
-
 from pysb import *
 
 Model()
diff --git a/python/tests/splines_utils.py b/python/tests/splines_utils.py
index 29024d3b73..6565ac80a4 100644
--- a/python/tests/splines_utils.py
+++ b/python/tests/splines_utils.py
@@ -8,7 +8,7 @@
 import os
 import uuid
 from tempfile import mkdtemp
-from typing import Any, Optional, Union
+from typing import Any
 from collections.abc import Sequence
 
 import amici
@@ -45,7 +45,7 @@ def evaluate_spline(
 
 def integrate_spline(
     spline: AbstractSpline,
-    params: Union[dict, None],
+    params: dict | None,
     tt: Sequence[float],
     initial_value: float = 0,
 ):
@@ -119,12 +119,12 @@ def species_to_index(name) -> int:
 def create_petab_problem(
     splines: list[AbstractSpline],
     params_true: dict,
-    initial_values: Optional[np.ndarray] = None,
+    initial_values: np.ndarray | None = None,
     use_reactions: bool = False,
     measure_upsample: int = 6,
     sigma: float = 1.0,
     t_extrapolate: float = 0.25,
-    folder: Optional[str] = None,
+    folder: str | None = None,
     model_name: str = "test_splines",
 ):
     """
@@ -283,9 +283,9 @@ def simulate_splines(
     params_true,
     initial_values=None,
     *,
-    folder: Optional[str] = None,
+    folder: str | None = None,
     keep_temporary: bool = False,
-    benchmark: Union[bool, int] = False,
+    benchmark: bool | int = False,
     rtol: float = 1e-12,
     atol: float = 1e-12,
     maxsteps: int = 500_000,
@@ -505,8 +505,8 @@ def check_splines(
     discard_annotations: bool = False,
     use_adjoint: bool = False,
     skip_sensitivity: bool = False,
-    debug: Union[bool, str] = False,
-    parameter_lists: Optional[Sequence[Sequence[int]]] = None,
+    debug: bool | str = False,
+    parameter_lists: Sequence[Sequence[int]] | None = None,
     llh_rtol: float = 1e-8,
     sllh_atol: float = 1e-8,
     x_rtol: float = 1e-11,
@@ -515,7 +515,7 @@ def check_splines(
     w_atol: float = 1e-11,
     sx_rtol: float = 1e-10,
     sx_atol: float = 1e-10,
-    groundtruth: Optional[Union[str, dict[str, Any]]] = None,
+    groundtruth: str | dict[str, Any] | None = None,
     **kwargs,
 ):
     """
@@ -771,8 +771,8 @@ def check_splines_full(
     check_piecewise: bool = True,
     check_forward: bool = True,
     check_adjoint: bool = True,
-    folder: Optional[str] = None,
-    groundtruth: Optional[Union[dict, str]] = "compute",
+    folder: str | None = None,
+    groundtruth: dict | str | None = "compute",
     return_groundtruth: bool = False,
     **kwargs,
 ):
diff --git a/python/tests/test_conserved_quantities_demartino.py b/python/tests/test_conserved_quantities_demartino.py
index ca40946db3..2ed778b85e 100644
--- a/python/tests/test_conserved_quantities_demartino.py
+++ b/python/tests/test_conserved_quantities_demartino.py
@@ -1,4 +1,5 @@
 """Tests for conservation laws / conserved moieties"""
+
 import os
 from time import perf_counter
 
diff --git a/python/tests/test_edata.py b/python/tests/test_edata.py
index 27c67de61e..fab49c160e 100644
--- a/python/tests/test_edata.py
+++ b/python/tests/test_edata.py
@@ -1,4 +1,5 @@
 """Tests related to amici.ExpData via Python"""
+
 import amici
 import numpy as np
 from amici.testing import skip_on_valgrind
diff --git a/python/tests/test_events.py b/python/tests/test_events.py
index 065cdeb126..05eddab59f 100644
--- a/python/tests/test_events.py
+++ b/python/tests/test_events.py
@@ -1,4 +1,5 @@
 """Tests for SBML events, including piecewise expressions."""
+
 from copy import deepcopy
 
 import amici
diff --git a/python/tests/test_heavisides.py b/python/tests/test_heavisides.py
index c3bea26a0c..26de4f575e 100644
--- a/python/tests/test_heavisides.py
+++ b/python/tests/test_heavisides.py
@@ -1,4 +1,5 @@
 """Tests for SBML events, including piecewise expressions."""
+
 import numpy as np
 import pytest
 from util import (
diff --git a/python/tests/test_petab_simulate.py b/python/tests/test_petab_simulate.py
index a8240bff33..e1da7768e3 100644
--- a/python/tests/test_petab_simulate.py
+++ b/python/tests/test_petab_simulate.py
@@ -1,4 +1,5 @@
 """Tests for petab_simulate.py."""
+
 import tempfile
 from pathlib import Path
 
diff --git a/python/tests/test_rdata.py b/python/tests/test_rdata.py
index 8e0f78655e..80ec3b80e6 100644
--- a/python/tests/test_rdata.py
+++ b/python/tests/test_rdata.py
@@ -1,4 +1,5 @@
 """Test amici.ReturnData(View)-related functionality"""
+
 import amici
 import numpy as np
 import pytest
diff --git a/python/tests/test_sbml_import.py b/python/tests/test_sbml_import.py
index aaab5688cc..f0400396f8 100644
--- a/python/tests/test_sbml_import.py
+++ b/python/tests/test_sbml_import.py
@@ -1,4 +1,5 @@
 """Tests related to amici.sbml_import"""
+
 import os
 import re
 from numbers import Number
diff --git a/python/tests/util.py b/python/tests/util.py
index dde10eb454..58e17137a6 100644
--- a/python/tests/util.py
+++ b/python/tests/util.py
@@ -1,4 +1,5 @@
 """Tests for SBML events, including piecewise expressions."""
+
 import sys
 import tempfile
 from pathlib import Path
diff --git a/tests/benchmark-models/evaluate_benchmark.py b/tests/benchmark-models/evaluate_benchmark.py
index 0c6e2e4122..0fe80f6625 100644
--- a/tests/benchmark-models/evaluate_benchmark.py
+++ b/tests/benchmark-models/evaluate_benchmark.py
@@ -3,6 +3,7 @@
 """
 Aggregate computation times from different benchmarks and plot
 """
+
 import os
 
 import matplotlib.pyplot as plt
diff --git a/tests/benchmark-models/test_petab_benchmark.py b/tests/benchmark-models/test_petab_benchmark.py
index 753c88e500..976ff3dc05 100644
--- a/tests/benchmark-models/test_petab_benchmark.py
+++ b/tests/benchmark-models/test_petab_benchmark.py
@@ -1,4 +1,5 @@
 """Tests for simulate_petab on PEtab benchmark problems."""
+
 import os
 from pathlib import Path
 
diff --git a/tests/benchmark-models/test_petab_model.py b/tests/benchmark-models/test_petab_model.py
index 8f52a341c4..da3d37b5fb 100755
--- a/tests/benchmark-models/test_petab_model.py
+++ b/tests/benchmark-models/test_petab_model.py
@@ -3,6 +3,7 @@
 """
 Simulate a PEtab problem and compare results to reference values
 """
+
 import argparse
 import contextlib
 import importlib