Upgrade ruff and enable isort rules (#2983)

Sort imports.

Author: dweindl

.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: v5.0.0
+  rev: v6.0.0
   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: v0.12.0
+  rev: v0.14.1
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,7 +28,7 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.20.0
+    rev: v3.21.0
     hooks:
     -   id: pyupgrade
         args: ["--py310-plus"]

doc/conf.py

@@ -10,6 +10,7 @@
 import sys
 from enum import EnumType
 from unittest import mock
+
 import sphinx
 from sphinx.transforms.post_transforms import ReferencesResolver
 
@@ -19,8 +20,8 @@
     # for unclear reasons, the import of exhale_multiproject_monkeypatch
     #  fails on some systems, because the the location of the editable install
     #  is not automatically added to sys.path ¯\_(ツ)_/¯
-    from importlib.metadata import Distribution
     import json
+    from importlib.metadata import Distribution
     from urllib.parse import unquote_plus, urlparse
 
     dist = Distribution.from_name("sphinx-contrib-exhale-multiproject")

doc/examples/example_errors.ipynb

@@ -22,22 +22,22 @@
     "from contextlib import suppress\n",
     "from pathlib import Path\n",
     "\n",
+    "import amici\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "\n",
-    "import amici\n",
     "from amici import (\n",
-    "    simulation_status_to_str,\n",
-    "    SteadyStateSensitivityMode,\n",
+    "    SbmlImporter,\n",
     "    SensitivityMethod,\n",
     "    SensitivityOrder,\n",
+    "    SteadyStateSensitivityMode,\n",
+    "    import_model_module,\n",
     "    run_simulation,\n",
+    "    simulation_status_to_str,\n",
     ")\n",
     "from amici.petab.petab_import import import_petab_problem\n",
-    "from amici.petab.simulations import simulate_petab, RDATAS, EDATAS\n",
-    "from amici.plotting import plot_state_trajectories, plot_jacobian\n",
+    "from amici.petab.simulations import EDATAS, RDATAS, simulate_petab\n",
+    "from amici.plotting import plot_jacobian, plot_state_trajectories\n",
     "from petab.v1.sbml import get_sbml_model\n",
-    "from amici import SbmlImporter, import_model_module\n",
     "\n",
     "try:\n",
     "    import benchmark_models_petab\n",

doc/examples/example_jax/ExampleJax.ipynb

@@ -317,8 +317,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from amici.petab.simulations import simulate_petab\n",
     "import amici\n",
+    "from amici.petab.simulations import simulate_petab\n",
     "\n",
     "amici_solver = amici_model.create_solver()\n",
     "amici_solver.set_sensitivity_order(amici.SensitivityOrder.first)\n",