pre-commit autoupdate

.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: v4.6.0
+  rev: v5.0.0
   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: v0.6.7
+  rev: v0.8.6
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,7 +28,7 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.19.1
     hooks:
     -   id: pyupgrade
         args: ["--py310-plus"]

python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb

@@ -124,8 +124,7 @@
     "for reaction in sbml_model.getListOfReactions():\n",
     "    reactants = \" + \".join(\n",
     "        [\n",
-    "            \"%s %s\"\n",
-    "            % (\n",
+    "            \"{} {}\".format(\n",
     "                int(r.getStoichiometry()) if r.getStoichiometry() > 1 else \"\",\n",
     "                r.getSpecies(),\n",
     "            )\n",
@@ -134,8 +133,7 @@
     "    )\n",
     "    products = \" + \".join(\n",
     "        [\n",
-    "            \"%s %s\"\n",
-    "            % (\n",
+    "            \"{} {}\".format(\n",
     "                int(r.getStoichiometry()) if r.getStoichiometry() > 1 else \"\",\n",
     "                r.getSpecies(),\n",
     "            )\n",
@@ -144,7 +142,7 @@
     "    )\n",
     "    reversible = \"<\" if reaction.getReversible() else \"\"\n",
     "    print(\n",
-    "        \"%3s: %10s %1s->%10s\\t\\t[%s]\"\n",
+    "        \"%3s: %10s %1s->%10s\\t\\t[%s]\"  # noqa: UP031\n",
     "        % (\n",
     "            reaction.getId(),\n",
     "            reactants,\n",
@@ -370,7 +368,7 @@
     "\n",
     "# np.set_printoptions(threshold=8, edgeitems=2)\n",
     "for key, value in rdata.items():\n",
-    "    print(\"%12s: \" % key, value)"
+    "    print(f\"{key:12s}: \", value)"
    ]
   },
   {
@@ -664,15 +662,15 @@
     "Since the Eigenvalues of the Jacobian are negative and since the Jacobian at steady state is a fixed matrix, this system has a simple algebraic solution:\n",
     "\n",
     "   $$p(t) = e^{t J(x^*, \\theta)^T} p_{\\text{end}}.$$\n",
-    "   \n",
+    "\n",
     "As a consequence, the quadratures in adjoint computation also reduce to a matrix-vector product:\n",
     "\n",
     "   $$Q(x, \\theta) = Q(x^*, \\theta) = p_{\\text{integral}} * \\frac{\\partial f}{\\partial \\theta}$$\n",
     "\n",
     "with\n",
     "\n",
-    "   $$p_{\\text{integral}} = \\int_0^\\infty p(s) ds = (J(x^*, \\theta)^T)^{-1} p_{\\text{end}}.$$ \n",
-    "   \n",
+    "   $$p_{\\text{integral}} = \\int_0^\\infty p(s) ds = (J(x^*, \\theta)^T)^{-1} p_{\\text{end}}.$$\n",
+    "\n",
     "However, this solution is given in terms of a linear system of equations defined by the transposed Jacobian of the right hand side. Hence, if the (transposed) Jacobian is singular, it is not applicable.\n",
     "In this case, standard integration must be carried out."
    ]
@@ -922,7 +920,7 @@
     "\n",
     "for key, value in rdata.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)"
+    "        print(f\"{key:20s}:\", value)"
    ]
   },
   {
@@ -960,7 +958,7 @@
     "\n",
     "for key, value in rdata.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)"
+    "        print(f\"{key:20s}:\", value)"
    ]
   },
   {
@@ -993,7 +991,7 @@
     "\n",
     "for key, value in rdata_reduced.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)"
+    "        print(f\"{key:20s}:\", value)"
    ]
   },
   {
@@ -1044,7 +1042,7 @@
     "\n",
     "for key, value in rdata_reduced.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)\n",
+    "        print(f\"{key:20s}:\", value)\n",
     "print(\"Gradient:\", rdata_reduced[\"sllh\"])"
    ]
   },
@@ -1079,7 +1077,7 @@
     "\n",
     "for key, value in rdata_reduced.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)\n",
+    "        print(f\"{key:20s}:\", value)\n",
     "print(\"Gradient:\", rdata_reduced[\"sllh\"])"
    ]
   },
@@ -1117,7 +1115,7 @@
     "\n",
     "for key, value in rdata_reduced.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)\n",
+    "        print(f\"{key:20s}:\", value)\n",
     "print(\"Gradient:\", rdata_reduced[\"sllh\"])"
    ]
   },
@@ -1160,7 +1158,7 @@
     "\n",
     "for key, value in rdata.items():\n",
     "    if key[0:6] == \"preeq_\":\n",
-    "        print(\"%20s: \" % key, value)\n",
+    "        print(f\"{key:20s}:\", value)\n",
     "print(\"Gradient:\", rdata[\"sllh\"])"
    ]
   },

python/examples/example_errors.ipynb

@@ -76,9 +76,7 @@
    "outputs": [],
    "source": [
     "petab_problem = benchmark_models_petab.get_problem(\"Fujita_SciSignal2010\")\n",
-    "amici_model = import_petab_problem(\n",
-    "    petab_problem, verbose=False, compile_=None\n",
-    ")\n",
+    "amici_model = import_petab_problem(petab_problem, verbose=False, compile_=None)\n",
     "\n",
     "np.random.seed(2991)\n",
     "problem_parameters = dict(\n",
@@ -422,9 +420,7 @@
    "outputs": [],
    "source": [
     "petab_problem = benchmark_models_petab.get_problem(\"Weber_BMC2015\")\n",
-    "amici_model = import_petab_problem(\n",
-    "    petab_problem, verbose=False, compile_=None\n",
-    ")\n",
+    "amici_model = import_petab_problem(petab_problem, verbose=False, compile_=None)\n",
     "\n",
     "np.random.seed(4)\n",
     "problem_parameters = dict(\n",

python/examples/example_petab/petab.ipynb

@@ -28,12 +28,12 @@
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "## Importing a PEtab problem"
-   ],
    "metadata": {
     "collapsed": false
-   }
+   },
+   "source": [
+    "## Importing a PEtab problem"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -134,6 +134,10 @@
   },
   {
    "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [],
    "source": [
     "app = PetabProblem(petab_problem)\n",
@@ -143,43 +147,41 @@
     "\n",
     "# ExpData for a single condition:\n",
     "edata = app.get_edata(\"model1_data1\")"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "execution_count": null
+   ]
   },
   {
    "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "rdata = runAmiciSimulation(amici_model, solver=amici_model.getSolver(), edata=edata)\n",
-    "rdata"
-   ],
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "execution_count": null
+   "outputs": [],
+   "source": [
+    "rdata = runAmiciSimulation(\n",
+    "    amici_model, solver=amici_model.getSolver(), edata=edata\n",
+    ")\n",
+    "rdata"
+   ]
   },
   {
    "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "plot_state_trajectories(rdata)"
-   ],
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "execution_count": null
+   "outputs": [],
+   "source": [
+    "plot_state_trajectories(rdata)"
+   ]
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "For further information, check out the [AMICI documentation](https://amici.readthedocs.io/en/latest/)."
-   ],
    "metadata": {
     "collapsed": false
-   }
+   },
+   "source": [
+    "For further information, check out the [AMICI documentation](https://amici.readthedocs.io/en/latest/)."
+   ]
   }
  ],
  "metadata": {

python/examples/example_presimulation/ExampleExperimentalConditions.ipynb

@@ -89,8 +89,7 @@
     "for reaction in sbml_model.getListOfReactions():\n",
     "    reactants = \" + \".join(\n",
     "        [\n",
-    "            \"%s %s\"\n",
-    "            % (\n",
+    "            \"{} {}\".format(\n",
     "                int(r.getStoichiometry()) if r.getStoichiometry() > 1 else \"\",\n",
     "                r.getSpecies(),\n",
     "            )\n",
@@ -99,8 +98,7 @@
     "    )\n",
     "    products = \" + \".join(\n",
     "        [\n",
-    "            \"%s %s\"\n",
-    "            % (\n",
+    "            \"{} {}\".format(\n",
     "                int(r.getStoichiometry()) if r.getStoichiometry() > 1 else \"\",\n",
     "                r.getSpecies(),\n",
     "            )\n",
@@ -109,7 +107,7 @@
     "    )\n",
     "    reversible = \"<\" if reaction.getReversible() else \"\"\n",
     "    print(\n",
-    "        \"%3s: %10s %1s->%10s\\t\\t[%s]\"\n",
+    "        \"%3s: %10s %1s->%10s\\t\\t[%s]\"  # noqa: UP031\n",
     "        % (\n",
     "            reaction.getName(),\n",
     "            reactants,\n",
@@ -334,7 +332,7 @@
    "metadata": {},
    "source": [
     "For many biological systems, it is reasonable to assume that they start in a\n",
-    " steady state. In this example we want to specify an experiment where a pretreatment with a drug is performed _before_ the kinase is added. We assume that the pretreatment is sufficiently long such that the system reaches steadystate before the kinase is added. To implement this in amici, we can specify `fixedParametersPreequilibration` in the `ExpData` object. This automatically adds a preequilibration phase where the model is run to steadystate, before regular simulation starts. Here we set `DRUG_0=3` and `KIN_0=0` for the preequilibration. This means that there is no kinase available in the preequilibration phase. "
+    " steady state. In this example we want to specify an experiment where a pretreatment with a drug is performed _before_ the kinase is added. We assume that the pretreatment is sufficiently long such that the system reaches steadystate before the kinase is added. To implement this in amici, we can specify `fixedParametersPreequilibration` in the `ExpData` object. This automatically adds a preequilibration phase where the model is run to steadystate, before regular simulation starts. Here we set `DRUG_0=3` and `KIN_0=0` for the preequilibration. This means that there is no kinase available in the preequilibration phase."
    ]
   },
   {

python/sdist/amici/_codegen/model_class.py

@@ -82,12 +82,7 @@ def get_model_override_implementation(
             eval_signature=remove_argument_types(func_info.arguments(ode)),
         )
     )
-    return "{return_type} f{fun}({signature}) override {{{body}}}\n".format(
-        return_type=func_info.return_type,
-        fun=fun,
-        signature=func_info.arguments(ode),
-        body=body,
-    )
+    return f"{func_info.return_type} f{fun}({func_info.arguments(ode)}) override {{{body}}}\n"
 
 
 def get_sunindex_override_implementation(

python/sdist/amici/cxxcodeprinter.py

@@ -75,12 +75,7 @@ def _print_min_max(self, expr, cpp_fun: str, sympy_fun):
         )
         if len(expr.args) == 1:
             return self._print(arg0)
-        return "{}{}({}, {})".format(
-            self._ns,
-            cpp_fun,
-            self._print(arg0),
-            self._print(sympy_fun(*expr.args[1:])),
-        )
+        return f"{self._ns}{cpp_fun}({self._print(arg0)}, {self._print(sympy_fun(*expr.args[1:]))})"
 
     def _print_Min(self, expr):
         from sympy.functions.elementary.miscellaneous import Min

python/sdist/amici/import_utils.py

@@ -8,7 +8,6 @@
 from typing import (
     Any,
     SupportsFloat,
-    Union,
 )
 from collections.abc import Callable
 from collections.abc import Iterable, Sequence
@@ -30,7 +29,7 @@ class SBMLException(Exception):
     pass
 
 
-SymbolDef = dict[sp.Symbol, Union[dict[str, sp.Expr], sp.Expr]]
+SymbolDef = dict[sp.Symbol, dict[str, sp.Expr] | sp.Expr]
 
 
 # Monkey-patch toposort CircularDependencyError to handle non-sortable objects,
@@ -407,7 +406,7 @@ def _parse_special_functions(sym: sp.Expr, toplevel: bool = True) -> sp.Expr:
     if sym.__class__.__name__ == "plus" and not sym.args:
         return sp.Float(0.0)
 
-    if isinstance(sym, (sp.Function, sp.Mul, sp.Add, sp.Pow)):
+    if isinstance(sym, (sp.Function | sp.Mul | sp.Add | sp.Pow)):
         sym._args = args
 
     elif toplevel and isinstance(sym, BooleanAtom):
@@ -637,7 +636,7 @@ def cast_to_sym(
     :return:
         typecast value
     """
-    if isinstance(value, (sp.RealNumber, numbers.Number)):
+    if isinstance(value, (sp.RealNumber | numbers.Number)):
         value = sp.Float(float(value))
     elif isinstance(value, BooleanAtom):
         value = sp.Float(float(bool(value)))

python/sdist/amici/jax/petab.py

@@ -1,4 +1,5 @@
 """PEtab wrappers for JAX models.""" ""
+
 import shutil
 from numbers import Number
 from collections.abc import Iterable

python/sdist/amici/logging.py

@@ -127,8 +127,8 @@ def set_log_level(logger: logging.Logger, log_level: int | bool) -> None:
 
         if logger.getEffectiveLevel() != log_level:
             logger.debug(
-                "Changing log_level from %d to %d"
-                % (logger.getEffectiveLevel(), log_level)
+                f"Changing log_level from {logger.getEffectiveLevel()} "
+                f"to {log_level}"
             )
             logger.setLevel(log_level)