maint: ruff, modernize (#3131)

* update ruff
* modernize & reformat

Author: dweindl

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.14.1
+  rev: v0.15.2
   hooks:
     # Run the linter.
     - id: ruff

doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb

@@ -31,7 +31,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import petab.v1 as petab\n",
     "from amici.importers.petab import *\n",
     "from petab.v2 import Problem\n",
     "\n",
@@ -403,7 +402,9 @@
     "nps = jax_problem._np_numeric[ic, :]\n",
     "\n",
     "# Load parameters for the specified condition\n",
-    "p = jax_problem.load_model_parameters(jax_problem._petab_problem.experiments[0], is_preeq=False)\n",
+    "p = jax_problem.load_model_parameters(\n",
+    "    jax_problem._petab_problem.experiments[0], is_preeq=False\n",
+    ")\n",
     "\n",
     "\n",
     "# Define a function to compute the gradient with respect to dynamic timepoints\n",
@@ -576,7 +577,6 @@
    "outputs": [],
    "source": [
     "from amici.sim.sundials import SensitivityMethod, SensitivityOrder\n",
-    "from amici.sim.sundials.petab.v1 import simulate_petab\n",
     "\n",
     "# Import the PEtab problem as a standard AMICI model\n",
     "pi = PetabImporter(\n",

python/sdist/amici/_symbolic/de_model.py

@@ -2648,7 +2648,7 @@ def get_implicit_roots(self) -> list[sp.Expr]:
             for e in self._events
             if not e.has_explicit_trigger_times()
         ]
-    
+
     def has_algebraic_states(self) -> bool:
         """
         Checks whether the model has algebraic states
@@ -2666,7 +2666,7 @@ def has_event_assignments(self) -> bool:
             boolean indicating if event assignments are present
         """
         return any(event.updates_state for event in self._events)
-    
+
     def has_priority_events(self) -> bool:
         """
         Checks whether the model has events with priorities defined
@@ -2675,7 +2675,7 @@ def has_priority_events(self) -> bool:
             boolean indicating if priority events are present
         """
         return any(event.get_priority() is not None for event in self._events)
-    
+
     def has_implicit_event_assignments(self) -> bool:
         """
         Checks whether the model has event assignments with implicit triggers
@@ -2686,9 +2686,13 @@ def has_implicit_event_assignments(self) -> bool:
         """
         fixed_symbols = set([k._symbol for k in self._fixed_parameters])
         allowed_symbols = fixed_symbols | {amici_time_symbol}
-        # TODO: update to use has_explicit_trigger_times once 
+        # TODO: update to use has_explicit_trigger_times once
         # https://github.com/AMICI-dev/AMICI/issues/3126 is resolved
-        return any(event.updates_state and event._has_implicit_triggers(allowed_symbols) for event in self._events)
+        return any(
+            event.updates_state
+            and event._has_implicit_triggers(allowed_symbols)
+            for event in self._events
+        )
 
     def toposort_expressions(
         self, reorder: bool = True

python/sdist/amici/_symbolic/de_model_components.py

@@ -740,7 +740,7 @@ def __init__(
         :param priority: The priority of the event assignment.
 
         :param is_negative_event:
-            Whether this event is a "negative" event, i.e., an event that is 
+            Whether this event is a "negative" event, i.e., an event that is
             added to mirror an existing event with inverted trigger condition
             to avoid immediate retriggering of the original event (JAX simulations).
 
@@ -863,17 +863,16 @@ def has_explicit_trigger_times(
         """
         if allowed_symbols is None:
             return len(self._t_root) > 0
-        
+
         return len(self._t_root) > 0 and all(
             t.is_Number or t.free_symbols.issubset(allowed_symbols)
             for t in self._t_root
         )
-    
+
     def _has_implicit_triggers(
         self, allowed_symbols: set[sp.Symbol] | None = None
     ) -> bool:
-        """Check whether the event has implicit triggers.
-        """
+        """Check whether the event has implicit triggers."""
         t = self.get_val()
         return not t.free_symbols.issubset(allowed_symbols)
 

python/sdist/amici/constants.py

@@ -8,7 +8,7 @@
 import enum
 
 
-class SymbolId(str, enum.Enum):
+class SymbolId(enum.StrEnum):
     """
     Defines the different fields in the symbol dict to which sbml entities
     get parsed to.

python/sdist/amici/importers/petab/_petab_importer.py

@@ -23,8 +23,8 @@
 from amici import get_model_dir
 from amici._symbolic import DEModel, Event
 from amici.importers.utils import MeasurementChannel, amici_time_symbol
-from amici.logging import get_logger
 from amici.jax.petab import JAXProblem
+from amici.logging import get_logger
 
 from .v1.sbml_import import _add_global_parameter
 
@@ -608,7 +608,7 @@ def create_simulator(
             model_module = self.import_module(force_import=force_import)
             model = model_module.Model()
             return JAXProblem(model, self.petab_problem)
-        
+
         model = self.import_module(force_import=force_import).get_model()
         em = ExperimentManager(model=model, petab_problem=self.petab_problem)
         return PetabSimulator(em=em)

python/sdist/amici/importers/pysb/__init__.py

@@ -10,7 +10,6 @@
 import itertools
 import logging
 import os
-import re
 import sys
 from collections.abc import Callable, Iterable
 from pathlib import Path
@@ -31,9 +30,7 @@
     FixedParameter,
     FreeParameter,
     LogLikelihoodY,
-    NoiseParameter,
     Observable,
-    ObservableParameter,
     SigmaY,
 )
 from amici.logging import get_logger, log_execution_time, set_log_level

python/sdist/amici/importers/sbml/__init__.py

@@ -1902,7 +1902,7 @@ def _process_events(self) -> None:
 
             if self.jax:
                 # Add a negative event for JAX models to handle
-                # TODO: remove once condition function directions can be 
+                # TODO: remove once condition function directions can be
                 # traced through diffrax solve
                 neg_event_id = event_id + "_negative"
                 neg_event_sym = sp.Symbol(neg_event_id)

python/sdist/amici/importers/sbml/splines.py

@@ -1511,10 +1511,9 @@ def _spline_user_functions(
         "AmiciSplineSensitivity": [
             (
                 lambda *args: True,
-                lambda spline_id,
-                x,
-                param_id,
-                *p: f"sspl_{spline_ids.index(spline_id)}_{p_index[param_id]}",
+                lambda spline_id, x, param_id, *p: (
+                    f"sspl_{spline_ids.index(spline_id)}_{p_index[param_id]}"
+                ),
             )
         ],
     }

python/sdist/amici/importers/utils.py

@@ -71,7 +71,7 @@ def __init__(self, data):
 annotation_namespace = "https://github.com/AMICI-dev/AMICI"
 
 
-class ObservableTransformation(str, enum.Enum):
+class ObservableTransformation(enum.StrEnum):
     """
     Different modes of observable transformation.
     """