run ruff

python/sdist/amici/__init__.template.py

@@ -16,6 +16,6 @@
     )
 
 from .TPL_MODELNAME import *  # noqa: F403, F401
-from .TPL_MODELNAME import getModel as get_model # noqa: F401
+from .TPL_MODELNAME import getModel as get_model  # noqa: F401
 
 __version__ = "TPL_PACKAGE_VERSION"

python/sdist/amici/de_export.py

@@ -587,7 +587,7 @@ def smart_multiply(
 
 
 def smart_is_zero_matrix(
-    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix]
+    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix],
 ) -> bool:
     """A faster implementation of sympy's is_zero_matrix
 

python/sdist/amici/gradient_check.py

@@ -6,7 +6,7 @@
 """
 
 import copy
-from typing import Callable, List, Optional, Sequence
+from typing import List, Optional, Sequence
 
 import numpy as np
 

python/sdist/amici/import_utils.py

@@ -72,7 +72,7 @@ class ObservableTransformation(str, enum.Enum):
 
 
 def noise_distribution_to_observable_transformation(
-    noise_distribution: Union[str, Callable]
+    noise_distribution: Union[str, Callable],
 ) -> ObservableTransformation:
     """
     Parse noise distribution string and extract observable transformation
@@ -93,7 +93,7 @@ def noise_distribution_to_observable_transformation(
 
 
 def noise_distribution_to_cost_function(
-    noise_distribution: Union[str, Callable]
+    noise_distribution: Union[str, Callable],
 ) -> Callable[[str], str]:
     """
     Parse noise distribution string to a cost function definition amici can
@@ -423,7 +423,7 @@ 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]]
+    args: Sequence[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]],
 ) -> Tuple[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]]:
     """
     Denest piecewise functions that contain piecewise as condition

python/sdist/amici/petab/util.py

@@ -66,7 +66,7 @@ def get_states_in_condition_table(
             spm = pysb.pattern.SpeciesPatternMatcher(
                 model=petab_problem.model.model
             )
-        except NotImplementedError as e:
+        except NotImplementedError:
             raise NotImplementedError(
                 "Requires https://github.com/pysb/pysb/pull/570. "
                 "To use this functionality, update pysb via "

python/sdist/amici/plotting.py

@@ -56,8 +56,7 @@ def plot_state_trajectories(
     elif model is not None and prefer_names:
         labels = np.asarray(model.getStateNames())[list(state_indices)]
         labels = [
-            l if l else model.getStateIds()[ix]
-            for ix, l in enumerate(labels)
+            l if l else model.getStateIds()[ix] for ix, l in enumerate(labels)
         ]
     elif model is not None:
         labels = np.asarray(model.getStateIds())[list(state_indices)]

python/sdist/amici/pysb_import.py

@@ -410,7 +410,7 @@ def _process_pysb_species(pysb_model: pysb.Model, ode_model: DEModel) -> None:
                 sp.Symbol(f"__s{ix}"), f"{specie}", init, xdot[ix]
             )
         )
-    logger.debug(f"Finished Processing PySB species ")
+    logger.debug("Finished Processing PySB species ")
 
 
 @log_execution_time("processing PySB parameters", logger)
@@ -1353,7 +1353,7 @@ def has_fixed_parameter_ic(
 
 
 def extract_monomers(
-    complex_patterns: Union[pysb.ComplexPattern, List[pysb.ComplexPattern]]
+    complex_patterns: Union[pysb.ComplexPattern, List[pysb.ComplexPattern]],
 ) -> List[str]:
     """
     Constructs a list of monomer names contained in complex patterns.

python/sdist/amici/sbml_import.py

@@ -21,7 +21,6 @@
     List,
     Optional,
     Sequence,
-    Set,
     Tuple,
     Union,
 )
@@ -1165,7 +1164,7 @@ def _process_reactions(self):
                     # accounts for possibly variable compartments.
                     self.stoichiometric_matrix[
                         species["index"], reaction_index
-                    ] += (sign * stoichiometry * species["conversion_factor"])
+                    ] += sign * stoichiometry * species["conversion_factor"]
             if reaction.isSetId():
                 sym_math = self._local_symbols[reaction.getId()]
             else:
@@ -2360,9 +2359,9 @@ def _replace_in_all_expressions(
         # rule (at the end of the _process_species method), hence needs to be
         # processed here too.
         self.compartments = {
-            smart_subs(c, old, new)
-            if replace_identifiers
-            else c: smart_subs(v, old, self._make_initial(new))
+            smart_subs(c, old, new) if replace_identifiers else c: smart_subs(
+                v, old, self._make_initial(new)
+            )
             for c, v in self.compartments.items()
         }
 

python/sdist/amici/sbml_utils.py

@@ -519,7 +519,7 @@ def mathml2sympy(
 
 
 def _parse_logical_operators(
-    math_str: Union[str, float, None]
+    math_str: Union[str, float, None],
 ) -> Union[str, float, None]:
     """
     Parses a math string in order to replace logical operators by a form

python/sdist/amici/splines.py

@@ -1510,7 +1510,10 @@ 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/swig_wrappers.py

@@ -54,7 +54,7 @@ def _capture_cstdout():
 
 
 def _get_ptr(
-    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData]
+    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData],
 ) -> Union[
     "amici_swig.Model",
     "amici_swig.ExpData",

python/tests/conftest.py

@@ -2,7 +2,6 @@
 import copy
 import importlib
 import os
-import shutil
 import sys
 
 import amici

python/tests/petab_test_problems/lotka_volterra/model/writer.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 
-import petab
 import yaml2sbml
 
 yaml2sbml_yaml = "lotka_volterra.yaml"

python/tests/test_edata.py

@@ -2,7 +2,6 @@
 import amici
 import numpy as np
 from amici.testing import skip_on_valgrind
-from test_sbml_import import model_units_module
 
 
 @skip_on_valgrind

tests/generateTestConfig/example_steadystate.py

@@ -2,7 +2,7 @@
 import sys
 
 import numpy as np
-from example import AmiciExample, dict2attrs
+from example import AmiciExample
 
 
 class ExampleSteadystate(AmiciExample):