ruff

Author: dweindl

pypesto/objective/amici/amici.py

@@ -41,7 +41,6 @@
     try:
         import amici
         import amici.petab.petab_importer
-        import pandas as pd
         from amici.petab.parameter_mapping import ParameterMapping
     except ImportError:
         pass
@@ -705,7 +704,7 @@ def update_from_problem(
 
         id_to_val = {
             self.x_ids[x_idx]: x_val
-            for x_idx, x_val in zip(x_fixed_indices, x_fixed_vals)
+            for x_idx, x_val in zip(x_fixed_indices, x_fixed_vals, strict=True)
         }
         for condition_mapping in self.parameter_mapping:
             for (

pypesto/petab/objective_creator.py

@@ -9,11 +9,10 @@
 import shutil
 import warnings
 from abc import ABC, abstractmethod
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
 from dataclasses import dataclass
 from typing import (
     Any,
-    Callable,
 )
 
 import numpy as np
@@ -49,7 +48,6 @@
     import amici.petab.petab_importer
     import amici.petab.simulations
     from amici.petab.import_helpers import check_model
-    import amici.sim.sundials as asd
 except ImportError:
     amici = None
 try:
@@ -322,7 +320,11 @@ def create_objective(
         # fill in dummy parameters (this is needed since some objective
         #  initialization e.g. checks for preeq parameters)
         problem_parameters = dict(
-            zip(self.petab_problem.x_ids, self.petab_problem.x_nominal_scaled)
+            zip(
+                self.petab_problem.x_ids,
+                self.petab_problem.x_nominal_scaled,
+                strict=True,
+            )
         )
         amici.petab.conditions.fill_in_parameters(
             edatas=edatas,
@@ -651,7 +653,7 @@ def _check_noise_formulae(
         to_change = []
         # check that noise formulae are valid
         for i_edata, (edata, par_map) in enumerate(
-            zip(edatas, parameter_mapping)
+            zip(edatas, parameter_mapping, strict=True)
         ):
             for j_formula, noise_formula in enumerate(edata.noise_formulae):
                 # constant values are allowed
@@ -763,7 +765,7 @@ def create_parameter_mapping(self):
         if not overrides:
             return mapping
         for (_, condition), mapping_per_condition in zip(
-            simulation_conditions.iterrows(), mapping
+            simulation_conditions.iterrows(), mapping, strict=True
         ):
             for override in overrides:
                 preeq_id = condition.get(PREEQUILIBRATION_CONDITION_ID)

pypesto/petab/util.py

@@ -6,8 +6,10 @@
     import petab.v1 as petab
     from petab.v1.C import (
         ESTIMATE,
+        LIN,
         NOISE_PARAMETERS,
         OBSERVABLE_ID,
+        PARAMETER_SCALE_UNIFORM,
     )
 except ImportError:
     petab = None
@@ -140,6 +142,7 @@ def _setup(
                     petab.parameters.get_priors_from_df(
                         parameter_df, mode=petab.INITIALIZATION
                     ),
+                    strict=True,
                 )
             )
         else: