linting fixes

biosimulators · Nov 7, 2024 · 825a465 · 825a465
1 parent 137224f
commit 825a465
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Showing 2 changed files with 24 additions and 6 deletions.
diff --git a/biosimulators_copasi/data_model.py b/biosimulators_copasi/data_model.py
@@ -10,7 +10,7 @@
 from typing import Union, get_type_hints
 
 import COPASI
-from biosimulators_utils.sedml.data_model import UniformTimeCourseSimulation, SteadyStateSimulation, Variable, Algorithm
+from biosimulators_utils.sedml.data_model import UniformTimeCourseSimulation, SteadyStateSimulation, Variable
 
 import basico
 import pandas
@@ -91,6 +91,7 @@ def __eq__(self, other: CopasiAlgorithmParameter) -> bool:
     def __ne__(self, other: RelativeToleranceParameter) -> bool:
         return not self.__eq__(other)
 
+
 class Resolution(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "resolution"
@@ -109,6 +110,7 @@ def set_value(self, new_value: float):
             raise ValueError
         self._value = new_value
 
+
 class DerivationFactor(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "derivationfactor"
@@ -127,6 +129,7 @@ def set_value(self, new_value: float):
             raise ValueError
         self._value = new_value
 
+
 class UseNewton(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "useNewton"
@@ -145,6 +148,7 @@ def set_value(self, new_value: bool):
             raise ValueError
         self._value = new_value
 
+
 class UseIntegration(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "useIntegration"
@@ -163,6 +167,7 @@ def set_value(self, new_value: bool):
             raise ValueError
         self._value = new_value
 
+
 class UseBackIntegration(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "useBackIntegration"
@@ -181,6 +186,7 @@ def set_value(self, new_value: bool):
             raise ValueError
         self._value = new_value
 
+
 class AcceptNegativeConcentrations(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "acceptNegativeConcentrations"
@@ -199,6 +205,7 @@ def set_value(self, new_value: bool):
             raise ValueError
         self._value = new_value
 
+
 class IterationLimit(CopasiAlgorithmParameter):
     KISAO_ID: str = "KISAO_0000486"
     ID: str = "iterationLimit"
@@ -217,6 +224,7 @@ def set_value(self, new_value: int):
             raise ValueError
         self._value = new_value
 
+
 class MaxForwardIntegrationDuration(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "maxForwardIntegrationDuration"
@@ -235,6 +243,7 @@ def set_value(self, new_value: float):
             raise ValueError
         self._value = new_value
 
+
 class MaxReverseIntegrationDuration(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "maxReverseIntegrationDuration"
@@ -253,6 +262,7 @@ def set_value(self, new_value: float):
             raise ValueError
         self._value = new_value
 
+
 class TargetCriterion(CopasiAlgorithmParameter):
     KISAO_ID: str = ""  # To be created
     ID: str = "targetCriterion"
@@ -279,6 +289,7 @@ def set_value(self, new_value: str):
             raise ValueError
         self._value = new_value
 
+
 class RelativeToleranceParameter(CopasiAlgorithmParameter):
     KISAO_ID: str = "KISAO_0000209"
     ID: str = "r_tol"
@@ -638,6 +649,7 @@ def __eq__(self, other):
         event_support_equality = self.CAN_SUPPORT_EVENTS == other.CAN_SUPPORT_EVENTS
         return kisao_equality and id_equality and name_equality and event_support_equality
 
+
 class SteadyStateAlgorithm(CopasiAlgorithm):
     KISAO_ID: str = None
     ID: str = None
@@ -684,6 +696,7 @@ def get_overrides(self) -> dict:
         overrides.update(self.target_criterion.get_override_repr())
         return overrides
 
+
 class CopasiHybridAlternatingNewtonLSODASolver(SteadyStateAlgorithm):
     KISAO_ID: str = "KISAO_0000411"  # Placeholder until it gets its own solver
     ID: str = "steadystatestandard"
@@ -703,6 +716,7 @@ def __init__(self, use_integration: bool = True, use_back_integration: bool = Fa
     def get_copasi_id(self) -> str:
         return CopasiHybridAlternatingNewtonLSODASolver.ID
 
+
 class PureNewtonRootFindingAlgorithm(SteadyStateAlgorithm):
     KISAO_ID: str = "KISAO_0000409"
     ID: str = "steadystatenewton"
@@ -719,6 +733,7 @@ def __init__(self, resolution: float = 1e-09, derivation_factor: float = 0.001,
     def get_copasi_id(self) -> str:
         return PureNewtonRootFindingAlgorithm.ID
 
+
 class PureIntegrationRootFindingAlgorithm(SteadyStateAlgorithm):
     KISAO_ID: str = ""  # No applicable term yet
     ID: str = "steadystateintegration"
@@ -734,9 +749,11 @@ def __init__(self, use_integration: bool = True, use_back_integration: bool = Fa
         super().__init__(True, use_integration, use_back_integration, resolution, derivation_factor,
                          accept_negative_concentrations, iteration_limit, max_forward_duration, max_back_duration,
                          target_criterion_distance, target_criterion_rate, units)
+
     def get_copasi_id(self) -> str:
         return PureIntegrationRootFindingAlgorithm.ID
 
+
 class GibsonBruckAlgorithm(CopasiAlgorithm):
     KISAO_ID: str = "KISAO_0000027"
     ID: str = "stochastic"
@@ -1340,4 +1357,4 @@ def generate_data_handler(self, output_selection: list[str]):
     @staticmethod
     def _get_times(number_of_steps: int, output_start_time: float, output_end_time: float) -> "list[float]":
         time_range: float = output_end_time - output_start_time
-        return [(i * time_range) / number_of_steps for i in range(number_of_steps)] + [output_start_time]
+        return [(i * time_range) / number_of_steps for i in range(number_of_steps)] + [output_start_time]
diff --git a/biosimulators_copasi/utils.py b/biosimulators_copasi/utils.py
@@ -45,12 +45,12 @@ def get_algorithm(kisao_id: str, events_were_requested: bool = False, config: Co
            :obj:`CopasiAlgorithm`: The copasi algorithm deemed suitable
         """
     algorithm_kisao_to_class_map: dict[str, CopasiAlgorithm] = \
-        { CopasiAlgorithmType[alg_name].value.KISAO_ID: CopasiAlgorithmType[alg_name].value
-          for alg_name, _ in CopasiAlgorithmType.__members__.items() }
+        {CopasiAlgorithmType[alg_name].value.KISAO_ID: CopasiAlgorithmType[alg_name].value
+         for alg_name, _ in CopasiAlgorithmType.__members__.items()}
 
     legal_alg_kisao_ids = \
-        [ kisao for kisao, obj in algorithm_kisao_to_class_map.items()
-        if not events_were_requested or obj.CAN_SUPPORT_EVENTS ]
+        [kisao for kisao, obj in algorithm_kisao_to_class_map.items()
+         if not events_were_requested or obj.CAN_SUPPORT_EVENTS]
 
     if kisao_id in legal_alg_kisao_ids:
         constructor = algorithm_kisao_to_class_map[kisao_id]
@@ -76,6 +76,7 @@ def get_algorithm(kisao_id: str, events_were_requested: bool = False, config: Co
 
     raise ValueError(f"No suitable equivalent for '{kisao_id}' could be found with the provided substitution policy")
 
+
 def set_algorithm_parameter_values(copasi_algorithm: CopasiAlgorithm, requested_changes: list) \
         -> tuple[list[AlgorithmParameterChange], list[AlgorithmParameterChange]]:
     """ Set a parameter of a COPASI simulation function