add trailing commas

src/rfbzero/crossover.py

@@ -51,7 +51,7 @@ def crossover(
  c_red_ncls: float,
  volume_cls: float,
  volume_ncls: float,
- time_step: float
+ time_step: float,
  ) -> tuple[float, float, float, float, float, float]:
  """
  Calculation of crossover species, considering permeabilities of oxidized/reduced species.

src/rfbzero/experiment.py

@@ -38,7 +38,7 @@ def __init__(
  time_step: float,
  charge_first: bool = True,
  products_cls: list[str] = None,
- products_ncls: list[str] = None
+ products_ncls: list[str] = None,
  ) -> None:
  self.duration = duration
  self.time_step = time_step
@@ -258,7 +258,7 @@ def __init__(
  update_concentrations: Callable[[float], tuple[dict[str, float], dict[str, float]]],
  current: float,
  current_lim_cls: float = None,
- current_lim_ncls: float = None
+ current_lim_ncls: float = None,
  ) -> None:
  self.charge = charge
  self.cell_model = cell_model
@@ -330,7 +330,7 @@ def __init__(
  update_concentrations: Callable[[float], tuple[dict[str, float], dict[str, float]]],
  current: float,
  voltage_limit: float,
- voltage_limit_capacity_check: bool = True
+ voltage_limit_capacity_check: bool = True,
  ) -> None:
  super().__init__(charge, cell_model, results, update_concentrations, current)
  self.voltage_limit = voltage_limit
@@ -399,7 +399,7 @@ def cycle_step(self) -> CyclingStatus:
  ocv,
  n_act,
  n_mt,
- total_overpotential
+ total_overpotential,
  )
 
  return self._check_time(cycling_status)
@@ -441,7 +441,7 @@ def __init__(
  voltage_limit: float,
  current_estimate: float,
  current_lim_cls: float = None,
- current_lim_ncls: float = None
+ current_lim_ncls: float = None,
  ) -> None:
  super().__init__(charge, cell_model, results, update_concentrations, current_estimate,
  current_lim_cls, current_lim_ncls)
@@ -479,7 +479,7 @@ def cycle_step(self) -> CyclingStatus:
  self.charge,
  self.current,
  self.voltage_limit,
- ocv
+ ocv,
  )
 
  if abs(self.current) <= abs(self.current_cutoff):
@@ -503,7 +503,7 @@ def solver(current) -> float:
  loss_solve, *_ = self.cell_model._total_overpotential(
  current.item(),
  self.current_lim_cls,
- self.current_lim_ncls
+ self.current_lim_ncls,
  )
  return self.voltage_limit - ocv - self.__current_direction() * loss_solve
 
@@ -567,7 +567,7 @@ def _validate_cycle_values(
  value: Optional[float],
  value_charge: Optional[float],
  value_discharge: Optional[float],
- name: str
+ name: str,
  ) -> tuple[float, float]:
  """Checks validity of user inputs for current limits and/or cutoffs."""
  if value is not None and (value_charge is not None or value_discharge is not None):
@@ -595,7 +595,7 @@ def _validate_protocol(
  degradation: Optional[DegradationMechanism],
  cls_degradation: Optional[DegradationMechanism],
  ncls_degradation: Optional[DegradationMechanism],
- crossover: Optional[Crossover]
+ crossover: Optional[Crossover],
  ) -> tuple[CyclingResults, Callable[[float], tuple[dict[str, float], dict[str, float]]]]:
  """Checks validity of user inputs for voltage limits and optional degradation and crossover mechanisms."""
  if not self.voltage_limit_discharge < cell_model.ocv_50_soc < self.voltage_limit_charge:
@@ -677,7 +677,7 @@ def __init__(
  ) -> None:
  super().__init__(voltage_limit_charge, voltage_limit_discharge, charge_first)
  self.current_charge, self.current_discharge = self._validate_cycle_values(
- current, current_charge, current_discharge, 'current'
+ current, current_charge, current_discharge, 'current',
  )
 
  def run(
@@ -687,7 +687,7 @@ def run(
  degradation: DegradationMechanism = None,
  cls_degradation: DegradationMechanism = None,
  ncls_degradation: DegradationMechanism = None,
- crossover: Crossover = None
+ crossover: Crossover = None,
  ) -> CyclingResults:
  """
  Applies the constant current (CC) protocol and (optional) degradation/crossover mechanisms to a cell model.
@@ -715,7 +715,7 @@ def run(
  """
 
  results, update_concentrations = self._validate_protocol(
- duration, cell_model, degradation, cls_degradation, ncls_degradation, crossover
+ duration, cell_model, degradation, cls_degradation, ncls_degradation, crossover,
  )
 
  def get_cycle_mode(charge: bool) -> _ConstantCurrentCycleMode:
@@ -726,7 +726,7 @@ def get_cycle_mode(charge: bool) -> _ConstantCurrentCycleMode:
  results,
  update_concentrations,
  self.current_charge if charge else self.current_discharge,
- self.voltage_limit_charge if charge else self.voltage_limit_discharge
+ self.voltage_limit_charge if charge else self.voltage_limit_discharge,
  )
 
  cycle_mode = get_cycle_mode(self.charge_first)
@@ -788,7 +788,7 @@ def __init__(
  ) -> None:
  super().__init__(voltage_limit_charge, voltage_limit_discharge, charge_first)
  self.current_cutoff_charge, self.current_cutoff_discharge = self._validate_cycle_values(
- current_cutoff, current_cutoff_charge, current_cutoff_discharge, 'current_cutoff'
+ current_cutoff, current_cutoff_charge, current_cutoff_discharge, 'current_cutoff',
  )
 
  def run(
@@ -798,7 +798,7 @@ def run(
  degradation: DegradationMechanism = None,
  cls_degradation: DegradationMechanism = None,
  ncls_degradation: DegradationMechanism = None,
- crossover: Crossover = None
+ crossover: Crossover = None,
  ) -> CyclingResults:
  """
  Applies the constant voltage (CV) cycling protocol and (optional) degradation/crossover mechanisms to a cell
@@ -827,7 +827,7 @@ def run(
  """
 
  results, update_concentrations = self._validate_protocol(
- duration, cell_model, degradation, cls_degradation, ncls_degradation, crossover
+ duration, cell_model, degradation, cls_degradation, ncls_degradation, crossover,
  )
 
  def get_cycle_mode(charge: bool) -> _ConstantVoltageCycleMode:
@@ -838,7 +838,7 @@ def get_cycle_mode(charge: bool) -> _ConstantVoltageCycleMode:
  update_concentrations,
  self.current_cutoff_charge if charge else self.current_cutoff_discharge,
  self.voltage_limit_charge if charge else self.voltage_limit_discharge,
- 0.0
+ 0.0,
  )
 
  cycle_mode = get_cycle_mode(self.charge_first)
@@ -904,10 +904,10 @@ def __init__(
  ) -> None:
  super().__init__(voltage_limit_charge, voltage_limit_discharge, charge_first)
  self.current_cutoff_charge, self.current_cutoff_discharge = self._validate_cycle_values(
- current_cutoff, current_cutoff_charge, current_cutoff_discharge, 'current_cutoff'
+ current_cutoff, current_cutoff_charge, current_cutoff_discharge, 'current_cutoff',
  )
  self.current_charge, self.current_discharge = self._validate_cycle_values(
- current, current_charge, current_discharge, 'current'
+ current, current_charge, current_discharge, 'current',
  )
 
  def run(
@@ -917,7 +917,7 @@ def run(
  degradation: DegradationMechanism = None,
  cls_degradation: DegradationMechanism = None,
  ncls_degradation: DegradationMechanism = None,
- crossover: Crossover = None
+ crossover: Crossover = None,
  ) -> CyclingResults:
  """
  Applies the constant current constant voltage (CCCV) cycling protocol and (optional) degradation/crossover
@@ -945,7 +945,7 @@ def run(
 
  """
  results, update_concentrations = self._validate_protocol(
- duration, cell_model, degradation, cls_degradation, ncls_degradation, crossover
+ duration, cell_model, degradation, cls_degradation, ncls_degradation, crossover,
  )
 
  def get_cc_cycle_mode(charge: bool) -> _ConstantCurrentCycleMode:
@@ -956,7 +956,7 @@ def get_cc_cycle_mode(charge: bool) -> _ConstantCurrentCycleMode:
  update_concentrations,
  self.current_charge if charge else self.current_discharge,
  self.voltage_limit_charge if charge else self.voltage_limit_discharge,
- voltage_limit_capacity_check=False
+ voltage_limit_capacity_check=False,
  )
 
  def get_cv_cycle_mode(
@@ -974,7 +974,7 @@ def get_cv_cycle_mode(
  self.voltage_limit_charge if charge else self.voltage_limit_discharge,
  current_estimate,
  current_lim_cls,
- current_lim_ncls
+ current_lim_ncls,
  )
 
  cycle_mode: _CycleMode = get_cc_cycle_mode(self.charge_first)
@@ -994,8 +994,11 @@ def get_cv_cycle_mode(
  if is_cc_mode:
  if cycling_status == CyclingStatus.VOLTAGE_LIMIT_REACHED:
  is_cc_mode = False
- cycle_mode = get_cv_cycle_mode(cycle_mode.charge, cycle_mode.current,
- cycle_mode.current_lim_cls, cycle_mode.current_lim_ncls)
+ cycle_mode = get_cv_cycle_mode(cycle_mode.charge,
+ cycle_mode.current,
+ cycle_mode.current_lim_cls,
+ cycle_mode.current_lim_ncls,
+ )
  cycling_status = CyclingStatus.NORMAL
  elif cycling_status == CyclingStatus.NEGATIVE_CONCENTRATIONS:
  # Record info for the half cycle

src/rfbzero/redox_flow_cell.py

@@ -106,7 +106,7 @@ def __init__(
  roughness_factor: float = 26.0,
  num_electrons_cls: int = 1,
  num_electrons_ncls: int = 1,
- temperature: float = 298.0
+ temperature: float = 298.0,
  ) -> None:
  self.volume_cls = volume_cls
  self.volume_ncls = volume_ncls
@@ -381,7 +381,7 @@ def _coulomb_counter(
  current: float,
  cls_degradation: DegradationMechanism = None,
  ncls_degradation: DegradationMechanism = None,
- cross_over: Crossover = None
+ cross_over: Crossover = None,
  ) -> tuple[dict[str, float], dict[str, float]]:
  """
  Updates all species' concentrations at each time step. Contributions from faradaic current, (optional)