Adds SLF001 to ruff - private member access

CONTRIBUTING.md

@@ -21,7 +21,7 @@ pip install -e .[all,dev]
 
 Before you commit any code, please perform the following checks using [Nox](https://nox.thea.codes/en/stable/index.html):
 
-- [All tests pass](#testing): `$ nox -s unit`
+- [All tests pass](#testing): `$ nox -s quick`
 
 ### Installing and using pre-commit
 
@@ -83,16 +83,20 @@ PyBOP follows the [PEP8 recommendations](https://www.python.org/dev/peps/pep-000
 
 ### Ruff
 
-We use [ruff](https://github.com/charliermarsh/ruff) to check our PEP8 adherence. To try this on your system, navigate to the PyBOP directory in a console and type
+We use [ruff](https://github.com/charliermarsh/ruff) to lint and ensure adherence to Python PEP standards. To manually trigger `ruff`, navigate to the PyBOP directory in a console and type
 
 ```bash
 python -m pip install pre-commit
 pre-commit run ruff
 ```
 
-ruff is configured inside the file `pre-commit-config.yaml`, allowing us to ignore some errors. If you think this should be added or removed, please submit an [issue](https://guides.github.com/features/issues/).
+ruff is configured inside the file `pyproject.toml`, allowing us to ignore some errors. If you think a rule should be added or removed, please submit an [issue](https://guides.github.com/features/issues/).
 
-When you commit your changes they will be checked against ruff automatically (see [Pre-commit checks](#pre-commit-checks)).
+When you commit your changes they will be checked against ruff automatically (see [Pre-commit checks](#pre-commit-checks)). If you are having issues getting your commit to pass the linting, it
+is possible to skip linting for single lines (this should only be done as a **last resort**) by adding a line comment of `#noqa: $ruff_rule` where the `$ruff_rule` is replaced with the rule in question.
+It is also possible to skip linting altogether by committing your changes by using the
+`--no-verify` command-line flag.
+These rules can be found in the ruff configuration in `pyproject.toml` or in the failed pre-commit output. Please note the lint skipping in the pull request for reviewers.
 
 ### Naming
 

benchmarks/benchmark_model.py

@@ -79,7 +79,7 @@ def time_model_simulate(self, model, parameter_set):
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
         """
-        self.problem._model.simulate(inputs=self.inputs, t_eval=self.t_eval)
+        self.problem.model.simulate(inputs=self.inputs, t_eval=self.t_eval)
 
     def time_model_simulateS1(self, model, parameter_set):
         """
@@ -89,4 +89,4 @@ def time_model_simulateS1(self, model, parameter_set):
             model (pybop.Model): The model class being benchmarked.
             parameter_set (str): The name of the parameter set being used.
         """
-        self.problem._model.simulateS1(inputs=self.inputs, t_eval=self.t_eval)
+        self.problem.model.simulateS1(inputs=self.inputs, t_eval=self.t_eval)

examples/notebooks/optimiser_calibration.ipynb

@@ -482,7 +482,7 @@
    "source": [
     "for optim, sigma in zip(optims, sigmas):\n",
     "    print(\n",
-    "        f\"| Sigma: {sigma} | Num Iterations: {optim._iterations} | Best Cost: {optim.pints_optimiser.f_best()} | Results: {optim.pints_optimiser.x_best()} |\"\n",
+    "        f\"| Sigma: {sigma} | Num Iterations: {optim.result.n_iterations} | Best Cost: {optim.pints_optimiser.f_best()} | Results: {optim.pints_optimiser.x_best()} |\"\n",
     "    )"
    ]
   },

examples/notebooks/spm_electrode_design.ipynb

@@ -276,7 +276,7 @@
    ],
    "source": [
     "if cost.update_capacity:\n",
-    "    problem._model.approximate_capacity(x)\n",
+    "    problem.model.approximate_capacity(x)\n",
     "pybop.quick_plot(problem, problem_inputs=x, title=\"Optimised Comparison\");"
    ]
   },

examples/scripts/exp_UKF.py

@@ -40,7 +40,7 @@
 # Verification step: make another prediction using the Observer class
 model.build(parameters=parameters)
 simulator = pybop.Observer(parameters, model, signal=["2y"])
-simulator._time_data = t_eval
+simulator.time_data = t_eval
 measurements = simulator.evaluate(true_inputs)
 
 # Verification step: Compare by plotting

examples/scripts/spme_max_energy.py

@@ -57,7 +57,7 @@
 
 # Plot the timeseries output
 if cost.update_capacity:
-    problem._model.approximate_capacity(x)
+    problem.model.approximate_capacity(x)
 pybop.quick_plot(problem, problem_inputs=x, title="Optimised Comparison")
 
 # Plot the cost landscape with optimisation path

examples/standalone/cost.py

@@ -43,9 +43,9 @@ def __init__(self, problem=None):
         )
         self.x0 = self.parameters.initial_value()
 
-    def _evaluate(self, inputs):
+    def compute(self, inputs):
         """
-        Calculate the cost for a given parameter value.
+        Compute the cost for a given parameter value.
 
         The cost function is defined as cost(x) = x^2 + 42, where x is the
         parameter value.

pybop/costs/_likelihoods.py

@@ -39,10 +39,13 @@ def __init__(self, problem: BaseProblem, sigma0: Union[list[float], float]):
         self._offset = -0.5 * self.n_time_data * np.log(2 * np.pi * self.sigma2)
         self._multip = -1 / (2.0 * self.sigma2)
 
-    def _evaluate(self, inputs: Inputs) -> float:
+    def compute(self, inputs: Inputs) -> float:
         """
-        Evaluates the Gaussian log-likelihood for the given parameters with known sigma.
+        Compute the Gaussian log-likelihood for the given parameters with known sigma.
+
+        This method only computes the likelihood, without calling the problem.evaluateS1.
         """
+
         if not self.verify_prediction(self.y):
             return -np.inf
 
@@ -59,14 +62,16 @@ def _evaluate(self, inputs: Inputs) -> float:
 
         return e.item() if self.n_outputs == 1 else np.sum(e)
 
-    def _evaluateS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
+    def computeS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
         """
-        Calculates the log-likelihood and gradient.
+        Compute the Gaussian log-likelihood and it's gradient for the given parameters with known sigma.
+
+        This method only computes the likelihood, without calling the problem.evaluateS1.
         """
         if not self.verify_prediction(self.y):
             return -np.inf, -self._de * np.ones(self.n_parameters)
 
-        likelihood = self._evaluate(inputs)
+        likelihood = self.compute(inputs)
 
         r = np.asarray(
             [self._target[signal] - self.y[signal] for signal in self.signal]
@@ -168,9 +173,11 @@ def dsigma_scale(self, new_value):
             raise ValueError("dsigma_scale must be non-negative")
         self._dsigma_scale = new_value
 
-    def _evaluate(self, inputs: Inputs) -> float:
+    def compute(self, inputs: Inputs) -> float:
         """
-        Evaluates the Gaussian log-likelihood for the given parameters.
+        Compute the Gaussian log-likelihood for the given parameters.
+
+        This method only computes the likelihood, without calling the problem.evaluateS1.
 
         Parameters
         ----------
@@ -207,9 +214,11 @@ def _evaluate(self, inputs: Inputs) -> float:
 
         return e.item() if self.n_outputs == 1 else np.sum(e)
 
-    def _evaluateS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
+    def computeS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
         """
-        Calculates the log-likelihood and sensitivities.
+        Compute the Gaussian log-likelihood and it's gradient for the given parameters.
+
+        This method only computes the likelihood, without calling the problem.evaluateS1.
 
         Parameters
         ----------
@@ -231,7 +240,7 @@ def _evaluateS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
         if not self.verify_prediction(self.y):
             return -np.inf, -self._de * np.ones(self.n_parameters)
 
-        likelihood = self._evaluate(inputs)
+        likelihood = self.compute(inputs)
 
         r = np.asarray(
             [self._target[signal] - self.y[signal] for signal in self.signal]
@@ -279,16 +288,20 @@ def __init__(self, problem, likelihood, sigma0=None, gradient_step=1e-3):
             raise ValueError(f"{self.likelihood} must be a subclass of BaseLikelihood")
 
         self.parameters = self.likelihood.parameters
-        self._has_separable_problem = self.likelihood._has_separable_problem
+        self._has_separable_problem = self.likelihood.has_separable_problem
 
-    def _evaluate(self, inputs: Inputs) -> float:
+    def compute(self, inputs: Inputs) -> float:
         """
-        Calculate the maximum a posteriori cost for a given set of parameters.
+        Compute the Maximum a Posteriori for the given parameters.
+
+        If self._has_separable_problem is True, then this method only computes the
+        likelihood, without calling the problem.evaluate(). Else, problem.evaluate()
+        is called before computing the likelihood.
 
         Parameters
         ----------
         inputs : Inputs
-            The parameters for which to evaluate the cost.
+            The parameters for which to compute the cost.
 
         Returns
         -------
@@ -309,10 +322,13 @@ def _evaluate(self, inputs: Inputs) -> float:
         posterior = log_likelihood + log_prior
         return posterior
 
-    def _evaluateS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
+    def computeS1(self, inputs: Inputs) -> tuple[float, np.ndarray]:
         """
-        Compute the maximum a posteriori with respect to the parameters.
-        The method passes the likelihood gradient to the optimiser without modification.
+        Compute the Maximum a Posteriori, and it's gradient for the given parameters.
+
+        If self._has_separable_problem is True, then this method only computes the
+        likelihood, without calling the problem.evaluateS1(). Else, problem.evaluateS1()
+        is called before computing the likelihood.
 
         Parameters
         ----------

pybop/costs/_weighted_cost.py

@@ -22,7 +22,7 @@ class WeightedCost(BaseCost):
         A list of values with which to weight the cost values.
     _has_identical_problems : bool
         If True, the shared problem will be evaluated once and saved before the
-        self._evaluate() method of each cost is called (default: False).
+        self.compute() method of each cost is called (default: False).
     _has_separable_problem: bool
         If True, the shared problem is seperable from the cost function and
         will be evaluated for each problem before the cost evaluation is
@@ -54,7 +54,7 @@ def __init__(self, *costs, weights: Optional[list[float]] = None):
 
         # Check if all costs depend on the same problem
         self._has_identical_problems = all(
-            cost._has_separable_problem and cost.problem is self.costs[0].problem
+            cost.has_separable_problem and cost.problem is self.costs[0].problem
             for cost in self.costs
         )
 
@@ -80,9 +80,9 @@ def __init__(self, *costs, weights: Optional[list[float]] = None):
         # Weighted costs do not use this functionality
         self._has_separable_problem = False
 
-    def _evaluate(self, inputs: Inputs):
+    def compute(self, inputs: Inputs):
         """
-        Calculate the weighted cost for a given set of parameters.
+        Compute the weighted cost for a given set of parameters.
 
         Parameters
         ----------
@@ -105,15 +105,15 @@ def _evaluate(self, inputs: Inputs):
             inputs = cost.parameters.as_dict()
             if self._has_identical_problems:
                 cost.y = self.y
-            elif cost._has_separable_problem:
+            elif cost.has_separable_problem:
                 cost.y = cost.problem.evaluate(
                     inputs, update_capacity=self.update_capacity
                 )
-            e[i] = cost._evaluate(inputs)
+            e[i] = cost.compute(inputs)
 
         return np.dot(e, self.weights)
 
-    def _evaluateS1(self, inputs: Inputs):
+    def computeS1(self, inputs: Inputs):
         """
         Compute the weighted cost and its gradient with respect to the parameters.
 
@@ -140,9 +140,9 @@ def _evaluateS1(self, inputs: Inputs):
             inputs = cost.parameters.as_dict()
             if self._has_identical_problems:
                 cost.y, cost.dy = (self.y, self.dy)
-            elif cost._has_separable_problem:
+            elif cost.has_separable_problem:
                 cost.y, cost.dy = cost.problem.evaluateS1(inputs)
-            e[i], de[:, i] = cost._evaluateS1(inputs)
+            e[i], de[:, i] = cost.computeS1(inputs)
 
         e = np.dot(e, self.weights)
         de = np.dot(de, self.weights)

pybop/costs/base_cost.py

@@ -24,7 +24,7 @@ class BaseCost:
         The number of outputs in the model.
     _has_separable_problem : bool
         If True, the problem is separable from the cost function and will be
-        evaluated in advance of the call to self._evaluate() (default: False).
+        evaluated in advance of the call to self.compute() (default: False).
     """
 
     def __init__(self, problem: Optional[BaseProblem] = None):
@@ -38,7 +38,7 @@ def __init__(self, problem: Optional[BaseProblem] = None):
         self.dy = None
         self.set_fail_gradient()
         if isinstance(self.problem, BaseProblem):
-            self._target = self.problem._target
+            self._target = self.problem.target
             self.parameters.join(self.problem.parameters)
             self.n_outputs = self.problem.n_outputs
             self.signal = self.problem.signal
@@ -53,6 +53,10 @@ def n_parameters(self):
     def has_separable_problem(self):
         return self._has_separable_problem
 
+    @property
+    def target(self):
+        return self._target
+
     def __call__(self, inputs: Union[Inputs, list]):
         """
         Call the evaluate function for a given set of parameters.
@@ -61,7 +65,8 @@ def __call__(self, inputs: Union[Inputs, list]):
 
     def evaluate(self, inputs: Union[Inputs, list]):
         """
-        Call the evaluate function for a given set of parameters.
+        This method calls the forward model via problem.evaluateS1(inputs),
+        and computes the cost for the given output by calling self.computeS1(inputs).
 
         Parameters
         ----------
@@ -88,24 +93,25 @@ def evaluate(self, inputs: Union[Inputs, list]):
                     inputs, update_capacity=self.update_capacity
                 )
 
-            return self._evaluate(inputs)
+            return self.compute(inputs)
 
         except NotImplementedError as e:
             raise e
 
         except Exception as e:
             raise ValueError(f"Error in cost calculation: {e}") from e
 
-    def _evaluate(self, inputs: Inputs):
+    def compute(self, inputs: Inputs):
         """
-        Calculate the cost function value for a given set of parameters.
+        Calculates the cost function value for a given set of parameters.
 
+        This method only computes the cost, without calling the problem.evaluate.
         This method must be implemented by subclasses.
 
         Parameters
         ----------
         inputs : Inputs
-            The parameters for which to evaluate the cost.
+            The parameters for which to compute the cost.
 
         Returns
         -------
@@ -121,12 +127,17 @@ def _evaluate(self, inputs: Inputs):
 
     def evaluateS1(self, inputs: Union[Inputs, list]):
         """
-        Call _evaluateS1 for a given set of parameters.
+        This method calls the forward model via problem.evaluateS1(inputs),
+        and computes the cost for the given output by calling self.computeS1(inputs).
+
+        This method includes the gradient of the cost function computed by
+        calling self.computeS1(inputs) with the sensitivity information provided by
+        the forward model via problem.evaluateS1(inputs).
 
         Parameters
         ----------
         inputs : Inputs or array-like
-            The parameters for which to compute the cost and gradient.
+            The parameters for which to evaluate the cost and gradient.
 
         Returns
         -------
@@ -147,18 +158,21 @@ def evaluateS1(self, inputs: Union[Inputs, list]):
             if self._has_separable_problem:
                 self.y, self.dy = self.problem.evaluateS1(inputs)
 
-            return self._evaluateS1(inputs)
+            return self.computeS1(inputs)
 
         except NotImplementedError as e:
             raise e
 
         except Exception as e:
             raise ValueError(f"Error in cost calculation: {e}") from e
 
-    def _evaluateS1(self, inputs: Inputs):
+    def computeS1(self, inputs: Inputs):
         """
         Compute the cost and its gradient with respect to the parameters.
 
+        This method only computes the cost, without calling the problem.evaluateS1.
+        This method must be implemented by subclasses.
+
         Parameters
         ----------
         inputs : Inputs