Merge branch 'develop' into i1863-idklu-casadi

CHANGELOG.md

@@ -1,8 +1,15 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
 ## Features
+
 -   Added a casadi version of the IDKLU solver, which is used for `model.convert_to_format = "casadi"` ([#2002](https://github.com/pybamm-team/PyBaMM/pull/2002))
 
+## Bug fixes
+
+-   Remove old deprecation errors, including those in `parameter_values.py` that caused the simulation if, for example, the reaction rate is re-introduced manually ([#2022](https://github.com/pybamm-team/PyBaMM/pull/2022))
+
+## Breaking changes
+
 # [v22.3](https://github.com/pybamm-team/PyBaMM/tree/v22.3) - 2022-03-31
 
 ## Features

pybamm/expression_tree/symbol.py

@@ -878,10 +878,6 @@ def has_symbol_of_classes(self, symbol_classes):
         """
         return any(isinstance(symbol, symbol_classes) for symbol in self.pre_order())
 
-    def simplify(self, simplified_symbols=None, clear_domains=True):
-        """`simplify()` has now been removed."""
-        raise pybamm.ModelError("simplify is deprecated as it now has no effect")
-
     def to_casadi(self, t=None, y=None, y_dot=None, inputs=None, casadi_symbols=None):
         """
         Convert the expression tree to a CasADi expression tree.

pybamm/models/full_battery_models/lithium_ion/dfn.py

@@ -19,6 +19,12 @@ class DFN(BaseModel):
         option to False allows users to change any number of the submodels before
         building the complete model (submodels cannot be changed after the model is
         built).
+    Examples
+    --------
+    >>> import pybamm
+    >>> model = pybamm.lithium_ion.DFN()
+    >>> model.name
+    'Doyle-Fuller-Newman model'
 
     References
     ----------

pybamm/parameters/parameter_values.py

@@ -177,18 +177,6 @@ def update_from_chemistry(self, chemistry):
         if "lithium plating" in chemistry:
             component_groups += ["lithium plating"]
 
-        if "anode" in chemistry.keys():
-            raise KeyError(
-                "The 'anode' notation has been deprecated, "
-                "'negative electrode' should be used instead."
-            )
-
-        if "cathode" in chemistry.keys():
-            raise KeyError(
-                "The 'cathode' notation has been deprecated, "
-                "'positive electrode' should be used instead."
-            )
-
         for component_group in component_groups:
             # Make sure component is provided
             try:
@@ -352,43 +340,9 @@ def check_parameter_values(self, values):
                 "'Typical current [A]' cannot be zero. A possible alternative is to "
                 "set 'Current function [A]' to `0` instead."
             )
-        if "C-rate" in values:
-            raise ValueError(
-                "The 'C-rate' parameter has been deprecated, "
-                "use 'Current function [A]' instead. The Nominal "
-                "cell capacity can be accessed as 'Nominal cell "
-                "capacity [A.h]', and used to calculate current from C-rate."
-            )
-        if "Cell capacity [A.h]" in values:
-            raise ValueError(
-                "The 'Cell capacity [A.h]' parameter has been deprecated, "
-                "'Nominal cell capacity [A.h]' should be used instead."
-            )
+
         for param in values:
-            if "surface area density" in param:
-                raise ValueError(
-                    "Parameters involving 'surface area density' have been renamed to "
-                    "'surface area to volume ratio' ('{}' found)".format(param)
-                )
-            elif "reaction rate" in param:
-                raise ValueError(
-                    "Parameters involving 'reaction rate' have been replaced with "
-                    "'exchange-current density' ('{}' found)".format(param)
-                )
-            elif "particle distribution in x" in param:
-                raise ValueError(
-                    "The parameter '{}' has been deprecated".format(param)
-                    + "The particle radius is now set as a function of x directly "
-                    "instead of providing a reference value and a distribution."
-                )
-            elif "surface area to volume ratio distribution in x" in param:
-                raise ValueError(
-                    "The parameter '{}' has been deprecated".format(param)
-                    + "The surface area to volume ratio is now set as a function "
-                    "of x directly instead of providing a reference value and a "
-                    "distribution."
-                )
-            elif "propotional term" in param:
+            if "propotional term" in param:
                 raise ValueError(
                     f"The parameter '{param}' has been renamed to "
                     "'... proportional term [s-1]', and its value should now be divided"

pybamm/simulation.py

@@ -963,7 +963,7 @@ def step(
 
         return self.solution
 
-    def plot(self, output_variables=None, quick_plot_vars=None, **kwargs):
+    def plot(self, output_variables=None, **kwargs):
         """
         A method to quickly plot the outputs of the simulation. Creates a
         :class:`pybamm.QuickPlot` object (with keyword arguments 'kwargs') and
@@ -973,19 +973,12 @@ def plot(self, output_variables=None, quick_plot_vars=None, **kwargs):
         ----------
         output_variables: list, optional
             A list of the variables to plot.
-        quick_plot_vars: list, optional
-            A list of the variables to plot. Deprecated, use output_variables instead.
         **kwargs
             Additional keyword arguments passed to
             :meth:`pybamm.QuickPlot.dynamic_plot`.
             For a list of all possible keyword arguments see :class:`pybamm.QuickPlot`.
         """
 
-        if quick_plot_vars is not None:
-            raise NotImplementedError(
-                "'quick_plot_vars' has been deprecated. Use 'output_variables' instead."
-            )
-
         if self._solution is None:
             raise ValueError(
                 "Model has not been solved, please solve the model before plotting."

pybamm/solvers/base_solver.py

@@ -48,19 +48,13 @@ def __init__(
         root_method=None,
         root_tol=1e-6,
         extrap_tol=0,
-        max_steps="deprecated",
     ):
         self.method = method
         self.rtol = rtol
         self.atol = atol
         self.root_tol = root_tol
         self.root_method = root_method
         self.extrap_tol = extrap_tol
-        if max_steps != "deprecated":
-            raise ValueError(
-                "max_steps has been deprecated, and should be set using the "
-                "solver-specific extra-options dictionaries instead"
-            )
         self.models_set_up = {}
 
         # Defaults, can be overwritten by specific solver

pybamm/solvers/idaklu_solver.py

@@ -51,7 +51,6 @@ def __init__(
         root_method="casadi",
         root_tol=1e-6,
         extrap_tol=0,
-        max_steps="deprecated",
     ):
 
         if idaklu_spec is None:  # pragma: no cover
@@ -64,7 +63,6 @@ def __init__(
             root_method,
             root_tol,
             extrap_tol,
-            max_steps,
         )
         self.name = "IDA KLU solver"
 

pybamm/solvers/scikits_dae_solver.py

@@ -56,13 +56,12 @@ def __init__(
         root_tol=1e-6,
         extrap_tol=0,
         extra_options=None,
-        max_steps="deprecated",
     ):
         if scikits_odes_spec is None:
             raise ImportError("scikits.odes is not installed")
 
         super().__init__(
-            method, rtol, atol, root_method, root_tol, extrap_tol, max_steps
+            method, rtol, atol, root_method, root_tol, extrap_tol
         )
         self.name = "Scikits DAE solver ({})".format(method)
 

pybamm/solvers/scikits_ode_solver.py

@@ -49,19 +49,13 @@ def __init__(
         rtol=1e-6,
         atol=1e-6,
         extrap_tol=0,
-        linsolver="deprecated",
         extra_options=None,
     ):
         if scikits_odes_spec is None:
             raise ImportError("scikits.odes is not installed")
 
         super().__init__(method, rtol, atol, extrap_tol=extrap_tol)
         self.extra_options = extra_options or {}
-        if linsolver != "deprecated":
-            raise ValueError(
-                "linsolver has been deprecated. Pass 'linsolver' to extra_options "
-                "dictionary instead"
-            )
         self.ode_solver = True
         self.name = "Scikits ODE solver ({})".format(method)
 

pybamm/util.py

@@ -13,7 +13,6 @@
 import subprocess
 import sys
 import timeit
-import warnings
 from collections import defaultdict
 from platform import system
 
@@ -265,22 +264,6 @@ def load_function(filename):
     if filename.endswith(".py"):
         filename = filename.replace(".py", "")
 
-    # Replace `lead-acid` with `lead_acid`
-    if "lead-acid" in filename:
-        warnings.simplefilter("always", DeprecationWarning)
-        warnings.warn(
-            "lead-acid is deprecated, use lead_acid instead", DeprecationWarning
-        )
-        filename = filename.replace("lead-acid", "lead_acid")
-
-    # Replace `lithium-ion` with `lithium_ion`
-    if "lithium-ion" in filename:
-        warnings.simplefilter("always", DeprecationWarning)
-        warnings.warn(
-            "lithium-ion is deprecated, use lithium_ion instead", DeprecationWarning
-        )
-        filename = filename.replace("lithium-ion", "lithium_ion")
-
     # Assign path to _ and filename to tail
     _, tail = os.path.split(filename)
 

tests/unit/test_expression_tree/test_symbol.py

@@ -319,14 +319,6 @@ def test_symbol_evaluates_to_constant_number(self):
         a = 3 * pybamm.t + 2
         self.assertFalse(a.evaluates_to_constant_number())
 
-    def test_simplify(self):
-        a = pybamm.Parameter("A")
-        # test error
-        with self.assertRaisesRegex(
-            pybamm.ModelError, "simplify is deprecated as it now has no effect"
-        ):
-            (a + a).simplify()
-
     def test_simplify_if_constant(self):
         m = pybamm.Matrix(np.zeros((10, 10)))
         m_simp = pybamm.simplify_if_constant(m)

tests/unit/test_parameters/test_parameter_values.py

@@ -137,26 +137,9 @@ def test_update(self):
             param.update({"b": 1})
 
     def test_check_parameter_values(self):
-        # Cell capacity [A.h] deprecated
-        with self.assertRaisesRegex(ValueError, "Cell capacity"):
-            pybamm.ParameterValues({"Cell capacity [A.h]": 1})
         # Can't provide a current density of 0, as this will cause a ZeroDivision error
         with self.assertRaisesRegex(ValueError, "Typical current"):
             pybamm.ParameterValues({"Typical current [A]": 0})
-        with self.assertRaisesRegex(
-            ValueError, "The 'C-rate' parameter has been deprecated"
-        ):
-            pybamm.ParameterValues({"C-rate": 0})
-        with self.assertRaisesRegex(ValueError, "surface area density"):
-            pybamm.ParameterValues({"Negative surface area density": 1})
-        with self.assertRaisesRegex(ValueError, "reaction rate"):
-            pybamm.ParameterValues({"Negative reaction rate": 1})
-        with self.assertRaisesRegex(ValueError, "particle distribution"):
-            pybamm.ParameterValues({"Negative particle distribution in x": 1})
-        with self.assertRaisesRegex(ValueError, "surface area to volume ratio"):
-            pybamm.ParameterValues(
-                {"Negative electrode surface area to volume ratio distribution in x": 1}
-            )
         with self.assertRaisesRegex(ValueError, "propotional term"):
             pybamm.ParameterValues(
                 {"Negative electrode LAM constant propotional term": 1}
@@ -1002,17 +985,6 @@ def some_function(self):
         self.assertEqual(df[1]["b"], "[function]some_function")
         self.assertEqual(df[1]["c"], "[data]some_data")
 
-    def test_deprecate_anode_cathode(self):
-        chemistry = pybamm.parameter_sets.Ecker2015.copy()
-        chemistry["anode"] = chemistry.pop("negative electrode")
-        with self.assertRaisesRegex(KeyError, "anode"):
-            pybamm.ParameterValues(chemistry)
-
-        chemistry = pybamm.parameter_sets.Ecker2015.copy()
-        chemistry["cathode"] = chemistry.pop("positive electrode")
-        with self.assertRaisesRegex(KeyError, "cathode"):
-            pybamm.ParameterValues(chemistry)
-
 
 if __name__ == "__main__":
     print("Add -v for more debug output")

tests/unit/test_simulation.py

@@ -362,10 +362,6 @@ def test_plot(self):
         sim.solve(t_eval=t_eval)
         sim.plot(testing=True)
 
-        # test quick_plot_vars deprecation error
-        with self.assertRaisesRegex(NotImplementedError, "'quick_plot_vars'"):
-            sim.plot(quick_plot_vars=["var"])
-
     def test_create_gif(self):
         sim = pybamm.Simulation(pybamm.lithium_ion.SPM())
         sim.solve(t_eval=[0, 10])

tests/unit/test_solvers/test_base_solver.py

@@ -20,10 +20,6 @@ def test_base_solver_init(self):
         solver.rtol = 1e-7
         self.assertEqual(solver.rtol, 1e-7)
 
-        # max_steps deprecated
-        with self.assertRaisesRegex(ValueError, "max_steps has been deprecated"):
-            pybamm.BaseSolver(max_steps=10)
-
     def test_root_method_init(self):
         solver = pybamm.BaseSolver(root_method="casadi")
         self.assertIsInstance(solver.root_method, pybamm.CasadiAlgebraicSolver)

tests/unit/test_solvers/test_scikits_solvers.py

@@ -11,11 +11,6 @@
 
 @unittest.skipIf(not pybamm.have_scikits_odes(), "scikits.odes not installed")
 class TestScikitsSolvers(unittest.TestCase):
-    def test_init(self):
-        # linsolver deprecated
-        with self.assertRaisesRegex(ValueError, "linsolver has been deprecated"):
-            pybamm.ScikitsOdeSolver(linsolver="lapackdense")
-
     def test_model_ode_integrate_failure(self):
         # Turn off warnings to ignore sqrt error
         warnings.simplefilter("ignore")

tests/unit/test_util.py

@@ -25,32 +25,6 @@ class TestUtil(unittest.TestCase):
     """
 
     def test_load_function(self):
-        # Test replace function and deprecation warning for lithium-ion
-        with self.assertWarns(Warning):
-            warn_path = os.path.join(
-                "pybamm",
-                "input",
-                "parameters",
-                "lithium-ion",
-                "negative_electrodes",
-                "graphite_Chen2020",
-                "graphite_LGM50_electrolyte_exchange_current_density_Chen2020.py",
-            )
-            pybamm.load_function(warn_path)
-
-        # Test replace function and deprecation warning for lead-acid
-        with self.assertWarns(Warning):
-            warn_path = os.path.join(
-                "pybamm",
-                "input",
-                "parameters",
-                "lead-acid",
-                "negative_electrodes",
-                "lead_Sulzer2019",
-                "lead_exchange_current_density_Sulzer2019.py",
-            )
-            pybamm.load_function(warn_path)
-
         # Test function load with absolute path
         abs_test_path = os.path.join(
             pybamm.root_dir(),