Merge pull request #415 from pybop-team/patch-pybammv24.5

BradyPlanden · web-flow · commit 737a4f8e4e1e · 2024-07-31T13:26:01.000+01:00
Release v24.6.1
diff --git a/.gitignore b/.gitignore
@@ -314,3 +314,6 @@ $RECYCLE.BIN/
 # Airspeed Velocity
 *.asv/
 results/
+
+# Pycharm
+*.idea/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,14 @@
 
 ## Features
 
+## Bug Fixes
+
+## Breaking Changes
+
+# [v24.6.1](https://github.com/pybop-team/PyBOP/tree/v24.6.1) - 2024-07-31
+
+## Features
+- [#313](https://github.com/pybop-team/PyBOP/pull/313/) - Fixes for PyBaMM v24.5, drops support for PyBaMM v23.9, v24.1
 
 ## Bug Fixes
 
diff --git a/CITATION.cff b/CITATION.cff
@@ -11,5 +11,5 @@ authors:
     family-names: Courtier
   - given-names: David
     family-names: Howey
-version: "24.6" # Update this when you release a new version
+version: "24.6.1" # Update this when you release a new version
 repository-code: 'https://www.github.com/pybop-team/pybop'
diff --git a/docs/_static/switcher.json b/docs/_static/switcher.json
@@ -6,7 +6,7 @@
     {
       "name": "v24.6 (stable)",
       "version": "v24.6",
-      "url": "https://pybop-docs.readthedocs.io/en/v24.6/",
+      "url": "https://pybop-docs.readthedocs.io/en/v24.6.1/",
       "preferred": true
     },
     {
diff --git a/examples/scripts/gitt.py b/examples/scripts/gitt.py
@@ -36,10 +36,10 @@
 model = pybop.lithium_ion.WeppnerHuggins(parameter_set=parameter_set)
 
 parameters = pybop.Parameter(
-    "Positive electrode diffusivity [m2.s-1]",
+    "Positive particle diffusivity [m2.s-1]",
     prior=pybop.Gaussian(5e-14, 1e-13),
     bounds=[1e-16, 1e-11],
-    true_value=parameter_set["Positive electrode diffusivity [m2.s-1]"],
+    true_value=parameter_set["Positive particle diffusivity [m2.s-1]"],
 )
 
 problem = pybop.FittingProblem(
diff --git a/examples/scripts/parameters/example_BPX.json b/examples/scripts/parameters/example_BPX.json
@@ -1,7 +1,7 @@
 {
     "Header": {
-          "BPX": 0.1,
-          "Title": "Parameterisation example of an LFP|graphite 2 Ah cylindrical 18650 cell.",
+          "BPX": 0.4,
+          "Title": "Parameterisation example of an LFP|graphite 2 Ah cylindrical 18650 cell. File downloaded on 19/3/24 from https://github.com/FaradayInstitution/BPX/blob/main/examples/lfp_18650_cell_BPX.json",
           "Description": "LFP|graphite 2 Ah cylindrical 18650 cell. Parameterisation by About:Energy Limited (aboutenergy.io), December 2022, based on cell cycling data, and electrode data gathered after cell teardown. Electrolyte properties from Nyman et al. 2008 (doi:10.1016/j.electacta.2008.04.023). Negative electrode entropic coefficient data are from O'Regan et al. 2022 (doi:10.1016/j.electacta.2022.140700). Positive electrode entropic coefficient data are from Gerver and Meyers 2011 (doi:10.1149/1.3591799). Other thermal properties are estimated.",
           "Model": "DFN"
     },
@@ -70,9 +70,6 @@
                 "Thickness [m]": 2e-05,
                 "Porosity": 0.47,
                 "Transport efficiency": 0.3222
-          },
-          "User-defined": {
-                "Source:": "An example BPX json file downloaded on 19/3/24 from https://github.com/FaradayInstitution/BPX/blob/main/examples/lfp_18650_cell_BPX.json"
           }
     }
 }
diff --git a/examples/scripts/spm_UKF.py b/examples/scripts/spm_UKF.py
@@ -22,7 +22,7 @@
 
 # Make a prediction with measurement noise
 sigma = 0.001
-t_eval = np.arange(0, 300, 2)
+t_eval = np.arange(0, 900, 0.5)
 values = model.predict(t_eval=t_eval)
 corrupt_values = values["Voltage [V]"].data + np.random.normal(0, sigma, len(t_eval))
 
@@ -42,8 +42,8 @@
 signal = ["Voltage [V]"]
 n_states = model.n_states
 n_signals = len(signal)
-covariance = np.diag([0] * 19 + [sigma**2] + [0] * 19 + [sigma**2])
-process_noise = np.diag([0] * 19 + [1e-6] + [0] * 19 + [1e-6])
+covariance = np.diag([0] * 20 + [sigma**2] + [0] * 20 + [sigma**2])
+process_noise = np.diag([0] * 20 + [1e-6] + [0] * 20 + [1e-6])
 measurement_noise = np.diag([sigma**2])
 observer = pybop.UnscentedKalmanFilterObserver(
     parameters,
diff --git a/pybop/_experiment.py b/pybop/_experiment.py
@@ -49,6 +49,4 @@ def __init__(
             period,
             temperature,
             termination,
-            drive_cycles,
-            cccv_handling,
         )
diff --git a/pybop/costs/fitting_costs.py b/pybop/costs/fitting_costs.py
@@ -161,7 +161,7 @@ def _evaluate(self, inputs: Inputs, grad=None):
 
         e = np.asarray(
             [
-                np.sum(((prediction[signal] - self._target[signal]) ** 2))
+                np.sum((prediction[signal] - self._target[signal]) ** 2)
                 for signal in self.signal
             ]
         )
diff --git a/pybop/models/base_model.py b/pybop/models/base_model.py
@@ -11,7 +11,7 @@
 
 
 @dataclass
-class TimeSeriesState(object):
+class TimeSeriesState:
     """
     The current state of a time series model that is a pybamm model.
     """
@@ -119,9 +119,13 @@ def build(
             self.set_params()
 
             self._mesh = pybamm.Mesh(self.geometry, self.submesh_types, self.var_pts)
-            self._disc = pybamm.Discretisation(self.mesh, self.spatial_methods)
+            self._disc = pybamm.Discretisation(
+                mesh=self.mesh,
+                spatial_methods=self.spatial_methods,
+                check_model=check_model,
+            )
             self._built_model = self._disc.process_model(
-                self._model_with_set_params, inplace=False, check_model=check_model
+                self._model_with_set_params, inplace=False
             )
 
             # Clear solver and setup model
@@ -230,9 +234,13 @@ def rebuild(
 
         self.set_params(rebuild=True)
         self._mesh = pybamm.Mesh(self.geometry, self.submesh_types, self.var_pts)
-        self._disc = pybamm.Discretisation(self.mesh, self.spatial_methods)
+        self._disc = pybamm.Discretisation(
+            mesh=self.mesh,
+            spatial_methods=self.spatial_methods,
+            check_model=check_model,
+        )
         self._built_model = self._disc.process_model(
-            self._model_with_set_params, inplace=False, check_model=check_model
+            self._model_with_set_params, inplace=False
         )
 
         # Clear solver and setup model
diff --git a/pybop/models/lithium_ion/weppner_huggins.py b/pybop/models/lithium_ion/weppner_huggins.py
@@ -36,7 +36,7 @@ def __init__(self, name="Weppner & Huggins model", **model_kwargs):
         # Model kwargs (build, options) are not implemented, keeping here for consistent interface
         if model_kwargs is not dict(build=True):
             unused_kwargs_warning = "The input model_kwargs are not currently used by the Weppner & Huggins model."
-            warnings.warn(unused_kwargs_warning, UserWarning)
+            warnings.warn(unused_kwargs_warning, UserWarning, stacklevel=2)
 
         super().__init__({}, name)
 
@@ -65,7 +65,7 @@ def __init__(self, name="Weppner & Huggins model", **model_kwargs):
         # Parameters
         ######################
 
-        d_s = Parameter("Positive electrode diffusivity [m2.s-1]")
+        d_s = Parameter("Positive particle diffusivity [m2.s-1]")
 
         c_s_max = Parameter("Maximum concentration in positive electrode [mol.m-3]")
 
diff --git a/pybop/observers/unscented_kalman.py b/pybop/observers/unscented_kalman.py
@@ -152,7 +152,7 @@ def get_current_covariance(self) -> Covariance:
 
 
 @dataclass
-class SigmaPoint(object):
+class SigmaPoint:
     """
     A sigma point is a point in the state space that is used to estimate the mean and covariance of a random variable.
     """
@@ -162,7 +162,7 @@ class SigmaPoint(object):
     w_c: float
 
 
-class SquareRootUKF(object):
+class SquareRootUKF:
     """
     van der Menve, R., & Wan, E. A. (2001). THE SQUARE-ROOT UNSCENTED KALMAN FILTER FOR STATE AND PARAMETER-ESTIMATION.
     https://doi.org/10.1109/ICASSP.2001.940586
diff --git a/pybop/parameters/parameter_set.py b/pybop/parameters/parameter_set.py
@@ -67,7 +67,7 @@ def import_parameters(self, json_path=None):
 
         # Read JSON file
         if not self.params and self.json_path:
-            with open(self.json_path, "r") as file:
+            with open(self.json_path) as file:
                 self.params = json.load(file)
         else:
             raise ValueError(
diff --git a/pyproject.toml b/pyproject.toml
@@ -26,7 +26,7 @@ classifiers = [
 ]
 requires-python = ">=3.9, <3.13"
 dependencies = [
-  "pybamm>=23.9",
+  "pybamm>=24.5",
   "numpy>=1.16, <2.0",
   "scipy>=1.3",
   "pints>=0.5",
@@ -73,14 +73,15 @@ Homepage = "https://github.com/pybop-team/PyBOP"
 Documentation = "https://pybop-docs.readthedocs.io"
 Repository = "https://github.com/pybop-team/PyBOP"
 Releases = "https://github.com/pybop-team/PyBOP/releases"
-Changelog = "https://github.com/pybop-team/PyBOP/CHANGELOG.md"
+Changelog = "https://github.com/pybop-team/PyBOP/blob/develop/CHANGELOG.md"
 
 [tool.pytest.ini_options]
 addopts = "--showlocals -v -n auto"
 
 [tool.ruff]
 extend-include = ["*.ipynb"]
 extend-exclude = ["__init__.py"]
+fix = true
 
 [tool.ruff.lint]
 extend-select = ["I"]
diff --git a/scripts/ci/build_matrix.sh b/scripts/ci/build_matrix.sh
@@ -11,8 +11,11 @@
 
 python_version=("3.9" "3.10" "3.11" "3.12")
 os=("ubuntu-latest" "windows-latest" "macos-13" "macos-14")
-# This command fetches the last two PyBaMM versions excluding release candidates from PyPI
-pybamm_version=($(curl -s https://pypi.org/pypi/pybamm/json | jq -r '.releases | keys[]' | grep -v rc | tail -n 2 | paste -sd " " -))
+# This command fetches the last PyBaMM version excluding release candidates from PyPI
+pybamm_version=($(curl -s https://pypi.org/pypi/pybamm/json | jq -r '.releases | keys[]' | grep -v rc | tail -n 1 | paste -sd " " -))
+
+# This command fetches the last PyBaMM versions including release candidates from PyPI
+#pybamm_version=($(curl -s https://pypi.org/pypi/pybamm/json | jq -r '.releases | keys[]' | tail -n 1 | paste -sd " " -))
 
 # open dict
 json='{
@@ -40,7 +43,7 @@ json+='
   ]
 }'
 
-# Filter out incompatible combinations
-json=$(echo "$json" | jq -c 'del(.include[] | select(.pybamm_version == "23.9" and .python_version == "3.12"))')
+# Example for filtering out incompatible combinations
+#json=$(echo "$json" | jq -c 'del(.include[] | select(.pybamm_version == "23.9" and .python_version == "3.12"))')
 
 echo "$json" | jq -c .
diff --git a/tests/integration/test_model_experiment_changes.py b/tests/integration/test_model_experiment_changes.py
@@ -22,7 +22,7 @@ class TestModelAndExperimentChanges:
             ),
             pybop.Parameters(
                 pybop.Parameter(  # non-geometric parameter
-                    "Positive electrode diffusivity [m2.s-1]",
+                    "Positive particle diffusivity [m2.s-1]",
                     prior=pybop.Gaussian(3.43e-15, 1e-15),
                     bounds=[1e-15, 5e-15],
                     true_value=4e-15,
diff --git a/tests/unit/test_cost.py b/tests/unit/test_cost.py
@@ -179,7 +179,8 @@ def test_costs(self, cost):
                 cost([1.1])
 
             # Test option setting
-            cost.set_fail_gradient(1)
+            cost.set_fail_gradient(10)
+            assert cost._de == 10
 
         if isinstance(cost, pybop.SumSquaredError):
             e, de = cost.evaluateS1([0.5])
@@ -263,4 +264,4 @@ def test_design_costs(
 
             # Compute after updating nominal capacity
             cost = cost_class(problem, update_capacity=True)
-            cost([0.4])
+            assert np.isfinite(cost([0.4]))
diff --git a/tests/unit/test_experiment.py b/tests/unit/test_experiment.py
@@ -18,9 +18,9 @@ def test_experiment(self):
         pybop_experiment = pybop.Experiment(protocol)
         pybamm_experiment = pybamm.Experiment(protocol)
 
-        assert [
-            step.to_dict() for step in pybop_experiment.operating_conditions_steps
-        ] == [step.to_dict() for step in pybamm_experiment.operating_conditions_steps]
+        assert [step.to_dict() for step in pybop_experiment.steps] == [
+            step.to_dict() for step in pybamm_experiment.steps
+        ]
 
         assert pybop_experiment.cycle_lengths == pybamm_experiment.cycle_lengths
 
diff --git a/tests/unit/test_models.py b/tests/unit/test_models.py
@@ -358,11 +358,13 @@ def test_non_converged_solution(self):
                 "Voltage [V]": np.zeros(100),
             }
         )
-
         problem = pybop.FittingProblem(model, parameters=parameters, dataset=dataset)
-        res = problem.evaluate([-0.2, -0.2])
-        _, res_grad = problem.evaluateS1([-0.2, -0.2])
+
+        # Simulate the DFN with active material values of 0.
+        # The solution elements will not change as the solver will not converge.
+        output = problem.evaluate([0, 0])
+        output_S1, _ = problem.evaluateS1([0, 0])
 
         for key in problem.signal:
-            assert np.isinf(res.get(key, [])).any()
-        assert np.isinf(res_grad).any()
+            assert np.allclose(output.get(key, [])[0], output.get(key, []))
+            assert np.allclose(output_S1.get(key, [])[0], output_S1.get(key, []))
diff --git a/tests/unit/test_observer_unscented_kalman.py b/tests/unit/test_observer_unscented_kalman.py
@@ -93,6 +93,15 @@ def test_cholupdate(self):
         SquareRootUKF.cholupdate(R1_, u.copy(), 1.0)
         np.testing.assert_array_almost_equal(R1, R1_)
 
+        # Test hypot
+        f = 10.0
+        j = 20.0
+        out_1 = f * np.sqrt(1 + 1.0 * f**2 / j**2)
+        np.testing.assert_allclose(SquareRootUKF.hypot(f, j, 1.0), out_1)
+
+        j = 10.0
+        np.testing.assert_allclose(SquareRootUKF.hypot(f, j, 1.0), float(0))
+
     @pytest.mark.unit
     def test_unscented_kalman_filter(self, dataset, observer):
         t_eval = dataset["Time [s]"]
@@ -116,6 +125,11 @@ def test_unscented_kalman_filter(self, dataset, observer):
                 decimal=4,
             )
 
+        # Test get covariance
+        cov = observer.get_current_measure()
+        assert cov.shape == (1, 1)
+        assert float(0) <= cov[0]
+
     @pytest.mark.unit
     def test_observe_no_measurement(self, observer):
         with pytest.raises(ValueError):

Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@`
`6`	`6`	`{`
`7`	`7`	`"name": "v24.6 (stable)",`
`8`	`8`	`"version": "v24.6",`
`9`		`- "url": "https://pybop-docs.readthedocs.io/en/v24.6/",`
	`9`	`+ "url": "https://pybop-docs.readthedocs.io/en/v24.6.1/",`
`10`	`10`	`"preferred": true`
`11`	`11`	`},`
`12`	`12`	`{`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"Header": {`
`3`		`- "BPX": 0.1,`
`4`		`- "Title": "Parameterisation example of an LFP\|graphite 2 Ah cylindrical 18650 cell.",`
	`3`	`+ "BPX": 0.4,`
	`4`	`+ "Title": "Parameterisation example of an LFP\|graphite 2 Ah cylindrical 18650 cell. File downloaded on 19/3/24 from https://github.com/FaradayInstitution/BPX/blob/main/examples/lfp_18650_cell_BPX.json",`
`5`	`5`	"Description": "LFP\|graphite 2 Ah cylindrical 18650 cell. Parameterisation by About:Energy Limited (aboutenergy.io), December 2022, based on cell cycling data, and electrode data gathered after cell teardown. Electrolyte properties from Nyman et al. 2008 (doi:10.1016/j.electacta.2008.04.023). Negative electrode entropic coefficient data are from O'Regan et al. 2022 (doi:10.1016/j.electacta.2022.140700). Positive electrode entropic coefficient data are from Gerver and Meyers 2011 (doi:10.1149/1.3591799). Other thermal properties are estimated.",
`6`	`6`	`"Model": "DFN"`
`7`	`7`	`},`
`@@ -70,9 +70,6 @@`
`70`	`70`	`"Thickness [m]": 2e-05,`
`71`	`71`	`"Porosity": 0.47,`
`72`	`72`	`"Transport efficiency": 0.3222`
`73`		`- },`
`74`		`- "User-defined": {`
`75`		`- "Source:": "An example BPX json file downloaded on 19/3/24 from https://github.com/FaradayInstitution/BPX/blob/main/examples/lfp_18650_cell_BPX.json"`
`76`	`73`	`}`
`77`	`74`	`}`
`78`	`75`	`}`
Original file line number	Diff line number	Diff line change
`@@ -49,6 +49,4 @@ def __init__(`
`49`	`49`	`period,`
`50`	`50`	`temperature,`
`51`	`51`	`termination,`
`52`		`- drive_cycles,`
`53`		`- cccv_handling,`
`54`	`52`	`)`
Original file line number	Diff line number	Diff line change
`@@ -161,7 +161,7 @@ def _evaluate(self, inputs: Inputs, grad=None):`
`161`	`161`
`162`	`162`	`e = np.asarray(`
`163`	`163`	`[`
`164`		`- np.sum(((prediction[signal] - self._target[signal]) ** 2))`
	`164`	`+ np.sum((prediction[signal] - self._target[signal]) ** 2)`
`165`	`165`	`for signal in self.signal`
`166`	`166`	`]`
`167`	`167`	`)`