Update BPX version and make PyBaMM compatible with Pydantic V2 (#4701)

* Force version second attempt

* Fix typo

* Fixing some tests

* Rename some parameters

* Fix typo

* Remove strings with typos

* Fix another bug

* Revert file

* Fix attribute parsing

* Force version

* Fix pin

* Update changelog

CHANGELOG.md

@@ -10,6 +10,7 @@
 
 ## Breaking changes
 
+- Updated BPX to v0.5.0 and made changes for the switch to Pydantic V2 ([#4701](https://github.com/pybamm-team/PyBaMM/pull/4701))
 - Summary variables now calculated only when called, accessed via a class in the same manner as other variables rather than a dictionary. ([#4621](https://github.com/pybamm-team/PyBaMM/pull/4621))
 - The conda distribution (`pybamm`) now installs all optional dependencies available on conda-forge. Use the new `pybamm-base` conda
 package to install PyBaMM with only the required dependencies. ([conda-forge/pybamm-feedstock#70](https://github.com/conda-forge/pybamm-feedstock/pull/70))

pyproject.toml

@@ -91,7 +91,7 @@ cite = [
 ]
 # Battery Parameter eXchange format
 bpx = [
-    "bpx==0.4.0",
+    "bpx>=0.5.0,<0.6.0",
 ]
 # Low-overhead progress bars
 tqdm = [

src/pybamm/parameters/bpx.py

@@ -398,8 +398,7 @@ def _conductivity(c_e, T, Ea, sigma_ref, constant=False):
     # Add user-defined parameters, if any
     user_defined = bpx.parameterisation.user_defined
     if user_defined:
-        for name in user_defined.__dict__.keys():
-            value = getattr(user_defined, name)
+        for name, value in user_defined:
             value = process_float_function_table(value, name)
             if callable(value):
                 pybamm_dict[name] = partial(_callable_func, fun=value)
@@ -447,7 +446,7 @@ def _bpx_to_domain_param_dict(instance: BPX, pybamm_dict: dict, domain: Domain)
     Turns a BPX instance in to a dictionary of parameters for PyBaMM for a given domain
     """
     # Loop over fields in BPX instance and add to pybamm dictionary
-    for name, field in instance.__fields__.items():
+    for name, field in instance.model_fields.items():
         value = getattr(instance, name)
         # Handle blended electrodes, where the field is now an instance of
         # ElectrodeBlended or ElectrodeBlendedSPM
@@ -460,16 +459,16 @@ def _bpx_to_domain_param_dict(instance: BPX, pybamm_dict: dict, domain: Domain)
             for i, phase_name in enumerate(particle_instance.keys()):
                 phase_instance = particle_instance[phase_name]
                 # Loop over fields in phase instance and add to pybamm dictionary
-                for name, field in phase_instance.__fields__.items():
-                    value = getattr(phase_instance, name)
+                for name_to_add, field_to_add in phase_instance.model_fields.items():
+                    value = getattr(phase_instance, name_to_add)
                     pybamm_name = PHASE_NAMES[i] + _get_pybamm_name(
-                        field.field_info.alias, domain
+                        field_to_add.alias, domain
                     )
-                    value = process_float_function_table(value, name)
+                    value = process_float_function_table(value, name_to_add)
                     pybamm_dict[pybamm_name] = value
         # Handle other fields, which correspond directly to parameters
         else:
-            pybamm_name = _get_pybamm_name(field.field_info.alias, domain)
+            pybamm_name = _get_pybamm_name(field.alias, domain)
             value = process_float_function_table(value, name)
             pybamm_dict[pybamm_name] = value
     return pybamm_dict

tests/unit/test_parameters/test_bpx.py

@@ -4,11 +4,12 @@
 import copy
 import numpy as np
 import pytest
+from typing import Any
 
 
 class TestBPX:
     def setup_method(self):
-        self.base = {
+        self.base: dict[str, Any] = {
             "Header": {
                 "BPX": 1.0,
                 "Title": "Parametrisation example",
@@ -116,7 +117,7 @@ def test_bpx(self):
                     },
                 },
             },
-            copy.copy(self.base),
+            copy.deepcopy(self.base),
         ]
 
         model = pybamm.lithium_ion.DFN()
@@ -132,9 +133,6 @@ def test_bpx(self):
             with tempfile.NamedTemporaryFile(
                 suffix=filename, delete=False, mode="w"
             ) as tmp:
-                # write to a temporary file so we can
-                # get the source later on using inspect.getsource
-                # (as long as the file still exists)
                 json.dump(obj, tmp)
                 tmp.flush()
 
@@ -153,13 +151,13 @@ def test_no_already_exists_in_BPX(self):
         with tempfile.NamedTemporaryFile(
             suffix="test.json", delete=False, mode="w"
         ) as test_file:
-            json.dump(copy.copy(self.base), test_file)
+            json.dump(copy.deepcopy(self.base), test_file)
             test_file.flush()
             params = pybamm.ParameterValues.create_from_bpx(test_file.name)
             assert "check_already_exists" not in params.keys()
 
     def test_constant_functions(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         bpx_obj["Parameterisation"]["Electrolyte"].update(
             {
                 "Conductivity [S.m-1]": 1,
@@ -183,9 +181,6 @@ def test_constant_functions(self):
         with tempfile.NamedTemporaryFile(
             suffix=filename, delete=False, mode="w"
         ) as tmp:
-            # write to a tempory file so we can
-            # get the source later on using inspect.getsource
-            # (as long as the file still exists)
             json.dump(bpx_obj, tmp)
             tmp.flush()
 
@@ -210,7 +205,7 @@ def check_constant_output(func):
             check_constant_output(De)
 
     def test_table_data(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         data = {"x": [0, 1], "y": [0, 1]}
         bpx_obj["Parameterisation"]["Electrolyte"].update(
             {
@@ -237,9 +232,6 @@ def test_table_data(self):
         with tempfile.NamedTemporaryFile(
             suffix=filename, delete=False, mode="w"
         ) as tmp:
-            # write to a temporary file so we can
-            # get the source later on using inspect.getsource
-            # (as long as the file still exists)
             json.dump(bpx_obj, tmp)
             tmp.flush()
 
@@ -263,20 +255,17 @@ def test_table_data(self):
                 assert isinstance(dUdT, pybamm.Interpolant)
 
     def test_bpx_soc_error(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         with pytest.raises(ValueError, match="Target SOC"):
             pybamm.ParameterValues.create_from_bpx_obj(bpx_obj, target_soc=10)
 
     def test_bpx_arrhenius(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
 
         filename = "tmp.json"
         with tempfile.NamedTemporaryFile(
             suffix=filename, delete=False, mode="w"
         ) as tmp:
-            # write to a tempory file so we can
-            # get the source later on using inspect.getsource
-            # (as long as the file still exists)
             json.dump(bpx_obj, tmp)
             tmp.flush()
 
@@ -327,7 +316,7 @@ def arrhenius_assertion(pv, param_key, Ea_key):
             arrhenius_assertion(pv, param_key, Ea_key)
 
     def test_bpx_blended(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         bpx_obj["Parameterisation"]["Positive electrode"] = {
             "Thickness [m]": 5.23e-05,
             "Conductivity [S.m-1]": 0.789,
@@ -367,9 +356,6 @@ def test_bpx_blended(self):
         with tempfile.NamedTemporaryFile(
             suffix=filename, delete=False, mode="w"
         ) as tmp:
-            # write to a tempory file so we can
-            # get the source later on using inspect.getsource
-            # (as long as the file still exists)
             json.dump(bpx_obj, tmp)
             tmp.flush()
 
@@ -393,7 +379,7 @@ def test_bpx_blended(self):
             sim.solve(calc_esoh=False)
 
     def test_bpx_blended_error(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         bpx_obj["Parameterisation"]["Positive electrode"] = {
             "Thickness [m]": 5.23e-05,
             "Conductivity [S.m-1]": 0.789,
@@ -446,17 +432,14 @@ def test_bpx_blended_error(self):
         with tempfile.NamedTemporaryFile(
             suffix=filename, delete=False, mode="w"
         ) as tmp:
-            # write to a tempory file so we can
-            # get the source later on using inspect.getsource
-            # (as long as the file still exists)
             json.dump(bpx_obj, tmp)
             tmp.flush()
 
             with pytest.raises(NotImplementedError, match="PyBaMM does not support"):
                 pybamm.ParameterValues.create_from_bpx(tmp.name)
 
     def test_bpx_user_defined(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         data = {"x": [0, 1], "y": [0, 1]}
         bpx_obj["Parameterisation"]["User-defined"] = {
             "User-defined scalar parameter": 1.0,
@@ -468,9 +451,6 @@ def test_bpx_user_defined(self):
         with tempfile.NamedTemporaryFile(
             suffix=filename, delete=False, mode="w"
         ) as tmp:
-            # write to a tempory file so we can
-            # get the source later on using inspect.getsource
-            # (as long as the file still exists)
             json.dump(bpx_obj, tmp)
             tmp.flush()
 
@@ -488,21 +468,21 @@ def test_bpx_user_defined(self):
             )
 
     def test_bpx_activation_energy_default(self):
-        bpx_obj = copy.copy(self.base)
-        bpx_obj["Parameterisation"]["Negative electrode"][
+        bpx_obj = copy.deepcopy(self.base)
+        del bpx_obj["Parameterisation"]["Negative electrode"][
             "Diffusivity activation energy [J.mol-1]"
-        ] = None
+        ]
         with tempfile.NamedTemporaryFile(
             suffix="test.json", delete=False, mode="w"
         ) as test_file:
-            json.dump(copy.copy(bpx_obj), test_file)
+            json.dump(copy.deepcopy(bpx_obj), test_file)
             test_file.flush()
             param = pybamm.ParameterValues.create_from_bpx(test_file.name)
             assert param[
                 "Negative electrode diffusivity activation energy [J.mol-1]"
             ] == pytest.approx(0.0, rel=1e-12)
 
     def test_bpx_from_obj(self):
-        bpx_obj = copy.copy(self.base)
+        bpx_obj = copy.deepcopy(self.base)
         param = pybamm.ParameterValues.create_from_bpx_obj(bpx_obj)
         assert isinstance(param, pybamm.ParameterValues)