Merge branch 'develop' into feat-eval-at-edge

Author: brosaplanella

.github/workflows/run_periodic_tests.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest, macos-13, macos-latest, windows-latest ]
+        os: [ ubuntu-latest, macos-15-intel, macos-latest, windows-latest ]
         python-version: ["3.10", "3.11", "3.12"]
     name: Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
 
@@ -48,7 +48,7 @@ jobs:
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
-        if: matrix.os == 'macos-13' || matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-15-intel' || matrix.os == 'macos-latest'
         env:
           HOMEBREW_NO_INSTALL_CLEANUP: 1
           HOMEBREW_NO_AUTO_UPDATE: 1

.github/workflows/test_on_push.yml

@@ -48,7 +48,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-15-intel, macos-latest, windows-latest]
         python-version: ["3.10", "3.11", "3.12"]
     name: Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
 
@@ -74,7 +74,7 @@ jobs:
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
-        if: matrix.os == 'macos-13' || matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-15-intel' || matrix.os == 'macos-latest'
         env:
           HOMEBREW_NO_INSTALL_CLEANUP: 1
           HOMEBREW_NO_AUTO_UPDATE: 1

.lycheeignore

@@ -3,6 +3,7 @@ https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v%7BSUITESPARSE_VERSI
 https://github.com/LLNL/sundials/releases/download/v%7BSUNDIALS_VERSION%7D/sundials-%7BSUNDIALS_VERSION%7D.tar.gz
 https://mac.r-project.org/openmp/openmp-%7BOPENMP_VERSION%7D-darwin20-Release.tar.gz
 https://github.com/pybamm-team/pybamm-data/releases/download/%7Bself.version%7D
+https://github.com/pybamm-team/PyBaMM/tree/v%7Brelease_version%7D
 
 # Errors in docs/source/user_guide/getting_started.md
 file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/api_docs

CHANGELOG.md

@@ -2,19 +2,26 @@
 
 ## Features
 
+- Added the `num_steps_no_progress` and `t_no_progress` options in the `IDAKLUSolver` to early terminate the simulation if little progress is detected. ([#5201](https://github.com/pybamm-team/PyBaMM/pull/5201))
 - Added helper functions to import external 3D meshes in PyBaMM ([#5162](https://github.com/pybamm-team/PyBaMM/pull/5162))
 - Added support for algebraic and differential surface form in composite models. ([#5165](https://github.com/pybamm-team/PyBaMM/pull/5165))
 - Adds a composite electrode electrode soh model ([#5160](https://github.com/pybamm-team/PyBaMM/pull/5129))
 - Generalises `set_initial_soc` to `set_initial_state` and adds Thevenin initial state setting. ([#5129](https://github.com/pybamm-team/PyBaMM/pull/5129))
 
 ## Bug fixes
 
+- Added explicit warning in installation docs about unmaintained Conda recipe due to pybammsolvers split (Fixes #5155). See pull request [#5206](https://github.com/pybamm-team/PyBaMM/pull/5206)
+- Fixed a bug where time-based Heaviside or modulo discontinuities could trigger out-of-bounds errors in time arrays. ([#5205](https://github.com/pybamm-team/PyBaMM/pull/5205))
+- Fixed a bug using a time-varying input with heaviside or modulo functions using the `IDAKLUSolver`. ([#4994](https://github.com/pybamm-team/PyBaMM/pull/4994))
 - Fix a bug in setting initial stoichiometries where the reference temperature was used instead of the initial temperature. ([#5189](https://github.com/pybamm-team/PyBaMM/pull/5189))
 - Fix a bug in the calculation of "Bulk" OCP terms in hysteresis models ([#5169](https://github.com/pybamm-team/PyBaMM/pull/5169))
 - Fixed a bug where the final duration of a drive cycle would not be inferred correctly. ([#5153](https://github.com/pybamm-team/PyBaMM/pull/5153))
+- Fixes a bug where sensitivities for 1D+ variables calculated using the `output_variables` options were incorrect ([#5118](https://github.com/pybamm-team/PyBaMM/pull/5118))
+- Fix Bruggeman coefficient computation from BPX porosity and transport efficiency instead of hard-coding, remove redundant values, and add a unit test for verification. ([#5196](https://github.com/pybamm-team/PyBaMM/pull/5196))
 
 # [v25.8.0](https://github.com/pybamm-team/PyBaMM/tree/v25.8.0) - 2025-08-04
 
+
 ## Features
 
 - Added `plot_3d_cross_section` & `plot_3d_heatmap` functions to support plotting for 3D thermal simulations. ([#5130](https://github.com/pybamm-team/PyBaMM/pull/5130))
@@ -77,7 +84,7 @@
 
 ## Breaking changes
 
-- Remove sensitivity functionality for Casadi and Scipy solvers, only `pybamm.IDAKLU` solver can calculate sensitivities. ([#4975](https://github.com/pybamm-team/PyBaMM/pull/4975))
+- Remove sensitivity functionality for Casadi and Scipy solvers, only `pybamm.IDAKLUSolver` can calculate sensitivities. ([#4975](https://github.com/pybamm-team/PyBaMM/pull/4975))
 
 # [v25.4.2](https://github.com/pybamm-team/PyBaMM/tree/v25.4.2) - 2025-04-17
 
@@ -603,7 +610,7 @@ package to install PyBaMM with only the required dependencies. ([conda-forge/pyb
 - Removed code for generating `ModelingToolkit` problems ([#2432](https://github.com/pybamm-team/PyBaMM/pull/2432))
 - Removed `FirstOrder` and `Composite` lead-acid models, and some submodels specific to those models ([#2431](https://github.com/pybamm-team/PyBaMM/pull/2431))
 
-# [v22.10.post1](https://github.com/pybamm-team/PyBaMM/tree/v22.10.post1) - 2022-10-31
+# v22.10.post1 - 2022-10-31
 
 ## Breaking changes
 
@@ -635,7 +642,7 @@ package to install PyBaMM with only the required dependencies. ([conda-forge/pyb
 - Removed `get_infinite_nested_dict`, `BaseModel.check_default_variables_dictionaries`, and `Discretisation.create_jacobian` methods, which were not used by any other functionality in the repository ([#2384](https://github.com/pybamm-team/PyBaMM/pull/2384))
 - Dropped support for Python 3.7 after the release of Numpy v1.22.0 ([#2379](https://github.com/pybamm-team/PyBaMM/pull/2379))
 - Removed parameter cli tools (add/edit/remove parameters). Parameter sets can now more easily be added via python scripts. ([#2342](https://github.com/pybamm-team/PyBaMM/pull/2342))
-- Parameter sets should now be provided as single python files containing all parameters and functions. Parameters provided as "data" (e.g. OCP vs SOC) can still be csv files, but must be either in the same folder as the parameter file or in a subfolder called "data/". See for example [Ai2020](https://github.com/pybamm-team/PyBaMM/tree/develop/pybamm/input/parameters/lithium_ion/Ai2020.py) ([#2342](https://github.com/pybamm-team/PyBaMM/pull/2342))
+- Parameter sets should now be provided as single python files containing all parameters and functions. Parameters provided as "data" (e.g. OCP vs SOC) can still be csv files, but must be either in the same folder as the parameter file or in a subfolder called "data/". See for example [Ai2020](https://github.com/pybamm-team/PyBaMM/blob/develop/src/pybamm/input/parameters/lithium_ion/Ai2020.py) ([#2342](https://github.com/pybamm-team/PyBaMM/pull/2342))
 
 # [v22.9](https://github.com/pybamm-team/PyBaMM/tree/v22.9) - 2022-09-30
 
@@ -1339,7 +1346,7 @@ This release introduces many new features and optimizations. All models can now
 - Removed `Outer` and `Kron` nodes as no longer used ([#777](https://github.com/pybamm-team/PyBaMM/pull/777))
 - Moved `results` to separate repositories ([#761](https://github.com/pybamm-team/PyBaMM/pull/761))
 - The parameters "Bruggeman coefficient" must now be specified separately as "Bruggeman coefficient (electrolyte)" and "Bruggeman coefficient (electrode)"
-- The current classes (`GetConstantCurrent`, `GetUserCurrent` and `GetUserData`) have now been removed. Please refer to the [`change-input-current` notebook](https://github.com/pybamm-team/PyBaMM/blob/develop/docs/source/examples/notebooks/change-input-current.ipynb) for information on how to specify an input current
+- The current classes (`GetConstantCurrent`, `GetUserCurrent` and `GetUserData`) have now been removed. Please refer to the [`change-input-current` notebook](https://github.com/pybamm-team/PyBaMM/blob/develop/docs/source/examples/notebooks/parameterization/change-input-current.ipynb) for information on how to specify an input current
 - Parameter functions must now use pybamm functions instead of numpy functions (e.g. `pybamm.exp` instead of `numpy.exp`), as these are then used to construct the expression tree directly. Generally, pybamm syntax follows numpy syntax; please get in touch if a function you need is missing.
 - The current must now be updated by changing "Current function [A]" or "C-rate" instead of "Typical current [A]"
 

benchmarks/README.md

@@ -32,7 +32,7 @@ asv run v0.3..develop
 
 Further information on how to run benchmarks with `asv` can be found in the documentation at [Using airspeed velocity](https://asv.readthedocs.io/en/stable/using.html).
 
-`asv` is configured using a file `asv.conf.json` located at the root of the PyBaMM repository. See the [asv reference](https://asv.readthedocs.io/en/stable/reference.html) for details on available settings and options.
+`asv` is configured using a file `asv.conf.json` located at the root of the PyBaMM repository. See the [asv reference](https://asv.readthedocs.io/en/stable/user_reference.html) for details on available settings and options.
 
 Benchmark results are stored in a directory `results/` at the location of the configuration file. There is one result file per commit, per machine.
 

docs/source/user_guide/installation/index.rst

@@ -29,6 +29,11 @@ It can be installed using ``pip`` or ``conda``, or from source.
 
       conda install -c conda-forge pybamm-base
 
+.. warning::
+
+   The PyBaMM Conda recipe is not currently maintained and lags several releases behind.
+   As a result, installations via Conda will provide an outdated version.
+   To access the latest version, consider installing PyBaMM using pip.
 
 Optional solvers
 ----------------
@@ -60,8 +65,8 @@ PyBaMM requires the following dependencies.
 =================================================================== ==========================
 Package                                                             Supported version(s)
 =================================================================== ==========================
-`PyBaMM solvers <https://github.com/pybamm-team/pybammsolvers>`__     0.0.4
-`NumPy <https://numpy.org>`__                                         >= 1.23.5, <2
+`PyBaMM solvers <https://github.com/pybamm-team/pybammsolvers>`__     >= 0.2.0, <0.4.0
+`NumPy <https://numpy.org>`__                                         Whatever recent versions work
 `SciPy <https://docs.scipy.org/doc/scipy/>`__                         Whatever recent versions work. >= 1.9.3
 `CasADi <https://web.casadi.org/docs/>`__                             Whatever recent versions work. >= 3.6.7
 `Xarray <https://docs.xarray.dev/en/stable/>`__                       Whatever recent versions work. >= 2022.6.0

pyproject.toml

@@ -28,8 +28,8 @@ classifiers = [
     "Topic :: Scientific/Engineering",
 ]
 dependencies = [
-    "pybammsolvers",
-    "numpy>=1.23.5,<2.0.0",
+    "pybammsolvers>=0.3.0,<0.4.0",
+    "numpy",
     "scipy>=1.11.4",
     "casadi==3.6.7",
     "xarray>=2022.6.0",
@@ -113,7 +113,7 @@ dev = [
     "hypothesis",
 ]
 jax = [
-    "jax>=0.4.36,<0.6.0",
+    "jax>=0.4.36,<0.7.0",
 ]
 # Contains all optional dependencies, except for jax, and dev dependencies
 all = [

src/pybamm/expression_tree/operations/serialise.py

@@ -786,11 +786,10 @@ def convert_symbol_to_json(
         >>> from pybamm.expression_tree.operations.serialise import Serialise
         >>> s = pybamm.Scalar(5)
         >>> Serialise.convert_symbol_to_json(s)
-        {'type': 'Scalar', 'value': 5.0}
-
+        {'type': 'Scalar', 'value': np.float64(5.0)}
         >>> v = pybamm.Variable("c")
         >>> Serialise.convert_symbol_to_json(v)
-        {'type': 'Variable', 'name': 'c', 'domains': {'primary': [], 'secondary': [], 'tertiary': [], 'quaternary': []}, 'bounds': [{'type': 'Scalar', 'value': -inf}, {'type': 'Scalar', 'value': inf}]}
+        {'type': 'Variable', 'name': 'c', 'domains': {'primary': [], 'secondary': [], 'tertiary': [], 'quaternary': []}, 'bounds': [{'type': 'Scalar', 'value': np.float64(-inf)}, {'type': 'Scalar', 'value': np.float64(inf)}]}
         """
 
         if isinstance(symbol, numbers.Number | list):

src/pybamm/models/base_model.py

@@ -12,9 +12,6 @@
 import pybamm
 from pybamm.expression_tree.operations.serialise import Serialise
 
-# Only throw the default solver warning once
-warnings.filterwarnings("once", message="The default solver changed to IDAKLUSolver*")
-
 
 class BaseModel:
     """
@@ -421,11 +418,6 @@ def default_solver(self):
         if len(self.rhs) == 0 and len(self.algebraic) != 0:
             return pybamm.CasadiAlgebraicSolver()
         else:
-            warnings.warn(
-                "The default solver changed to IDAKLUSolver after the v25.4.0. release. "
-                "You can swap back to the previous default by using `pybamm.CasadiSolver()` instead.",
-                stacklevel=2,
-            )
             return pybamm.IDAKLUSolver()
 
     @property

src/pybamm/parameters/bpx.py

@@ -145,10 +145,6 @@ def bpx_to_param_dict(bpx: BPX) -> dict:
     # activity
     pybamm_dict["Thermodynamic factor"] = 1.0
 
-    # assume Bruggeman relation for effective electrolyte properties
-    for domain in [negative_electrode, separator, positive_electrode]:
-        pybamm_dict[domain.pre_name + "Bruggeman coefficient (electrolyte)"] = 1.5
-
     # solid phase properties reported in BPX are already "effective",
     # so no correction is applied
     for domain in [negative_electrode, positive_electrode]:
@@ -216,10 +212,11 @@ def bpx_to_param_dict(bpx: BPX) -> dict:
     pybamm_dict.update({"Total heat transfer coefficient [W.m-2.K-1]": 0})
 
     # transport efficiency
+    # Compute Bruggeman coefficient from BPX-specified porosity and transport efficiency
     for domain in [negative_electrode, separator, positive_electrode]:
-        pybamm_dict[domain.pre_name + "porosity"] = pybamm_dict[
-            domain.pre_name + "transport efficiency"
-        ] ** (1.0 / 1.5)
+        pybamm_dict[domain.pre_name + "Bruggeman coefficient (electrolyte)"] = math.log(
+            pybamm_dict[domain.pre_name + "transport efficiency"]
+        ) / math.log(pybamm_dict[domain.pre_name + "porosity"])
 
     def _get_activation_energy(var_name):
         return pybamm_dict.get(var_name) or 0.0