Merge pull request #825 from pybop-team/25.10

Release v25.10

Author: NicolaCourtier

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,37 +1,18 @@
 # Description
 
-Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context.
 
-## Issue reference
-Fixes # (issue-number)
-
-## Review
-Before you mark your PR as ready for review, please ensure that you've considered the following:
-- Updated the [CHANGELOG.md](https://github.com/pybop-team/PyBOP/blob/develop/CHANGELOG.md) in reverse chronological order (newest at the top) with a concise description of the changes, including the PR number.
-- Noted any breaking changes, including details on how it might impact existing functionality.
+Fixes # (issue)
 
 ## Type of change
-- [ ] New Feature: A non-breaking change that adds new functionality.
-- [ ] Optimization: A code change that improves performance.
-- [ ] Examples: A change to existing or additional examples.
-- [ ] Bug Fix: A non-breaking change that addresses an issue.
-- [ ] Documentation: Updates to documentation or new documentation for new features.
-- [ ] Refactoring: Non-functional changes that improve the codebase.
-- [ ] Style: Non-functional changes related to code style (formatting, naming, etc).
-- [ ] Testing: Additional tests to improve coverage or confirm functionality.
-- [ ] Other: (Insert description of change)
-
-# Key checklist:
-
-- [ ] No style issues: `$ pre-commit run` (or `$ nox -s pre-commit`) (see [CONTRIBUTING.md](https://github.com/pybop-team/PyBOP/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
-- [ ] All unit tests pass: `$ nox -s tests`
-- [ ] The documentation builds: `$ nox -s doctest`
 
-You can run integration tests, unit tests, and doctests together at once, using `$ nox -s quick`.
+Please add a line in the relevant section of [CHANGELOG.md](https://github.com/pybop-team/PyBOP/blob/develop/CHANGELOG.md) to document the change (include PR #).
 
-## Further checks:
-- [ ] Code is well-commented, especially in complex or unclear areas.
-- [ ] Added tests that prove my fix is effective or that my feature works.
-- [ ] Checked that coverage remains or improves, and added tests if necessary to maintain or increase coverage.
+# Important checks:
 
-Thank you for contributing to our project! Your efforts help us to deliver great software.
+Please confirm the following before marking the PR as ready for review:
+- No style issues: `$ pre-commit run` or `$ nox -s pre-commit` (see [CONTRIBUTING.md](https://github.com/pybop-team/PyBOP/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
+- All tests pass: `nox -s tests`
+- The documentation builds: `nox -s doctest`
+- Code is commented for hard-to-understand areas
+- Tests added that prove fix is effective or that feature works

.github/workflows/scheduled_tests.yaml

@@ -93,7 +93,10 @@ jobs:
           python -m pip install --upgrade pip nox[uv]
 
       - name: Unit tests with nox
-        run: python -m nox -s coverage
+        run: python -m nox -s unit
+
+      - name: Integration tests with nox
+        run: python -m nox -s integration
 
       - name: Run examples with nox
         run: python -m nox -s examples
@@ -133,7 +136,8 @@ jobs:
           eval "$(pyenv init -)"
           pyenv activate pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
           python -m pip install --upgrade pip nox[uv]
-          python -m nox -s coverage
+          python -m nox -s unit
+          python -m nox -s integration
           python -m nox -s examples
 
       - name: Uninstall pyenv-virtualenv & python

.github/workflows/test_on_pull_request.yaml

@@ -63,7 +63,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-13, macos-14]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         exclude: # We run the coverage tests on macos-14 with Python 3.12
           - os: macos-14
             python-version: "3.12"
@@ -109,6 +109,28 @@ jobs:
         run: |
           nox -s examples
 
+  # Notebooks on macos-14
+  example_notebooks:
+    needs: style
+    runs-on: macos-14
+    strategy:
+      fail-fast: false
+    name: Test notebooks (macos-14 / Python 3.12)
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip nox[uv] openpyxl ipywidgets
+
+      - name: Run notebooks
+        run: |
+          nox -s notebooks
+
   # Quick benchmarks on macos-14
   benchmarks:
     needs: style

.pre-commit-config.yaml

@@ -1,10 +1,11 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
+  autoupdate_schedule: monthly
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.3"
+    rev: "v0.13.3"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -13,7 +14,7 @@ repos:
         types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
         - id: check-added-large-files
           args: ['--maxkb=2000']

CHANGELOG.md

@@ -8,6 +8,44 @@
 
 ## Breaking Changes
 
+# [v25.10](https://github.com/pybop-team/PyBOP/tree/v25.10) - 2025-10-31
+
+This release presents a major restructure of PyBOP's base classes. We move from setting up a model, problem, cost,
+then optimiser to defining a simulator, cost, problem, and then optimiser. A `pybop.pybamm.Simulator` is designed
+to simulate a `pybamm.BaseModel`. Optimisation parameters can be passed through a `pybamm.ParameterValues` class.
+To understand how to update your use of PyBOP, please take a look at the example notebooks and scripts.
+
+## Breaking Changes
+
+- [#820](https://github.com/pybop-team/PyBOP/pull/820) - Remove the `name` property from `pybop.Parameter`
+- [#821](https://github.com/pybop-team/PyBOP/pull/821) - Remove the `papers` folder and update Readme.
+- [#809](https://github.com/pybop-team/PyBOP/pull/809) - Major restructure, including:
+- Deprecate Python 3.9 support
+- Update initial state setting (requires PyBaMM > 25.8)
+- Remove jax methods
+- Add PyBaMM and PyBaMM-EIS simulators for rebuilding and running simulations for a given set of input parameters
+- Remove PyBaMM wrappers and enable use of PyBaMM model, parameter values and experiment classes
+- Remove observers
+- Remove standalone class examples
+- Improve logging
+- Remove Optimisation and MCMCSampler wrapper classes
+- Remove Fisher information computation
+- Rename `apply_transform` argument to `transformed`
+- Remove the `update_capacity` option from the `DesignProblem`
+- Update sensitivities retrieval (for PyBaMM 25.8)
+- Remove uninformative examples
+- Move optimiser and sampler options into defined classes
+- Add PyBaMM utilities, design variable definitions and the `add_variable_to_model` function
+- Allow plotting via functions on the `OptimisationResult`
+- Separate the cost classes from the `Problem`
+- Replace `FittingProblem` and `DesignProblem` by a single `Problem` class
+- Rename and reimplement `MultiFittingProblem` as `MetaProblem`
+- Add `BaseSimulator` as a generic base class for the `pybop.pybamm.Simulator` and `pybop.pybamm.EISSimulator`
+- Enable `pybop.Parameter` objects to be passed directly to an instance of `pybamm.ParameterValues`
+- Update the method for setting formation concentrations to be part of the model definition
+- Rename some example scripts and notebooks
+- Update the docs and test workflows
+
 # [v25.6](https://github.com/pybop-team/PyBOP/tree/v25.6) - 2025-07-16
 
 ## Features

CITATION.cff

@@ -31,5 +31,5 @@ keywords:
 journal: "arXiv"
 date-released: 2024-12-20
 doi: 10.48550/arXiv.2412.15859
-version: "25.6" # Update this alongside new releases
+version: "25.10" # Update this alongside new releases
 repository-code: 'https://www.github.com/pybop-team/pybop'

README.md

@@ -19,9 +19,12 @@
 
 </div>
 
-PyBOP provides a complete set of tools for parameterisation and optimisation of battery models, using both Bayesian and frequentist approaches, with [example workflows](https://github.com/pybop-team/PyBOP/tree/main/examples/) to assist the user. PyBOP can be used to parameterise various battery models, including electrochemical and equivalent circuit models available in [PyBaMM](https://pybamm.org/). PyBOP prioritises clear and informative diagnostics for the user, while also allowing for advanced probabilistic methods.
+PyBOP provides tools for the parameterisation and optimisation of battery models, using both Bayesian and frequentist approaches, with [example workflows](https://github.com/pybop-team/PyBOP/tree/main/examples/) to assist the user. PyBOP can be used to parameterise various battery models, including the electrochemical and equivalent circuit models available in [PyBaMM](https://pybamm.org/).
 
-The diagram below shows the conceptual framework of PyBOP. This package is currently under development, so users can expect the API to evolve with future releases.
+📌 PyBOP v25.10 presents a [major restructure](https://github.com/pybop-team/PyBOP/tree/main/CHANGELOG.md) of PyBOP's base classes. We move from setting up
+a model, problem, cost, then optimiser to defining a simulator, cost, problem, and then optimiser. A `pybop.pybamm.Simulator` is designed to simulate a
+`pybamm.BaseModel`. Optimisation parameters can be passed through a `pybamm.ParameterValues` class.
+To understand how to update your use of PyBOP, please take a look at the example notebooks and scripts.
 
 <p align="center">
     <img src="https://raw.githubusercontent.com/pybop-team/PyBOP/develop/assets/PyBOP-high-level.svg" alt="pybop_arch.svg" width="700" />
@@ -49,7 +52,9 @@ pip install pybop==v24.3
 
 To check that PyBOP is installed correctly, run one of the examples in the following section. For a development installation, see the [Contribution Guide](https://github.com/pybop-team/PyBOP/blob/develop/CONTRIBUTING.md#Installation). More installation information is available in our [documentation](https://pybop-docs.readthedocs.io/en/latest/installation.html) and the [extended installation instructions](https://docs.pybamm.org/en/latest/source/user_guide/installation/gnu-linux-mac.html) for PyBaMM.
 
-## Using PyBOP
+
+## Use Cases
+
 PyBOP has two intended uses:
 
 1. Parameter inference from battery test data.
@@ -58,48 +63,36 @@ PyBOP has two intended uses:
 
 These include a wide variety of optimisation problems that require careful consideration due to the choice of battery model, data availability and/or the choice of design parameters.
 
+### Publications
+
+Please take inspiration from the following journal articles which show how PyBOP is being used for research:
+
+- "Physics-based battery model parametrisation from impedance data" by [Hallemans et al. (2025)](https://doi.org/10.1149/1945-7111/add41b) with [open-source code and data](https://github.com/Battery-Intelligence-Lab/Hallemans-2025-JES)
+
 ### Jupyter Notebooks
 
 Explore our [example notebooks](https://github.com/pybop-team/PyBOP/blob/develop/examples) for hands-on demonstrations:
 
-- [Gravimetric design optimisation (SPMe)](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/design_optimisation/energy_based_electrode_design.ipynb)
-- [Non-linear constrained ECM parameter identification](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/battery_parameterisation/ecm_trust-constr.ipynb)
-- [Optimiser comparison for parameter identification](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/comparison_examples/multi_optimiser_identification.ipynb)
-- [Parameter identification for spatial pouch cell model](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/battery_parameterisation/pouch_cell_identification.ipynb)
-- [Estimating ECM parameters from HPPC pulse](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/battery_parameterisation/equivalent_circuit_identification_hppc.ipynb)
+- [Getting started with gradient-based optimisation](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/getting_started/optimising_with_adamw.ipynb)
+- [Estimating ECM parameters from a HPPC pulse](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/battery_parameterisation/equivalent_circuit_identification_hppc.ipynb)
+- [Identifying ECM parameters with nonlinear constraints](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/battery_parameterisation/ecm_scipy_constraints.ipynb)
+- [Parameter identification for a spatial pouch cell model](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/battery_parameterisation/pouch_cell_identification.ipynb)
+- [Energy-based electrode design optimisation](https://nbviewer.org/github/pybop-team/PyBOP/blob/develop/examples/notebooks/design_optimisation/energy_based_electrode_design.ipynb)
 
 ### Python Scripts
 
 Find additional script-based examples in the [examples directory](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/):
 
-- [UKF parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/comparison_examples/unscented_kalman_filter.py)
-- [BPX format parameter import/export](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/getting_started/simple_BPX.py)
-- [Electrochemical Impendence Spectroscopy (EIS) parameter identification](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/battery_parameterisation/simple_eis.py)
-- [Maximum a Posteriori parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/comparison_examples/maximum_a_posteriori.py)
-- [Gradient-based parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/comparison_examples/adamw.py)
+- [Getting started with SciPy minimize](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/getting_started/optimising_with_scipy_minimize.py)
+- [Estimating diffusivity from GITT data](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/battery_parameterisation/gitt_fitting.py)
+- [Maximum a Posteriori parameter identification](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/comparison_examples/maximum_a_posteriori.py)
+- [Using electrochemical impedance spectroscopy (EIS) data](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/battery_parameterisation/simple_eis.py)
+- [Getting started with MCMC samplers](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/getting_started/monte_carlo_sampling.py)
 
 
-### Supported Methods
-The table below lists the currently supported [models](https://github.com/pybop-team/PyBOP/tree/develop/pybop/models), [optimisers](https://github.com/pybop-team/PyBOP/tree/develop/pybop/optimisers), and [cost functions](https://github.com/pybop-team/PyBOP/tree/develop/pybop/costs) in PyBOP.
-
-<p align="center">
-
-| Battery Models                                | Cost Functions                     | Optimization Algorithms                                            |
-|-----------------------------------------------|------------------------------------|--------------------------------------------------------------------|
-| Single Particle Model (SPM)                   | Sum of Squared Error (SSE)         | Covariance Matrix Adaptation Evolution Strategy (CMA-ES) <tr></tr> |
-| Single Particle Model with Electrolyte (SPMe) | Root Mean Squared Error (RMSE)     | Particle Swarm Optimization (PSO) <tr></tr>                        |
-| Doyle-Fuller-Newman (DFN)                     | Mean Squared Error (MSE)           | Exponential Natural Evolution Strategy (xNES) <tr></tr>            |
-| Many Particle Model (MPM)                     | Mean Absolute Error (MAE)          | Separable Natural Evolution Strategy (sNES)  <tr></tr>             |
-| Multi-Species Multi-Reaction (MSMR)           | Minkowski                          | Weight Decayed Adaptive Moment Estimation (AdamW) <tr></tr>        |
-| Weppner-Huggins                               | Sum of Power                       | Improved Resilient Backpropagation (iRProp-) <tr></tr>             |
-| Equivalent Circuit Models (ECM)               | Gaussian Log Likelihood            | SciPy Minimize & Differential Evolution  <tr></tr>                 |
-| Grouped-parameter SPM (GroupedSPM)            | Log Posterior                      | Cuckoo Search  <tr></tr>                                           |
-| Grouped-parameter SPMe (GroupedSPMe)          | Gravimetric Energy / Power Density | Simulated Annealing  <tr></tr>                                     |
-|                                               | Volumetric Energy / Power Density  | Random Search <tr></tr>                                            |
-|                                               |                                    | Gradient Descent <tr></tr>                                         |
-|                                               |                                    | Nelder Mead <tr></tr>                                              |
-
-</p>
+### Grouped Models
+In addition to the models available in PyBaMM, PyBOP currently hosts some grouped-parameter versions of common battery models which are
+purpose-built for parameter esimation and can be found under [models](https://github.com/pybop-team/PyBOP/tree/develop/pybop/models).
 
 
 ## Code of Conduct