Merge branch 'develop' into 92-transformations-for-varying-scale-para…

…meters

.github/release_workflow.md

@@ -11,6 +11,7 @@ To create a new release, follow these steps:
    -  Increment the following;
          -  The version number in the `pyproject.toml` and `CITATION.cff` files following CalVer versioning.
          -  The`CHANGELOG.md` version with the changes for the new version.
+         -  Add a new entry for the documentation site version switcher located at `docs/_static/switcher.json`
    -  Open a PR to the `main` branch. Once the PR is merged, proceed to the next step.
 
 2. **Tag the Release:**

.github/workflows/periodic_benchmarks.yaml

@@ -22,6 +22,11 @@ jobs:
     runs-on: [self-hosted, macOS, ARM64]
     if: github.repository == 'pybop-team/PyBOP'
     steps:
+      - name: Cleanup build folder
+        run: |
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+
       - uses: actions/checkout@v4
 
       - name: Install python & create virtualenv

.github/workflows/release_action.yaml

@@ -72,7 +72,7 @@ jobs:
           ./dist/*.tar.gz
           ./dist/*.whl
     - name: Publish artifacts and signatures to GitHub Releases
-      uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564  # v2.0.4
+      uses: softprops/action-gh-release@v2
       with:
         # `dist/` contains the built packages, and the
         # sigstore-produced signatures and certificates.

.github/workflows/scheduled_tests.yaml

@@ -113,6 +113,11 @@ jobs:
       matrix: ${{fromJson(needs.filter_pybamm_matrix.outputs.filtered_pybop_matrix)}}
 
     steps:
+      - name: Cleanup build folder
+        run: |
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+
       - uses: actions/checkout@v4
       - name: Install python & create virtualenv
         shell: bash

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.8"
+    rev: "v0.5.1"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -3,10 +3,24 @@
 ## Features
 
 
+## Bug Fixes
+
+
+## Breaking Changes
+
+# [v24.6](https://github.com/pybop-team/PyBOP/tree/v24.6) - 2024-07-08
+
+## Features
+
+- [#319](https://github.com/pybop-team/PyBOP/pull/319/) - Adds `CuckooSearch` optimiser with corresponding tests.
+- [#359](https://github.com/pybop-team/PyBOP/pull/359/) - Aligning Inputs between problem, observer and model.
+- [#379](https://github.com/pybop-team/PyBOP/pull/379) - Adds model.simulateS1 to weekly benchmarks.
+- [#174](https://github.com/pybop-team/PyBOP/issues/174) - Adds new logo and updates Readme for accessibility.
 - [#316](https://github.com/pybop-team/PyBOP/pull/316) - Adds Adam with weight decay (AdamW) optimiser, adds depreciation warning for pints.Adam implementation.
 - [#271](https://github.com/pybop-team/PyBOP/issues/271) - Aligns the output of the optimisers via a generalisation of Result class.
 - [#315](https://github.com/pybop-team/PyBOP/pull/315) - Updates __init__ structure to remove circular import issues and minimises dependancy imports across codebase for faster PyBOP module import. Adds type-hints to BaseModel and refactors rebuild parameter variables.
 - [#236](https://github.com/pybop-team/PyBOP/issues/236) - Restructures the optimiser classes, adds a new optimisation API through direct construction and keyword arguments, and fixes the setting of `max_iterations`, and `_minimising`. Introduces `pybop.BaseOptimiser`, `pybop.BasePintsOptimiser`, and `pybop.BaseSciPyOptimiser` classes.
+- [#322](https://github.com/pybop-team/PyBOP/pull/322) - Add `Parameters` class to store and access multiple parameters in one object.
 - [#321](https://github.com/pybop-team/PyBOP/pull/321) - Updates Prior classes with BaseClass, adds a `problem.sample_initial_conditions` method to improve stability of SciPy.Minimize optimiser.
 - [#249](https://github.com/pybop-team/PyBOP/pull/249) - Add WeppnerHuggins model and GITT example.
 - [#304](https://github.com/pybop-team/PyBOP/pull/304) - Decreases the testing suite completion time.
@@ -24,7 +38,12 @@
 
 ## Bug Fixes
 
-
+- [#393](https://github.com/pybop-team/PyBOP/pull/393) - General integration test fixes. Adds UserWarning when using Plot2d with prior generated bounds.
+- [#338](https://github.com/pybop-team/PyBOP/pull/338) - Fixes GaussianLogLikelihood class, adds integration tests, updates non-bounded parameter implementation by applying bounds from priors and `boundary_multiplier` argument. Bugfixes to CMAES construction.
+- [#339](https://github.com/pybop-team/PyBOP/issues/339) - Updates the calculation of the cyclable lithium capacity in the spme_max_energy example.
+- [#387](https://github.com/pybop-team/PyBOP/issues/387) - Adds keys to ParameterSet and updates ECM OCV check.
+- [#380](https://github.com/pybop-team/PyBOP/pull/380) - Restore self._boundaries construction for `pybop.PSO`
+- [#372](https://github.com/pybop-team/PyBOP/pull/372) - Converts `np.array` to `np.asarray` for Numpy v2.0 support.
 - [#165](https://github.com/pybop-team/PyBOP/issues/165) - Stores the attempted and best parameter values and the best cost for each iteration in the log attribute of the optimiser and updates the associated plots.
 - [#354](https://github.com/pybop-team/PyBOP/issues/354) - Fixes the calculation of the gradient in the `RootMeanSquaredError` cost.
 - [#347](https://github.com/pybop-team/PyBOP/issues/347) - Resets options between MSMR tests to cope with a bug in PyBaMM v23.9 which is fixed in PyBaMM v24.1.
@@ -38,6 +57,13 @@
 - [#270](https://github.com/pybop-team/PyBOP/pull/270) - Updates PR template.
 - [#91](https://github.com/pybop-team/PyBOP/issues/91) - Adds a check on the number of parameters for CMAES and makes XNES the default optimiser.
 
+## Breaking Changes
+
+- [#322](https://github.com/pybop-team/PyBOP/pull/322) - Add `Parameters` class to store and access multiple parameters in one object (API change).
+- [#285](https://github.com/pybop-team/PyBOP/pull/285) - Drop support for Python 3.8.
+- [#251](https://github.com/pybop-team/PyBOP/pull/251) - Drop support for PyBaMM v23.5
+- [#236](https://github.com/pybop-team/PyBOP/issues/236) - Restructures the optimiser classes (API change).
+
 # [v24.3.1](https://github.com/pybop-team/PyBOP/tree/v24.3.1) - 2024-06-17
 
 ## Features

CITATION.cff

@@ -11,5 +11,5 @@ authors:
     family-names: Courtier
   - given-names: David
     family-names: Howey
-version: "24.3.1" # Update this when you release a new version
+version: "24.6" # Update this when you release a new version
 repository-code: 'https://www.github.com/pybop-team/pybop'

CONTRIBUTING.md

@@ -70,7 +70,7 @@ You now have everything you need to start making changes!
 ### C. Merging your changes with PyBOP
 
 10. [Test your code!](#testing)
-12. If you added a major new feature, perhaps it should be showcased in an [example notebook](#example-notebooks).
+12. If you added a major new feature, perhaps it should be showcased in an [example notebook](https://github.com/pybop-team/PyBOP/tree/develop/examples/notebooks).
 13. If you've added new functionality, please add additional tests to ensure ample code coverage in PyBOP.
 13. When you feel your code is finished, or at least warrants serious discussion, create a [pull request](https://help.github.com/articles/about-pull-requests/) (PR) on [PyBOP's GitHub page](https://github.com/pybop-team/PyBOP).
 14. Once a PR has been created, it will be reviewed by any member of the community. Changes might be suggested which you can make by simply adding new commits to the branch. When everything's finished, someone with the right GitHub permissions will merge your changes into PyBOP main repository.
@@ -314,8 +314,6 @@ Configuration files:
 pyproject.toml
 ```
 
-Note that this file must be kept in sync with the version number in [pybop/**init**.py](https://github.com/pybop-team/PyBOP/blob/develop/pybop/__init__.py).
-
 ### Continuous Integration using GitHub actions
 
 Each change pushed to the PyBOP GitHub repository will trigger the test and benchmark suites to be run, using [GitHub actions](https://github.com/features/actions).

README.md

@@ -1,6 +1,7 @@
 <div align="center">
 
-  ![logo](https://raw.githubusercontent.com/pybop-team/PyBOP/develop/assets/Temp_Logo.png)
+  <img src="https://raw.githubusercontent.com/pybop-team/PyBOP/develop/assets/logo/PyBOP_logo_flat.png" alt="logo.svg" width="700" />
+
   # Python Battery Optimisation and Parameterisation
 
 
@@ -25,8 +26,7 @@ PyBOP provides a complete set of tools for parameterisation and optimisation of
 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.
 
 <p align="center">
-    <!-- <img src="https://raw.githubusercontent.com/pybop-team/PyBOP/develop/assets/pybop_architecture.svg" alt="pybop_arch.svg" width="600" /> -->
-    <img src="assets/PyBOP-high-level.svg" alt="pybop_arch.svg" width="700" />
+    <img src="https://raw.githubusercontent.com/pybop-team/PyBOP/develop/assets/PyBOP-high-level.svg" alt="pybop_arch.svg" width="700" />
 </p>
 
 ## Installation