Merge branch 'develop' into jaxify-idaklu-implementation

# Conflicts:
#	CHANGELOG.md
#	examples/notebooks/battery_parameterisation/single_pulse_circuit_model.ipynb

.github/workflows/lychee_links.yaml

@@ -35,7 +35,7 @@ jobs:
             --max-retries 5
             --skip-missing
             --exclude-loopback
-            --accept 200,429,999
+            --accept 200,403,429,999
             --exclude "https://tiles.stadiamaps.com/*|https://b.tile.openstreetmap.org/*"
             --exclude "https://cartodb-basemaps-c.global.ssl.fastly.net/*"
             --exclude "https://events.mapbox.com/*|https://events.mapbox.cn/*|https://api.mapbox.cn/*"

.github/workflows/release_action.yaml

@@ -40,10 +40,11 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
+        merge-multiple: true
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
 
@@ -61,10 +62,11 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
+        merge-multiple: true
     - name: Sign the dists with Sigstore
       uses: sigstore/[email protected]
       with:
@@ -95,10 +97,11 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
+        merge-multiple: true
     - name: Publish distribution 📦 to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.7.1"
+    rev: "v0.8.1"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -34,7 +34,7 @@ repos:
         - id: rst-inline-touching-normal
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: ['--keep-output', '--drop-empty-cells']

CHANGELOG.md

@@ -3,6 +3,11 @@
 ## Features
 
 - [#481](https://github.com/pybop-team/PyBOP/pull/481) - Adds experimental support for PyBaMM's jaxified IDAKLU solver. Includes Jax-specific cost functions `pybop.JaxSumSquareError` and `pybop.JaxLogNormalLikelihood`. Adds `Jax` optional dependency to PyBaMM dependency.
+- [#570](https://github.com/pybop-team/PyBOP/pull/570) - Updates the contour and surface plots, adds mixed chain effective sample size computation, x0 to optim.log
+- [#566](https://github.com/pybop-team/PyBOP/pull/566) - Adds `UnitHyperCube` transformation class, fixes incorrect application of gradient transformation.
+- [#569](https://github.com/pybop-team/PyBOP/pull/569) - Adds parameter specific learning rate functionality to GradientDescent optimiser.
+- [#282](https://github.com/pybop-team/PyBOP/issues/282) - Restructures the examples directory.
+- [#396](https://github.com/pybop-team/PyBOP/issues/396) - Adds `ecm_with_tau.py` example script.
 - [#452](https://github.com/pybop-team/PyBOP/issues/452) - Extends `cell_mass` and `approximate_capacity` for half-cell models.
 - [#544](https://github.com/pybop-team/PyBOP/issues/544) - Allows iterative plotting using `StandardPlot`.
 - [#541](https://github.com/pybop-team/PyBOP/pull/541) - Adds `ScaledLogLikelihood` and `BaseMetaLikelihood` classes.
@@ -14,6 +19,7 @@
 ## Optimisations
 
 - [#512](https://github.com/pybop-team/PyBOP/pull/513) - Refactors `LogPosterior` with attributes pointing to composed likelihood object.
+- [#551](https://github.com/pybop-team/PyBOP/pull/551) - Refactors Optimiser arguments, `population_size` and `max_iterations` as default args, improves optimiser docstrings
 
 ## Bug Fixes
 

README.md

@@ -64,21 +64,21 @@ These include a wide variety of optimisation problems that require careful consi
 
 Explore our [example notebooks](https://github.com/pybop-team/PyBOP/blob/develop/examples) for hands-on demonstrations:
 
-- [Gravimetric design optimisation (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/energy_based_electrode_design.ipynb)
-- [Non-linear constrained ECM parameter identification](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/ecm_trust-constr.ipynb)
-- [Optimiser comparison for parameter identification](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/multi_optimiser_identification.ipynb)
-- [Parameter identification for spatial pouch cell model](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/pouch_cell_identification.ipynb)
-- [Estimating ECM parameters from HPPC pulse](https://github.com/pybop-team/PyBOP/blob/develop/examples/notebooks/equivalent_circuit_identification_hppc.ipynb)
+- [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)
 
 ### 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/spm_UKF.py)
-- [BPX format parameter import/export](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/BPX_spm.py)
-- [Electrochemical Impendence Spectroscopy (EIS) parameter identification](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/eis_fitting.py)
-- [Maximum a Posteriori parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/BPX_spm.py)
-- [Gradient-based parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/spm_AdamW.py)
+- [UKF parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/comparison_examples/spm_UKF.py)
+- [BPX format parameter import/export](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/getting_started/BPX_spm.py)
+- [Electrochemical Impendence Spectroscopy (EIS) parameter identification](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/battery_parameterisation/eis_fitting.py)
+- [Maximum a Posteriori parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/getting_started/BPX_spm.py)
+- [Gradient-based parameter identification (SPM)](https://github.com/pybop-team/PyBOP/blob/develop/examples/scripts/comparison_examples/spm_AdamW.py)
 
 
 ### Supported Methods

benchmarks/benchmark_optim_construction.py

@@ -19,7 +19,7 @@ def setup(self, model, parameter_set, optimiser):
         Args:
             model (pybop.Model): The model class to be benchmarked.
             parameter_set (str): The name of the parameter set to be used.
-            optimiser (pybop.Optimiser): The optimizer class to be used.
+            optimiser (pybop.Optimiser): The optimiser class to be used.
         """
         # Set random seed
         set_random_seed()

benchmarks/benchmark_parameterisation.py

@@ -124,4 +124,4 @@ def time_optimiser_ask(self, model, parameter_set, optimiser):
             optimiser (pybop.Optimiser): The optimizer class being used.
         """
         if optimiser not in [pybop.SciPyMinimize, pybop.SciPyDifferentialEvolution]:
-            self.optim.pints_optimiser.ask()
+            self.optim.optimiser.ask()

benchmarks/benchmark_track_parameterisation.py

@@ -29,7 +29,7 @@ def setup(self, model, parameter_set, optimiser):
         Args:
             model (pybop.Model): The model class to be benchmarked.
             parameter_set (str): The name of the parameter set to be used.
-            optimiser (pybop.Optimiser): The optimizer class to be used.
+            optimiser (pybop.Optimiser): The optimiser class to be used.
         """
         # Set random seed
         set_random_seed()
@@ -121,7 +121,7 @@ def results_tracking(self, model, parameter_set, optimiser):
         Args:
             model (pybop.Model): The model class being benchmarked (unused).
             parameter_set (str): The name of the parameter set being used (unused).
-            optimiser (pybop.Optimiser): The optimizer class being used (unused).
+            optimiser (pybop.Optimiser): The optimiser class being used (unused).
         """
         results = self.optim.run()
         return results.x