Merge branch 'develop' into migrate-to-sbc

.all-contributorsrc

@@ -970,6 +970,27 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "MarcBerliner",
+      "name": "Marc Berliner",
+      "avatar_url": "https://avatars.githubusercontent.com/u/34451391?v=4",
+      "profile": "http://marcberliner.com",
+      "contributions": [
+        "code",
+        "doc",
+        "infra",
+        "maintenance"
+      ]
+    },
+    {
+      "login": "Aswinr24",
+      "name": "Aswinr24",
+      "avatar_url": "https://avatars.githubusercontent.com/u/135364633?v=4",
+      "profile": "https://github.com/Aswinr24",
+      "contributions": [
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/lychee_url_checker.yml

@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@v1.10.0
+        uses: lycheeverse/lychee-action@v2.0.2
         with:
           # arguments with file types to check
           args: >-

.github/workflows/periodic_benchmarks.yml

@@ -48,7 +48,7 @@ jobs:
           asv run --machine "GitHubRunner" NEW --show-stderr -v
 
       - name: Upload results as artifact
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: asv_periodic_results
           path: results

.github/workflows/publish_pypi.yml

@@ -94,7 +94,7 @@ jobs:
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
             python -m pytest -m cibw {project}/tests/unit
       - name: Upload Windows wheels
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: wheels_windows
           path: ./wheelhouse/*.whl
@@ -133,7 +133,7 @@ jobs:
             python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for Linux
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: wheels_manylinux
           path: ./wheelhouse/*.whl
@@ -265,7 +265,7 @@ jobs:
             python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for macOS (amd64, arm64)
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: wheels_${{ matrix.os }}
           path: ./wheelhouse/*.whl
@@ -285,7 +285,7 @@ jobs:
         run: pipx run build --sdist
 
       - name: Upload SDist
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: sdist
           path: ./dist/*.tar.gz

.github/workflows/run_benchmarks_over_history.yml

@@ -46,7 +46,7 @@ jobs:
           ${{ github.event.inputs.commit_start }}..${{ github.event.inputs.commit_end }}
 
       - name: Upload results as artifact
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: asv_over_history_results
           path: results

.github/workflows/run_periodic_tests.yml

@@ -156,7 +156,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.python-version == '3.12'
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 

.github/workflows/scorecard.yml

@@ -59,7 +59,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
+        uses: actions/upload-artifact@184d73b71b93c222403b2e7f1ffebe4508014249 # v4.4.1
         with:
           name: SARIF file
           path: results.sarif
@@ -68,6 +68,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@294a9d92911152fe08befb9ec03e240add280cb3 # v3.26.8
+        uses: github/codeql-action/upload-sarif@f779452ac5af1c261dce0346a8f964149f49322b # v3.26.13
         with:
           sarif_file: results.sarif

.github/workflows/test_on_push.yml

@@ -208,7 +208,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.python-version == '3.12'
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 

.gitignore

@@ -64,6 +64,7 @@ coverage.xml
 htmlcov/
 
 # virtual environment
+.venv
 env/
 venv/
 venv3.5/

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.7"
+    rev: "v0.6.9"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -13,13 +13,13 @@ repos:
         types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.18.0"
+    rev: "1.19.0"
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==23.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
         - id: check-added-large-files
         - id: check-case-conflict

CHANGELOG.md

@@ -2,11 +2,16 @@
 
 ## Features
 
+- Adds an option "voltage as a state" that can be "false" (default) or "true". If "true" adds an explicit algebraic equation for the voltage. ([#4507](https://github.com/pybamm-team/PyBaMM/pull/4507))
+- Improved `QuickPlot` accuracy for simulations with Hermite interpolation. ([#4483](https://github.com/pybamm-team/PyBaMM/pull/4483))
+- Added Hermite interpolation to the (`IDAKLUSolver`) that improves the accuracy and performance of post-processing variables. ([#4464](https://github.com/pybamm-team/PyBaMM/pull/4464))
+- Added `BasicDFN` model for sodium-ion batteries ([#4451](https://github.com/pybamm-team/PyBaMM/pull/4451))
 - Added sensitivity calculation support for `pybamm.Simulation` and `pybamm.Experiment` ([#4415](https://github.com/pybamm-team/PyBaMM/pull/4415))
 - Added OpenMP parallelization to IDAKLU solver for lists of input parameters ([#4449](https://github.com/pybamm-team/PyBaMM/pull/4449))
 - Added phase-dependent particle options to LAM
   ([#4369](https://github.com/pybamm-team/PyBaMM/pull/4369))
 - Added a lithium ion equivalent circuit model with split open circuit voltages for each electrode (`SplitOCVR`). ([#4330](https://github.com/pybamm-team/PyBaMM/pull/4330))
+- Added the `pybamm.DiscreteTimeSum` expression node to sum an expression over a sequence of data times, and accompanying `pybamm.DiscreteTimeData` class to store the data times and values ([#4501](https://github.com/pybamm-team/PyBaMM/pull/4501))
 
 ## Optimizations
 
@@ -16,10 +21,12 @@
 
 ## Bug Fixes
 
+- Added `_from_json()` functionality to `Sign` which was erroneously omitted previously. ([#4517](https://github.com/pybamm-team/PyBaMM/pull/4517))
 - Fixed bug where IDAKLU solver failed when `output variables` were specified and an extrapolation event is present. ([#4440](https://github.com/pybamm-team/PyBaMM/pull/4440))
 
 ## Breaking changes
 
+- Removed all instances of `param = self.param` and now directly access `self.param` across the codebase. This change simplifies parameter references and enhances readability. ([#4484](https://github.com/pybamm-team/PyBaMM/pull/4494))
 - Removed the deprecation warning for the chemistry argument in
   ParameterValues ([#4466](https://github.com/pybamm-team/PyBaMM/pull/4466))
 - The parameters "... electrode OCP entropic change [V.K-1]" and "... electrode volume change" are now expected to be functions of stoichiometry only instead of functions of both stoichiometry and maximum concentration ([#4427](https://github.com/pybamm-team/PyBaMM/pull/4427))

CMakeLists.txt

@@ -111,6 +111,8 @@ pybind11_add_module(idaklu
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/Expression.hpp
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionSet.hpp
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp
+  src/pybamm/solvers/c_solvers/idaklu/observe.hpp
+  src/pybamm/solvers/c_solvers/idaklu/observe.cpp
   # IDAKLU expressions - concrete implementations
   ${IDAKLU_EXPR_CASADI_SOURCE_FILES}
   ${IDAKLU_EXPR_IREE_SOURCE_FILES}

README.md

@@ -15,7 +15,7 @@
 [![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/pybamm-team/PyBaMM/badge)](https://scorecard.dev/viewer/?uri=github.com/pybamm-team/PyBaMM)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-91-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-93-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>

all_contributors.md

@@ -122,6 +122,10 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/pipliggins"><img src="https://avatars.githubusercontent.com/u/55396775?v=4?s=100" width="100px;" alt="Pip Liggins"/><br /><sub><b>Pip Liggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=pipliggins" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=pipliggins" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/medha-14"><img src="https://avatars.githubusercontent.com/u/143182673?v=4?s=100" width="100px;" alt="Medha Bhardwaj"/><br /><sub><b>Medha Bhardwaj</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=medha-14" title="Code">💻</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="http://marcberliner.com"><img src="https://avatars.githubusercontent.com/u/34451391?v=4?s=100" width="100px;" alt="Marc Berliner"/><br /><sub><b>Marc Berliner</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=MarcBerliner" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=MarcBerliner" title="Documentation">📖</a> <a href="#infra-MarcBerliner" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-MarcBerliner" title="Maintenance">🚧</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Aswinr24"><img src="https://avatars.githubusercontent.com/u/135364633?v=4?s=100" width="100px;" alt="Aswinr24"/><br /><sub><b>Aswinr24</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=Aswinr24" title="Tests">⚠️</a></td>
+    </tr>
   </tbody>
 </table>
 

docs/conf.py

@@ -341,7 +341,7 @@
 
 {% set github_docname =
 'github/pybamm-team/pybamm/blob/develop/docs/' +
-env.doc2path(env.docname, base=None) %}
+env.doc2path(env.docname, base=None) | string() %}
 
 {% set notebooks_version = env.config.html_context.notebooks_version %}
 {% set github_download_url = env.config.html_context.github_download_url %}

docs/source/examples/index.rst

@@ -68,6 +68,7 @@ The notebooks are organised into subfolders, and can be viewed in the galleries
     notebooks/models/SEI-on-cracks.ipynb
     notebooks/models/simulate-3E-cell.ipynb
     notebooks/models/simulating-ORegan-2022-parameter-set.ipynb
+    notebooks/models/sodium-ion.ipynb
     notebooks/models/SPM.ipynb
     notebooks/models/SPMe.ipynb
     notebooks/models/submodel_cracking_DFN_or_SPM.ipynb

pyproject.toml

@@ -83,6 +83,7 @@ plot = [
     "matplotlib>=3.6.0",
 ]
 cite = [
+    "setuptools", # Fix for a pybtex issue
     "pybtex>=0.24.0",
 ]
 # Battery Parameter eXchange format
@@ -150,6 +151,7 @@ Ramadass2004 = "pybamm.input.parameters.lithium_ion.Ramadass2004:get_parameter_v
 Xu2019 = "pybamm.input.parameters.lithium_ion.Xu2019:get_parameter_values"
 ECM_Example = "pybamm.input.parameters.ecm.example_set:get_parameter_values"
 MSMR_Example = "pybamm.input.parameters.lithium_ion.MSMR_example_set:get_parameter_values"
+Chayambuka2022 = "pybamm.input.parameters.sodium_ion.Chayambuka2022:get_parameter_values"
 
 [tool.scikit-build]
 minimum-version = "build-system.requires"
@@ -206,6 +208,8 @@ extend-select = [
     "YTT",           # flake8-2020
     "TID252",        # relative-imports
     "S101",          # to identify use of assert statement
+    "PT027",         # remove unittest style assertion
+    "PT009",         # Use pytest.raises instead of unittest-style
 ]
 ignore = [
     "E741",        # Ambiguous variable name