[GSOC 2025] Saving and Loading Parameter Sets

.github/workflows/benchmark_on_push.yml

@@ -20,7 +20,7 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Set up Python 3.12

.github/workflows/docker.yml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -31,7 +31,7 @@ jobs:
         with:
           cache-binary: false
       - name: Login to Docker Hub
-        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3.4.0
+        uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
         with:
             username: ${{ secrets.DOCKERHUB_USERNAME }}
             password: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/lychee_url_checker.yml

@@ -23,20 +23,20 @@ jobs:
 
       # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
+        uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # v4.2.4
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
           restore-keys: cache-lychee-
 
       # check URLs with Lychee
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@82202e5e9c2f4ef1a55a3d02563e1cb6041e5332 # v2.4.1
+        uses: lycheeverse/lychee-action@5c4ee84814c983aa7164eaee476f014e53ff3963 # v2.5.0
         with:
           # arguments with file types to check
           args: >-

.github/workflows/periodic_benchmarks.yml

@@ -28,7 +28,7 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -78,14 +78,14 @@ jobs:
         run: pip install asv
 
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
           persist-credentials: false
 
       - name: Download results artifact(s)
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
         with:
           path: results
           merge-multiple: true

.github/workflows/publish_pypi.yml

@@ -13,7 +13,7 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: true
       - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
@@ -39,7 +39,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
         with:
           path: deploy
           merge-multiple: true

.github/workflows/run_benchmarks_over_history.yml

@@ -37,7 +37,7 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Set up Python 3.12
@@ -140,14 +140,14 @@ jobs:
         run: pip install asv
 
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
           persist-credentials: false
 
       - name: Download results artifact(s)
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.6.2
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v4.6.2
         with:
           name: asv_over_history_results
           path: results

.github/workflows/run_periodic_tests.yml

@@ -36,7 +36,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -103,7 +103,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -141,7 +141,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -175,7 +175,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 

.github/workflows/scorecard.yml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -65,6 +65,6 @@ 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@181d5eefc20863364f96762470ba6f862bdef56b # v3.29.2
+        uses: github/codeql-action/upload-sarif@96f518a34f7a870018057716cc4d7a5c014bd61c # v3.29.5
         with:
           sarif_file: results.sarif

.github/workflows/test_on_push.yml

@@ -24,7 +24,7 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Setup Python
@@ -54,12 +54,12 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -132,13 +132,13 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         with:
           packages: graphviz pandoc
           execute_install_scripts: true
@@ -179,12 +179,12 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -222,12 +222,12 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         with:
           packages: gfortran gcc graphviz
           execute_install_scripts: true

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.4"
+    rev: "v0.12.9"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -19,7 +19,7 @@ repos:
          additional_dependencies: [black==23.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
         - id: check-added-large-files
         - id: check-case-conflict
@@ -44,6 +44,6 @@ repos:
         - id: sp-repo-review
 
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.11.0
+    rev: v1.12.1
     hooks:
       - id: zizmor

CHANGELOG.md

@@ -1,6 +1,17 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
 ## Features
+
+- 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))
+
+# [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))
 - Added a `Basic3DThermalSPM` with two way coupling. ([#5112](https://github.com/pybamm-team/PyBaMM/pull/5112))
 - Enables the passing of `inputs` throughout `set_initial_soc`. ([#5122](https://github.com/pybamm-team/PyBaMM/pull/5122))
 - Adds `on_failure` option to `BaseSolver` with options for `"warn"`, `"ignore"`, and `"raise"` to change behaviour on solver failure. Defaults to "raise" to retain historic functionality. ([#5105](https://github.com/pybamm-team/PyBaMM/pull/5105))
@@ -17,6 +28,10 @@
 
 ## Bug fixes
 
+- Fixed non-deterministic plotting CI issues ([#5150](https://github.com/pybamm-team/PyBaMM/pull/5150))
+- Fix non-deterministic ShapeError in 3D FEM gradient method ([#5143](https://github.com/pybamm-team/PyBaMM/pull/5143))
+- Fixes negative electrode boundary values for half-cell voltage contributions. ([#5139](https://github.com/pybamm-team/PyBaMM/pull/5139))
+- Makes `A_cc` L_z * L_y * number of layers ([#5138](https://github.com/pybamm-team/PyBaMM/pull/5138))
 - Fixes `TimeIntegral` expression node summation when dependent on an input parameter. ([#5119](https://github.com/pybamm-team/PyBaMM/pull/5119))
 - Fixed a bug that ignored the default duration of drive cycles for `CRate` steps and a bug that overwrote custom `period` arguments for drive cycles. ([#5090](https://github.com/pybamm-team/PyBaMM/pull/5090))
 - Converts sensitivities to numpy objects, fixing bug in `DiscreteTimeSum` sensitivity calculation ([#5037](https://github.com/pybamm-team/PyBaMM/pull/5037))
@@ -28,6 +43,7 @@
 
 ## Breaking changes
 
+- Changed behavior of drive cycle steps in `pybamm.Experiment`s to treat each time point as a discontinuity, consistent with how input interpolants work. This ensures more accurate simulation of drive cycles with rapid changes. ([#5141](https://github.com/pybamm-team/PyBaMM/pull/5141))
 - Removed the IREE code from the IDAKLU solver ([#5080](https://github.com/pybamm-team/PyBaMM/pull/5080))
 - Removed support for Python 3.9 ([#5052](https://github.com/pybamm-team/PyBaMM/pull/5052))
 - In OCP hysteresis models, users need to explicitly give the equilibrium, delithiation, and lithiation OCPs when using a hysteresis model. E.g., you must provide all three of "Negative electrode OCP [V]", "Negative electrode delithiation OCP [V]", and "Negative electrode lithiation OCP [V]". ([#4893](https://github.com/pybamm-team/PyBaMM/pull/4893))

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "25.6.0"
+version: "25.8.0"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

docs/source/api/plotting/index.rst

@@ -8,3 +8,5 @@ Plotting
   plot_2D
   plot_voltage_components
   plot_summary_variables
+  plot_3d_cross_section
+  plot_3d_heatmap

docs/source/api/plotting/plot_3d_cross_section.rst

@@ -0,0 +1,4 @@
+Plot Cross Section
+==================
+
+.. autofunction:: pybamm.plot_3d_cross_section

docs/source/api/plotting/plot_3d_heatmap.rst

@@ -0,0 +1,4 @@
+Plot 3D Heatmap
+===============
+
+.. autofunction:: pybamm.plot_3d_heatmap

docs/source/examples/notebooks/models/electrode-state-of-health.ipynb

@@ -336,7 +336,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -365,7 +365,7 @@
     "    Q_n = parameter_values.evaluate(param.n.Q_init)\n",
     "    Q_p = parameter_values.evaluate(param.p.Q_init)\n",
     "\n",
-    "    Q = parameter_values.evaluate(param.Q / param.n_electrodes_parallel)\n",
+    "    Q = parameter_values.evaluate(param.Q)\n",
     "    esoh_solver = pybamm.lithium_ion.ElectrodeSOHSolver(\n",
     "        parameter_values, param, known_value=\"cell capacity\"\n",
     "    )\n",