Merge branch 'develop' into geometric-input-params

.all-contributorsrc

@@ -1,6 +1,7 @@
 {
+  "skipCi": false,
   "files": [
-    "all_contributors.md",
+    "all_contributors.md"
   ],
   "imageSize": 100,
   "commit": false,
@@ -999,14 +1000,22 @@
       "contributions": [
         "doc"
       ]
+    },
+    {
+      "login": "AndEsterson",
+      "name": "Andrew Esterson",
+      "avatar_url": "https://avatars.githubusercontent.com/u/55912083?v=4",
+      "profile": "https://github.com/AndEsterson",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,
   "projectName": "PyBaMM",
   "projectOwner": "pybamm-team",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "skipCi": true,
   "commitConvention": "angular",
   "commitType": "docs"
 }

.github/workflows/docker.yml

@@ -21,7 +21,7 @@ jobs:
         uses: docker/setup-qemu-action@49b3bc8e6bdd4a60e6116a5414239cba5943d3cf # v3.2.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3.7.1
+        uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3.8.0
 
       - name: Login to Docker Hub
         uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567 # v3.3.0

.github/workflows/scorecard.yml

@@ -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@aa578102511db1f4524ed59b8cc2bae4f6e88195 # v3.27.6
+        uses: github/codeql-action/upload-sarif@df409f7d9260372bd5f19e5b04e83cb3c43714ae # v3.27.9
         with:
           sarif_file: results.sarif

.github/workflows/test_on_push.yml

@@ -3,7 +3,6 @@ name: PyBaMM
 on:
   workflow_dispatch:
   pull_request:
-    paths-ignore: [".all-contributorsrc", "all_contributors.md"]
 
 env:
   PYBAMM_DISABLE_TELEMETRY: "true"

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.8.2"
+    rev: "v0.8.3"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -1,10 +1,15 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
 ## Features
+
+- Made composite electrode model compatible with particle size distribution ([#4687](https://github.com/pybamm-team/PyBaMM/pull/4687))
+- Added `Symbol.post_order()` method to return an iterable that steps through the tree in post-order fashion. ([#4684](https://github.com/pybamm-team/PyBaMM/pull/4684))
 - Added two more submodels (options) for the SEI: Lars von Kolzenberg (2020) model and Tunneling Limit model ([#4394](https://github.com/pybamm-team/PyBaMM/pull/4394))
 
+
 ## Breaking changes
 
+- Summary variables now calculated only when called, accessed via a class in the same manner as other variables rather than a dictionary. ([#4621](https://github.com/pybamm-team/PyBaMM/pull/4621))
 - The conda distribution (`pybamm`) now installs all optional dependencies available on conda-forge. Use the new `pybamm-base` conda
 package to install PyBaMM with only the required dependencies. ([conda-forge/pybamm-feedstock#70](https://github.com/conda-forge/pybamm-feedstock/pull/70))
 - Separated extrapolation options for `pybamm.BoundaryValue` and `pybamm.BoundaryGradient`, and updated the default to be "linear" for the value and "quadratic" for the gradient. ([#4614](https://github.com/pybamm-team/PyBaMM/pull/4614))

all_contributors.md

@@ -1,6 +1,6 @@
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-94-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-95-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
@@ -68,7 +68,7 @@ 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/bardsleypt"><img src="https://avatars.githubusercontent.com/u/54084289?v=4?s=100" width="100px;" alt="bardsleypt"/><br /><sub><b>bardsleypt</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Abardsleypt" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=bardsleypt" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/ndrewwang"><img src="https://avatars.githubusercontent.com/u/56122552?v=4?s=100" width="100px;" alt="ndrewwang"/><br /><sub><b>ndrewwang</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Andrewwang" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=ndrewwang" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/MichaPhilipp"><img src="https://avatars.githubusercontent.com/u/58085966?v=4?s=100" width="100px;" alt="MichaPhilipp"/><br /><sub><b>MichaPhilipp</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AMichaPhilipp" title="Bug reports">🐛</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/abillscmu"><img src="https://avatars.githubusercontent.com/u/48105066?v=4?s=100" width="100px;" alt="Alec Bills"/><br /><sub><b>Alec Bills</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=abillscmu" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/aabills"><img src="https://avatars.githubusercontent.com/u/48105066?v=4?s=100" width="100px;" alt="Alec Bills"/><br /><sub><b>Alec Bills</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=aabills" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/agriyakhetarpal"><img src="https://avatars.githubusercontent.com/u/74401230?v=4?s=100" width="100px;" alt="Agriya Khetarpal"/><br /><sub><b>Agriya Khetarpal</b></sub></a><br /><a href="#infra-agriyakhetarpal" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=agriyakhetarpal" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=agriyakhetarpal" title="Documentation">📖</a> <a href="https://github.com/pybamm-team/PyBaMM/pulls?q=is%3Apr+reviewed-by%3Aagriyakhetarpal" title="Reviewed Pull Requests">👀</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/awadell1"><img src="https://avatars.githubusercontent.com/u/5857298?v=4?s=100" width="100px;" alt="Alex Wadell"/><br /><sub><b>Alex Wadell</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=awadell1" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=awadell1" title="Tests">⚠️</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=awadell1" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/iatzak"><img src="https://avatars.githubusercontent.com/u/112731474?v=4?s=100" width="100px;" alt="iatzak"/><br /><sub><b>iatzak</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=iatzak" title="Documentation">📖</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Aiatzak" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=iatzak" title="Code">💻</a></td>
@@ -131,6 +131,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <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>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/isaacbasil"><img src="https://avatars.githubusercontent.com/u/123981577?v=4?s=100" width="100px;" alt="isaacbasil"/><br /><sub><b>isaacbasil</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=isaacbasil" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/AndEsterson"><img src="https://avatars.githubusercontent.com/u/55912083?v=4?s=100" width="100px;" alt="Andrew Esterson"/><br /><sub><b>Andrew Esterson</b></sub></a><br /><a href="#infra-AndEsterson" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
   </tbody>
 </table>

docs/source/api/solvers/index.rst

@@ -13,3 +13,4 @@ Solvers
   algebraic_solvers
   solution
   processed_variable
+  summary_variables

docs/source/api/solvers/summary_variables.rst

@@ -0,0 +1,5 @@
+Summary Variables
+======================
+
+.. autoclass:: pybamm.SummaryVariables
+  :members:

docs/source/examples/notebooks/models/loss_of_active_materials.ipynb

@@ -443,6 +443,8 @@
     "second = 0.1\n",
     "parameter_values.update(\n",
     "    {\n",
+    "        \"Primary: Negative electrode reference concentration for free of deformation [mol.m-3]\": 0.0,\n",
+    "        \"Secondary: Negative electrode reference concentration for free of deformation [mol.m-3]\": 0.0,\n",
     "        \"Primary: Negative electrode LAM constant proportional term [s-1]\": 1e-4 / 3600,\n",
     "        \"Secondary: Negative electrode LAM constant proportional term [s-1]\": 1e-4\n",
     "        / 3600\n",

docs/source/examples/notebooks/models/using-submodels.ipynb

@@ -527,10 +527,10 @@
     "    model.param, \"positive\", model.options, cracks=True\n",
     ")\n",
     "model.submodels[\"Negative lithium plating\"] = pybamm.lithium_plating.NoPlating(\n",
-    "    model.param, \"Negative\"\n",
+    "    model.param, \"negative\"\n",
     ")\n",
     "model.submodels[\"Positive lithium plating\"] = pybamm.lithium_plating.NoPlating(\n",
-    "    model.param, \"Positive\"\n",
+    "    model.param, \"positive\"\n",
     ")"
    ]
   },

docs/source/examples/notebooks/simulations_and_experiments/simulating-long-experiments.ipynb

@@ -541,7 +541,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "right-skiing",
    "metadata": {},
    "outputs": [
@@ -638,7 +638,7 @@
     }
    ],
    "source": [
-    "sorted(sol.summary_variables.keys())"
+    "sorted(sol.summary_variables.all_variables)"
    ]
   },
   {
@@ -1936,7 +1936,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "venv",
    "language": "python",
    "name": "python3"
   },
@@ -1950,7 +1950,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.11.10"
   },
   "toc": {
    "base_numbering": 1,
@@ -1964,11 +1964,6 @@
    "toc_position": {},
    "toc_section_display": true,
    "toc_window_display": true
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "612adcc456652826e82b485a1edaef831aa6d5abc680d008e93d513dd8724f14"
-   }
   }
  },
  "nbformat": 4,

docs/source/user_guide/installation/index.rst

@@ -63,6 +63,8 @@ Package                                                             Minimum supp
 `pandas <https://pypi.org/project/pandas/>`__                       1.5.0
 `pooch <https://www.fatiando.org/pooch/>`__                         1.8.1
 `posthog <https://posthog.com/>`__                                  3.6.5
+`pyyaml <https://pyyaml.org/>`__
+`platformdirs <https://platformdirs.readthedocs.io/en/latest/>`__
 =================================================================== ==========================
 
 .. _install.optional_dependencies:
@@ -102,13 +104,21 @@ Installable with ``pip install "pybamm[docs]"``
 Dependency                                                                                        Minimum Version    pip extra          Notes
 ================================================================================================= ================== ================== =======================================================================
 `sphinx <https://www.sphinx-doc.org/en/master/>`__                                                \-                 docs               Sphinx makes it easy to create intelligent and beautiful documentation.
+`sphinx_rtd_theme <https://pypi.org/project/sphinx-rtd-theme/>`__                                 \-                 docs               This Sphinx theme provides a great reader experience for documentation.
 `pydata-sphinx-theme <https://pydata-sphinx-theme.readthedocs.io/en/stable/>`__                   \-                 docs               A clean, Bootstrap-based Sphinx theme.
 `sphinx_design <https://sphinx-design.readthedocs.io/en/latest/>`__                               \-                 docs               A sphinx extension for designing.
 `sphinx-copybutton <https://sphinx-copybutton.readthedocs.io/en/latest/>`__                       \-                 docs               To copy codeblocks.
 `myst-parser <https://myst-parser.readthedocs.io/en/latest/>`__                                   \-                 docs               For technical & scientific documentation.
 `sphinx-inline-tabs <https://sphinx-inline-tabs.readthedocs.io/en/latest/>`__                     \-                 docs               Add inline tabbed content to your Sphinx documentation.
 `sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io/en/latest/>`__                 \-                 docs               For BibTeX citations.
 `sphinx-autobuild <https://sphinx-extensions.readthedocs.io/en/latest/sphinx-autobuild.html>`__   \-                 docs               For re-building docs once triggered.
+`sphinx-last-updated-by-git <https://pypi.org/project/sphinx-last-updated-by-git/>`__             \-                 docs               To get the "last updated" time for each Sphinx page from Git.
+`nbsphinx <https://nbsphinx.readthedocs.io/en/0.9.5/>`__                                          \-                 docs               Sphinx extension that provides a source parser for .ipynb files
+`ipykernel <https://pypi.org/project/ipykernel/>`__                                               \-                 docs               Provides the IPython kernel for Jupyter.
+`ipywidgets <https://ipywidgets.readthedocs.io/en/latest/>`__                                     \-                 docs               Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
+`sphinx-gallery <https://pypi.org/project/sphinx-gallery/>`__                                     \-                 docs               Builds an HTML gallery of examples from any set of Python scripts.
+`sphinx-hoverxref <https://sphinx-hoverxref.readthedocs.io/en/latest/index.html>`__               \-                 docs               Sphinx extension to show a floating window.
+`sphinx-docsearch <https://sphinx-docsearch.readthedocs.io/>`__                                   \-                 docs               To replaces Sphinx’s built-in search with Algolia DocSearch.
 ================================================================================================= ================== ================== =======================================================================
 
 .. _install.examples_dependencies:
@@ -142,7 +152,9 @@ Dependency
 `pytest <https://docs.pytest.org/en/stable/>`__                                  6.0.0              dev                For running the test suites.
 `pytest-doctestplus <https://github.com/scientific-python/pytest-doctestplus>`__ \-                 dev                For running doctests.
 `pytest-xdist <https://pytest-xdist.readthedocs.io/en/latest/>`__                \-                 dev                For running tests in parallel across distributed workers.
+`pytest-mock <https://pytest-mock.readthedocs.io/en/latest/index.html>`__        \-                 dev                Provides a mocker fixture.
 `nbmake <https://github.com/treebeardtech/nbmake/>`__                            \-                 dev                A ``pytest`` plugin for executing Jupyter notebooks.
+`importlib-metadata <https://pypi.org/project/importlib-metadata/>`__            \-                 dev                Used to read metadata from Python packages.
 ================================================================================ ================== ================== =============================================================
 
 .. _install.cite_dependencies:

pyproject.toml

@@ -91,7 +91,7 @@ cite = [
 ]
 # Battery Parameter eXchange format
 bpx = [
-    "bpx>=0.4.0",
+    "bpx==0.4.0",
 ]
 # Low-overhead progress bars
 tqdm = [

src/pybamm/__init__.py

@@ -163,6 +163,7 @@
 from .solvers.processed_variable_time_integral import ProcessedVariableTimeIntegral
 from .solvers.processed_variable import ProcessedVariable, process_variable
 from .solvers.processed_variable_computed import ProcessedVariableComputed
+from .solvers.summary_variable import SummaryVariables
 from .solvers.base_solver import BaseSolver
 from .solvers.dummy_solver import DummySolver
 from .solvers.algebraic_solver import AlgebraicSolver

src/pybamm/callbacks.py

@@ -212,7 +212,7 @@ def on_cycle_end(self, logs):
 
         voltage_stop = logs["stopping conditions"]["voltage"]
         if voltage_stop is not None:
-            min_voltage = logs["summary variables"]["Minimum voltage [V]"]
+            min_voltage = logs["Minimum voltage [V]"]
             if min_voltage > voltage_stop[0]:
                 self.logger.notice(
                     f"Minimum voltage is now {min_voltage:.3f} V "