Merge pull request #2821 from pybamm-team/develop

Make release v23.3

.all-contributorsrc

@@ -579,7 +579,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/83979298?v=4",
       "profile": "https://github.com/jeromtom",
       "contributions": [
-        "doc"
+        "doc",
+        "code",
+        "test"
       ]
     },
     {
@@ -590,6 +592,25 @@
       "contributions": [
         "example"
       ]
+    },
+    {
+      "login": "jsbrittain",
+      "name": "jsbrittain",
+      "avatar_url": "https://avatars.githubusercontent.com/u/98161205?v=4",
+      "profile": "http://www.jsbrittain.com/",
+      "contributions": [
+        "code",
+        "test"
+      ]
+    },
+    {
+      "login": "arjxn-py",
+      "name": "Arjun",
+      "avatar_url": "https://avatars.githubusercontent.com/u/104268427?v=4",
+      "profile": "https://github.com/arjxn-py",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/lychee_url_checker.yml

@@ -0,0 +1,55 @@
+name: Check URLs with Lychee
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+  schedule:
+    # Run everyday at 3 am UTC
+    - cron: "0 3 * * *"
+
+jobs:
+  linkChecker:
+    runs-on: ubuntu-latest
+    steps:
+
+      # cache Lychee results to avoid hitting rate limits  
+      - name: Restore lychee cache
+        uses: actions/cache@v3
+        with:
+          path: .lycheecache
+          key: cache-lychee-${{ github.sha }}
+          restore-keys: cache-lychee-
+
+      # check URLs with Lychee
+      - uses: actions/checkout@v3
+
+      # use stable version for now to avoid breaking changes
+      - name: Lychee URL checker
+        uses: lycheeverse/lychee-action@v1.6.1
+        with:
+          # arguments with file types to check
+          args: >-
+            --cache
+            --no-progress
+            --max-cache-age 2d
+            --timeout 10
+            --max-retries 5
+            --skip-missing
+            --exclude-loopback
+            --exclude https://twitter.com/pybamm_
+            --exclude "https://doi\.org|www.sciencedirect\.com/*"
+            --accept 200,429
+            --exclude-path ./CHANGELOG.md 
+            --exclude-path ./scripts/update_version.py
+            './**/*.rst'
+            './**/*.md'
+            './**/*.py'
+            './**/*.ipynb'
+          # fail the action on broken links
+          fail: true
+        env:
+          # to be used in case rate limits are surpassed
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.gitignore

@@ -62,7 +62,7 @@ dist/
 coverage.xml
 htmlcov/
 
-# virtual enviroment
+# virtual environment
 env/
 venv/
 venv3.5/
@@ -74,6 +74,7 @@ lib64
 share/
 pyvenv.cfg
 .vscode
+.ruff_cache/
 
 # sundials
 sundials

.lycheeignore

@@ -0,0 +1,17 @@
+# a list of links/files to be ignored by lychee link checker (see workflow file)
+
+# Errors in docs/source/user_guide/getting_started.md
+file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/api_docs
+
+# Errors in docs/source/user_guide/fundamentals/index.md
+file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/fundamentals/base_battery_model
+file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/fundamentals/parameter_sets
+file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/fundamentals/quick_plot
+file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/fundamentals/plot_voltage_components
+
+# Errors in docs/source/user_guide/index.md
+file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/api_docs
+
+# Errors in examples/notebooks/README.md
+file:///home/runner/work/PyBaMM/PyBaMM/examples/notebooks/using-submodels.ipynb
+file:///home/runner/work/PyBaMM/PyBaMM/examples/notebooks/create-model.ipynb

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
       - id: black
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.253"
+    rev: "v0.0.259"
     hooks:
       - id: ruff
         args: [--ignore=E741, --exclude=__init__.py]

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Optionally declare the Python requirements required to build your docs
+python:
+    install:
+      - requirements: docs/requirements.txt
+      - method: pip
+        path: .

CHANGELOG.md

@@ -1,12 +1,47 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v23.3](https://github.com/pybamm-team/PyBaMM/tree/v23.3) - 2023-03-31
+
+## Features
+
+- Added option to limit the number of integrators stored in CasadiSolver, which is particularly relevant when running simulations back-to-back [#2823](https://github.com/pybamm-team/PyBaMM/pull/2823)
+- Added new variables, related to electrode balance, for the `ElectrodeSOH` model ([#2807](https://github.com/pybamm-team/PyBaMM/pull/2807))
+- Added method to calculate maximum theoretical energy. ([#2777](https://github.com/pybamm-team/PyBaMM/pull/2777)) and add to summary variables ([#2781](https://github.com/pybamm-team/PyBaMM/pull/2781))
+- Renamed "Terminal voltage [V]" to just "Voltage [V]". "Terminal voltage [V]" can still be used and will return the same value as "Voltage [V]". ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+- Added "Negative electrode surface potential difference at separator interface [V]", which is the value of the surface potential difference (`phi_s - phi_e`) at the anode/separator interface, commonly controlled in fast-charging algorithms to avoid plating. Also added "Positive electrode surface potential difference at separator interface [V]". ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+- Added "Bulk open-circuit voltage [V]", which is the open-circuit voltage as calculated from the bulk particle concentrations. The old variable "Measured open circuit voltage [V]", which referred to the open-circuit potential as calculated from the surface particle concentrations, has been renamed to "Surface open-circuit voltage [V]". ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740)) "Bulk open-circuit voltage [V]" was briefly named "Open-circuit voltage [V]", but this was changed in ([#2845](https://github.com/pybamm-team/PyBaMM/pull/2845))
+- Added an example for `plot_voltage_components`, explaining what the different voltage components are. ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+
+## Bug fixes
+
+- Fixed excessive RAM consumption when running multiple simulations ([#2823](https://github.com/pybamm-team/PyBaMM/pull/2823))
+- Fixed a bug where variable bounds could not contain `InputParameters` ([#2795](https://github.com/pybamm-team/PyBaMM/pull/2795))
+- Improved `model.latexify()` to have a cleaner and more readable output ([#2764](https://github.com/pybamm-team/PyBaMM/pull/2764))
+- Fixed electrolyte conservation in the case of concentration-dependent transference number ([#2758](https://github.com/pybamm-team/PyBaMM/pull/2758))
+- Fixed `plot_voltage_components` so that the sum of overpotentials is now equal to the voltage ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+- Fixed use of last_state as starting_solution in Simulation.solve() ([#2822](https://github.com/pybamm-team/PyBaMM/pull/2822))
+
+## Optimizations
+
+- Migrated to [Lychee](https://github.com/lycheeverse/lychee-action) workflow for checking URLs ([#2734](https://github.com/pybamm-team/PyBaMM/pull/2734))
+
+## Breaking changes
+
+- `ElectrodeSOH.solve` now returns a `{str: float}` dict instead of a `pybamm.Solution` object (to avoid having to do `.data[0]` every time). In any code that uses `sol = ElectrodeSOH.solve()`, `sol[key].data[0]` should be replaced with `sol[key]`. ([#2779](https://github.com/pybamm-team/PyBaMM/pull/2779))
+- Removed "... cation signed stoichiometry" and "... electrons in reaction" parameters, they are now hardcoded. ([#2778](https://github.com/pybamm-team/PyBaMM/pull/2778))
+- When using `solver.step()`, the first time point in the step is shifted by `pybamm.settings.step_start_offset` (default 1 ns) to avoid having duplicate times in the solution steps from the end of one step and the start of the next. ([#2773](https://github.com/pybamm-team/PyBaMM/pull/2773))
+- Renamed "Measured open circuit voltage [V]" to "Surface open-circuit voltage [V]". This variable was calculated from surface particle concentrations, and hence "hid" the overpotential from particle gradients. The new variable "Bulk open-circuit voltage [V]" is calculated from bulk particle concentrations instead. ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+- Renamed all references to "open circuit" to be "open-circuit" instead. ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+- Renamed parameter "1 + dlnf/dlnc" to "Thermodynamic factor". ([#2727](https://github.com/pybamm-team/PyBaMM/pull/2727))
+- All PyBaMM models are now dimensional. This has been benchmarked against dimensionless models and found to give around the same solve time. Implementing dimensional models greatly reduces the barrier to entry for adding new models. However, this comes with several breaking changes: (i) the `timescale` and `length_scales` attributes of a model have been removed (they are no longer needed) (ii) several dimensionless variables are no longer defined, but the corresponding dimensional variables can still be accessed by adding the units to the name (iii) some parameters used only for non-dimensionalization, such as "Typical current [A]", have been removed ([#2419](https://github.com/pybamm-team/PyBaMM/pull/2419))
+
 # [v23.2](https://github.com/pybamm-team/PyBaMM/tree/v23.2) - 2023-02-28
 
 ## Features
 
-- Added an option for using a banded jacobian and sundials banded solvers for the IDAKLU solve [#2677](https://github.com/pybamm-team/PyBaMM/pull/2677)
-- The "particle size" option can now be a tuple to allow different behaviour in each electrode([#2672](https://github.com/pybamm-team/PyBaMM/pull/2672)).
-- Added temperature control to experiment class. [#2518](https://github.com/pybamm-team/PyBaMM/pull/2518)
+- Added an option for using a banded jacobian and sundials banded solvers for the IDAKLU solve ([#2677](https://github.com/pybamm-team/PyBaMM/pull/2677))
+- The "particle size" option can now be a tuple to allow different behaviour in each electrode ([#2672](https://github.com/pybamm-team/PyBaMM/pull/2672)).
+- Added temperature control to experiment class. ([#2518](https://github.com/pybamm-team/PyBaMM/pull/2518))
 
 ## Bug fixes
 

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "23.2"
+version: "23.3"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

CONTRIBUTING.md

@@ -400,7 +400,7 @@ Editable notebooks are made available using [Google Colab](https://colab.researc
 GitHub does some magic with particular filenames. In particular:
 
 - The first page people see when they go to [our GitHub page](https://github.com/pybamm-team/PyBaMM) displays the contents of [README.md](README.md), which is written in the [Markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) format. Some guidelines can be found [here](https://help.github.com/articles/about-readmes/).
-- The license for using PyBaMM is stored in [LICENSE](LICENSE), and [automatically](https://help.github.com/articles/adding-a-license-to-a-repository/) linked to by GitHub.
+- The license for using PyBaMM is stored in [LICENSE](LICENSE.txt), and [automatically](https://help.github.com/articles/adding-a-license-to-a-repository/) linked to by GitHub.
 - This file, [CONTRIBUTING.md](CONTRIBUTING.md) is recognised as the contribution guidelines and a link is [automatically](https://github.com/blog/1184-contributing-guidelines) displayed when new issues or pull requests are created.
 
 ## Acknowledgements

README.md

@@ -14,7 +14,7 @@
 [![black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-53-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-54-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -247,8 +247,10 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/ayeankit"><img src="https://avatars.githubusercontent.com/u/72691866?v=4?s=100" width="100px;" alt="Ankit Kumar"/><br /><sub><b>Ankit Kumar</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=ayeankit" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://aniketsinghrawat.vercel.app/"><img src="https://avatars.githubusercontent.com/u/31622972?v=4?s=100" width="100px;" alt="Aniket Singh Rawat"/><br /><sub><b>Aniket Singh Rawat</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=dikwickley" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/jeromtom"><img src="https://avatars.githubusercontent.com/u/83979298?v=4?s=100" width="100px;" alt="Jerom Palimattom Tom"/><br /><sub><b>Jerom Palimattom Tom</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=jeromtom" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/jeromtom"><img src="https://avatars.githubusercontent.com/u/83979298?v=4?s=100" width="100px;" alt="Jerom Palimattom Tom"/><br /><sub><b>Jerom Palimattom Tom</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=jeromtom" title="Documentation">📖</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=jeromtom" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=jeromtom" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="http://bradyplanden.github.io"><img src="https://avatars.githubusercontent.com/u/55357039?v=4?s=100" width="100px;" alt="Brady Planden"/><br /><sub><b>Brady Planden</b></sub></a><br /><a href="#example-BradyPlanden" title="Examples">💡</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://www.jsbrittain.com/"><img src="https://avatars.githubusercontent.com/u/98161205?v=4?s=100" width="100px;" alt="jsbrittain"/><br /><sub><b>jsbrittain</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=jsbrittain" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=jsbrittain" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/arjxn-py"><img src="https://avatars.githubusercontent.com/u/104268427?v=4?s=100" width="100px;" alt="Arjun"/><br /><sub><b>Arjun</b></sub></a><br /><a href="#infra-arjxn-py" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
   </tbody>
 </table>

docs/conf.py

@@ -26,7 +26,7 @@
 author = "The PyBaMM Team"
 
 # The short X.Y version
-version = "23.2"
+version = "23.3"
 # The full version, including alpha/beta/rc tags
 release = version
 
@@ -50,6 +50,7 @@
     "sphinx_design",
     "sphinx_copybutton",
     "myst_parser",
+    "sphinx_extend_parent",
 ]
 
 
@@ -135,12 +136,14 @@
             "url": "https://github.com/pybamm-team/PyBaMM/tree/develop/CONTRIBUTING.md",
         },
     ],
-    # Add light/dark mode and documentation version switcher:
-    # "navbar_end": ["theme-switcher", "version-switcher", "navbar-icon-links"],
-    # "switcher": {
-    #     "version_match": switcher_version,
-    #     "json_url": "https://numpy.org/doc/_static/versions.json",
-    # },
+    "switcher": {
+        "version_match": release,
+        "json_url": "https://pybamm.readthedocs.io/en/latest/_static/versions.json",  # noqa: E501
+    },
+    # turn to False to not fail build if json_url is not found
+    "check_switcher": True,
+    # for dark mode toggle, version switcher, and social media links
+    "navbar_end": ["theme-switcher", "version-switcher", "navbar-icon-links"],
     "use_edit_page_button": True,
 }
 

docs/source/_static/pybamm.css

@@ -38,7 +38,7 @@ h3 {
 
 /* Style the active version button.
 
-- dev: orange
+- latest: orange
 - stable: green
 - old, PR: red
 
@@ -48,24 +48,23 @@ Wong, B. Points of view: Color blindness.
 Nat Methods 8, 441 (2011). https://doi.org/10.1038/nmeth.1618
 */
 
-/* If the active version has the name "dev", style it orange */
-#version_switcher_button[data-active-version-name*="dev"] {
+/* If the active version has the name "latest", style it orange */
+.version-switcher__button[data-active-version-name*="latest"] {
   background-color: #e69f00;
   border-color: #e69f00;
   color: #000000;
 }
 
 /* green for `stable` */
-#version_switcher_button[data-active-version-name*="stable"] {
+.version-switcher__button[data-active-version-name*="stable"] {
   background-color: #009e73;
   border-color: #009e73;
 }
 
 /* red for `old` */
-#version_switcher_button:not(
-    [data-active-version-name*="stable"],
-    [data-active-version-name*="dev"],
-    [data-active-version-name=""]
+.version-switcher__button:not(
+    [data-active-version-name*="latest"],
+    [data-active-version-name*="stable"]
   ) {
   background-color: #980f0f;
   border-color: #980f0f;