Merge branch 'develop' into patch-2

Author: valentinsulzer

.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"
       ]
     },
     {

.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/[email protected]
+        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}}

.github/workflows/url_checker.yml

@@ -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

.gitignore

@@ -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

.lycheeignore

@@ -9,7 +9,7 @@ repos:
       - id: black
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.253"
+    rev: "v0.0.255"
     hooks:
       - id: ruff
         args: [--ignore=E741, --exclude=__init__.py]

.pre-commit-config.yaml

@@ -2,28 +2,38 @@
 
 ## Features
 
-- Renamed "Terminal voltage [V]" to just "Voltage [V]". "Terminal voltage [V]" can still be used and will return the same value as "Voltage [V]".
+- 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 "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))
 - Added an example for `plot_voltage_components`, explaining what the different voltage components are. ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
+- 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))
 
 ## Bug fixes
 
+- 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))
 
+## 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 "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
 

CHANGELOG.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

CONTRIBUTING.md

@@ -247,7 +247,7 @@ 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>
     </tr>
   </tbody>

README.md

@@ -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,
 }