Merge branch 'develop' of https://github.com/pybamm-team/PyBaMM into …

…nox-cleanup

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
 # activated pre-commit - https://github.com/pybamm-team/PyBaMM/pull/2272
 0054efe388d2d17301f7e0554449eac9a7d3b7fc
+# activated pre-commit for notebooks - https://github.com/pybamm-team/PyBaMM/pull/3110
+a63e49ece0f9336d1f5c2562f7459e555c6e6693

.gitignore

@@ -134,5 +134,9 @@ results/
 !docs/source/examples/notebooks/models/spm1.png
 !docs/source/examples/notebooks/models/spm2.png
 
+# do not ignore images in _static folder in docs
+!docs/_static/favicon/favicon.png
+!docs/_static/pybamm_logo.png
+
 # tests
 test_callback.log

.pre-commit-config.yaml

@@ -3,13 +3,21 @@ ci:
   autofix_commit_msg: "style: pre-commit fixes"
 
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
-    hooks:
-      - id: black
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.278"
+    rev: "v0.0.281"
     hooks:
       - id: ruff
-        args: [--ignore=E741, --exclude=__init__.py]
+        args: [--fix, --ignore=E741, --exclude=__init__.py]
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-ruff
+        additional_dependencies: [ruff==0.0.280]
+        args: ["--fix","--ignore=E501,E402"]
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.15.0"
+    hooks:
+       - id: blacken-docs
+         additional_dependencies: [black==22.12.0]

.readthedocs.yaml

@@ -11,6 +11,11 @@ sphinx:
   configuration: docs/conf.py
   fail_on_warning: false
 
+formats:
+  - pdf
+  - epub
+  - htmlzip
+
 # Set the version of Python and other tools you might need
 build:
   # Install Graphviz to build SVG files

CHANGELOG.md

@@ -2,13 +2,20 @@
 
 ## Breaking changes
 
+- Added option to use an empirical hysteresis model for the diffusivity and exchange-current density ([#3194](https://github.com/pybamm-team/PyBaMM/pull/3194))
+- Double-layer capacity can now be provided as a function of temperature ([#3174](https://github.com/pybamm-team/PyBaMM/pull/3174))
+- `pybamm_install_jax` is deprecated. It is now replaced with `pip install pybamm[jax]` ([#3163](https://github.com/pybamm-team/PyBaMM/pull/3163))
 - PyBaMM now has optional dependencies that can be installed with the pattern `pip install pybamm[option]` e.g. `pybamm[plot]` ([#3044](https://github.com/pybamm-team/PyBaMM/pull/3044))
 
 ## Bug fixes
 
+- Fixed a bug where the "basic" lithium-ion models gave incorrect results when using nonlinear particle diffusivity ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))
+- Particle size distributions now work with SPMe and NewmanTobias models ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))
+- Fix to simulate c_rate steps with drive cycles ([#3186](https://github.com/pybamm-team/PyBaMM/pull/3186))
 - Parameters in `Prada2013` have been updated to better match those given in the paper, which is a 2.3 Ah cell, instead of the mix-and-match with the 1.1 Ah cell from Lain2019.
-- Error generated when invalid parameter values are passed.
-- Thevenin() model is now constructed with standard variables: `Time [s], Time [min], Time [h]` ([#3143](https://github.com/pybamm-team/PyBaMM/pull/3143)) 
+- Error generated when invalid parameter values are passed. ([#3132](https://github.com/pybamm-team/PyBaMM/pull/3132))
+- Thevenin() model is now constructed with standard variables: `Time [s], Time [min], Time [h]` ([#3143](https://github.com/pybamm-team/PyBaMM/pull/3143))
+- Fix SEI Example Notebook ([#3166](https://github.com/pybamm-team/PyBaMM/pull/3166))
 
 # [v23.5](https://github.com/pybamm-team/PyBaMM/tree/v23.5) - 2023-06-18
 
@@ -27,7 +34,7 @@
 
 ## Bug fixes
 
-- Realign 'count' increment in CasadiSolver._integrate() ([#2986](https://github.com/pybamm-team/PyBaMM/pull/2986))
+- Realign 'count' increment in CasadiSolver.\_integrate() ([#2986](https://github.com/pybamm-team/PyBaMM/pull/2986))
 - Fix `pybamm_install_odes` and update the required SUNDIALS version ([#2958](https://github.com/pybamm-team/PyBaMM/pull/2958))
 - Fixed a bug where all data included in a BPX was incorrectly assumed to be given as a function of time.([#2957](https://github.com/pybamm-team/PyBaMM/pull/2957))
 - Remove brew install for Mac from the recommended developer installation options for SUNDIALS ([#2925](https://github.com/pybamm-team/PyBaMM/pull/2925))

CONTRIBUTING.md

@@ -74,23 +74,7 @@ pre-commit run ruff
 
 ruff is configured inside the file `pre-commit-config.yaml`, allowing us to ignore some errors. If you think this should be added or removed, please submit an [issue](#issues)
 
-When you commit your changes they will be checked against ruff automatically (see [infrastructure](#infrastructure)).
-
-### Black
-
-We use [black](https://black.readthedocs.io/en/stable/) to automatically configure our code to adhere to PEP8. Black can be used in two ways:
-
-1. Command line: navigate to the PyBaMM directory in a console and type
-
-```bash
-black {source_file_or_directory}
-```
-
-2. Editor: black can be [configured](https://test-black.readthedocs.io/en/latest/editor_integration.html) to automatically reformat a Python script each time the script is saved in an editor.
-
-If you want to use black in your editor, you may need to change the max line length in your editor settings.
-
-Even when code has been formatted by black, you should still make sure that it adheres to the PEP8 standard set by [ruff](#ruff).
+When you commit your changes they will be checked against ruff automatically (see [Pre-commit checks](#pre-commit-checks)).
 
 ### Naming
 
@@ -219,13 +203,20 @@ This also means that, if you can't fix the bug yourself, it will be much easier
 2. Set break points, either in your IDE or using the Python debugging module. To use the latter, add the following line where you want to set the break point
 
    ```python
-   import ipdb; ipdb.set_trace()
+   import ipdb
+
+   ipdb.set_trace()
    ```
 
    This will start the [Python interactive debugger](https://gist.github.com/mono0926/6326015). If you want to be able to use magic commands from `ipython`, such as `%timeit`, then set
 
    ```python
-   from IPython import embed; embed(); import ipdb; ipdb.set_trace()
+   from IPython import embed
+
+   embed()
+   import ipdb
+
+   ipdb.set_trace()
    ```
 
    at the break point instead.
@@ -237,14 +228,17 @@ This also means that, if you can't fix the bug yourself, it will be much easier
       try:
           do_something_complicated()
       except ValueError:
-          import ipdb; ipdb.set_trace()
+          import ipdb
+
+          ipdb.set_trace()
       ```
 
       This will start the debugger at the point where the `ValueError` was raised, and allow you to investigate further. Sometimes, it is more informative to put the try-except block further up the call stack than exactly where the error is raised.
    2. Warnings. If functions are raising warnings instead of errors, it can be hard to pinpoint where this is coming from. Here, you can use the `warnings` module to convert warnings to errors:
 
       ```python
       import warnings
+
       warnings.simplefilter("error")
       ```
 
@@ -270,7 +264,12 @@ This also means that, if you can't fix the bug yourself, it will be much easier
 Sometimes, a bit of code will take much longer than you expect to run. In this case, you can set
 
 ```python
-from IPython import embed; embed(); import ipdb; ipdb.set_trace()
+from IPython import embed
+
+embed()
+import ipdb
+
+ipdb.set_trace()
 ```
 
 as above, and then use some of the profiling tools. In order of increasing detail:
@@ -389,7 +388,7 @@ Documentation is built using https://readthedocs.org/ and published on http://do
 
 ### Google Colab
 
-Editable notebooks are made available using [Google Colab](https://colab.research.google.com/notebooks/intro.ipynb) [here](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/develop/).
+Editable notebooks are made available using [Google Colab](https://colab.research.google.com/notebooks/intro.ipynb) [here](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/main/).
 
 ### GitHub
 
@@ -402,4 +401,4 @@ GitHub does some magic with particular filenames. In particular:
 ## Acknowledgements
 
 This CONTRIBUTING.md file, along with large sections of the code infrastructure,
-was copied from the excellent [Pints GitHub repo](https://github.com/pints-team/pints)
+was copied from the excellent [Pints GitHub repo](https://github.com/pints-team/pints)

README.md

@@ -11,7 +11,7 @@
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/main/)
 [![DOI](https://zenodo.org/badge/DOI/10.5334/jors.309.svg)](https://doi.org/10.5334/jors.309)
 [![release](https://img.shields.io/github/v/release/pybamm-team/PyBaMM?color=yellow)](https://github.com/pybamm-team/PyBaMM/releases)
-[![black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
+[![code style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
 [![All Contributors](https://img.shields.io/badge/all_contributors-60-orange.svg)](#-contributors)
@@ -82,7 +82,7 @@ sim.plot()
 
 However, much greater customisation is available. It is possible to change the physics, parameter values, geometry, submesh type, number of submesh points, methods for spatial discretisation and solver for integration (see DFN [script](https://github.com/pybamm-team/PyBaMM/blob/develop/examples/scripts/DFN.py) or [notebook](https://github.com/pybamm-team/PyBaMM/blob/develop/docs/source/examples/notebooks/models/DFN.ipynb)).
 
-For new users we recommend the [Getting Started](https://github.com/pybamm-team/PyBaMM/tree/develop/docs/source/examples/notebooks/getting_started/) guides. These are intended to be very simple step-by-step guides to show the basic functionality of PyBaMM, and can either be downloaded and used locally, or used online through [Google Colab](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/develop).
+For new users we recommend the [Getting Started](https://github.com/pybamm-team/PyBaMM/tree/develop/docs/source/examples/notebooks/getting_started/) guides. These are intended to be very simple step-by-step guides to show the basic functionality of PyBaMM, and can either be downloaded and used locally, or used online through [Google Colab](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/main/).
 
 Further details can be found in a number of [detailed examples](https://github.com/pybamm-team/PyBaMM/tree/develop/examples), hosted here on
 github. In addition, there is a [full API documentation](https://docs.pybamm.org/en/latest/source/api/index.html),
@@ -94,7 +94,7 @@ Note that the examples on the default `develop` branch are tested on the latest
 
 ## Versioning
 
-PyBaMM uses [CalVer](https://calver.org/), which means that we make new releases every month with the version number `YY.MM`. There is no difference between releases that increment the year and releases that increment the month; in particular, releases that increment the month may introduce breaking changes. Breaking changes for each release are communicated via the [CHANGELOG](CHANGELOG.md), and come with deprecation warnings or errors that are kept for at least one year (12 releases). If you find a breaking change that is not documented, or think it should be undone, please open an issue on [GitHub](https://github.com/pybamm-team/pybamm).
+PyBaMM makes releases every four months and we use [CalVer](https://calver.org/), which means that the version number is `YY.MM`. The releases happen, approximately, at the end of January, May and September. There is no difference between releases that increment the year and releases that increment the month; in particular, releases that increment the month may introduce breaking changes. Breaking changes for each release are communicated via the [CHANGELOG](CHANGELOG.md), and come with deprecation warnings or errors that are kept for at least one year (3 releases). If you find a breaking change that is not documented, or think it should be undone, please open an issue on [GitHub](https://github.com/pybamm-team/pybamm).
 
 ## 🚀 Installing PyBaMM
 

docs/source/_static/pybamm.css → docs/_static/pybamm.css

@@ -36,40 +36,6 @@ h3 {
   letter-spacing: -0.03em;
 }
 
-/* Style the active version button.
-
-- latest: orange
-- stable: green
-- old, PR: red
-
-Colors from:
-
-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 "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"] {
-  background-color: #009e73;
-  border-color: #009e73;
-}
-
-/* red for `old` */
-.version-switcher__button:not(
-    [data-active-version-name*="latest"],
-    [data-active-version-name*="stable"]
-  ) {
-  background-color: #980f0f;
-  border-color: #980f0f;
-}
-
 /* Main page overview cards */
 
 .sd-card {
@@ -167,3 +133,82 @@ html[data-theme="dark"] h3 {
 .tooltipster-sidetip.tooltipster-shadow.tooltipster-left .tooltipster-arrow-border {
   border-left-color: var(--pst-color-background) !important;
 }
+
+/* Custom styles for Algolia DocSearch v3 items and modals */
+/* to make them congruous with PST on light and dark themes */
+
+@import url("https://cdn.jsdelivr.net/npm/@docsearch/css@3");
+
+.DocSearch-Modal {
+  margin: 150px auto auto;
+  background: var(--pst-color-background);
+}
+
+.DocSearch-Container {
+  z-index: 2000;
+}
+
+kbd.DocSearch-Commands-Key {
+  border: 0;
+  box-shadow: var(--docsearch-key-shadow);
+  margin: 1px 5px 1px 0px;
+  padding: inherit;
+}
+
+.DocSearch-Button-Key {
+  width: 24px;
+}
+/* Do not add custom padding for keyboard buttons */
+
+kbd:not(.compound) {
+  padding: 0rem 0rem;
+}
+
+html[data-theme="dark"] kbd.DocSearch-Commands-Key {
+  color: var(--pst-color-border);
+}
+
+html[data-theme="dark"] .DocSearch-Commands-Key {
+  background: linear-gradient(-26.5deg,#30474f,#31355b)
+}
+
+.DocSearch-Hit-source {
+  background: var(--pst-color-background);
+}
+.DocSearch-Button {
+  border-radius: 6px;
+}
+
+.DocSearch-Footer {
+  background: var(--pst-color-background);
+}
+
+/* Should be for both light and dark */
+
+:root {
+  --docsearch-primary-color: var(--pst-color-info);
+  --docsearch-searchbox-focus-background: var(--pst-color-background);
+  --docsearch-footer-background: var(--pst-color-on-background)
+}
+
+/* Logo in dark theme */
+
+html[data-theme="dark"] .DocSearch-Logo svg path.cls-1,
+html[data-theme="dark"] .DocSearch-Logo svg path.cls-2,
+html[data-theme="dark"] .DocSearch-Logo svg rect.cls-1 {
+ fill: var(--pst-color-white);
+}
+
+/* Logo in light theme */
+
+html[data-theme="light"] .DocSearch-Logo svg path.cls-1,
+html[data-theme="light"] .DocSearch-Logo svg path.cls-2,
+html[data-theme="light"] .DocSearch-Logo svg rect.cls-1 {
+  fill: var(--pst-color-primary);
+}
+
+/* Search field dark theme corrections */
+
+html[data-theme="dark"] .DocSearch-Button {
+  background: var(--pst-color-on-surface);
+}

docs/_templates/algolia-searchbox.html

@@ -0,0 +1,4 @@
+<!-- Algolia overrides the PyData theme's searchbox with this template -->
+<div role="search">
+  <div id="algolia-docsearch"></div>
+</div>