Merge branch 'develop' into i2376-bpx

.all-contributorsrc

@@ -521,6 +521,26 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "agriyakhetarpal",
+      "name": "Agriya Khetarpal",
+      "avatar_url": "https://avatars.githubusercontent.com/u/74401230?v=4",
+      "profile": "https://github.com/agriyakhetarpal",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "awadell1",
+      "name": "Alex Wadell",
+      "avatar_url": "https://avatars.githubusercontent.com/u/5857298?v=4",
+      "profile": "https://github.com/awadell1",
+      "contributions": [
+        "code",
+        "test",
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/ISSUE_TEMPLATE/new_parameter_set.yml

@@ -0,0 +1,28 @@
+name: New Parameter Set
+description: Add a third party parameter set to PyBaMM's documentation
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Third-party parameter sets can be added to PyBaMM by registering an entry
+        point with `pybamm-parameter-sets` as described in our
+        [documentation](https://pybamm.readthedocs.io/en/latest/source/parameters/parameter_sets.html).
+  - type: input
+    id: parameter-set-url
+    attributes:
+      label: Where can we find your parameter set?
+      description: Provide the Github URL or PyPi package name for your parameter set
+      placeholder: https://github.com/AwesomeOrg/NewParameterSet
+    validations:
+      required: true
+  - type: dropdown
+    id: open-source-approved
+    attributes:
+      label: Is your package open source?
+      description: See the [Open Source Initiative's List of Approved Licenses](https://opensource.org/licenses)
+      options: ["Yes", "No"]
+  - type: textarea
+    id: feedback
+    attributes:
+      label: Any additional information?
+      description: Thank you for making parameter set! Is there anything else we should know about it?

.github/workflows/test_on_push.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Setup python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.9
 
       - name: Check style
         run: |
@@ -46,7 +46,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9]
 
     steps:
       - uses: actions/checkout@v3
@@ -96,7 +96,7 @@ jobs:
         if: matrix.os != 'windows-latest'
         run: tox -e julia
 
-      - name: Run unit tests for GNU/Linux with Python 3.7 and 3.8
+      - name: Run unit tests for GNU/Linux with Python 3.8
         if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.9
         run: python -m tox -e unit
 

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.2
+    rev: v3.0.0-alpha.3
     hooks:
       - id: prettier
         exclude: assets/js/webapp\.js

.readthedocs.yml

@@ -16,3 +16,5 @@ python:
   version: 3.8
   install:
     - requirements: docs/requirements.txt
+    - method: pip
+      path: .

CHANGELOG.md

@@ -1,18 +1,30 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v22.10](https://github.com/pybamm-team/PyBaMM/tree/v22.10) - 2022-10-31
+
+## Features
+
+- Third-party parameter sets can be added by registering entry points to `pybamm_parameter_set` ([#2396](https://github.com/pybamm-team/PyBaMM/pull/2396))
+- Added three-dimensional interpolation ([#2380](https://github.com/pybamm-team/PyBaMM/pull/2380))
+
 ## Bug fixes
 
+- `pybamm.have_julia()` now checks that julia is properly configured ([#2402](https://github.com/pybamm-team/PyBaMM/pull/2402))
 - For simulations with events that cause the simulation to stop early, the sensitivities could be evaluated incorrectly to zero ([#2337](https://github.com/pybamm-team/PyBaMM/pull/2337))
 
 ## Optimizations
 
+- Reformatted how simulations with experiments are built ([#2395](https://github.com/pybamm-team/PyBaMM/pull/2395))
 - Added small perturbation to initial conditions for casadi solver. This seems to help the solver converge better in some cases ([#2356](https://github.com/pybamm-team/PyBaMM/pull/2356))
 - Added `ExplicitTimeIntegral` functionality to move variables which do not appear anywhere on the rhs to a new location, and to integrate those variables explicitly when `get` is called by the solution object. ([#2348](https://github.com/pybamm-team/PyBaMM/pull/2348))
 - Added more rules for simplifying expressions ([#2211](https://github.com/pybamm-team/PyBaMM/pull/2211))
 - Sped up calculations of Electrode SOH variables for summary variables ([#2210](https://github.com/pybamm-team/PyBaMM/pull/2210))
 
 ## Breaking change
 
+- Removed `pybamm.SymbolReplacer` as it is no longer needed to set up simulations with experiments, which is the only place where it was being used ([#2395](https://github.com/pybamm-team/PyBaMM/pull/2395))
+- Removed `get_infinite_nested_dict`, `BaseModel.check_default_variables_dictionaries`, and `Discretisation.create_jacobian` methods, which were not used by any other functionality in the repository ([#2384](https://github.com/pybamm-team/PyBaMM/pull/2384))
+- Dropped support for Python 3.7 after the release of Numpy v1.22.0 ([#2379](https://github.com/pybamm-team/PyBaMM/pull/2379))
 - Removed parameter cli tools (add/edit/remove parameters). Parameter sets can now more easily be added via python scripts. ([#2342](https://github.com/pybamm-team/PyBaMM/pull/2342))
 - Parameter sets should now be provided as single python files containing all parameters and functions. Parameters provided as "data" (e.g. OCP vs SOC) can still be csv files, but must be either in the same folder as the parameter file or in a subfolder called "data/". See for example [Ai2020](https://github.com/pybamm-team/PyBaMM/tree/develop/pybamm/input/parameters/lithium_ion/Ai2020.py) ([#2342](https://github.com/pybamm-team/PyBaMM/pull/2342))
 

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "22.9"
+version: "22.10"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

CONTRIBUTING.md

@@ -295,7 +295,7 @@ PyBaMM is documented in several ways.
 
 First and foremost, every method and every class should have a [docstring](https://www.python.org/dev/peps/pep-0257/) that describes in plain terms what it does, and what the expected input and output is.
 
-These docstrings can be fairly simple, but can also make use of [reStructuredText](http://docutils.sourceforge.net/docs/user/rst/quickref.html), a markup language designed specifically for writing [technical documentation](https://en.wikipedia.org/wiki/ReStructuredText). For example, you can link to other classes and methods by writing `` :class:`pybamm.Model`  `` and `` :meth:`run()`  ``.
+These docstrings can be fairly simple, but can also make use of [reStructuredText](http://docutils.sourceforge.net/docs/user/rst/quickref.html), a markup language designed specifically for writing [technical documentation](https://en.wikipedia.org/wiki/ReStructuredText). For example, you can link to other classes and methods by writing ``:class:`pybamm.Model` `` and ``:meth:`run()` ``.
 
 In addition, we write a (very) small bit of documentation in separate reStructuredText files in the `docs` directory. Most of what these files do is simply import docstrings from the source code. But they also do things like add tables and indexes. If you've added a new class to a module, search the `docs` directory for that module's `.rst` file and add your class (in alphabetical order) to its index. If you've added a whole new module, copy-paste another module's file and add a link to your new file in the appropriate `index.rst` file.
 

README.md

@@ -14,7 +14,7 @@
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
 
-[![All Contributors](https://img.shields.io/badge/all_contributors-46-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-48-orange.svg)](#-contributors)
 
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
@@ -214,6 +214,8 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center"><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"><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"><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"><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></td>
+      <td align="center"><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>
     </tr>
   </tbody>
 </table>

docs/conf.py

@@ -14,7 +14,7 @@
 #
 import os
 import sys
-
+import pybamm
 import guzzle_sphinx_theme
 
 sys.path.insert(0, os.path.abspath("../"))
@@ -27,7 +27,7 @@
 author = "The PyBaMM Team"
 
 # The short X.Y version
-version = "22.9"
+version = "22.10"
 # The full version, including alpha/beta/rc tags
 release = version
 
@@ -213,3 +213,28 @@
     # "scipy": ("http://docs.scipy.org/doc/scipy/reference", None),
     "matplotlib": ("https://matplotlib.org", None),
 }
+
+# -- Jinja templating --------------------------------------------------------
+# Credit to: https://ericholscher.com/blog/2016/jul/25/integrating-jinja-rst-sphinx/
+
+
+def rstjinja(app, docname, source):
+    """
+    Render our pages as a jinja template for fancy templating goodness.
+    """
+    # Make sure we're outputting HTML
+    if app.builder.format != "html":
+        return
+    src = source[0]
+    rendered = app.builder.templates.render_string(src, app.config.html_context)
+    source[0] = rendered
+
+
+def setup(app):
+    app.connect("source-read", rstjinja)
+
+
+# Context for Jinja Templates
+html_context = {
+    "parameter_sets": pybamm.parameter_sets,
+}

docs/index.rst

@@ -101,9 +101,8 @@ There are many ways to contribute to PyBaMM:
 .. toctree::
     :maxdepth: 1
 
-    tutorials/add-parameter-values
     tutorials/add-model
     tutorials/add-spatial-method
     tutorials/add-solver
 
-Before contributing, please read the `Contribution Guidelines <https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md>`_.
+Before contributing, please read the `Contribution Guidelines <https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md>`_.

docs/install/GNU-linux.rst

@@ -7,7 +7,7 @@
 Prerequisites
 =============
 
-To use and/or contribute to PyBaMM, you must have Python 3.7, 3.8, or 3.9 installed.
+To use and/or contribute to PyBaMM, you must have Python 3.8 or 3.9 installed.
 
 To install Python 3 on Debian-based distribution (Debian, Ubuntu, Linux
 mint), open a terminal and run
@@ -46,7 +46,7 @@ User install
 
 We recommend to install PyBaMM within a virtual environment, in order
 not to alter any distribution python files.
-First, make sure you are using python 3.7, 3.8, or 3.9.
+First, make sure you are using python 3.8 or 3.9.
 To create a virtual environment ``env`` within your current directory type:
 
 .. code:: bash

docs/install/install-from-source.rst

@@ -25,7 +25,7 @@ or download the source archive on the repository's homepage.
 
 To install PyBaMM, you will need:
 
-- Python 3 (PyBaMM supports versions 3.7, 3.8, and 3.9)
+- Python 3 (PyBaMM supports versions 3.8 and 3.9)
 - The python headers file for your current python version.
 - A BLAS library (for instance `openblas <https://www.openblas.net/>`_).
 - A C compiler (ex: ``gcc``).
@@ -177,7 +177,7 @@ The default command
 will run the full test suite (integration and unit tests).
 This can take several minutes.
 
-Is is often sufficient to run the unit tests only. To do so, use
+It is often sufficient to run the unit tests only. To do so, use
 
    .. code:: bash
 

docs/install/windows.rst

@@ -6,13 +6,13 @@ Windows
 Prerequisites
 -------------
 
-To use and/or contribute to PyBaMM, you must have Python 3.7, 3.8, or 3.9 installed.
+To use and/or contribute to PyBaMM, you must have Python 3.8 or 3.9 installed.
 
 To install Python 3 download the installation files from `Python’s
 website <https://www.python.org/downloads/windows/>`__. Make sure to
 tick the box on ``Add Python 3.X to PATH``. For more detailed
 instructions please see the `official Python on Windows
-guide <https://docs.python.org/3.7/using/windows.html>`__.
+guide <https://docs.python.org/3.9/using/windows.html>`__.
 
 Install PyBaMM
 --------------