#2382 merge develop

.all-contributorsrc

@@ -530,6 +530,17 @@
       "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

@@ -55,12 +55,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Set up Julia
-        if: matrix.os != 'windows-latest'
-        uses: julia-actions/setup-julia@v1
-        with:
-          version: 1.7
-
       - name: Install Linux system dependencies
         if: matrix.os == 'ubuntu-latest'
         run: |
@@ -92,10 +86,6 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: tox -e pybamm-requires
 
-      - name: Install Julia
-        if: matrix.os != 'windows-latest'
-        run: tox -e julia
-
       - 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

.gitignore

@@ -112,9 +112,6 @@ test.json
 # tox
 .tox/
 
-# julia
-Manifest.toml
-
 # vcpkg
 vcpkg_installed/
 

.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.4
     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 +1,50 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+## Features
+
+- Added `scale` and `reference` attributes to `Variable` objects, which can be use to make the ODE/DAE solver better conditioned ([#2440](https://github.com/pybamm-team/PyBaMM/pull/2440))
+- SEI reactions can now be asymmetric ([#2425](https://github.com/pybamm-team/PyBaMM/pull/2425))
+
+## Optimizations
+
+- Added more rules for simplifying expressions, especially around Concatenations. Also, meshes constructed from multiple domains are now cached ([#2443](https://github.com/pybamm-team/PyBaMM/pull/2443))
+- Added more rules for simplifying expressions. Constants in binary operators are now moved to the left by default (e.g. `x*2` returns `2*x`) ([#2424](https://github.com/pybamm-team/PyBaMM/pull/2424))
+
+## Breaking changes
+
+- Renamed entry point for parameter sets to `pybamm_parameter_sets` ([#2475](https://github.com/pybamm-team/PyBaMM/pull/2475))
+- Removed code for generating `ModelingToolkit` problems ([#2432](https://github.com/pybamm-team/PyBaMM/pull/2432))
+- Removed `FirstOrder` and `Composite` lead-acid models, and some submodels specific to those models ([#2431](https://github.com/pybamm-team/PyBaMM/pull/2431))
+
+# [v22.10.post1](https://github.com/pybamm-team/PyBaMM/tree/v22.10.post1) - 2022-10-31
+
+## Breaking changes
+
+- Removed all julia generation code ([#2453](https://github.com/pybamm-team/PyBaMM/pull/2453)). Julia code will be hosted at [PyBaMM.jl](https://github.com/tinosulzer/PyBaMM.jl) from now on.
+
+# [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`~~`pybamm_parameter_sets` ([#2396](https://github.com/pybamm-team/PyBaMM/pull/2396), changed in [#2475](https://github.com/pybamm-team/PyBaMM/pull/2475))
+- 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))

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-47-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-48-orange.svg)](#-contributors)
 
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
@@ -68,7 +68,9 @@ Additional supporting material can be found
 
 Note that the examples on the default `develop` branch are tested on the latest `develop` commit. This may sometimes cause errors when running the examples on the pybamm pip package, which is synced to the `main` branch. You can switch to the `main` branch on github to see the version of the examples that is compatible with the latest pip release.
 
-<!-- For further examples, see the list of repositories that use PyBaMM [here](https://github.com/pybamm-team/pybamm-example-results). -->
+## 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).
 
 ## 🚀 Installing PyBaMM
 
@@ -215,6 +217,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <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>

benchmarks/different_model_options.py

@@ -124,10 +124,12 @@ class TimeBuildModelSEI:
             "none",
             "constant",
             "reaction limited",
+            "reaction limited (asymmetric)",
             "solvent-diffusion limited",
             "electron-migration limited",
             "interstitial-diffusion limited",
             "ec reaction limited",
+            "ec reaction limited (asymmetric)",
         ],
     )
 
@@ -143,10 +145,12 @@ class TimeSolveSEI:
             "none",
             "constant",
             "reaction limited",
+            "reaction limited (asymmetric)",
             "solvent-diffusion limited",
             "electron-migration limited",
             "interstitial-diffusion limited",
             "ec reaction limited",
+            "ec reaction limited (asymmetric)",
         ],
     )
 

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/source/models/lead_acid/index.rst

@@ -6,5 +6,4 @@ Lead Acid Models
 
   base_lead_acid_model
   loqs
-  higher_order
   full

docs/source/models/submodels/current_collector/index.rst

@@ -5,8 +5,6 @@ Current Collector
   :maxdepth: 1
 
   base_current_collector
-  composite_potential_pair
   effective_resistance_current_collector
   homogeneous_current_collector
   potential_pair
-  quite_conductive_potential_pair

docs/source/models/submodels/electrolyte_diffusion/index.rst

@@ -6,5 +6,4 @@ Electrolyte Diffusion
   base_electrolyte_diffusion
   constant_concentration
   leading_order_diffusion
-  composite_diffusion
   full_diffusion