Merge branch 'develop' into main-fix-merge

Author: priyanshuone6

.all-contributorsrc

@@ -293,7 +293,9 @@
       "contributions": [
         "test",
         "code",
-        "bug"
+        "bug",
+        "review",
+        "maintenance"
       ]
     },
     {
@@ -406,6 +408,16 @@
       "contributions": [
         "doc"
       ]
+    },
+    {
+      "login": "wigging",
+      "name": "Gavin Wiggins",
+      "avatar_url": "https://avatars.githubusercontent.com/u/6828967?v=4",
+      "profile": "https://gavinw.me",
+      "contributions": [
+        "bug",
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,6 +4,9 @@ about: Create a report to help us improve
 
 ---
 
+- PyBaMM version - `$ python -m pip show pybamm`:
+- Python version - `$ python --version`:
+
 **Describe the bug**
 A clear and concise description of what the bug is.
 

.github/workflows/update_vcpkg_baseline.yml

@@ -0,0 +1,42 @@
+name: Update vcpkg-configuration baseline
+
+on:
+  push:
+    branches:
+    - develop
+    paths:
+    - vcpkg-configuration.json
+  schedule:
+    # Run at 3 am UTC on 20th every month
+    - cron: 0 3 20 * *
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install wheel
+        pip install --editable .
+    - name: Update baseline
+      run: python scripts/update_vcpkg_baseline.py
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v3
+      with:
+        delete-branch: true
+        branch-suffix: short-commit-hash
+        commit-message: update baseline
+        title: Update vcpkg-configuration.json baseline
+        body: |
+            Update baseline of vcpkg-configuration.json with the latest commit id
+
+            Auto-generated pull request

CHANGELOG.md

@@ -1,3 +1,14 @@
+# [Unreleased](https://github.com/pybamm-team/PyBaMM)
+
+## Features
+
+-   Added `plot_summary_variables` to plot and compare summary variables ([#1678](https://github.com/pybamm-team/PyBaMM/pull/1678))
+-   The DFN model can now be used directly (instead of `BasicDFNHalfCell`) to simulate a half-cell ([#1600](https://github.com/pybamm-team/PyBaMM/pull/1600))
+
+## Breaking changes
+
+-   The substring 'negative electrode' has been removed from variables related to SEI and lithium plating (e.g. 'Total negative electrode SEI thickness [m]' replaced by 'Total SEI thickness [m]') ([#1654](https://github.com/pybamm-team/PyBaMM/pull/1654))
+
 # [v21.08](https://github.com/pybamm-team/PyBaMM/tree/v21.08) - 2021-08-26
 
 This release introduces:
@@ -57,6 +68,7 @@ example notebook ([#1602](https://github.com/pybamm-team/PyBaMM/pull/1602))
 -   Made parameters importable through pybamm ([#1475](https://github.com/pybamm-team/PyBaMM/pull/1475))
 
 ## Breaking changes
+
 -   Refactored the `particle` submodel module, with the models having no size distribution now found in `particle.no_distribution`, and those with a size distribution in `particle.size_distribution`. Renamed submodels to indicate the transport model (Fickian diffusion, polynomial profile) and if they are "x-averaged". E.g., `FickianManyParticles` and `FickianSingleParticle` are now `no_distribution.FickianDiffusion` and `no_distribution.XAveragedFickianDiffusion` ([#1602](https://github.com/pybamm-team/PyBaMM/pull/1602))
 -   Changed sensitivity API. Removed `ProcessedSymbolicVariable`, all sensitivity now handled within the solvers and `ProcessedVariable` ()  ([#1552](https://github.com/pybamm-team/PyBaMM/pull/1552))
 -   The `Yang2017` parameter set has been removed as the complete parameter set is not publicly available in the literature ([#1577](https://github.com/pybamm-team/PyBaMM/pull/1577))

FindSuiteSparse.cmake

@@ -64,7 +64,7 @@ find_library(SUITESPARSE_CONFIG_LIB
   PATH_SUFFIXES "lib" "lib32" "lib64" "Lib"
   NO_DEFAULT_PATH
 )
-# now also include the deafult paths
+# now also include the default paths
 find_library(SUITESPARSE_CONFIG_LIB
   NAMES "suitesparseconfig"
   PATH_SUFFIXES "lib" "lib32" "lib64" "Lib"
@@ -93,7 +93,7 @@ foreach(_component ${SUITESPARSE_COMPONENTS})
     PATH_SUFFIXES "lib" "lib32" "lib64" "${_component}" "${_component}/Lib"
     NO_DEFAULT_PATH
   )
-  #now  also include the deafult paths
+  #now  also include the default paths
   find_library(${_component}_LIBRARY
     NAMES "${_componentLower}"
     PATH_SUFFIXES "lib" "lib32" "lib64" "${_component}" "${_component}/Lib"

README.md

@@ -11,7 +11,7 @@
 [![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)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-35-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-36-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -69,12 +69,19 @@ We strongly recommend to install PyBaMM within a python virtual environment, in
 For instructions on how to create a virtual environment for PyBaMM, see [the documentation](https://pybamm.readthedocs.io/en/latest/install/GNU-linux.html#user-install).
 
 ### Using pip
+[![pypi](https://img.shields.io/pypi/v/pybamm?color=blue)](https://pypi.org/project/pybamm/)
+[![downloads](https://img.shields.io/pypi/dm/pybamm?color=blue)](https://pypi.org/project/pybamm/)
+
 ```bash
 pip install pybamm
 ```
 
 ### Using conda
 PyBaMM is available as a conda package through the conda-forge channel.
+
+[![conda_forge](https://img.shields.io/conda/vn/conda-forge/pybamm?color=green)](https://anaconda.org/conda-forge/pybamm)
+[![downloads](https://img.shields.io/conda/dn/conda-forge/pybamm?color=green)](https://anaconda.org/conda-forge/pybamm)
+
 ```bash
 conda install -c conda-forge pybamm
 ```
@@ -163,7 +170,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
   <tr>
     <td align="center"><a href="https://github.com/weilongai"><img src="https://avatars1.githubusercontent.com/u/41424174?v=4?s=100" width="100px;" alt=""/><br /><sub><b>WEILONG AI</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=weilongai" title="Code">💻</a> <a href="#example-weilongai" title="Examples">💡</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=weilongai" title="Tests">⚠️</a></td>
     <td align="center"><a href="https://github.com/lonnbornj"><img src="https://avatars2.githubusercontent.com/u/35983543?v=4?s=100" width="100px;" alt=""/><br /><sub><b>lonnbornj</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=lonnbornj" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=lonnbornj" title="Tests">⚠️</a> <a href="#example-lonnbornj" title="Examples">💡</a></td>
-    <td align="center"><a href="https://github.com/priyanshuone6"><img src="https://avatars.githubusercontent.com/u/64051212?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Priyanshu Agarwal</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=priyanshuone6" title="Tests">⚠️</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=priyanshuone6" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Apriyanshuone6" title="Bug reports">🐛</a></td>
+    <td align="center"><a href="https://github.com/priyanshuone6"><img src="https://avatars.githubusercontent.com/u/64051212?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Priyanshu Agarwal</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=priyanshuone6" title="Tests">⚠️</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=priyanshuone6" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Apriyanshuone6" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/pulls?q=is%3Apr+reviewed-by%3Apriyanshuone6" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-priyanshuone6" title="Maintenance">🚧</a></td>
     <td align="center"><a href="https://github.com/DrSOKane"><img src="https://avatars.githubusercontent.com/u/42972513?v=4?s=100" width="100px;" alt=""/><br /><sub><b>DrSOKane</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=DrSOKane" title="Code">💻</a> <a href="#example-DrSOKane" title="Examples">💡</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=DrSOKane" title="Documentation">📖</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=DrSOKane" title="Tests">⚠️</a></td>
     <td align="center"><a href="https://github.com/Saransh-cpp"><img src="https://avatars.githubusercontent.com/u/74055102?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Saransh Chopra</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=Saransh-cpp" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=Saransh-cpp" title="Tests">⚠️</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=Saransh-cpp" title="Documentation">📖</a></td>
     <td align="center"><a href="https://github.com/DavidMStraub"><img src="https://avatars.githubusercontent.com/u/10965193?v=4?s=100" width="100px;" alt=""/><br /><sub><b>David Straub</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3ADavidMStraub" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=DavidMStraub" title="Code">💻</a></td>
@@ -178,6 +185,9 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="https://github.com/chuckliu1979"><img src="https://avatars.githubusercontent.com/u/13491954?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chuck Liu</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achuckliu1979" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=chuckliu1979" title="Code">💻</a></td>
     <td align="center"><a href="https://github.com/partben"><img src="https://avatars.githubusercontent.com/u/88316576?v=4?s=100" width="100px;" alt=""/><br /><sub><b>partben</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=partben" title="Documentation">📖</a></td>
   </tr>
+  <tr>
+    <td align="center"><a href="https://gavinw.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
+  </tr>
 </table>
 
 <!-- markdownlint-restore -->

docs/source/models/lithium_ion/electrode_soh.rst

@@ -0,0 +1,10 @@
+Electrode SOH models
+====================
+
+.. autoclass:: pybamm.lithium_ion.ElectrodeSOH
+    :members:
+
+.. autoclass:: pybamm.lithium_ion.ElectrodeSOHHalfCell
+    :members:
+
+.. autofunction:: pybamm.lithium_ion.get_initial_stoichiometries

docs/source/models/lithium_ion/index.rst

@@ -10,3 +10,4 @@ Lithium-ion Models
   dfn
   newman_tobias
   yang2017
+  electrode_soh

docs/source/models/submodels/electrode/ohm/index.rst

@@ -8,3 +8,4 @@ Ohmic
   composite_ohm
   full_ohm
   surface_form_ohm
+  li_metal_explicit

docs/source/models/submodels/electrode/ohm/li_metal_explicit.rst

@@ -0,0 +1,5 @@
+Explicit potential drop for lithium metal
+=========================================
+
+.. autoclass:: pybamm.electrode.ohm.LithiumMetalExplicit
+    :members: