Merge pull request #1879 from pybamm-team/develop

Make release 21.12

.all-contributorsrc

@@ -344,7 +344,8 @@
         "test",
         "doc",
         "tutorial",
-        "review"
+        "review",
+        "maintenance"
       ]
     },
     {
@@ -445,6 +446,25 @@
         "bug",
         "code"
       ]
+    },
+    {
+      "login": "dion-w",
+      "name": "Dion Wilde",
+      "avatar_url": "https://avatars.githubusercontent.com/u/91852142?v=4",
+      "profile": "https://github.com/dion-w",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "ehtec",
+      "name": "Elias Hohl",
+      "avatar_url": "https://avatars.githubusercontent.com/u/48386220?v=4",
+      "profile": "https://www.ehtec.co",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/release_checklist.md

@@ -4,4 +4,4 @@
   - `CITATION.cff`
   - `vcpkg.json`
 - Update CHANGELOG.md with a summary of the release
-- Update jax and jaxlib to latest version in `pybamm.util.install_jax` and fix any bugs that arise
+- Update jax and jaxlib to latest version in `pybamm.util` and fix any bugs that arise

.github/workflows/build_sdist.yml

@@ -11,25 +11,21 @@ on:
     types: [completed]
 
 jobs:
-  # If build_wheels fails, exit this workflow
-  exit-workflow:
-    name: Exit workflow if build_wheels fails
-    runs-on: ubuntu-latest
-    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
-    steps:
-      - run: exit 1
-
 
-  build_sdist:
+  build-sdist:
     name: Build sdist
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: [3.8]
-    if: |
-      ${{ github.event.workflow_run.conclusion == 'success' }} ||
-      github.event_name == 'workflow_dispatch'
+
     steps:
+      - name: Fail the job if build_wheels fails
+        if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+        uses: actions/github-script@v5
+        with:
+          script: core.setFailed('workflow build_wheels failed')
+
       - uses: actions/checkout@v2
 
       - name: Set up Python ${{ matrix.python-version }}
@@ -53,7 +49,7 @@ jobs:
 
   publish-pypi:
     name: Upload sdist to PyPI
-    needs: build_sdist
+    needs: build-sdist
     runs-on: ubuntu-latest
     steps:
       - name: Download sdist

.github/workflows/test_on_push.yml

@@ -1,8 +1,7 @@
 name: PyBaMM
 
 on:
-  push:
-
+  workflow_dispatch:
   pull_request:
 
   # everyday at 3 am UTC
@@ -11,7 +10,23 @@ on:
 
 jobs:
 
+  pre_job:
+    runs-on: ubuntu-latest
+    # Map a step output to a job output
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          # All of these options are optional, so you can remove them if you are happy with the defaults
+          concurrent_skipping: 'never'
+          cancel_others: 'true'
+          paths_ignore: '["**/README.md"]'
+
   style:
+    needs: pre_job
+    if: ${{ needs.pre_job.outputs.should_skip != 'true' }}
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
@@ -80,6 +95,10 @@ jobs:
       if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
       run: tox -e coverage
 
+    - name: Upload coverage report
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
+      uses: codecov/[email protected]
+
     - name: Run integration tests for GNU/Linux
       if: matrix.os == 'ubuntu-latest'
       run: python -m tox -e integration
@@ -100,6 +119,3 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       run: tox -e examples
 
-    - name: Upload coverage report
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
-      uses: codecov/[email protected]

CHANGELOG.md

@@ -1,8 +1,24 @@
+# [v21.12](https://github.com/pybamm-team/PyBaMM/tree/v21.11) - 2021-12-29
+
+## Features
+
+-   Added new kinetics models for asymmetric Butler-Volmer, linear kinetics, and Marcus-Hush-Chidsey ([#1858](https://github.com/pybamm-team/PyBaMM/pull/1858))
+-   Experiments can be set to terminate when a voltage is reached (across all steps) ([#1832](https://github.com/pybamm-team/PyBaMM/pull/1832))
+-   Added cylindrical geometry and finite volume method ([#1824](https://github.com/pybamm-team/PyBaMM/pull/1824))
+
+## Bug fixes
+
+-   `PyBaMM` is now importable in `Linux` systems where `jax` is already installed ([#1874](https://github.com/pybamm-team/PyBaMM/pull/1874))
+-   Simulations with drive cycles now support `initial_soc` ([#1842](https://github.com/pybamm-team/PyBaMM/pull/1842))
+-   Fixed bug in expression tree simplification ([#1831](https://github.com/pybamm-team/PyBaMM/pull/1831))
+-   Solid tortuosity is now correctly calculated with Bruggeman coefficient of the respective electrode ([#1773](https://github.com/pybamm-team/PyBaMM/pull/1773))
+
 # [v21.11](https://github.com/pybamm-team/PyBaMM/tree/v21.11) - 2021-11-30
 
 ## Features
 
 -   The name of a parameter set can be passed to `ParameterValues` as a string, e.g. `ParameterValues("Chen2020")` ([#1822](https://github.com/pybamm-team/PyBaMM/pull/1822))
+-   Added submodels for interface utilisation ([#1821](https://github.com/pybamm-team/PyBaMM/pull/1821))
 -   Reformatted SEI growth models into a single submodel with conditionals ([#1808](https://github.com/pybamm-team/PyBaMM/pull/1808))
 -   Stress-induced diffusion is now a separate model option instead of being automatically included when using the particle mechanics submodels ([#1797](https://github.com/pybamm-team/PyBaMM/pull/1797))
 -   `Experiment`s with drive cycles can be solved ([#1793](https://github.com/pybamm-team/PyBaMM/pull/1793))
@@ -22,7 +38,7 @@
 -   The `chemistry` keyword argument in `ParameterValues` has been deprecated. Use `ParameterValues(chem)` instead of `ParameterValues(chemistry=chem)` ([#1822](https://github.com/pybamm-team/PyBaMM/pull/1822))
 -   Raise error when trying to convert an `Interpolant` with the "pchip" interpolator to CasADI ([#1791](https://github.com/pybamm-team/PyBaMM/pull/1791))
 -   Raise error if `Concatenation` is used directly with `Variable` objects (`concatenation` should be used instead) ([#1789](https://github.com/pybamm-team/PyBaMM/pull/1789))
--   Made jax, jaxlib and the PyBaMM JaxSolver optional ([#1767](https://github.com/pybamm-team/PyBaMM/pull/1767))
+-   Made jax, jaxlib and the PyBaMM JaxSolver optional ([#1767](https://github.com/pybamm-team/PyBaMM/pull/1767), [#1803](https://github.com/pybamm-team/PyBaMM/pull/1803))
 
 # [v21.10](https://github.com/pybamm-team/PyBaMM/tree/v21.10) - 2021-10-31
 

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "21.11"
+version: "21.12"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

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-38-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-40-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -176,7 +176,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <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> <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> <a href="#tutorial-priyanshuone6" title="Tutorials">✅</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> <a href="#tutorial-DrSOKane" title="Tutorials">✅</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> <a href="#tutorial-Saransh-cpp" title="Tutorials">✅</a> <a href="https://github.com/pybamm-team/PyBaMM/pulls?q=is%3Apr+reviewed-by%3ASaransh-cpp" title="Reviewed Pull Requests">👀</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> <a href="#tutorial-Saransh-cpp" title="Tutorials">✅</a> <a href="https://github.com/pybamm-team/PyBaMM/pulls?q=is%3Apr+reviewed-by%3ASaransh-cpp" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-Saransh-cpp" title="Maintenance">🚧</a></td>
   </tr>
   <tr>
     <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>
@@ -191,6 +191,8 @@ 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>
     <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>
+    <td align="center"><a href="https://github.com/dion-w"><img src="https://avatars.githubusercontent.com/u/91852142?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Dion Wilde</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Adion-w" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=dion-w" title="Code">💻</a></td>
+    <td align="center"><a href="https://www.ehtec.co"><img src="https://avatars.githubusercontent.com/u/48386220?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Elias Hohl</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=ehtec" title="Code">💻</a></td>
   </tr>
 </table>
 

docs/conf.py

@@ -26,9 +26,9 @@
 author = "The PyBaMM Team"
 
 # The short X.Y version
-version = "21.11"
+version = "21.12"
 # The full version, including alpha/beta/rc tags
-release = "21.11"
+release = "21.12"
 
 
 # -- General configuration ---------------------------------------------------

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

@@ -8,6 +8,5 @@ Submodels for (loss of) active material
 
   base_active_material
   constant_active_material
-  reaction_driven_active_material
-  stress_driven_active_material
+  loss_active_material
 

docs/source/models/submodels/active_material/loss_active_material.rst

@@ -0,0 +1,8 @@
+Loss of Active Material 
+=======================
+
+.. autoclass:: pybamm.active_material.LossActiveMaterial
+    :members:
+
+
+

docs/source/models/submodels/interface/diffusion_limited.rst

@@ -1,5 +1,5 @@
 Diffusion-limited
 =================
 
-.. autoclass:: pybamm.interface.DiffusionLimited
+.. autoclass:: pybamm.kinetics.DiffusionLimited
     :members:

docs/source/models/submodels/interface/first_order_kinetics.rst

@@ -1,8 +1,8 @@
 First-order Kinetics
 ====================
 
-.. autoclass:: pybamm.interface.FirstOrderKinetics
+.. autoclass:: pybamm.kinetics.FirstOrderKinetics
     :members:
 
-.. autoclass:: pybamm.interface.InverseFirstOrderKinetics
+.. autoclass:: pybamm.kinetics.InverseFirstOrderKinetics
     :members:

docs/source/models/submodels/interface/inverse_butler_volmer.rst

@@ -1,5 +1,5 @@
 Inverse Butler-Volmer
 =====================
 
-.. autoclass:: pybamm.interface.inverse_kinetics.InverseButlerVolmer
+.. autoclass:: pybamm.kinetics.InverseButlerVolmer
     :members:

docs/source/models/submodels/interface/kinetics.rst

@@ -1,16 +1,28 @@
 Kinetics
 ========
 
-.. autoclass:: pybamm.interface.BaseKinetics
+.. autoclass:: pybamm.kinetics.BaseKinetics
     :members:
 
-.. autoclass:: pybamm.interface.ButlerVolmer
+.. autoclass:: pybamm.kinetics.SymmetricButlerVolmer
     :members:
 
-.. autoclass:: pybamm.interface.NoReaction
+.. autoclass:: pybamm.kinetics.AsymmetricButlerVolmer
     :members:
 
-.. autoclass:: pybamm.interface.ForwardTafel
+.. autoclass:: pybamm.kinetics.Linear
+    :members:
+
+.. autoclass:: pybamm.kinetics.Marcus
+    :members:
+
+.. autoclass:: pybamm.kinetics.MarcusHushChidsey
+    :members:
+
+.. autoclass:: pybamm.kinetics.NoReaction
+    :members:
+
+.. autoclass:: pybamm.kinetics.ForwardTafel
     :members:
 
 .. .. autoclass:: pybamm.interface.BackwardTafel

examples/notebooks/Creating Models/1-an-ode-model.ipynb

@@ -296,7 +296,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -310,7 +310,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,

examples/notebooks/Creating Models/2-a-pde-model.ipynb

@@ -340,7 +340,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
   },
   "toc": {
    "base_numbering": 1,

examples/notebooks/Creating Models/3-negative-particle-problem.ipynb

@@ -362,7 +362,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
   },
   "toc": {
    "base_numbering": 1,

examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb

@@ -422,7 +422,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
   },
   "toc": {
    "base_numbering": 1,

examples/notebooks/Creating Models/5-half-cell-model.ipynb

@@ -648,7 +648,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.0"
   },
   "toc": {
    "base_numbering": 1,

examples/notebooks/Creating Models/6-a-simple-SEI-model.ipynb

@@ -728,7 +728,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -742,7 +742,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,