Merge branch 'develop' into i3558-repair-wheel

.all-contributorsrc

@@ -727,6 +727,43 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "chmabaur",
+      "name": "chmabaur",
+      "avatar_url": "https://avatars.githubusercontent.com/u/127507466?v=4",
+      "profile": "https://github.com/chmabaur",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "AbhishekChaudharii",
+      "name": "Abhishek Chaudhari",
+      "avatar_url": "https://avatars.githubusercontent.com/u/91185083?v=4",
+      "profile": "https://github.com/AbhishekChaudharii",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "shubhambhar007",
+      "name": "Shubham Bhardwaj",
+      "avatar_url": "https://avatars.githubusercontent.com/u/32607282?v=4",
+      "profile": "https://github.com/shubhambhar007",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "jlauber18",
+      "name": "Jonathan Lauber",
+      "avatar_url": "https://avatars.githubusercontent.com/u/28939653?v=4",
+      "profile": "https://github.com/jlauber18",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/benchmark_on_push.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

.github/workflows/docker.yml

@@ -48,8 +48,7 @@ jobs:
             echo "tag=all" >> "$GITHUB_OUTPUT"
           fi
 
-      - name: Build and push Docker image to Docker Hub (no solvers)
-        if: matrix.build-args == 'No solvers'
+      - name: Build and push Docker image to Docker Hub (${{ matrix.build-args }})
         uses: docker/build-push-action@v5
         with:
           context: .
@@ -58,29 +57,5 @@ jobs:
           push: true
           platforms: linux/amd64, linux/arm64
 
-      - name: Build and push Docker image to Docker Hub (with ODES and IDAKLU solvers)
-        if: matrix.build-args == 'ODES' || matrix.build-args == 'IDAKLU'
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: scripts/Dockerfile
-          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
-          push: true
-          build-args: ${{ matrix.build-args }}=true
-          platforms: linux/amd64, linux/arm64
-
-      - name: Build and push Docker image to Docker Hub (with ALL and JAX solvers)
-        if: matrix.build-args == 'ALL' || matrix.build-args == 'JAX'
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: scripts/Dockerfile
-          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
-          push: true
-          build-args: ${{ matrix.build-args }}=true
-          # exclude arm64 for JAX and ALL builds for now, see
-          # https://github.com/google/jax/issues/13608
-          platforms: linux/amd64
-
       - name: List built image(s)
         run: docker images

.github/workflows/periodic_benchmarks.yml

@@ -22,7 +22,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -59,7 +59,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

.github/workflows/publish_pypi.yml

@@ -33,7 +33,7 @@ jobs:
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -87,7 +87,7 @@ jobs:
       - uses: actions/checkout@v4
         name: Check out PyBaMM repository
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Set up Python
         with:
           python-version: 3.8
@@ -139,7 +139,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.github/workflows/release_reminder.yml

@@ -11,6 +11,7 @@ permissions:
 
 jobs:
   remind:
+    if: github.repository_owner == 'pybamm-team'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/run_benchmarks_over_history.yml

@@ -24,7 +24,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: Install nox and asv
@@ -48,12 +48,13 @@ jobs:
           path: results
 
   publish-results:
+    if: github.repository_owner == 'pybamm-team'
     name: Push and publish results
     needs: benchmarks
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: Install asv

.github/workflows/run_periodic_tests.yml

@@ -29,13 +29,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
       - name: Check style
         run: |
           python -m pip install pre-commit
+          git add .
           pre-commit run ruff
 
   build:
@@ -50,7 +51,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -112,6 +113,7 @@ jobs:
 
   #M-series Mac Mini
   build-apple-mseries:
+    if: github.repository_owner == 'pybamm-team'
     needs: style
     runs-on: [self-hosted, macOS, ARM64]
     env:

.github/workflows/test_on_push.yml

@@ -21,13 +21,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
       - name: Check style
         run: |
           python -m pip install pre-commit
+          git add .
           pre-commit run ruff
 
   run_unit_tests:
@@ -85,7 +86,7 @@ jobs:
 
       - name: Set up Python ${{ matrix.python-version }}
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
@@ -141,7 +142,7 @@ jobs:
 
       - name: Set up Python 3.11
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: 'pip'
@@ -221,7 +222,7 @@ jobs:
 
       - name: Set up Python ${{ matrix.python-version }}
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
@@ -278,7 +279,7 @@ jobs:
 
       - name: Set up Python 3.11
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: 'pip'
@@ -320,7 +321,7 @@ jobs:
 
       - name: Set up Python 3.11
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: 'pip'
@@ -374,7 +375,7 @@ jobs:
 
       - name: Set up Python 3.11
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: 'pip'

.github/workflows/update_version.yml

@@ -40,7 +40,7 @@ jobs:
           ref: '${{ env.NON_RC_VERSION }}'
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

.github/workflows/validation_benchmarks.yml

@@ -9,6 +9,7 @@ on:
 
 jobs:
   build:
+    if: github.repository_owner == 'pybamm-team'
     name: Dispatch to `pybamm-validation`
     runs-on: ubuntu-latest
     steps:

.github/workflows/work_precision_sets.yml

@@ -7,11 +7,12 @@ on:
 
 jobs:
   benchmarks_on_release:
+    if: github.repository_owner == 'pybamm-team'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
       - name: Get current date

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.6"
+    rev: "v0.1.7"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## Features
 
+- Added method to get QuickPlot axes by variable ([#3596](https://github.com/pybamm-team/PyBaMM/pull/3596))
+- Added custom experiment terminations ([#3596](https://github.com/pybamm-team/PyBaMM/pull/3596))
+- Mechanical parameters are now a function of stoichiometry and temperature ([#3576](https://github.com/pybamm-team/PyBaMM/pull/3576))
+- Added a new unary operator, `EvaluateAt`, that evaluates a spatial variable at a given position ([#3573](https://github.com/pybamm-team/PyBaMM/pull/3573))
+- Added a method, `insert_reference_electrode`, to `pybamm.lithium_ion.BaseModel` that insert a reference electrode to measure the electrolyte potential at a given position in space and adds new variables that mimic a 3E cell setup. ([#3573](https://github.com/pybamm-team/PyBaMM/pull/3573))
 - Serialisation added so models can be written to/read from JSON ([#3397](https://github.com/pybamm-team/PyBaMM/pull/3397))
 
 ## Bug fixes
@@ -11,6 +16,14 @@
 - Fixed bug in calculation of theoretical energy that made it very slow ([#3506](https://github.com/pybamm-team/PyBaMM/pull/3506))
 - The irreversible plating model now increments `f"{Domain} dead lithium concentration [mol.m-3]"`, not `f"{Domain} lithium plating concentration [mol.m-3]"` as it did previously. ([#3485](https://github.com/pybamm-team/PyBaMM/pull/3485))
 
+## Optimizations
+
+- Updated `jax` and `jaxlib` to the latest available versions and added Windows (Python 3.9+) support for the Jax solver ([#3550](https://github.com/pybamm-team/PyBaMM/pull/3550))
+
+## Breaking changes
+
+- Dropped support for the `[jax]` extra, i.e., the Jax solver when running on Python 3.8. The Jax solver is now available on Python 3.9 and above ([#3550](https://github.com/pybamm-team/PyBaMM/pull/3550))
+
 # [v23.9](https://github.com/pybamm-team/PyBaMM/tree/v23.9) - 2023-10-31
 
 ## Features

README.md

@@ -14,7 +14,7 @@
 [![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-66-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-70-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -270,6 +270,10 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://aitorres.com"><img src="https://avatars.githubusercontent.com/u/26191851?v=4?s=100" width="100px;" alt="Andrés Ignacio Torres"/><br /><sub><b>Andrés Ignacio Torres</b></sub></a><br /><a href="#infra-aitorres" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/Agnik7"><img src="https://avatars.githubusercontent.com/u/77234005?v=4?s=100" width="100px;" alt="Agnik Bakshi"/><br /><sub><b>Agnik Bakshi</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=Agnik7" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/RuiheLi"><img src="https://avatars.githubusercontent.com/u/84007676?v=4?s=100" width="100px;" alt="RuiheLi"/><br /><sub><b>RuiheLi</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=RuiheLi" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=RuiheLi" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/chmabaur"><img src="https://avatars.githubusercontent.com/u/127507466?v=4?s=100" width="100px;" alt="chmabaur"/><br /><sub><b>chmabaur</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achmabaur" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=chmabaur" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/AbhishekChaudharii"><img src="https://avatars.githubusercontent.com/u/91185083?v=4?s=100" width="100px;" alt="Abhishek Chaudhari"/><br /><sub><b>Abhishek Chaudhari</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=AbhishekChaudharii" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/shubhambhar007"><img src="https://avatars.githubusercontent.com/u/32607282?v=4?s=100" width="100px;" alt="Shubham Bhardwaj"/><br /><sub><b>Shubham Bhardwaj</b></sub></a><br /><a href="#infra-shubhambhar007" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/jlauber18"><img src="https://avatars.githubusercontent.com/u/28939653?v=4?s=100" width="100px;" alt="Jonathan Lauber"/><br /><sub><b>Jonathan Lauber</b></sub></a><br /><a href="#infra-jlauber18" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
   </tbody>
 </table>

docs/conf.py

@@ -76,6 +76,7 @@
 
 doctest_global_setup = """
 from docs import *
+import pybamm
 """
 
 # Add any paths that contain templates here, relative to this directory.

docs/source/api/experiment/experiment_steps.rst

@@ -18,3 +18,28 @@ directly:
 
 .. autoclass:: pybamm.step._Step
     :members:
+
+Step terminations
+-----------------
+
+Standard step termination events are implemented by the following classes, which are
+called when the termination is specified by a specific string. These classes can be
+either be called directly or via the string format specified in the class docstring
+
+.. autoclass:: pybamm.step.CrateTermination
+    :members:
+
+.. autoclass:: pybamm.step.CurrentTermination
+    :members:
+
+.. autoclass:: pybamm.step.VoltageTermination
+    :members:
+
+The following classes can be used to define custom terminations for an experiment
+step:
+
+.. autoclass:: pybamm.step.BaseTermination
+    :members:
+
+.. autoclass:: pybamm.step.CustomTermination
+    :members: