Merge branch 'develop' of https://github.com/pybamm-team/PyBaMM into …

…issue-2111-custom-transport-efficiency

# Conflicts:
#	CHANGELOG.md

.all-contributorsrc

@@ -717,6 +717,16 @@
       "contributions": [
         "doc"
       ]
+    },
+    {
+      "login": "RuiheLi",
+      "name": "RuiheLi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/84007676?v=4",
+      "profile": "https://github.com/RuiheLi",
+      "contributions": [
+        "code",
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/release_workflow.md

@@ -1,6 +1,6 @@
 # Release workflow
 
-This file contains the workflow required to make a `PyBaMM` release on GitHub and PyPI by the maintainers.
+This file contains the workflow required to make a `PyBaMM` release on GitHub, PyPI, and conda-forge by the maintainers.
 
 ## rc0 releases (automated)
 
@@ -75,5 +75,7 @@ Some other essential things to check throughout the release process -
 - As the release workflow is initiated by the `release` event, it's important to note that the default `GITHUB_REF` used by `actions/checkout` during the checkout process will correspond to the tag created during the release process. Consequently, the workflows will consistently build PyBaMM based on the commit associated with this tag. Should new commits be introduced to the `vYY.MM` branch, such as those addressing build issues, it becomes necessary to manually update this tag to point to the most recent commit -
   ```
   git tag -f <tag_name> <commit_hash>
-  git push origin <tag_name>  # can only be carried out by the maintainers
+  git push -f <pybamm-team/PyBaMM_remote_name> <tag_name>  # can only be carried out by the maintainers
   ```
+- If changes are made to the API, console scripts, entry points, new optional dependencies are added, support for major Python versions is dropped or added, or core project information and metadata are modified at the time of the release, make sure to update the `meta.yaml` file in the `recipe/` folder of the [conda-forge/pybamm-feedstock](https://github.com/conda-forge/pybamm-feedstock) repository accordingly by following the instructions in the [conda-forge documentation](https://conda-forge.org/docs/maintainer/updating_pkgs.html#updating-the-feedstock-repository) and re-rendering the recipe
+- The conda-forge release workflow will automatically be triggered following a stable PyPI release, and the aforementioned updates should be carried out directly in the main repository by pushing changes to the automated PR created by the conda-forge-bot. A manual PR can also be created if the updates are not included in the automated PR for some reason. This manual PR **must** bump the build number in `meta.yaml` and **must** be from a personal fork of the repository.

.github/workflows/docker.yml

@@ -1,4 +1,4 @@
-name: Build & Push Docker Images
+name: Build and push Docker images to Docker Hub
 
 on:
   workflow_dispatch:
@@ -7,69 +7,80 @@ on:
     - develop
 
 jobs:
-  pre_job:
+  build_docker_images:
+    # This workflow is only of value to PyBaMM and would always be skipped in forks
+    if: github.repository_owner == 'pybamm-team'
+    name: Image (${{ matrix.build-args }})
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        build-args: ["No solvers", "JAX", "ODES", "IDAKLU", "ALL"]
+      fail-fast: true
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Login to DockerHub
+      - name: Login to Docker Hub
         uses: docker/login-action@v3
         with:
             username: ${{ secrets.DOCKERHUB_USERNAME }}
             password: ${{ secrets.DOCKERHUB_TOKEN }}
 
-      - name: List built images
-        run: docker images
-
-      - name: Build and Push Docker Image (Without Solvers)
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: scripts/Dockerfile
-          tags: pybamm/pybamm:latest
-          push: true
+      - name: Create tags for Docker images based on build-time arguments
+        id: tags
+        run: |
+          if [ "${{ matrix.build-args }}" = "No solvers" ]; then
+            echo "tag=latest" >> "$GITHUB_OUTPUT"
+          elif [ "${{ matrix.build-args }}" = "JAX" ]; then
+            echo "tag=jax" >> "$GITHUB_OUTPUT"
+          elif [ "${{ matrix.build-args }}" = "ODES" ]; then
+            echo "tag=odes" >> "$GITHUB_OUTPUT"
+          elif [ "${{ matrix.build-args }}" = "IDAKLU" ]; then
+            echo "tag=idaklu" >> "$GITHUB_OUTPUT"
+          elif [ "${{ matrix.build-args }}" = "ALL" ]; then
+            echo "tag=all" >> "$GITHUB_OUTPUT"
+          fi
 
-      - name: Build and Push Docker Image (With JAX Solver)
+      - name: Build and push Docker image to Docker Hub (no solvers)
+        if: matrix.build-args == 'No solvers'
         uses: docker/build-push-action@v5
         with:
           context: .
           file: scripts/Dockerfile
-          tags: pybamm/pybamm:jax
+          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
           push: true
-          build-args: |
-            JAX=true
+          platforms: linux/amd64, linux/arm64
 
-      - name: Build and Push Docker Image (With ODES & DAE Solver)
+      - 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:odes
+          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
           push: true
-          build-args: |
-            ODES=true
+          build-args: ${{ matrix.build-args }}=true
+          platforms: linux/amd64, linux/arm64
 
-      - name: Build and Push Docker Image (With IDAKLU Solver)
+      - 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:idaklu
+          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
           push: true
-          build-args: |
-            IDAKLU=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: Build and Push Docker Image (With All Solvers)
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: scripts/Dockerfile
-          tags: pybamm/pybamm:latest
-          push: true
-          build-args: |
-            ALL=true
+      - name: List built image(s)
+        run: docker images

.github/workflows/publish_pypi.yml

@@ -10,7 +10,7 @@ on:
     inputs:
       target:
         description: 'Deployment target. Can be "pypi" or "testpypi"'
-        default: "pypi"
+        default: "testpypi"
       debug_enabled:
         type: boolean
         description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'

.github/workflows/run_periodic_tests.yml

@@ -84,44 +84,44 @@ jobs:
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=2.38.0.20190211
 
-      - name: Install standard python dependencies
+      - name: Install standard Python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools nox
+          python -m pip install --upgrade pip wheel setuptools
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s pybamm-requires
+        run: pipx run nox -s pybamm-requires
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        run: nox -s unit
+        run: pipx run nox -s unit
 
       - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: nox -s coverage
+        run: pipx run nox -s coverage
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/[email protected]
 
       - name: Run integration tests
-        run: nox -s integration
+        run: pipx run nox -s integration
 
       - name: Install docs dependencies and run doctests
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s doctests
+        run: pipx run nox -s doctests
 
       - name: Check if the documentation can be built
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s docs
+        run: pipx run nox -s docs
 
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s examples
+        run: pipx run nox -s examples
 
       - name: Run example scripts tests
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s scripts
+        run: pipx run nox -s scripts
 
   #M-series Mac Mini
   build-apple-mseries:

.github/workflows/test_on_push.yml

@@ -92,7 +92,7 @@ jobs:
 
       - name: Install PyBaMM dependencies
         run: |
-          pip install --upgrade pip wheel setuptools nox
+          pip install --upgrade pip wheel setuptools
           pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
@@ -111,10 +111,10 @@ jobs:
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s pybamm-requires
+        run: pipx run nox -s pybamm-requires
 
       - name: Run unit tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
-        run: nox -s unit
+        run: pipx run nox -s unit
 
   # Runs only on Ubuntu with Python 3.11
   check_coverage:
@@ -169,10 +169,10 @@ jobs:
           key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        run: nox -s pybamm-requires
+        run: pipx run nox -s pybamm-requires
 
       - name: Run unit tests for Ubuntu with Python 3.11 and generate coverage report
-        run: nox -s coverage
+        run: pipx run nox -s coverage
 
       - name: Upload coverage report
         uses: codecov/[email protected]
@@ -235,7 +235,7 @@ jobs:
 
       - name: Install PyBaMM dependencies
         run: |
-          pip install --upgrade pip wheel setuptools nox
+          pip install --upgrade pip wheel setuptools
           pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
@@ -254,10 +254,10 @@ jobs:
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s pybamm-requires
+        run: pipx run nox -s pybamm-requires
 
       - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
-        run: nox -s integration
+        run: pipx run nox -s integration
 
 # Runs only on Ubuntu with Python 3.11. Skips IDAKLU module compilation
 # for speedups, which is already tested in other jobs.
@@ -296,14 +296,14 @@ jobs:
 
       - name: Install PyBaMM dependencies
         run: |
-          pip install --upgrade pip wheel setuptools nox
+          pip install --upgrade pip wheel setuptools
           pip install -e .[all,docs]
 
       - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
-        run: nox -s doctests
+        run: pipx run nox -s doctests
 
       - name: Check if the documentation can be built for GNU/Linux with Python 3.11
-        run: nox -s docs
+        run: pipx run nox -s docs
 
   # Runs only on Ubuntu with Python 3.11
   run_example_tests:
@@ -341,7 +341,7 @@ jobs:
 
       - name: Install PyBaMM dependencies
         run: |
-          pip install --upgrade pip wheel setuptools nox
+          pip install --upgrade pip wheel setuptools
           pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
@@ -358,10 +358,10 @@ jobs:
           key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        run: nox -s pybamm-requires
+        run: pipx run nox -s pybamm-requires
 
       - name: Install dev dependencies and run example tests for GNU/Linux with Python 3.11
-        run: nox -s examples
+        run: pipx run nox -s examples
 
   # Runs only on Ubuntu with Python 3.11
   run_scripts_tests:
@@ -399,7 +399,7 @@ jobs:
 
       - name: Install PyBaMM dependencies
         run: |
-          pip install --upgrade pip wheel setuptools nox
+          pip install --upgrade pip wheel setuptools
           pip install -e .[all,docs]
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
@@ -416,7 +416,7 @@ jobs:
           key: nox-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        run: nox -s pybamm-requires
+        run: pipx run nox -s pybamm-requires
 
       - name: Install dev dependencies and run example scripts tests for GNU/Linux with Python 3.11
-        run: nox -s scripts
+        run: pipx run nox -s scripts

.pre-commit-config.yaml

@@ -4,17 +4,11 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.292"
+    rev: "v0.1.3"
     hooks:
       - id: ruff
-        args: [--fix, --ignore=E741, --exclude=__init__.py]
-
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
-    hooks:
-      - id: nbqa-ruff
-        additional_dependencies: [ruff==0.0.284]
-        args: ["--fix","--ignore=E501,E402"]
+        args: [--fix, --show-fixes]
+        types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.16.0"

CHANGELOG.md

@@ -1,9 +1,14 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
-# [v23.9rc0](https://github.com/pybamm-team/PyBaMM/tree/v23.9rc0) - 2023-10-31
+## Bug fixes
+
+- Fixed a bug where the JaxSolver would fails when using GPU support with no input parameters ([#3423](https://github.com/pybamm-team/PyBaMM/pull/3423))
 
 ## Features
 - Transport efficiency submodel has new options from the literature relating to different tortuosity factor models and also a new option called "tortuosity factor" for specifying the value or function directly as parameters ([#3437](https://github.com/pybamm-team/PyBaMM/pull/3437))
+
+# [v23.9rc0](https://github.com/pybamm-team/PyBaMM/tree/v23.9rc0) - 2023-10-31
+
 - The parameter "Ambient temperature [K]" can now be given as a function of position `(y,z)` and time `t`. The "edge" and "current collector" heat transfer coefficient parameters can also depend on `(y,z)` ([#3257](https://github.com/pybamm-team/PyBaMM/pull/3257))
 - Spherical and cylindrical shell domains can now be solved with any boundary conditions ([#3237](https://github.com/pybamm-team/PyBaMM/pull/3237))
 - Processed variables now get the spatial variables automatically, allowing plotting of more generic models ([#3234](https://github.com/pybamm-team/PyBaMM/pull/3234))
@@ -37,6 +42,7 @@
 - Error generated when invalid parameter values are passed ([#3132](https://github.com/pybamm-team/PyBaMM/pull/3132))
 - Parameters in `Prada2013` have been updated to better match those given in the paper, which is a 2.3 Ah cell, instead of the mix-and-match with the 1.1 Ah cell from Lain2019 ([#3096](https://github.com/pybamm-team/PyBaMM/pull/3096))
 - The `OneDimensionalX` thermal model has been updated to account for edge/tab cooling and account for the current collector volumetric heat capacity. It now gives the correct behaviour compared with a lumped model with the correct total heat transfer coefficient and surface area for cooling. ([#3042](https://github.com/pybamm-team/PyBaMM/pull/3042))
+- Fixed a bug where supplying an initial soc did not work with half cell models ([#3456](https://github.com/pybamm-team/PyBaMM/pull/3456))
 
 ## Optimizations
 
@@ -45,6 +51,7 @@
 
 ## Breaking changes
 
+- The parameter "Exchange-current density for lithium plating [A.m-2]" has been renamed to "Exchange-current density for lithium metal electrode [A.m-2]" when referring to the lithium plating reaction on the surface of a lithium metal electrode ([#3445](https://github.com/pybamm-team/PyBaMM/pull/3445))
 - Dropped support for i686 (32-bit) architectures on GNU/Linux distributions ([#3412](https://github.com/pybamm-team/PyBaMM/pull/3412))
 - The class `pybamm.thermal.OneDimensionalX` has been moved to `pybamm.thermal.pouch_cell.OneDimensionalX` to reflect the fact that the model formulation implicitly assumes a pouch cell geometry ([#3257](https://github.com/pybamm-team/PyBaMM/pull/3257))
 - The "lumped" thermal option now always used the parameters "Cell cooling surface area [m2]", "Cell volume [m3]" and "Total heat transfer coefficient [W.m-2.K-1]" to compute the cell cooling regardless of the chosen "cell geometry" option. The user must now specify the correct values for these parameters instead of them being calculated based on e.g. a pouch cell. An `OptionWarning` is raised to let users know to update their parameters ([#3257](https://github.com/pybamm-team/PyBaMM/pull/3257))

CMakeLists.txt

@@ -24,7 +24,10 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 set(CMAKE_EXPORT_COMPILE_COMMANDS 1)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-
+if(NOT MSVC)
+    # MSVC does not support variable length arrays (vla)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Werror=vla")
+endif()
 
 # casadi seems to compile without the newer versions of std::string
 add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)