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

…develop

.all-contributorsrc

@@ -1,6 +1,7 @@
 {
   "files": [
-    "all_contributors.md"
+    "all_contributors.md",
+    "README.md"
   ],
   "imageSize": 100,
   "commit": false,
@@ -865,6 +866,25 @@
       "contributions": [
         "doc"
       ]
+    },
+    {
+      "login": "mleot",
+      "name": "mleot",
+      "avatar_url": "https://avatars.githubusercontent.com/u/140573653?v=4",
+      "profile": "https://github.com/mleot",
+      "contributions": [
+        "code",
+        "test"
+      ]
+    },
+    {
+      "login": "abhicodes369",
+      "name": "Abhi ram",
+      "avatar_url": "https://avatars.githubusercontent.com/u/119055274?v=4",
+      "profile": "https://github.com/abhicodes369",
+      "contributions": [
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/CODEOWNERS

@@ -1,17 +1,17 @@
 # Automatically request reviews from maintainers
 
 # Package
-/pybamm/discretisations/ @martinjrobins @rtimms @tinosulzer
-/pybamm/experiment/ @brosaplanella @martinjrobins @rtimms @tinosulzer @TomTranter
-/pybamm/expression_tree/ @martinjrobins @rtimms @tinosulzer
-/pybamm/geometry/ @martinjrobins @rtimms @tinosulzer
-/pybamm/input/ @brosaplanella @DrSOKane @rtimms @tinosulzer @TomTranter @kratman
-/pybamm/meshes/ @martinjrobins @rtimms @tinosulzer @rtimms
-/pybamm/models/ @brosaplanella @DrSOKane @rtimms @tinosulzer @TomTranter @rtimms
-/pybamm/parameters/ @brosaplanella @DrSOKane @rtimms @tinosulzer @TomTranter @rtimms  @kratman
-/pybamm/plotting/ @martinjrobins @rtimms @Saransh-cpp @tinosulzer @rtimms  @kratman @agriyakhetarpal
-/pybamm/solvers/ @martinjrobins @rtimms @tinosulzer @TomTranter @rtimms
-/pybamm/spatial_methods/ @martinjrobins @rtimms @tinosulzer @rtimms
+/pybamm/discretisations/ @martinjrobins @rtimms @valentinsulzer
+/pybamm/experiment/ @brosaplanella @martinjrobins @rtimms @valentinsulzer @TomTranter
+/pybamm/expression_tree/ @martinjrobins @rtimms @valentinsulzer
+/pybamm/geometry/ @martinjrobins @rtimms @valentinsulzer
+/pybamm/input/ @brosaplanella @DrSOKane @rtimms @valentinsulzer @TomTranter @kratman
+/pybamm/meshes/ @martinjrobins @rtimms @valentinsulzer @rtimms
+/pybamm/models/ @brosaplanella @DrSOKane @rtimms @valentinsulzer @TomTranter @rtimms
+/pybamm/parameters/ @brosaplanella @DrSOKane @rtimms @valentinsulzer @TomTranter @rtimms  @kratman
+/pybamm/plotting/ @martinjrobins @rtimms @Saransh-cpp @valentinsulzer @rtimms  @kratman @agriyakhetarpal
+/pybamm/solvers/ @martinjrobins @rtimms @valentinsulzer @TomTranter @rtimms
+/pybamm/spatial_methods/ @martinjrobins @rtimms @valentinsulzer @rtimms
 /pybamm/* @pybamm-team/maintainers # the files directly under /pybamm/, will not recurse
 
 # CI/CD workflows

.github/workflows/publish_pypi.yml

@@ -83,7 +83,8 @@ jobs:
             CMAKE_GENERATOR_PLATFORM=x64
             CMAKE_BUILD_PARALLEL_LEVEL=${{ steps.get_num_cores.outputs.count }}
           CIBW_ARCHS: AMD64
-          CIBW_BEFORE_BUILD: python -m pip install setuptools wheel # skip CasADi and CMake
+          CIBW_BEFORE_BUILD: python -m pip install setuptools wheel delvewheel # skip CasADi and CMake
+          CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload Windows wheels

.github/workflows/run_periodic_tests.yml

@@ -6,7 +6,7 @@ on:
   workflow_dispatch:
   pull_request:
     branches:
-    - main
+      - main
 
   # Run every day at 3 am UTC
   schedule:
@@ -24,22 +24,98 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  style:
+  run_unit_tests:
+    name: Unit tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-12, macos-14, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        # Exclude Python 3.12 from unit tests since we run it in the coverage jobs
+        exclude:
+          - os: ubuntu-latest
+            python-version: "3.12"
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Install macOS system dependencies
+        if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
+        env:
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
+          # Speed up CI
+          NONINTERACTIVE: 1
+        # sometimes gfortran cannot be found, so reinstall gcc just to be sure
+        run: |
+          brew analytics off
+          brew install graphviz libomp
+          brew reinstall gcc
+
+      - name: Install Windows system dependencies
+        if: matrix.os == 'windows-latest'
+        run: choco install graphviz --version=8.0.5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
+        timeout-minutes: 10
+        if: matrix.os != 'windows-latest'
+        run: python -m nox -s pybamm-requires
+
+      - name: Run unit tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
+        run: python -m nox -s unit
+
+  check_coverage:
     runs-on: ubuntu-latest
+    name: Coverage tests (ubuntu-latest / Python 3.12)
+
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup python
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
           python-version: 3.12
 
-      - name: Check style
-        run: |
-          python -m pip install pre-commit
-          pre-commit run -a
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
+        timeout-minutes: 10
+        run: python -m nox -s pybamm-requires
 
-  build:
-    needs: style
+      - name: Run unit tests for Ubuntu with Python 3.12 and generate coverage report
+        run: python -m nox -s coverage
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v4.4.1
+        if: github.repository == 'pybamm-team/PyBaMM'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  run_integration_tests:
+    name: Integration tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -49,31 +125,35 @@ jobs:
     steps:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
 
       - name: Install Linux system dependencies
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev graphviz pandoc
-          sudo apt install texlive-full
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
         if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
+        env:
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
+          # Speed up CI
+          NONINTERACTIVE: 1
+        # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
-          brew install graphviz libomp
+          brew install graphviz
           brew reinstall gcc
 
       - name: Install Windows system dependencies
         if: matrix.os == 'windows-latest'
-        run: choco install graphviz --version=2.38.0.20190211
+        run: choco install graphviz --version=8.0.5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - name: Install nox
         run: python -m pip install nox
@@ -83,43 +163,97 @@ jobs:
         if: matrix.os != 'windows-latest'
         run: python -m nox -s pybamm-requires
 
-      - name: Run unit tests for GNU/Linux, macOS, and Windows with all Python versions
-        if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        run: python -m nox -s unit
+      - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
+        run: python -m nox -s integration
 
-      - 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: python -m nox -s coverage
+  # Skips IDAKLU module compilation for speedups, which is already tested in other jobs.
+  run_doctests:
+    runs-on: ubuntu-latest
+    name: Doctests (ubuntu-latest / Python 3.11)
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-      - name: Upload coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        uses: codecov/codecov-action@v4.3.1
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          python-version: 3.11
 
-      - name: Run integration tests
-        run: python -m nox -s integration
+      - name: Install nox
+        run: python -m pip install nox
 
-      - name: Install docs dependencies and run doctests
-        if: matrix.os == 'ubuntu-latest'
+      - name: Install docs dependencies and run doctests for GNU/Linux
         run: python -m nox -s doctests
 
-      - name: Check if the documentation can be built
-        if: matrix.os == 'ubuntu-latest'
+      - name: Check if the documentation can be built for GNU/Linux
         run: python -m nox -s docs
 
-      - name: Install dev dependencies and run example tests
-        if: matrix.os == 'ubuntu-latest'
+  run_example_tests:
+    runs-on: ubuntu-latest
+    name: Example notebooks (ubuntu-latest / Python 3.12)
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
+        timeout-minutes: 10
+        run: python -m nox -s pybamm-requires
+
+      - name: Run example notebooks tests for GNU/Linux with Python 3.12
         run: python -m nox -s examples
 
-      - name: Run example scripts tests
-        if: matrix.os == 'ubuntu-latest'
+  run_scripts_tests:
+    runs-on: ubuntu-latest
+    name: Example scripts (ubuntu-latest / Python 3.12)
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt install gfortran gcc graphviz libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
+        timeout-minutes: 10
+        run: python -m nox -s pybamm-requires
+
+      - name: Run example scripts tests for GNU/Linux with Python 3.12
         run: python -m nox -s scripts
 
   # M-series Mac Mini
   build-apple-mseries:
     if: github.repository_owner == 'pybamm-team'
-    needs: style
     runs-on: [self-hosted, macOS, ARM64]
     env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
@@ -130,7 +264,9 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
       - name: Install Python & create virtualenv
         shell: bash
         run: |