Migrate to scikit-build-core

.github/workflows/benchmark_on_push.yml

@@ -28,7 +28,7 @@ jobs:
 
       - name: Install python dependencies
         run: |
-          python -m uv pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m uv pip install --upgrade pip scikit-build-core wget cmake casadi numpy
           python -m uv pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS

.github/workflows/periodic_benchmarks.yml

@@ -36,7 +36,7 @@ jobs:
 
       - name: Install python dependencies
         run: |
-          python -m uv pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m uv pip install --upgrade pip scikit-build-core wget cmake casadi numpy
           python -m uv pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS
@@ -46,9 +46,6 @@ jobs:
         run: |
           asv machine --machine "GitHubRunner"
           asv run --machine "GitHubRunner" NEW --show-stderr -v
-        env:
-          SUNDIALS_INST: $HOME/.local
-          LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
         uses: actions/[email protected]

.github/workflows/publish_pypi.yml

@@ -15,6 +15,8 @@ on:
         description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
         required: false
         default: false
+  pull_request: # Temporarily trigger on PRs for debugging, remove later
+    types: [opened, synchronize, reopened]
 
 # Set options available for all jobs that use cibuildwheel
 env:
@@ -47,9 +49,6 @@ jobs:
           with open(output_file, "a", encoding="utf-8") as output_stream:
               output_stream.write(f"count={num_cpus}\n")
 
-      - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.12.0 https://github.com/pybind/pybind11.git -c advice.detachedHead=false
-
       - name: Install vcpkg on Windows
         run: |
           cd C:\
@@ -72,7 +71,10 @@ jobs:
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
 
       - name: Build 64-bit wheels on Windows
-        run: pipx run cibuildwheel --output-dir wheelhouse
+        uses: pypa/[email protected]
+        with:
+          package-dir: .
+          output-dir: wheelhouse
         env:
           CIBW_ENVIRONMENT: >
             PYBAMM_USE_VCPKG=ON
@@ -83,7 +85,7 @@ 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 delvewheel # skip CasADi and CMake
+          CIBW_BEFORE_BUILD: python -m pip install scikit-build-core delvewheel pybind11 # skip CasADi and CMake
           # Fix access violation because GHA runners have modified PATH that picks wrong
           # msvcp140.dll, see https://github.com/adang1345/delvewheel/issues/54
           CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair --add-path C:/Windows/System32 -w {dest_dir} {wheel}
@@ -110,17 +112,19 @@ jobs:
         with:
           python-version: 3.11
 
-      - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.12.0 https://github.com/pybind/pybind11.git -c advice.detachedHead=false
-
       - name: Build wheels on Linux
-        run: pipx run cibuildwheel --output-dir wheelhouse
+        uses: pypa/[email protected]
+        with:
+          package-dir: .
+          output-dir: wheelhouse
         env:
           CIBW_ARCHS_LINUX: x86_64
-          CIBW_BEFORE_ALL_LINUX: >
-            yum -y install openblas-devel lapack-devel &&
-            bash scripts/install_sundials.sh 6.0.3 6.5.0
-          CIBW_BEFORE_BUILD_LINUX: python -m pip install cmake casadi setuptools wheel
+          CIBW_BEFORE_BUILD_LINUX: |
+            set -e -x
+            yum update -y
+            yum -y install openblas-devel
+            python scripts/install_KLU_Sundials.py
+            python -m pip install cmake casadi scikit-build-core pybind11
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
           CIBW_TEST_EXTRAS: "all,dev,jax"
           CIBW_TEST_COMMAND: |
@@ -148,9 +152,6 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.12.0 https://github.com/pybind/pybind11.git -c advice.detachedHead=false
-
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
 
@@ -241,11 +242,12 @@ jobs:
 
             python scripts/install_KLU_Sundials.py
             python -m cibuildwheel --output-dir wheelhouse
+
         env:
           # 10.13 for Intel (macos-12/macos-13), 11.0 for Apple Silicon (macos-14 and macos-latest)
           MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-14' && '11.0' || '10.13' }}
           CIBW_ARCHS_MACOS: auto
-          CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
+          CIBW_BEFORE_BUILD: python -m pip install cmake casadi scikit-build-core delocate
           CIBW_REPAIR_WHEEL_COMMAND: |
             if [[ $(uname -m) == "x86_64" ]]; then
               delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
@@ -289,7 +291,10 @@ jobs:
 
   publish_pypi:
     # This job is only of value to PyBaMM and would always be skipped in forks
-    if: github.event_name != 'schedule' && github.repository == 'pybamm-team/PyBaMM'
+    if: >-
+      (github.event_name == 'workflow_dispatch' ||
+      github.event_name == 'release') &&
+      github.repository == 'pybamm-team/PyBaMM'
     name: Upload package to PyPI
     needs: [
       build_manylinux_wheels,

.github/workflows/run_periodic_tests.yml

@@ -26,27 +26,66 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  run_tests:
-    runs-on: ${{ matrix.os }}
+  run_windows_unit_integration_tests:
+    env:
+      PYBAMM_USE_VCPKG: ON
+      VCPKG_ROOT_DIR: C:\vcpkg
+      VCPKG_DEFAULT_TRIPLET: x64-windows-static-md
+      VCPKG_FEATURE_FLAGS: manifests,registries
+      CMAKE_GENERATOR: "Visual Studio 17 2022"
+    runs-on: windows-latest
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest, macos-12, macos-14, windows-latest ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
-    name: Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    name: Tests (windows-latest / Python ${{ matrix.python-version }})
 
     steps:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v4
 
-      - name: Install Linux system dependencies
-        if: matrix.os == 'ubuntu-latest'
+      - name: Install Windows system dependencies
+        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 vcpkg on Windows
         run: |
-          sudo apt-get update
-          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+          cd C:\
+          rm -r -fo 'C:\vcpkg'
+          git clone https://github.com/microsoft/vcpkg
+          cd vcpkg
+          .\bootstrap-vcpkg.bat
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Run unit tests for windows-latest with Python ${{ matrix.python-version }}
+        run: python -m nox -s unit
+
+      - name: Run integration tests for windows-latest with Python ${{ matrix.python-version }}
+        run: python -m nox -s integration
+
+  run_macos_unit_integration_tests:
+    runs-on: ${{ matrix.os }}
+    env:
+        PYBAMM_IDAKLU_EXPR_CASADI: ON
+        PYBAMM_IDAKLU_EXPR_IREE: ON
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-12, macos-14]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    name: Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
 
       - 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
@@ -59,9 +98,38 @@ jobs:
           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 macOS
+        timeout-minutes: 10
+        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
+
+      - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
+        run: python -m nox -s integration
+
+  run_linux_unit_integration_coverage_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    name: Tests (ubuntu-latest / Python ${{ matrix.python-version }})
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: sudo apt install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
@@ -74,31 +142,34 @@ jobs:
       - name: Install nox
         run: python -m uv pip install nox[uv]
 
-      - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         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 }}
-        if: matrix.os != 'ubuntu-latest' || matrix.python-version != '3.12'
+      - name: Run unit tests for GNU/Linux with Python ${{ matrix.python-version }}
+        if: matrix.python-version != '3.12'
         run: python -m nox -s unit
 
-      - name: Run coverage tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+      - name: Run coverage tests for GNU/Linux with Python ${{ matrix.python-version }}
+        if: matrix.python-version == '3.12'
         run: python -m nox -s coverage
 
       - name: Upload coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        if: matrix.python-version == '3.12'
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
-      - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
+      - name: Run integration tests for GNU/Linux with Python ${{ matrix.python-version }}
         run: python -m nox -s integration
 
   # Skips IDAKLU module compilation for speedups, which is already tested in other jobs.
   run_doctests:
+    env:
+      BUILD_IDAKLU: OFF
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
     name: Doctests (ubuntu-latest / Python 3.11)
 
     steps:
@@ -108,9 +179,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install Linux system dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install graphviz pandoc texlive-latex-extra dvipng
+        run: sudo apt install graphviz pandoc texlive-latex-extra dvipng
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -131,16 +200,16 @@ jobs:
 
   run_example_tests:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
     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
+        run: sudo apt install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
@@ -162,16 +231,16 @@ jobs:
 
   run_scripts_tests:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
     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
+        run: sudo apt install gfortran gcc graphviz libopenblas-dev texlive-latex-extra dvipng
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5