scikit-build-core CI Builds

.github/workflows/benchmark_on_push.yml

@@ -2,6 +2,7 @@ name: Run benchmarks on push
 on:
   push:
     branches: [main, develop]
+  workflow_dispatch:
 
 concurrency:
   # Cancel intermediate builds always
@@ -21,15 +22,20 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev
+          sudo apt install gfortran gcc libopenblas-dev liblapack-dev
 
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m pip install --upgrade pip scikit-build-core wget cmake casadi numpy
           python -m pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS
-        run: python scripts/install_KLU_Sundials.py
+        run: |
+          python scripts/install_KLU_Sundials.py
+          mkdir -p $(pwd)/sundials_KLU_libs/lib64/
+          export LD_LIBRARY_PATH=$(pwd)/sundials_KLU_libs/lib64/:$LD_LIBRARY_PATH
+          export PATH=$(pwd)/sundials_KLU_libs/lib64/:$PATH
+          echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
 
       - name: Fetch base branch
         run: |
@@ -46,6 +52,7 @@ jobs:
 
       - name: Run benchmarks
         run: |
+          export BUILD_IDAKLU=ON
           asv machine --machine "GitHubRunner"
           # Get IDs of branch and PR commits
           BASE_COMMIT=$(git rev-parse develop)

.github/workflows/docker.yml

@@ -9,7 +9,7 @@ on:
 jobs:
   build_docker_image:
     # This workflow is only of value to PyBaMM and would always be skipped in forks
-    if: github.repository_owner == 'pybamm-team'
+    # if: github.repository_owner == 'pybamm-team'
     name: Build image
     runs-on: ubuntu-latest
 
@@ -23,19 +23,19 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Login to Docker Hub
-        uses: docker/login-action@v3
-        with:
-            username: ${{ secrets.DOCKERHUB_USERNAME }}
-            password: ${{ secrets.DOCKERHUB_TOKEN }}
+      # - name: Login to Docker Hub
+      #   uses: docker/login-action@v3
+      #   with:
+      #       username: ${{ secrets.DOCKERHUB_USERNAME }}
+      #       password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build and push Docker image to Docker Hub
         uses: docker/build-push-action@v6
         with:
           context: .
           file: scripts/Dockerfile
           tags: pybamm/pybamm:latest
-          push: true
+          push: false
           platforms: linux/amd64, linux/arm64
 
       - name: List built image(s)

.github/workflows/periodic_benchmarks.yml

@@ -33,7 +33,7 @@ jobs:
 
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m pip install --upgrade pip scikit-build-core wget cmake casadi numpy
           python -m pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS
@@ -43,9 +43,6 @@ 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
           CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; print(pybamm.IDAKLUSolver())"
 
@@ -106,18 +108,27 @@ 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_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
+          CIBW_BEFORE_BUILD_LINUX: |
+            set -e -x
+
+            yum update -y
+            yum -y install openblas-devel lapack-devel
+            python scripts/install_KLU_Sundials.py
+            mkdir -p $(pwd)/sundials_KLU_libs/lib64/
+            export LD_LIBRARY_PATH=$(pwd)/sundials_KLU_libs/lib64/:$LD_LIBRARY_PATH
+            export PATH=$(pwd)/sundials_KLU_libs/lib64/:$PATH
+            echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
+
+            python -m pip install cmake casadi scikit-build-core pybind11
+          CIBW_REPAIR_WHEEL_COMMAND_LINUX: |
+            LD_LIBRARY_PATH=$(pwd)/sundials_KLU_libs/lib64/:$LD_LIBRARY_PATH auditwheel repair -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: |
             set -e -x
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
@@ -142,18 +153,16 @@ 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: Set macOS-specific environment variables
         run: echo "MACOSX_DEPLOYMENT_TARGET=11.0" >> $GITHUB_ENV
 
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel
-
       - name: Build wheels on macOS
-        shell: bash
-        run: |
+        uses: pypa/[email protected]
+        with:
+          package-dir: .
+          output-dir: wheelhouse
+        env:
+          CIBW_BEFORE_ALL: |
             set -e -x
 
             # Set LLVM-OpenMP URL
@@ -190,23 +199,25 @@ jobs:
               export PATH=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin:$PATH
             fi
 
-            # link libgfortran dylibs and place them in $HOME/.local/lib
-            # and then change rpath to $HOME/.local/lib for each of them
+            # link libgfortran dylibs and place them in sundials_KLU_libs/lib/
+            # and then change rpath to /sundials_KLU_libs/lib/ for each of them
             # Note: libgcc_s.1.dylib not available on macOS arm64; skip for now
-            mkdir -p $HOME/.local/lib
+
+            mkdir -p $(pwd)/sundials_KLU_libs/lib/
+
             if [[ $(uname -m) == "x86_64" ]]; then
               lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/lib
               for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.dylib libgcc_s.1.1.dylib; do
-                cp $lib_dir/$lib $HOME/.local/lib/
-                install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
-                codesign --force --sign - $HOME/.local/lib/$lib
+                cp $lib_dir/$lib $(pwd)/sundials_KLU_libs/lib/
+                install_name_tool -id $(pwd)/sundials_KLU_libs/lib/$lib $(pwd)/sundials_KLU_libs/lib/$lib
+                codesign --force --sign - $(pwd)/sundials_KLU_libs/lib/$lib
               done
             elif [[ $(uname -m) == "arm64" ]]; then
               lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/lib
               for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.1.dylib; do
-                cp $lib_dir/$lib $HOME/.local/lib/
-                install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
-                codesign --force --sign - $HOME/.local/lib/$lib
+                cp $lib_dir/$lib $(pwd)/sundials_KLU_libs/lib/
+                install_name_tool -id $(pwd)/sundials_KLU_libs/lib/$lib $(pwd)/sundials_KLU_libs/lib/$lib
+                codesign --force --sign - $(pwd)/sundials_KLU_libs/lib/$lib
               done
             fi
 
@@ -221,10 +232,10 @@ jobs:
               PREFIX="/opt/homebrew/Caskroom/miniforge/base/envs/pybamm-dev"
             fi
 
-            # Copy libomp.dylib from PREFIX to $HOME/.local/lib, needed for wheel repair
-            cp $PREFIX/lib/libomp.dylib $HOME/.local/lib/
-            install_name_tool -id $HOME/.local/lib/libomp.dylib $HOME/.local/lib/libomp.dylib
-            codesign --force --sign - $HOME/.local/lib/libomp.dylib
+            # Copy libomp.dylib from PREFIX to /sundials_KLU_libs/lib/, needed for wheel repair
+            cp $PREFIX/lib/libomp.dylib $(pwd)/sundials_KLU_libs/lib/
+            install_name_tool -id $(pwd)/sundials_KLU_libs/lib/libomp.dylib $(pwd)/sundials_KLU_libs/lib/libomp.dylib
+            codesign --force --sign - $(pwd)/sundials_KLU_libs/lib/libomp.dylib
 
             export CC=/usr/bin/clang
             export CXX=/usr/bin/clang++
@@ -233,15 +244,13 @@ jobs:
             export CXXFLAGS="$CXXFLAGS -I$PREFIX/include"
             export LDFLAGS="$LDFLAGS -L$PREFIX/lib -lomp"
 
-            # cibuildwheel not recognising its environment variable, so set manually
-            export CIBUILDWHEEL="1"
-
             python scripts/install_KLU_Sundials.py
-            python -m cibuildwheel --output-dir wheelhouse
-        env:
           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 pybind11
           CIBW_REPAIR_WHEEL_COMMAND: |
+            export LD_LIBRARY_PATH=$(pwd)/sundials_KLU_libs/lib/:$LD_LIBRARY_PATH
+            echo "$LD_LIBRARY_PATH"
+
             if [[ $(uname -m) == "x86_64" ]]; then
               delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
             elif [[ $(uname -m) == "arm64" ]]; then
@@ -282,7 +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/update_version.yml

@@ -48,7 +48,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install wheel
+          pip install scikit-build-core
           pip install --editable ".[all]"
 
       # update all the version strings and add CHANGELOG headings

.gitignore

@@ -29,6 +29,7 @@
 *__pycache__/
 *.cache
 .ipynb_checkpoints/
+.pytest_cache
 
 # Sphinx build files
 docs/_build/
@@ -55,8 +56,7 @@ matplotlibrc
 ideas/
 .idea/
 
-# setup.py files
-*.egg-info
+# distribution files
 dist/
 
 # coverage
@@ -85,6 +85,7 @@ sundials-*
 SuiteSparse-*
 build_sundials
 KLU_module_deps
+sundials_KLU_libs/include
 
 # downloads
 *.gz

CMakeLists.txt

@@ -17,6 +17,8 @@ if(DEFINED ENV{VCPKG_DEFAULT_TRIPLET} AND NOT DEFINED VCPKG_TARGET_TRIPLET)
     CACHE STRING "Vcpkg target triplet")
 endif()
 
+set(CUSTOM_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/sundials_KLU_libs)
+
 project(idaklu)
 
 set(CMAKE_CXX_STANDARD 14)
@@ -32,10 +34,12 @@ endif()
 # casadi seems to compile without the newer versions of std::string
 add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)
 
+# Add pybind11
 if(NOT PYBIND11_DIR)
   set(PYBIND11_DIR pybind11)
 endif()
-add_subdirectory(${PYBIND11_DIR})
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+find_package(pybind11 CONFIG REQUIRED)
 
 # Check Casadi build flag
 if(NOT DEFINED PYBAMM_IDAKLU_EXPR_CASADI)
@@ -104,10 +108,11 @@ pybind11_add_module(idaklu
   src/pybamm/solvers/c_solvers/idaklu/Expressions/Base/ExpressionTypes.hpp
   # IDAKLU expressions - concrete implementations
   ${IDAKLU_EXPR_CASADI_SOURCE_FILES}
-  ${IDAKLU_EXPR_IREE_SOURCE_FILES}
-)
+  ${IDAKLU_EXPR_IREE_SOURCE_FILES})
 
-if (NOT DEFINED USE_PYTHON_CASADI)
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+  set(USE_PYTHON_CASADI FALSE)
+else()
   set(USE_PYTHON_CASADI TRUE)
 endif()
 
@@ -140,7 +145,10 @@ set_target_properties(
 )
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
+
 # Sundials
+set(SUNDIALS_ROOT ${CUSTOM_INSTALL_DIR})
+message("SUNDIALS_ROOT: ${SUNDIALS_ROOT}")
 find_package(SUNDIALS REQUIRED)
 message("SUNDIALS found in ${SUNDIALS_INCLUDE_DIR}: ${SUNDIALS_LIBRARIES}")
 target_include_directories(idaklu PRIVATE ${SUNDIALS_INCLUDE_DIR})
@@ -149,14 +157,16 @@ target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES} casadi)
 # link suitesparse
 # if using vcpkg, use config mode to
 # find suitesparse. Otherwise, use FindSuiteSparse module
+set(SUITESPARSE_ROOT ${CUSTOM_INSTALL_DIR})
+message("SUITESPARSE_ROOT: ${SUITESPARSE_ROOT}")
 if(DEFINED VCPKG_ROOT_DIR)
-  find_package(SuiteSparse CONFIG REQUIRED)
+  find_package(SUITESPARSE CONFIG REQUIRED)
 else()
-  find_package(SuiteSparse REQUIRED)
+  find_package(SUITESPARSE REQUIRED)
   message("SuiteSparse found in ${SuiteSparse_INCLUDE_DIRS}: ${SuiteSparse_LIBRARIES}")
 endif()
-include_directories(${SuiteSparse_INCLUDE_DIRS})
-target_link_libraries(idaklu PRIVATE ${SuiteSparse_LIBRARIES})
+include_directories(${SUITESPARSE_INCLUDE_DIRS})
+target_link_libraries(idaklu PRIVATE ${SUITESPARSE_LIBRARIES})
 
 # IREE (MLIR compiler and runtime library) build settings
 if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
@@ -170,3 +180,5 @@ if(${PYBAMM_IDAKLU_EXPR_IREE} STREQUAL "ON" )
   target_link_libraries(idaklu PRIVATE iree_compiler_bindings_c_loader)
   target_link_libraries(idaklu PRIVATE iree_runtime_runtime)
 endif()
+
+install(TARGETS idaklu DESTINATION src/pybamm/solvers)