Specify pybind11 as a build-time dependency

.github/workflows/benchmark_on_push.yml

@@ -22,11 +22,11 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev
+          sudo apt-get install gfortran gcc libopenblas-dev
 
-      - name: Install python dependencies
+      - name: Install Python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m pip install --upgrade pip wheel setuptools wget cmake casadi pybind11[global]
           python -m pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS

.github/workflows/periodic_benchmarks.yml

@@ -55,6 +55,7 @@ jobs:
 
   publish-results:
     name: Push and publish results
+    if: github.repository == 'pybamm-team/pybamm'
     needs: benchmarks
     runs-on: ubuntu-latest
     steps:

.github/workflows/publish_pypi.yml

@@ -26,9 +26,6 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
-
       - name: Install vcpkg on Windows
         run: |
           cd C:\
@@ -76,9 +73,6 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
-
       # sometimes gfortran cannot be found, so reinstall gcc just to be sure
       - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-latest'
@@ -173,7 +167,7 @@ jobs:
   open_failure_issue:
     needs: [build_windows_wheels, build_wheels, build_sdist]
     name: Open an issue if build fails
-    if: ${{ always() && contains(needs.*.result, 'failure') }}
+    if: contains(needs.*.result, 'failure') && github.repository == 'pybamm-team/PyBaMM'
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4

.github/workflows/run_periodic_tests.yml

@@ -73,8 +73,8 @@ jobs:
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=2.38.0.20190211
 
-      - name: Install nox
-        run: python -m pip install nox
+      - name: Install nox and CMake
+        run: python -m pip install nox cmake
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
         if: matrix.os != 'windows-latest'

.github/workflows/test_on_push.yml

@@ -91,16 +91,15 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
 
-      - name: Install nox
-        run: python -m pip install nox
+      - name: Install nox and CMake
+        run: python -m pip install nox cmake
 
       - name: Cache pybamm-requires nox environment for GNU/Linux and macOS
         uses: actions/cache@v3
         if: matrix.os != 'windows-latest'
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
@@ -148,15 +147,14 @@ jobs:
           python-version: 3.11
           cache: 'pip'
 
-      - name: Install nox
-        run: python -m pip install nox
+      - name: Install nox and CMake
+        run: python -m pip install nox cmake
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
@@ -229,16 +227,15 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
 
-      - name: Install nox
-        run: python -m pip install nox
+      - name: Install nox and CMake
+        run: python -m pip install nox cmake
 
       - name: Cache pybamm-requires nox environment for GNU/Linux and macOS
         uses: actions/cache@v3
         if: matrix.os != 'windows-latest'
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
@@ -270,15 +267,15 @@ jobs:
       - name: Install Linux system dependencies
         uses: awalsh128/cache-apt-pkgs-action@v1.3.1
         with:
-          packages: gfortran gcc graphviz pandoc
+          packages: graphviz pandoc
           execute_install_scripts: true
 
       # dot -c is for registering graphviz fonts and plugins
-      - name: Install OpenBLAS and TeXLive for Linux
+      - name: Install TeXLive for Linux
         run: |
           sudo apt-get update
           sudo dot -c
-          sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
+          sudo apt-get install texlive-latex-extra dvipng
 
       - name: Set up Python 3.11
         id: setup-python
@@ -329,15 +326,14 @@ jobs:
           python-version: 3.11
           cache: 'pip'
 
-      - name: Install nox
-        run: python -m pip install nox
+      - name: Install nox and CMake
+        run: python -m pip install nox cmake
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
@@ -384,15 +380,14 @@ jobs:
           python-version: 3.11
           cache: 'pip'
 
-      - name: Install nox
-        run: python -m pip install nox
+      - name: Install nox and CMake
+        run: python -m pip install nox cmake
 
       - name: Cache pybamm-requires nox environment for GNU/Linux
         uses: actions/cache@v3
         with:
           path: |
             # Repository files
-            ${{ github.workspace }}/pybind11/
             ${{ github.workspace }}/install_KLU_Sundials/
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/

.gitignore

@@ -98,9 +98,6 @@ Makefile
 cmake_install.cmake
 *.so
 
-third-party/pybind11
-pybind11/
-
 # Build dependencies/
 KLU_module_deps
 

CHANGELOG.md

@@ -18,6 +18,7 @@
 
 ## Optimizations
 
+- Added `pybind11` as a build-time dependency, therefore simplifying the installation process ([#3560](https://github.com/pybamm-team/PyBaMM/pull/3560))
 - 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

CMakeLists.txt

@@ -32,11 +32,8 @@ endif()
 # casadi seems to compile without the newer versions of std::string
 add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)
 
-if(NOT PYBIND11_DIR)
-  set(PYBIND11_DIR pybind11)
-endif()
+find_package(pybind11 CONFIG REQUIRED)
 
-add_subdirectory(${PYBIND11_DIR})
 pybind11_add_module(idaklu
   pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp
   pybamm/solvers/c_solvers/idaklu/casadi_functions.hpp

asv.conf.json

@@ -4,10 +4,10 @@
   "version": 1,
 
   // The name of the project being benchmarked
-  "project": "PyBaMM",
+  "project": "pybamm",
 
   // The project's homepage
-  "project_url": "https://www.pybamm.org/",
+  "project_url": "https://pybamm.org/",
 
   // The URL or local path of the source code repository for the
   // project being benchmarked
@@ -23,12 +23,6 @@
   //
   // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
   // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
-  "build_command": [
-    "/bin/rm -rf pybind11",
-    "/usr/bin/git clone --depth 1 --branch v2.6.2 https://github.com/pybind/pybind11.git",
-    "python setup.py build",
-    "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
-  ],
 
   // List of branches to benchmark. If not provided, defaults to "master"
   // (for git) or "default" (for mercurial).
@@ -87,7 +81,7 @@
       "sympy": [],
       "bpx": [],
       "tqdm": [],
-      "matplotlib": [],
+      "matplotlib": []
     },
     "env": {
       "LD_LIBRARY_PATH": "/home/runner/.local/lib"

docs/source/user_guide/installation/install-from-source.rst

@@ -86,11 +86,9 @@ Manual install of build time requirements
 
 If you'd rather do things yourself,
 
-1. Make sure you have CMake installed
+1. Make sure you have CMake installed. CMake can be installed using ``pip``, ``brew``, or your system's package manager.
 2. Compile and install SuiteSparse (PyBaMM only requires the ``KLU`` component).
 3. Compile and install SUNDIALS.
-4. Clone the pybind11 repository in the ``PyBaMM/`` directory (make sure the directory is named ``pybind11``).
-
 
 PyBaMM ships with a Python script that automates points 2. and 3. You can run it with
 

noxfile.py

@@ -43,14 +43,6 @@ def run_pybamm_requires(session):
     if sys.platform != "win32":
         session.install("wget", "cmake", silent=False)
         session.run("python", "scripts/install_KLU_Sundials.py")
-        if not os.path.exists("./pybind11"):
-            session.run(
-                "git",
-                "clone",
-                "https://github.com/pybind/pybind11.git",
-                "pybind11/",
-                external=True,
-            )
     else:
         session.error("nox -s pybamm-requires is only available on Linux & macOS.")
 

pyproject.toml

@@ -2,11 +2,14 @@
 requires = [
     "setuptools>=64",
     "wheel",
-    # On Windows, use the CasADi vcpkg registry and CMake bundled from MSVC
+    # On Windows, use the CasADi vcpkg registry
     "casadi>=3.6.3; platform_system!='Windows'",
-    "cmake; platform_system!='Windows'",
+    "pybind11[global]>=2.11.1",
     ]
 build-backend = "setuptools.build_meta"
+# Note: CMake is required to compile the IDAKLU solver but is not bundled with
+# PyBaMM as a build-time dependency. If CMake is not installed, the IDAKLU
+# solver compilation does not proceed.
 
 [project]
 name = "pybamm"

scripts/Dockerfile

@@ -38,8 +38,6 @@ RUN pip install cmake
 
 RUN if [ "$IDAKLU" = "true" ]; then \
     python scripts/install_KLU_Sundials.py && \
-    rm -rf pybind11 && \
-    git clone https://github.com/pybind/pybind11.git && \
     pip install --user -e ".[all,dev,docs]"; \
     fi
 
@@ -54,8 +52,6 @@ RUN if [ "$JAX" = "true" ]; then \
 
 RUN if [ "$ALL" = "true" ]; then \
     python scripts/install_KLU_Sundials.py && \
-    rm -rf pybind11 && \
-    git clone https://github.com/pybind/pybind11.git && \
     pip install --user -e ".[all,dev,docs,jax,odes]"; \
     fi
 

setup.py

@@ -241,37 +241,35 @@ def run(self):
 
 
 def compile_KLU():
-    # Return whether or not the KLU extension should be compiled.
-    # Return True if:
-    # - Not running on Windows AND
-    # - CMake is found AND
-    # - The pybind11/ directory is found in the PyBaMM project directory
+    # Decide whether or not the KLU extension should be compiled.
+    # Return True if both of the following conditions are met:
+    #
+    # 1. CMake is found
+    # 2. pybind11 is found
+    #
+    # Otherwise, return False
+
     CMakeFound = True
     PyBind11Found = True
-    windows = (not system()) or system() == "Windows"
-
-    msg = "Running on Windows" if windows else "Not running on windows"
-    logger.info(msg)
 
+    # CMake
     try:
         subprocess.run(["cmake", "--version"])
         logger.info("Found CMake.")
     except OSError:
         CMakeFound = False
         logger.info("Could not find CMake. Skipping compilation of KLU module.")
 
-    pybamm_project_dir = os.path.dirname(os.path.abspath(__file__))
-    pybind11_dir = os.path.join(pybamm_project_dir, "pybind11")
+    # pybind11
     try:
-        open(os.path.join(pybind11_dir, "tools", "pybind11Tools.cmake"))
-        logger.info(f"Found pybind11 directory ({pybind11_dir})")
-    except FileNotFoundError:
+        from pybind11 import get_cmake_dir
+        pybind11_config = os.path.join(get_cmake_dir(), "pybind11Tools.cmake")
+        if not os.path.isfile(pybind11_config):
+            raise FileNotFoundError
+        logger.info("Found pybind11")
+    except ModuleNotFoundError or FileNotFoundError:
         PyBind11Found = False
-        msg = (
-            f"Could not find PyBind11 directory ({pybind11_dir})."
-            " Skipping compilation of KLU module."
-        )
-        logger.info(msg)
+        logger.info("Could not find pybind11. Skipping compilation of KLU module.")
 
     return CMakeFound and PyBind11Found