From 2db10e469bd89ad8d8e14d4edb68ee28a1e90fd6 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Thu, 21 Nov 2024 22:21:08 +0000
Subject: [PATCH] #20 Make castxml and clang system dependencies

---
 .github/workflows/test-cells-conda.yml  |  5 +++--
 .github/workflows/test-cells-ubuntu.yml |  7 +++++--
 .github/workflows/test-shapes-pip.yml   |  2 +-
 README.md                               |  6 ++++++
 examples/cells/CMakeLists.txt           | 25 ++++++++++++++-----------
 setup.cfg                               |  1 -
 6 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/test-cells-conda.yml b/.github/workflows/test-cells-conda.yml
index 306cd04..23e490a 100644
--- a/.github/workflows/test-cells-conda.yml
+++ b/.github/workflows/test-cells-conda.yml
@@ -30,7 +30,7 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake git
+          sudo apt-get install castxml clang cmake git
 
       - name: Setup Miniconda Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v3
@@ -81,7 +81,8 @@ jobs:
         run: mamba install boa conda-build conda-verify
 
       - name: Build
-        run: conda mambabuild recipe -m variants/python${{ matrix.python-version }}.yaml
+        run: |
+          conda mambabuild recipe -m variants/python${{ matrix.python-version }}.yaml
         working-directory: examples/cells/conda
 
       - name: Install
diff --git a/.github/workflows/test-cells-ubuntu.yml b/.github/workflows/test-cells-ubuntu.yml
index b1360c9..715b687 100644
--- a/.github/workflows/test-cells-ubuntu.yml
+++ b/.github/workflows/test-cells-ubuntu.yml
@@ -41,6 +41,8 @@ jobs:
           echo "VTK version: ${vtk_ver}"
 
           sudo apt-get install \
+            castxml \
+            clang \
             cmake \
             git \
             libboost-all-dev \
@@ -58,8 +60,9 @@ jobs:
 
           # Check installed package versions
           dpkg-query -W \
+            castxml \
+            clang \
             cmake \
-            g++ \
             git \
             libboost-all-dev \
             libpetsc-real-dev \
@@ -73,7 +76,7 @@ jobs:
             python3-vtk${vtk_ver}
 
       - name: Install cppwg
-        run: pipx install . --include-deps
+        run: pipx install .
 
       - name: Configure
         run: |
diff --git a/.github/workflows/test-shapes-pip.yml b/.github/workflows/test-shapes-pip.yml
index bea7477..a7d01b8 100644
--- a/.github/workflows/test-shapes-pip.yml
+++ b/.github/workflows/test-shapes-pip.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake git
+          sudo apt-get install castxml clang cmake git
 
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
diff --git a/README.md b/README.md
index 697dfd6..6927ced 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,12 @@ Automatically generate pybind11 Python wrapper code for C++ projects.
 
 ## Installation
 
+Install CastXML (required) and Clang (recommended). On Ubuntu, this would be:
+
+```bash
+sudo apt-get install castxml clang
+```
+
 Clone the repository and install cppwg:
 
 ```bash
diff --git a/examples/cells/CMakeLists.txt b/examples/cells/CMakeLists.txt
index acec276..433499b 100644
--- a/examples/cells/CMakeLists.txt
+++ b/examples/cells/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.16...3.22)
+cmake_minimum_required(VERSION 3.16...3.28)
 project(pycells LANGUAGES C CXX)
 
 set(CMAKE_CXX_STANDARD 17)
@@ -53,25 +53,27 @@ file(GLOB_RECURSE MAIN_SOURCES
     ${CMAKE_SOURCE_DIR}/src/cpp/*.hpp
 )
 add_library(cells SHARED ${MAIN_SOURCES})
-target_link_libraries(cells PUBLIC
-    ${Boost_LIBRARIES}
-    ${VTK_LIBRARIES}
-    ${PETSC_LIBRARIES}
-    ${MPI_C_LIBRARIES}
-    ${MPI_CXX_LIBRARIES}
-)
 target_include_directories(cells PUBLIC
     ${CMAKE_SOURCE_DIR}/src/cpp
     ${CMAKE_SOURCE_DIR}/src/cpp/cell
     ${CMAKE_SOURCE_DIR}/src/cpp/mesh
     ${CMAKE_SOURCE_DIR}/src/cpp/utils
     ${CMAKE_SOURCE_DIR}/src/cpp/visualization
+)
+target_include_directories(cells SYSTEM PUBLIC
     ${Boost_INCLUDE_DIR}
     ${VTK_INCLUDE_DIRS}
     ${PETSC_INCLUDES}
     ${MPI_C_INCLUDE_PATH}
     ${MPI_CXX_INCLUDE_PATH}
 )
+target_link_libraries(cells PUBLIC
+    ${Boost_LIBRARIES}
+    ${VTK_LIBRARIES}
+    ${PETSC_LIBRARIES}
+    ${MPI_C_LIBRARIES}
+    ${MPI_CXX_LIBRARIES}
+)
 
 # Set up the pycells module with pybind11
 file(GLOB WRAPPER_SOURCES
@@ -79,14 +81,14 @@ file(GLOB WRAPPER_SOURCES
     ${CMAKE_SOURCE_DIR}/dynamic/wrappers/all/*.hpp
 )
 pybind11_add_module(_pycells_all MODULE ${WRAPPER_SOURCES})
-target_link_libraries(_pycells_all PRIVATE cells)
 target_include_directories(_pycells_all PRIVATE
     ${CMAKE_SOURCE_DIR}/dynamic/wrappers/all
     ${CMAKE_SOURCE_DIR}/dynamic/typecasters/
     ${CMAKE_SOURCE_DIR}/dynamic/typecasters/thirdparty/dolfinx
     ${CMAKE_SOURCE_DIR}/dynamic/typecasters/thirdparty/smtk
-    ${PETSC4PY_INCLUDES}
 )
+target_include_directories(_pycells_all SYSTEM PRIVATE ${PETSC4PY_INCLUDES})
+target_link_libraries(_pycells_all PRIVATE cells)
 
 # Add install targets for scikit-build
 if(SKBUILD)
@@ -106,7 +108,8 @@ add_custom_target(pycells_wrappers
     COMMAND ${CPPWG} ${CMAKE_SOURCE_DIR}/src/cpp
             -w ${CMAKE_SOURCE_DIR}/dynamic/wrappers
             -p ${CMAKE_SOURCE_DIR}/dynamic/config.yaml
-            -i "$<JOIN:$<TARGET_PROPERTY:_pycells_all,INCLUDE_DIRECTORIES>,;>"
+            -i "$<JOIN:$<TARGET_PROPERTY:cells,INCLUDE_DIRECTORIES>,;>"
+               "$<JOIN:$<TARGET_PROPERTY:_pycells_all,INCLUDE_DIRECTORIES>,;>"
             -l ${CMAKE_BINARY_DIR}/cppwg.log
             --std c++17
     COMMAND_EXPAND_LISTS
diff --git a/setup.cfg b/setup.cfg
index 2022a7a..04f5f7a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,6 @@ python_requires = >=3.8
 install_requires =
     pyyaml>=6.0
     pygccxml>=2.2
-    castxml>=0.4
 
 [options.entry_points]
 console_scripts =