Fix SEGV w/ python and conda on macOS

.github/workflows/ci.yml

@@ -18,29 +18,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-11, windows-2019]
-        sofa_branch: [master]
-        python_version: ['3.8']
+        os: [ubuntu-22.04, macos-13, windows-2022]
+        sofa_branch: [v23.12]
+        python_version: ['3.10']
 
     steps:
-      - name: (Mac) Workaround for homebrew
-        shell: bash
-        if: runner.os == 'macOS'
-        run: |
-            rm -f /usr/local/bin/2to3
-            rm -f /usr/local/bin/idle3
-            rm -f /usr/local/bin/pydoc3
-            rm -f /usr/local/bin/python3
-            rm -f /usr/local/bin/python3-config
-            rm -f /usr/local/bin/2to3-3.11
-            rm -f /usr/local/bin/idle3.11
-            rm -f /usr/local/bin/pydoc3.11
-            rm -f /usr/local/bin/python3.11
-            rm -f /usr/local/bin/python3.11-config
-
       - name: Setup SOFA and environment
         id: sofa
-        uses: sofa-framework/sofa-setup-action@v4
+        uses: sofa-framework/sofa-setup-action@v5
         with:
           sofa_root: ${{ github.workspace }}/sofa
           sofa_version: ${{ matrix.sofa_branch }}
@@ -66,7 +51,7 @@ jobs:
           cmake_options="-GNinja \
             -DCMAKE_BUILD_TYPE=Release \
             -DCMAKE_INSTALL_PREFIX="$WORKSPACE_INSTALL_PATH" \
-            -DCMAKE_PREFIX_PATH="$SOFA_ROOT/lib/cmake" \
+            -DCMAKE_PREFIX_PATH="$SOFA_ROOT/lib/cmake:$pybind11_DIR" \
             -DPYTHON_ROOT=$PYTHON_ROOT -DPython_ROOT=$PYTHON_ROOT \
             -DPYTHON_EXECUTABLE=$PYTHON_EXE -DPython_EXECUTABLE=$PYTHON_EXE"
           if [ -e "$(command -v ccache)" ]; then
@@ -98,7 +83,7 @@ jobs:
           if [[ "${{ github.event.inputs.is_nightly }}" == "true" ]]; then
             ARTIFACT_VERSION="${ARTIFACT_VERSION}-nightly"
           fi
-          ARTIFACT_NAME="${PROJECT_NAME}_${ARTIFACT_VERSION}_python-${{ matrix.python_version }}_for-SOFA-${{ matrix.sofa_branch }}_${{ runner.os }}"
+          ARTIFACT_NAME="${PROJECT_NAME}_${ARTIFACT_VERSION}_python-${{ matrix.python_version }}_for-SOFA-${{ steps.sofa.outputs.sofa_version }}_${{ runner.os }}"
           echo "ARTIFACT_NAME=$ARTIFACT_NAME" | tee -a $GITHUB_ENV
 
       - name: Create artifact
@@ -177,7 +162,7 @@ jobs:
 
   deploy:
     name: Deploy artifacts
-    if: always() && startsWith(github.ref, 'refs/heads/') # we are on a branch (not a PR)
+    if: always() && startsWith(github.repository, 'sofa-framework') && (startsWith(github.ref, 'refs/heads/') || startsWith(github.ref, 'refs/tags/')) # we are not on a fork and on a branch or a tag (not a PR)
     needs: [build-and-test]
     runs-on: ubuntu-latest
     continue-on-error: true

CMake/SofaPython3Tools.cmake

@@ -114,44 +114,9 @@ function(SP3_add_python_module)
 
     find_package(pybind11 CONFIG QUIET REQUIRED)
 
-    # We are doing manually what's usually done with pybind11_add_module(${A_TARGET} SHARED "${A_SOURCES}")
-    # since we got some problems on MacOS using recent versions of pybind11 where the SHARED argument wasn't taken
-    # into account
-    python_add_library(${A_TARGET} SHARED "${A_SOURCES}")
+    pybind11_add_module(${A_TARGET} SHARED "${A_SOURCES}")
     add_library(SofaPython3::${A_TARGET} ALIAS ${A_TARGET})
 
-    if ("${pybind11_VERSION}" VERSION_GREATER_EQUAL "2.6.0")
-        target_link_libraries(${A_TARGET} PRIVATE pybind11::headers)
-        target_link_libraries(${A_TARGET} PRIVATE pybind11::embed)
-        target_link_libraries(${A_TARGET} PRIVATE pybind11::lto)
-        if(MSVC)
-            target_link_libraries(${A_TARGET} PRIVATE pybind11::windows_extras)
-        endif()
-
-        pybind11_extension(${A_TARGET})
-        pybind11_strip(${A_TARGET})
-    else()
-        target_link_libraries(${A_TARGET} PRIVATE pybind11::module)
-
-        # Equivalent to pybind11_extension(${A_TARGET}) which doesn't exists on pybind11 versions < 5
-        set_target_properties(${A_TARGET} PROPERTIES PREFIX "" SUFFIX "${PYTHON_MODULE_EXTENSION}")
-
-        if(NOT MSVC AND NOT ${CMAKE_BUILD_TYPE} MATCHES Debug|RelWithDebInfo)
-            # Equivalent to pybind11_strip(${A_TARGET}) which doesn't exists on pybind11 versions < 5
-            # Strip unnecessary sections of the binary on Linux/macOS
-            if(CMAKE_STRIP)
-                if(APPLE)
-                    set(x_opt -x)
-                endif()
-
-                add_custom_command(
-                        TARGET ${A_TARGET}
-                        POST_BUILD
-                        COMMAND ${CMAKE_STRIP} ${x_opt} $<TARGET_FILE:${A_TARGET}>)
-            endif()
-        endif()
-    endif()
-
     set_target_properties(${A_TARGET}
         PROPERTIES
             CXX_VISIBILITY_PRESET "hidden"

CMakeLists.txt

@@ -82,34 +82,6 @@ set_property(GLOBAL PROPERTY USE_FOLDERS ON)
 # Set the minimum python version to 3.7
 set(PYBIND11_PYTHON_VERSION 3.7)
 
-# Find Python3
-find_package(Python ${PYBIND11_PYTHON_VERSION} COMPONENTS Interpreter Development REQUIRED)
-
-# Save PYTHON_* vars
-set(PYTHON_VERSION_RESET "${PYTHON_VERSION}")
-set(PYTHON_EXECUTABLE_RESET "${PYTHON_EXECUTABLE}")
-set(PYTHON_LIBRARIES_RESET "${PYTHON_LIBRARIES}")
-set(PYTHON_INCLUDE_DIRS_RESET "${PYTHON_INCLUDE_DIRS}")
-set(PYTHON_LIBRARY_RESET "${PYTHON_LIBRARY}")
-set(PYTHON_INCLUDE_DIR_RESET "${PYTHON_INCLUDE_DIR}")
-
-# Change PYTHON_* vars before pybind11 find_package
-# to be sure that pybind11 relies on the right Python version
-set(PYTHON_VERSION "${Python_VERSION}" CACHE STRING "" FORCE)
-set(PYTHON_EXECUTABLE "${Python_EXECUTABLE}" CACHE FILEPATH "" FORCE)
-set(PYTHON_LIBRARIES "${Python_LIBRARIES}" CACHE STRING "" FORCE)
-set(PYTHON_INCLUDE_DIRS "${Python_INCLUDE_DIRS}" CACHE STRING "" FORCE)
-if(EXISTS "${Python_LIBRARY}")
-    set(PYTHON_LIBRARY "${Python_LIBRARY}" CACHE INTERNAL "" FORCE)
-elseif(EXISTS "${Python_LIBRARIES}")
-    set(PYTHON_LIBRARY "${Python_LIBRARIES}" CACHE INTERNAL "" FORCE)
-endif()
-if(EXISTS "${Python_INCLUDE_DIR}")
-    set(PYTHON_INCLUDE_DIR "${Python_INCLUDE_DIR}" CACHE INTERNAL "" FORCE)
-elseif(EXISTS "${Python_INCLUDE_DIRS}")
-    set(PYTHON_INCLUDE_DIR "${Python_INCLUDE_DIRS}" CACHE INTERNAL "" FORCE)
-endif()
-
 # Set the minimum pybind11 version to 2.3 (before that the pybind11::embed target did not exist)
 find_package(pybind11 2.3 CONFIG QUIET REQUIRED)
 
@@ -243,11 +215,3 @@ if (SP3_LINK_TO_USER_SITE AND SP3_PYTHON_PACKAGES_LINK_DIRECTORY)
         endif()
     endforeach()
 endif()
-
-# Reset PYTHON_* vars
-set(PYTHON_VERSION "${PYTHON_VERSION_RESET}" CACHE STRING "" FORCE)
-set(PYTHON_EXECUTABLE "${PYTHON_EXECUTABLE_RESET}" CACHE FILEPATH "" FORCE)
-set(PYTHON_LIBRARIES "${PYTHON_LIBRARIES_RESET}" CACHE STRING "" FORCE)
-set(PYTHON_INCLUDE_DIRS "${PYTHON_INCLUDE_DIRS_RESET}" CACHE STRING "" FORCE)
-set(PYTHON_LIBRARY "${PYTHON_LIBRARY_RESET}" CACHE INTERNAL "" FORCE)
-set(PYTHON_INCLUDE_DIR "${PYTHON_INCLUDE_DIR_RESET}" CACHE INTERNAL "" FORCE)

Plugin/CMakeLists.txt

@@ -35,7 +35,17 @@ add_library(SofaPython3::${PROJECT_NAME} ALIAS ${PROJECT_NAME})
 target_compile_definitions(${PROJECT_NAME} PRIVATE "-DSOFA_BUILD_SOFAPYTHON3")
 
 target_link_libraries(${PROJECT_NAME} PUBLIC Sofa.Simulation.Graph)
-target_link_libraries(${PROJECT_NAME} PUBLIC pybind11::module pybind11::embed)
+
+# The public linking with pybind lead to have a link with libpython which
+# propagates in the python module .so. On macOS, this extra link with libpython
+# lead to segv when importing the python module in versions of python that don't
+# have a dynamic link with libpython (such as the one provided by conda which is linked
+# statically), but works fine with versions that have such link.
+if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
+  target_link_libraries(${PROJECT_NAME} PRIVATE pybind11::pybind11 pybind11::python_link_helper)
+else()
+  target_link_libraries(${PROJECT_NAME} PUBLIC pybind11::embed)
+endif()
 
 set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME SofaPython3)
 

SofaPython3Config.cmake.in

@@ -8,47 +8,10 @@ set(SP3_PYTHON_PACKAGES_DIRECTORY @SP3_PYTHON_PACKAGES_DIRECTORY@)
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}")
 include(SofaPython3Tools)
 
-# Find Python3
-if(NOT Python_FOUND)
-    find_package(Python @Python_VERSION@ QUIET REQUIRED COMPONENTS Interpreter Development)
-endif()
 
 # Find pybind11
 if(NOT pybind11_FOUND)
-    # Save PYTHON_* vars
-    set(PYTHON_VERSION_RESET "${PYTHON_VERSION}")
-    set(PYTHON_EXECUTABLE_RESET "${PYTHON_EXECUTABLE}")
-    set(PYTHON_LIBRARIES_RESET "${PYTHON_LIBRARIES}")
-    set(PYTHON_INCLUDE_DIRS_RESET "${PYTHON_INCLUDE_DIRS}")
-    set(PYTHON_LIBRARY_RESET "${PYTHON_LIBRARY}")
-    set(PYTHON_INCLUDE_DIR_RESET "${PYTHON_INCLUDE_DIR}")
-
-    # Change PYTHON_* vars before pybind11 find_package
-    # to be sure that pybind11 relies on the right Python version
-    set(PYTHON_VERSION "${Python_VERSION}" CACHE STRING "" FORCE)
-    set(PYTHON_EXECUTABLE "${Python_EXECUTABLE}" CACHE FILEPATH "" FORCE)
-    set(PYTHON_LIBRARIES "${Python_LIBRARIES}" CACHE STRING "" FORCE)
-    set(PYTHON_INCLUDE_DIRS "${Python_INCLUDE_DIRS}" CACHE STRING "" FORCE)
-    if(EXISTS "${Python_LIBRARY}")
-        set(PYTHON_LIBRARY "${Python_LIBRARY}" CACHE INTERNAL "" FORCE)
-    elseif(EXISTS "${Python_LIBRARIES}")
-        set(PYTHON_LIBRARY "${Python_LIBRARIES}" CACHE INTERNAL "" FORCE)
-    endif()
-    if(EXISTS "${Python_INCLUDE_DIR}")
-        set(PYTHON_INCLUDE_DIR "${Python_INCLUDE_DIR}" CACHE INTERNAL "" FORCE)
-    elseif(EXISTS "${Python_INCLUDE_DIRS}")
-        set(PYTHON_INCLUDE_DIR "${Python_INCLUDE_DIRS}" CACHE INTERNAL "" FORCE)
-    endif()
-
     find_package(pybind11 @pybind11_VERSION@ QUIET REQUIRED CONFIG)
-
-    # Reset PYTHON_* vars
-    set(PYTHON_VERSION "${PYTHON_VERSION_RESET}" CACHE STRING "" FORCE)
-    set(PYTHON_EXECUTABLE "${PYTHON_EXECUTABLE_RESET}" CACHE FILEPATH "" FORCE)
-    set(PYTHON_LIBRARIES "${PYTHON_LIBRARIES_RESET}" CACHE STRING "" FORCE)
-    set(PYTHON_INCLUDE_DIRS "${PYTHON_INCLUDE_DIRS_RESET}" CACHE STRING "" FORCE)
-    set(PYTHON_LIBRARY "${PYTHON_LIBRARY_RESET}" CACHE INTERNAL "" FORCE)
-    set(PYTHON_INCLUDE_DIR "${PYTHON_INCLUDE_DIR_RESET}" CACHE INTERNAL "" FORCE)
 endif()
 
 # Find SofaPython3::XXXXX

Testing/CMakeLists.txt

@@ -16,6 +16,11 @@ set(SOURCE_FILES
 
 add_library(${PROJECT_NAME} SHARED ${HEADER_FILES} ${SOURCE_FILES})
 target_link_libraries(${PROJECT_NAME} PUBLIC Sofa.Testing SofaPython3::Plugin)
+# We wan't the pybind11 dependency to propagate to SofaPython3Testing consumers,
+# here Bindings.*.Tests
+if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
+  target_link_libraries(${PROJECT_NAME} PUBLIC pybind11::embed)
+endif()
 target_compile_definitions(${PROJECT_NAME} PRIVATE "-DSOFA_BUILD_SOFAPYTHON3")
 set_target_properties(${PROJECT_NAME} PROPERTIES FOLDER Testing)