Merge branch 'master' into header-hygiene-cabcode

CMakeLists.txt

@@ -247,6 +247,13 @@ include("${CODING_CONV_CMAKE}/3rdparty.cmake")
 cpp_cc_git_submodule(Random123)
 cpp_cc_git_submodule(eigen)
 
+if(NRN_ENABLE_CORENEURON)
+  file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/external/Random123/include/Random123"
+       DESTINATION "${CMAKE_BINARY_DIR}/include/")
+  file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/external/eigen/Eigen"
+       DESTINATION "${CMAKE_BINARY_DIR}/include/")
+endif()
+
 # =================================================================================================
 # Enable sanitizer support if the NRN_SANITIZERS variable is set. Comes befores PythonHelper.cmake.
 # =================================================================================================

bin/nrnivmodl-core.in

@@ -19,15 +19,7 @@ APP_NAME="$(basename "$0")"
 
 # directory and parent directory of this script
 PARENT_DIR="$(dirname "$BASH_SOURCE")/.."
-
-# prefer perl exe set by neuron wrappers in case of wheel
-PERL_EXE="${CORENRN_PERLEXE:-@PERL_EXECUTABLE@}"
-# in case of mac installer, wrapper is not used and hence
-# check if binary exist. otherwise, just rely on perl being
-# in default $PATH
-if [ ! -f "${PERL_EXE}" ]; then PERL_EXE="$(which perl)"; fi
-
-ROOT_DIR="$("${PERL_EXE}" -e "use Cwd 'abs_path'; print abs_path('$PARENT_DIR')")"
+ROOT_DIR="$(readlink -f "$PARENT_DIR")"
 
 # default arguments : number of parallel builds and default mod file path
 PARALLEL_BUILDS=4

bin/nrnivmodl_core_makefile.in

@@ -57,21 +57,17 @@ endif
 # binary used during build. If they don't exist then simply use python and
 # perl as the name of binaries.
 CORENRN_PYTHONEXE ?= @NRN_DEFAULT_PYTHON_EXECUTABLE@
-CORENRN_PERLEXE ?= @PERL_EXECUTABLE@
 ifeq ($(wildcard $(CORENRN_PYTHONEXE)),)
   CORENRN_PYTHONEXE=python
 endif
-ifeq ($(wildcard $(CORENRN_PERLEXE)),)
-  CORENRN_PERLEXE=perl
-endif
 
 CXXFLAGS = @CORENRN_CXX_FLAGS@
 CXX_COMPILE_CMD = $(CXX) $(CXXFLAGS) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ $(INCLUDES)
 CXX_LINK_EXE_CMD = $(CXX) $(CXXFLAGS) @CMAKE_EXE_LINKER_FLAGS@
 CXX_SHARED_LIB_CMD = $(CXX) $(CXXFLAGS) @CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS@ @CMAKE_SHARED_LIBRARY_CXX_FLAGS@ @CMAKE_SHARED_LINKER_FLAGS@
 
 # env variables required for mod2c or nmodl
-NMODL_ENV_VAR = @CORENRN_SANITIZER_ENABLE_ENVIRONMENT_STRING@ PYTHONPATH=${PYTHONPATH}:@CORENRN_NMODL_PYTHONPATH@:${CORENRN_LIB_DIR}/python MODLUNIT=$(CORENRN_SHARE_NMODL_DIR)/nrnunits.lib
+NMODL_ENV_VAR = @CORENRN_SANITIZER_ENABLE_ENVIRONMENT_STRING@ PYTHONPATH=${PYTHONPATH}:${CORENRN_LIB_DIR}/python MODLUNIT=$(CORENRN_SHARE_NMODL_DIR)/nrnunits.lib
 
 ifeq (@CORENRN_ENABLE_GPU@, ON)
     nmodl_arguments_c=@NMODL_ACC_BACKEND_ARGS@ @NMODL_COMMON_ARGS@
@@ -100,7 +96,6 @@ endif
 # Binary of NMODL depending on CMake option activated
 ifeq (@nmodl_FOUND@, TRUE)
     NMODL_BINARY_PATH = $(if $(NMODL_BINARY),$(NMODL_BINARY), @CORENRN_NMODL_BINARY@)
-    INCLUDES += -I@CORENRN_NMODL_INCLUDE@
 else
     NMODL_BINARY_PATH = $(if $(NMODL_BINARY),$(NMODL_BINARY), $(CORENRN_BIN_DIR)/@nmodl_binary_name@)
 endif
@@ -189,7 +184,7 @@ $(mod_cpp_files): $(MOD_TO_CPP_DIR)/%.cpp: $(MODS_PATH)/%.mod | $(MOD_TO_CPP_DIR
 
 # generate mod registration function. Dont overwrite if it's not changed
 $(MOD_FUNC_CPP): build_always | $(MOD_TO_CPP_DIR)
-	$(CORENRN_PERLEXE) $(CORENRN_SHARE_CORENRN_DIR)/mod_func.c.pl $(mod_files_names) > $(MOD_FUNC_CPP).tmp
+	bash $(CORENRN_SHARE_CORENRN_DIR)/mod_func.c.sh $(mod_files_names) > $(MOD_FUNC_CPP).tmp
 	diff -q $(MOD_FUNC_CPP).tmp $(MOD_FUNC_CPP) || \
 	mv $(MOD_FUNC_CPP).tmp $(MOD_FUNC_CPP)
 

ci/win_install_deps.cmd

@@ -28,7 +28,8 @@ C:\Python39\python.exe -m pip install  numpy==1.19.3 "cython < 3" || goto :error
 C:\Python310\python.exe -m pip install numpy==1.21.3 "cython < 3" || goto :error
 C:\Python311\python.exe -m pip install numpy==1.23.5 "cython < 3" || goto :error
 C:\Python312\python.exe -m pip install numpy==1.26.3 "cython < 3" || goto :error
-C:\Python312\python.exe -m pip install setuptools || goto :error
+:: setuptools 70.2 leads to an error
+C:\Python312\python.exe -m pip install setuptools==70.1.1 || goto :error
 
 :: install nsis
 nsis-3.05-setup.exe /S || goto :error

cmake/NanoBindMinimal.cmake

@@ -17,5 +17,4 @@ function(make_nanobind_target TARGET_NAME PYINC)
   endif()
   target_compile_features(${TARGET_NAME} PUBLIC cxx_std_17)
   set_property(TARGET ${TARGET_NAME} PROPERTY POSITION_INDEPENDENT_CODE True)
-  set_property(TARGET ${TARGET_NAME} PROPERTY INTERPROCEDURAL_OPTIMIZATION_RELEASE ON)
 endfunction()

cmake/coreneuron/packages/Findnmodl.cmake

@@ -17,15 +17,13 @@
 # ::
 #   set(CORENRN_NMODL_DIR "" CACHE PATH "Path to nmodl source-to-source compiler installation")
 #   find_package(nmodl REQUIRED)
-#   include_directories(${nmodl_INCLUDE_DIRS})
 #   target_link_libraries(foo ${nmodl_LIBRARIES})
 #
 # This module sets the following variables:
 #
 # ::
 #
 #   nmodl_FOUND   - set to true if the library is found
-#   nmodl_INCLUDE - list of required include directories
 #   nmodl_BINARY  - the nmodl binary
 # ~~~
 
@@ -35,13 +33,10 @@ find_program(
   NAMES nmodl${CMAKE_EXECUTABLE_SUFFIX}
   HINTS "${CORENRN_NMODL_DIR}/bin" QUIET)
 
-find_path(nmodl_INCLUDE "nmodl.hpp" HINTS "${CORENRN_NMODL_DIR}/include")
-find_path(nmodl_PYTHONPATH "nmodl/__init__.py" HINTS "${CORENRN_NMODL_DIR}/lib")
-
 # Checks 'REQUIRED', 'QUIET' and versions.
 include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(
   nmodl
   FOUND_VAR nmodl_FOUND
-  REQUIRED_VARS nmodl_BINARY nmodl_INCLUDE nmodl_PYTHONPATH)
+  REQUIRED_VARS nmodl_BINARY)

packaging/python/build_requirements.txt

@@ -1,2 +1,8 @@
 cython<3
 packaging
+numpy==1.17.5;python_version=='3.8'
+numpy==1.19.3;python_version=='3.9' and platform_machine=='x86_64'
+numpy==1.21.3;python_version=='3.9' and platform_machine=='arm64'
+numpy==1.21.3;python_version=='3.10'
+numpy==1.23.5;python_version=='3.11'
+numpy==1.26.0;python_version=='3.12'

packaging/python/build_wheels.bash

@@ -25,10 +25,11 @@ fi
 
 py_ver=""
 
-clone_install_nmodl_requirements() {
+clone_nmodl_and_add_requirements() {
     git config --global --add safe.directory /root/nrn
     git submodule update --init --recursive --force --depth 1 -- external/nmodl
-    pip install -r external/nmodl/requirements.txt
+    # We only want the _build_ dependencies
+    sed -e '/^# runtime dependencies/,$ d' external/nmodl/requirements.txt >> my_requirements.txt
 }
 
 
@@ -52,29 +53,6 @@ setup_venv() {
 }
 
 
-pip_numpy_install() {
-    # numpy is special as we want the minimum wheel version
-    numpy_ver="numpy"
-    case "$py_ver" in
-      36) numpy_ver="numpy==1.12.1" ;;
-      37) numpy_ver="numpy==1.14.6" ;;
-      38) numpy_ver="numpy==1.17.5" ;;
-      39) numpy_ver="numpy==1.19.3" ;;
-      310) numpy_ver="numpy==1.21.3" ;;
-      311) numpy_ver="numpy==1.23.5" ;;
-      312) numpy_ver="numpy==1.26.0" ;;
-      *) echo "Error: numpy version not specified for this python!" && exit 1;;
-    esac
-
-    # older version for apple m1 as building from source fails
-    if [[ `uname -m` == 'arm64' && "$py_ver" == "39" ]]; then
-      numpy_ver="numpy==1.21.3"
-    fi
-
-    echo " - pip install $numpy_ver"
-    pip install $numpy_ver
-}
-
 build_wheel_linux() {
     echo "[BUILD WHEEL] Building with interpreter $1"
     local skip=
@@ -83,11 +61,7 @@ build_wheel_linux() {
 
     echo " - Installing build requirements"
     pip install auditwheel
-    pip install -r packaging/python/build_requirements.txt
-    pip_numpy_install
-
-    echo " - Building..."
-    rm -rf dist build
+    cp packaging/python/build_requirements.txt my_requirements.txt
 
     CMAKE_DEFS="NRN_MPI_DYNAMIC=$3"
     if [ "$USE_STATIC_READLINE" == "1" ]; then
@@ -96,10 +70,17 @@ build_wheel_linux() {
 
     if [ "$2" == "coreneuron" ]; then
         setup_args="--enable-coreneuron"
-        clone_install_nmodl_requirements
+        clone_nmodl_and_add_requirements
         CMAKE_DEFS="${CMAKE_DEFS},LINK_AGAINST_PYTHON=OFF"
     fi
 
+    cat my_requirements.txt
+    pip install -r my_requirements.txt
+    pip check
+
+    echo " - Building..."
+    rm -rf dist build
+
     # Workaround for https://github.com/pypa/manylinux/issues/1309
     git config --global --add safe.directory "*"
 
@@ -135,15 +116,11 @@ build_wheel_osx() {
     (( $skip )) && return 0
 
     echo " - Installing build requirements"
-    pip install -U delocate -r packaging/python/build_requirements.txt
-    pip_numpy_install
-
-    echo " - Building..."
-    rm -rf dist build
+    cp packaging/python/build_requirements.txt my_requirements.txt
 
     if [ "$2" == "coreneuron" ]; then
         setup_args="--enable-coreneuron"
-        clone_install_nmodl_requirements
+        clone_nmodl_and_add_requirements
         CMAKE_DEFS="${CMAKE_DEFS},LINK_AGAINST_PYTHON=OFF"
     fi
 
@@ -152,6 +129,13 @@ build_wheel_osx() {
       CMAKE_DEFS="$CMAKE_DEFS,NRN_BINARY_DIST_BUILD=ON,NRN_WHEEL_STATIC_READLINE=ON"
     fi
 
+    cat my_requirements.txt
+    pip install -U delocate -r my_requirements.txt
+    pip check
+
+    echo " - Building..."
+    rm -rf dist build
+
     # We need to "fix" the platform tag if the Python installer is universal2
     # See:
     #     * https://github.com/pypa/setuptools/issues/2520

src/coreneuron/CMakeLists.txt

@@ -147,11 +147,6 @@ configure_file(${PROJECT_SOURCE_DIR}/src/coreneuron/config/config.cpp.in
 # =============================================================================
 include(OpenAccHelper)
 
-# =============================================================================
-# Common dependencies
-# =============================================================================
-find_package(Perl REQUIRED)
-
 # =============================================================================
 # Common build options
 # =============================================================================
@@ -259,21 +254,13 @@ if(NOT "${CORENRN_NMODL_DIR}" STREQUAL "" AND NOT nmodl_FOUND)
 endif()
 if(nmodl_FOUND)
   set(CORENRN_NMODL_BINARY ${nmodl_BINARY})
-  set(CORENRN_NMODL_INCLUDE ${nmodl_INCLUDE})
-  # path to python interface
-  set(ENV{PYTHONPATH} "${nmodl_PYTHONPATH}:$ENV{PYTHONPATH}")
-  set(CORENRN_NMODL_PYTHONPATH $ENV{PYTHONPATH})
 else()
   set(NMODL_ENABLE_PYTHON_BINDINGS
       OFF
       CACHE BOOL "Enable NMODL python bindings")
   nrn_add_external_project(nmodl DISABLE_ADD)
   add_subdirectory(${PROJECT_SOURCE_DIR}/external/nmodl ${CMAKE_BINARY_DIR}/external/nmodl)
   set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/nmodl${CMAKE_EXECUTABLE_SUFFIX})
-  set(CORENRN_NMODL_INCLUDE ${CMAKE_BINARY_DIR}/include)
-  set(ENV{PYTHONPATH} "$ENV{PYTHONPATH}")
-  set(nmodl_PYTHONPATH "${CMAKE_BINARY_DIR}/lib")
-  set(CORENRN_NMODL_PYTHONPATH "${nmodl_PYTHONPATH}:$ENV{PYTHONPATH}")
   set(NMODL_TARGET_TO_DEPEND nmodl)
   set(NMODL_PROJECT_BINARY_DIR ${CMAKE_BINARY_DIR}/external/nmodl)
   # install nrnunits.lib and libpywrapper.so from external/nmodl
@@ -360,23 +347,20 @@ if(NRN_ENABLE_MPI)
   list(APPEND CORENEURON_CODE_FILES "mpi/core/resolve.cpp")
 endif()
 
-file(COPY ${PROJECT_SOURCE_DIR}/external/Random123/include/Random123
-     DESTINATION ${CMAKE_BINARY_DIR}/include)
 list(APPEND CORENEURON_CODE_FILES ${PROJECT_BINARY_DIR}/coreneuron/config/config.cpp)
 
 set(ENGINEMECH_CODE_FILE "mechanism/mech/enginemech.cpp")
 
 # for external mod files we need to generate modl_ref function in mod_func.c
-set(MODFUNC_PERL_SCRIPT "mechanism/mech/mod_func.c.pl")
-
+set(MODFUNC_SHELL_SCRIPT "mechanism/mech/mod_func.c.sh")
 set(NMODL_UNITS_FILE "${CMAKE_BINARY_DIR}/share/mod2c/nrnunits.lib")
 
 # =============================================================================
 # Copy files that are required by nrnivmodl-core to the build tree at build time.
 # =============================================================================
 cpp_cc_build_time_copy(
-  INPUT "${CMAKE_CURRENT_SOURCE_DIR}/${MODFUNC_PERL_SCRIPT}"
-  OUTPUT "${CMAKE_BINARY_DIR}/share/coreneuron/mod_func.c.pl"
+  INPUT "${CMAKE_CURRENT_SOURCE_DIR}/${MODFUNC_SHELL_SCRIPT}"
+  OUTPUT "${CMAKE_BINARY_DIR}/share/coreneuron/mod_func.c.sh"
   NO_TARGET)
 cpp_cc_build_time_copy(
   INPUT "${CMAKE_CURRENT_SOURCE_DIR}/${ENGINEMECH_CODE_FILE}"
@@ -387,7 +371,7 @@ cpp_cc_build_time_copy(
   OUTPUT "${CMAKE_BINARY_DIR}/share/coreneuron/coreneuron.cpp"
   NO_TARGET)
 set(nrnivmodl_core_dependencies
-    "${CMAKE_BINARY_DIR}/share/coreneuron/mod_func.c.pl"
+    "${CMAKE_BINARY_DIR}/share/coreneuron/mod_func.c.sh"
     "${CMAKE_BINARY_DIR}/share/coreneuron/enginemech.cpp"
     "${CMAKE_BINARY_DIR}/share/coreneuron/coreneuron.cpp")
 # Set up build rules that copy builtin mod files from src/coreneuron/mechanism/mech/modfile/*.mod to
@@ -420,25 +404,6 @@ if(CORENRN_ENABLE_GPU)
   # https://forums.developer.nvidia.com/t/cannot-dynamically-load-a-shared-library-containing-both-openacc-and-cuda-code/210972
   # this cannot be included in the same shared library as the rest of the OpenACC code.
   set(CORENEURON_CUDA_FILES ${CMAKE_CURRENT_SOURCE_DIR}/permute/cellorder.cu)
-
-  # Eigen functions cannot be called directly from OpenACC regions, but Eigen is sort-of compatible
-  # with being compiled as CUDA code. Because of
-  # https://forums.developer.nvidia.com/t/cannot-dynamically-load-a-shared-library-containing-both-openacc-and-cuda-code/210972
-  # this has to mean `nvc++ -cuda` rather than `nvcc`. We explicitly instantiate Eigen functions for
-  # different matrix sizes in partial_piv_lu.cpp (with CUDA attributes but without OpenACC or OpenMP
-  # annotations) and dispatch to these from a wrapper in partial_piv_lu.h that does have
-  # OpenACC/OpenMP annotations.
-  if(EXISTS ${CORENRN_NMODL_INCLUDE}/partial_piv_lu/partial_piv_lu.cpp)
-    list(APPEND CORENEURON_CODE_FILES ${CORENRN_NMODL_INCLUDE}/partial_piv_lu/partial_piv_lu.cpp)
-    if(CORENRN_ENABLE_GPU
-       AND CORENRN_HAVE_NVHPC_COMPILER
-       AND CMAKE_BUILD_TYPE STREQUAL "Debug")
-      # In this case OpenAccHelper.cmake passes -gpu=debug, which makes these Eigen functions
-      # extremely slow. Downgrade that to -gpu=lineinfo for this file.
-      set_source_files_properties(${CORENRN_NMODL_INCLUDE}/partial_piv_lu/partial_piv_lu.cpp
-                                  PROPERTIES COMPILE_FLAGS "-gpu=lineinfo,nodebug -O1")
-    endif()
-  endif()
 endif()
 
 # =============================================================================
@@ -706,7 +671,7 @@ install(
   FILES_MATCHING
   PATTERN "*.h*"
   PATTERN "*.ipp")
-install(FILES ${MODFUNC_PERL_SCRIPT} ${ENGINEMECH_CODE_FILE} DESTINATION share/coreneuron)
+install(FILES ${MODFUNC_SHELL_SCRIPT} ${ENGINEMECH_CODE_FILE} DESTINATION share/coreneuron)
 
 # copy nmodl for nrnivmodl-core
 install(PROGRAMS ${CORENRN_NMODL_BINARY} DESTINATION bin)
@@ -724,9 +689,6 @@ if(CORENRN_ENABLE_SHARED)
   install(FILES ${corenrn_mech_library} DESTINATION lib)
 endif()
 
-# install random123 and nmodl headers
-install(DIRECTORY ${CMAKE_BINARY_DIR}/include/ DESTINATION include)
-
 # install mod files
 install(DIRECTORY ${CMAKE_BINARY_DIR}/share/modfile DESTINATION share)