cmake: export targets, allow building mechanisms via CMake, part 1

.github/workflows/wheels-template.yml

@@ -73,7 +73,7 @@ jobs:
         run: |
           brew install --cask xquartz
           brew uninstall cmake || echo "CMake was not pre-installed"
-          brew install flex bison cmake mpich
+          brew install flex bison cmake mpich ninja
           brew unlink mpich && brew install openmpi
           # Install newer version of Bash on MacOS
           brew install bash
@@ -127,7 +127,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt update
-          sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
+          sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev ninja-build
 
       - name: "Apply workaround for MPICH on Ubuntu 24.04"
         if: inputs.platform == 'ubuntu-24.04'
@@ -141,6 +141,22 @@ jobs:
           wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/libmpich12_4.2.0-5.1_amd64.deb'
           sudo dpkg --install mpich_4.2.0-5.1_amd64.deb libmpich12_4.2.0-5.1_amd64.deb
 
+      - name: Set env vars for testing (Linux)
+        if: startsWith(inputs.platform, "ubuntu")
+        run: |
+          echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+          echo CMAKE_GENERATOR=Ninja >> $GITHUB_ENV
+
+      - name: Set env vars for testing (MacOS)
+        if: startsWith(runner.os, "macOS")
+        run: |
+          if [[ "${{runner.os}}" == "macOS-15-intel" ]]; then
+            echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+          else
+            echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV
+          fi
+          echo CMAKE_GENERATOR=Ninja >> $GITHUB_ENV
+
       - name: Test wheel with ${{ inputs.python_version }}
         run: |
           minor_version="$(python${{ inputs.python_version }} -c 'import sys;print(sys.version_info.minor)')"

CMakeLists.txt

@@ -587,6 +587,8 @@ endif()
 # initialize CLI11 submodule
 cpp_cc_git_submodule(CLI11 BUILD PACKAGE CLI11 REQUIRED)
 
+# coreneuron targets will get propagated down from the subdirectory
+
 # =============================================================================
 # Enable NMODL code-generator support
 # =============================================================================
@@ -1117,6 +1119,52 @@ if(NRN_MACOS_BUILD AND NOT SKBUILD)
   nrn_macos_after_install()
 endif()
 
+# =============================================================================
+# Install CMake glue
+# =============================================================================
+configure_file(cmake/neuronMechMaker.cmake
+               "${PROJECT_BINARY_DIR}/lib/cmake/neuron/neuronMechMaker.cmake" COPYONLY)
+configure_file(cmake/mod_reg_nrn.cpp.in "${PROJECT_BINARY_DIR}/share/nrn/mod_reg_nrn.cpp.in"
+               COPYONLY)
+configure_file(cmake/mod_reg_corenrn.cpp.in
+               "${PROJECT_BINARY_DIR}/share/nrn/mod_reg_corenrn.cpp.in" COPYONLY)
+install(
+  TARGETS ${CORENRN_INSTALL_LIB_TARGETS}
+  EXPORT NeuronTargets
+  DESTINATION "${NRN_INSTALL_DATA_PREFIX}lib")
+install(
+  TARGETS ${CORENRN_INSTALL_BIN_TARGETS}
+  EXPORT NeuronTargets
+  DESTINATION "${NRN_INSTALL_DATA_PREFIX}bin")
+export(
+  EXPORT NeuronTargets
+  FILE ${PROJECT_BINARY_DIR}/lib/cmake/neuron/neuronTargets.cmake
+  NAMESPACE neuron::)
+
+install(
+  EXPORT NeuronTargets
+  FILE neuronTargets.cmake
+  NAMESPACE neuron::
+  DESTINATION "${NRN_INSTALL_DATA_PREFIX}lib/cmake/neuron")
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/neuronConfig.cmake.in
+               ${CMAKE_CURRENT_BINARY_DIR}/lib/cmake/neuron/neuronConfig.cmake @ONLY)
+
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/lib/cmake/neuron/neuronConfig.cmake
+        DESTINATION "${NRN_INSTALL_DATA_PREFIX}lib/cmake/neuron")
+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/neuronMechMaker.cmake
+        DESTINATION "${NRN_INSTALL_DATA_PREFIX}lib/cmake/neuron")
+
+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/mod_reg_nrn.cpp.in
+              ${CMAKE_CURRENT_SOURCE_DIR}/cmake/mod_reg_corenrn.cpp.in
+        DESTINATION "${NRN_INSTALL_DATA_PREFIX}share/nrn")
+
+# configuration and installation of nrnivmodl
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/nrnivmodl.cmake
+               ${CMAKE_CURRENT_BINARY_DIR}/lib/cmake/neuron/nrnivmodl/CMakeLists.txt @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/lib/cmake/neuron/nrnivmodl/CMakeLists.txt
+        DESTINATION "${NRN_INSTALL_DATA_PREFIX}lib/cmake/neuron/nrnivmodl")
+
 # =============================================================================
 # Copy bash executable for windows
 # =============================================================================

bin/CMakeLists.txt

@@ -47,7 +47,8 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nrnpyenv.sh.in ${PROJECT_BINARY_DIR}/
 # Make sure nrnivmodl and neurondemo are executable in the build folder, so we can execute it to
 # prepare test files. This can be done more elegantly in newer CMake versions; v3.19+ have
 # file(CHMOD ...) and v3.20+ support setting permissions directly in configure_file(...).
-set(NRN_CONFIG_EXE_FILES "nrnivmodl" "neurondemo")
+set(NRNIVMODL_NEURON ON)
+set(NRN_CONFIG_EXE_FILES "nrnivmodl" "neurondemo" "nrnivmodl-cmake")
 foreach(NRN_CONFIG_EXE_FILE ${NRN_CONFIG_EXE_FILES})
   configure_file("${NRN_CONFIG_EXE_FILE}.in" "tmp/${NRN_CONFIG_EXE_FILE}" @ONLY)
   file(
@@ -62,13 +63,39 @@ foreach(NRN_CONFIG_EXE_FILE ${NRN_CONFIG_EXE_FILES})
       WORLD_READ
       WORLD_EXECUTE)
 endforeach()
+unset(NRNIVMODL_NEURON)
+if(NRN_ENABLE_CORENEURON)
+  # nrnivmodl-all-cmake builds mechanisms for both NEURON and coreNEURON
+  set(NRNIVMODL_NEURON ON)
+  set(NRNIVMODL_CORENEURON ON)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nrnivmodl-cmake.in
+                 "${CMAKE_CURRENT_BINARY_DIR}/tmp/nrnivmodl-all-cmake" @ONLY)
+  file(
+    COPY "${CMAKE_CURRENT_BINARY_DIR}/tmp/nrnivmodl-all-cmake"
+    DESTINATION "${CMAKE_CURRENT_BINARY_DIR}"
+    FILE_PERMISSIONS
+      OWNER_READ
+      OWNER_WRITE
+      OWNER_EXECUTE
+      GROUP_READ
+      GROUP_EXECUTE
+      WORLD_READ
+      WORLD_EXECUTE)
+  unset(NRNIVMODL_NEURON)
+  unset(NRNIVMODL_CORENEURON)
+endif()
 file(REMOVE_RECURSE "${CMAKE_CURRENT_BINARY_DIR}/bin/tmp")
 
 # =============================================================================
 # Install targets
 # =============================================================================
 install(PROGRAMS ${PROJECT_BINARY_DIR}/bin/nrngui ${PROJECT_BINARY_DIR}/bin/neurondemo
-                 ${PROJECT_BINARY_DIR}/bin/nrnivmodl DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)
+                 ${PROJECT_BINARY_DIR}/bin/nrnivmodl ${PROJECT_BINARY_DIR}/bin/nrnivmodl-cmake
+        DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)
+if(NRN_ENABLE_CORENEURON)
+  install(PROGRAMS ${PROJECT_BINARY_DIR}/bin/nrnivmodl-all-cmake
+          DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)
+endif()
 
 install(FILES ${PROJECT_BINARY_DIR}/bin/nrnmech_makefile DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)
 install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/sortspike ${CMAKE_CURRENT_SOURCE_DIR}/mkthreadsafe

bin/nrnivmodl-cmake.in

@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+
+# =============================================================================
+# Simple wrapper for CMake that builds mechanisms from mod files
+# =============================================================================
+
+set -eu
+
+# Where the output files will be placed
+bindir="$(uname -m)"
+
+# The name of the current program
+program_name="$(basename "${0}")"
+
+# Where the `*.cmake` files are located
+NRN_CMAKE_PREFIX_PATH_DEFAULT="$(readlink -f "$(dirname "${0}")/../lib/cmake/")"
+if [ -n "${CMAKE_PREFIX_PATH:-}" ]; then
+    CMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH}:${NRN_CMAKE_PREFIX_PATH_DEFAULT}"
+else
+    CMAKE_PREFIX_PATH="${NRN_CMAKE_PREFIX_PATH_DEFAULT}"
+fi
+export CMAKE_PREFIX_PATH
+
+# On MacOS we need to set the deployment target to be equal to the one of NEURON
+if command -v xcrun >& /dev/null; then
+    @NRN_OSX_BUILD_TRUE@export SDKROOT="$(xcrun --sdk macosx --show-sdk-path)"
+    @NRN_OSX_BUILD_TRUE@export MACOSX_DEPLOYMENT_TARGET="@CMAKE_OSX_DEPLOYMENT_TARGET@"
+    if [ -z "${MACOSX_DEPLOYMENT_TARGET}" ]; then
+        unset MACOSX_DEPLOYMENT_TARGET
+    fi
+fi
+
+# We use the CMakeLists.txt from the NEURON installation directory to not have
+# to deal with any pre-existing CMakeLists.txt in the current directory
+srcdir="${NRN_CMAKE_PREFIX_PATH_DEFAULT}/neuron/nrnivmodl/"
+
+# In case of no files, default to using the files in the current dir
+if [ $# -lt 1 ]; then
+    set -- ./*.mod
+# In case of a single input, check if it's a directory; if it is, collect all mod files in it
+elif [ $# -eq 1 ] && [ -d "${1}" ]; then
+    printf "[%s] Collecting mod files under %s\n" "${program_name}" "$(readlink -f "${1}")"
+    set -- "${1}"/*.mod
+fi
+
+# After collecting the mod files, check each mod file actually exists
+for mod_file in "$@"; do
+    if [ ! -e "${mod_file}" ]; then
+        printf "[%s] ERROR: Mod file %s does not exist!\n" "${program_name}" "${mod_file}" >&2
+        exit 4
+    fi
+done
+
+# Convert all mod file paths to absolute paths because the source dir is in the NEURON install
+args=()
+for f in "$@"; do
+  resolved=$(readlink -f "$f") || exit 1
+  args+=("$resolved")
+done
+set -- "${args[@]}"
+
+# TODO what if the mod filenames contain semicolons?
+modfiles=$(IFS=";"; echo "$*")
+
+# Configure the mod files
+cmake \
+    -S "${srcdir}" \
+    -B "${bindir}" \
+    -DNRNIVMODL_MOD_FILES="${modfiles}" \
+    -DNRNIVMODL_NEURON=@NRNIVMODL_NEURON@ \
+    -DNRNIVMODL_CORENEURON=@NRNIVMODL_CORENEURON@
+
+# Actually build them
+cmake --build "${bindir}"

ci/azure-wheel-test-upload.yml

@@ -18,6 +18,7 @@ steps:
 
   - script: |
       export SKIP_EMBEDED_PYTHON_TEST=true
+      export CMAKE_BUILD_PARALLEL_LEVEL=4
       packaging/python/test_wheels.sh $(which python) $(ls -t wheelhouse/*.whl)
     displayName: 'Test with System Python'
 

ci/requirements.txt

@@ -2708,6 +2708,7 @@ sphinx==7.3.7 \
     #   sphinx-rtd-theme
     #   sphinxcontrib-jquery
     #   sphinxcontrib-mermaid
+    #   sphinxcontrib-moderncmakedomain
 sphinx-design==0.6.1 \
     --hash=sha256:b11f37db1a802a183d61b159d9a202314d4d2fe29c163437001324fe2f19549c \
     --hash=sha256:b44eea3719386d04d765c1a8257caca2b3e6f8421d7b3a5e742c0fd45f84e632
@@ -2750,6 +2751,10 @@ sphinxcontrib-mermaid==1.0.0 \
     --hash=sha256:2e8ab67d3e1e2816663f9347d026a8dee4a858acdd4ad32dd1c808893db88146 \
     --hash=sha256:60b72710ea02087f212028feb09711225fbc2e343a10d34822fe787510e1caa3
     # via -r docs/docs_requirements.txt
+sphinxcontrib-moderncmakedomain==3.29.0 \
+    --hash=sha256:22385d9956e9565311eca41a09f26688312e4997a7366cb965fa610d1fd1436c \
+    --hash=sha256:3587def241ff2577d0bbef11810a082e9dec1b78a3d4b4a066240b5f3dc1b5b2
+    # via -r docs/docs_requirements.txt
 sphinxcontrib-qthelp==2.0.0 \
     --hash=sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab \
     --hash=sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb

cmake/mod_reg_corenrn.cpp.in

@@ -0,0 +1,16 @@
+#include <cstdio>
+namespace coreneuron {
+extern int nrnmpi_myid;
+extern int nrn_nobanner_;
+
+@MECH_DECLARE@
+
+void modl_reg() {
+  if (!nrn_nobanner_) if (nrnmpi_myid < 1) {
+    fprintf(stderr, " Additional mechanisms from files\n");
+    @MECH_PRINT@
+    fprintf(stderr, "\n\n");
+  }
+  @MECH_REGISTRE@
+}
+} //namespace coreneuron

cmake/mod_reg_nrn.cpp.in

@@ -0,0 +1,16 @@
+#include <stdio.h>
+#include "hocdec.h"
+extern int nrnmpi_myid;
+extern int nrn_nobanner_;
+
+@MECH_DECLARE@
+
+extern "C" void modl_reg() {
+  if (!nrn_nobanner_) if (nrnmpi_myid < 1) {
+    fprintf(stderr, "Additional mechanisms from files\n");
+    @MECH_PRINT@
+    fprintf(stderr, "\n");
+  }
+  @MECH_REGISTRE@
+}
+

cmake/neuronConfig.cmake.in

@@ -0,0 +1,25 @@
+include(CMakeFindDependencyMacro)
+
+find_dependency(Threads)
+
+include("${CMAKE_CURRENT_LIST_DIR}/neuronTargets.cmake")
+
+get_filename_component(_dir "${CMAKE_CURRENT_LIST_FILE}" PATH)
+get_filename_component(_prefix "${_dir}/../../.." ABSOLUTE)
+
+set(NRN_ENABLE_CORENEURON @NRN_ENABLE_CORENEURON@)
+
+set(_NEURON_MAIN "${_prefix}/share/nrn/nrnmain.cpp")
+set(_NEURON_MAIN_INCLUDE_DIR "${_prefix}/include/nrncvode" "${_prefix}/include")
+set(_NEURON_MECH_REG "${_prefix}/share/nrn/mod_reg_nrn.cpp.in")
+
+set(_CORENEURON_BASE_MOD "${_prefix}/share/modfile")
+set(_CORENEURON_MAIN "${_prefix}/share/coreneuron/coreneuron.cpp")
+set(_CORENEURON_MECH_REG "${_prefix}/share/nrn/mod_reg_corenrn.cpp.in")
+set(_CORENEURON_MECH_ENG "${_prefix}/share/coreneuron/enginemech.cpp")
+set(_CORENEURON_RANDOM_INCLUDE "${_prefix}/include/coreneuron/utils/randoms" "${_prefix}/include")
+set(_CORENEURON_FLAGS @CORENRN_CXX_FLAGS@)
+
+set(_CORENEURON_MIN_CUDA_TOOLKIT_VERSION @CORENRN_CUDA_VERSION_SHORT@)
+
+include("${CMAKE_CURRENT_LIST_DIR}/neuronMechMaker.cmake")