Merge branch 'master' into slds

.github/workflows/coverage.yml

@@ -58,7 +58,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" numpy setuptools
+          python3 -m pip install 'mpi4py<4' cython numpy setuptools
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
           curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip
@@ -91,9 +91,9 @@ jobs:
       - name: Install Python@${{ env.PY_MIN_VERSION }} dependencies
         working-directory: ${{runner.workspace}}/nrn
         run: |
-          python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
           python -m pip install --upgrade -r ci_requirements.txt
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
       - name: Set up Python@${{ env.PY_MID_VERSION }}
         uses: actions/setup-python@v5
@@ -108,9 +108,9 @@ jobs:
       - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies
         working-directory: ${{runner.workspace}}/nrn
         run: |
-          python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
           python -m pip install --upgrade -r ci_requirements.txt
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
 
       - name: Build & Test

.github/workflows/docs.yml

@@ -78,11 +78,3 @@ jobs:
       - name: live debug session on failure (manual steps required, check `.github/docs.yml`)
         if: failure() && contains(github.event.pull_request.title, 'live-debug-docs')
         uses: mxschmitt/action-tmate@v3
-
-      - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@v4
-        if: env.OK_TO_DEPLOY_DOCS == 'true' && github.ref == 'refs/heads/master'
-        with:
-          branch: gh-pages # The branch the action should deploy to.
-          folder: ${{runner.workspace}}/nrn/docs/_build # The folder the action should deploy.
-          single-commit: true #have a single commit on the deployment branch instead of maintaining the full history

.github/workflows/neuron-ci.yml

@@ -70,7 +70,7 @@ jobs:
               # TODO: address-leak is the dream, but there are many problems,
               # including external ones from the MPI implementations
               sanitizer: address
-          - os: ubuntu-22.04
+          - os: ubuntu-24.04
             config:
               build_mode: cmake
               # Cannot use a non-instrumented OpenMP with TSan, and we don't
@@ -86,6 +86,13 @@ jobs:
               cmake_option: -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF
                 -DNRN_ENABLE_RX3D=OFF -DNMODL_SANITIZERS=address
               sanitizer: address
+          - os: macOS-14
+            config:
+              build_mode: cmake
+              # TODO: investigate rxd test timeouts in this build and re-enable them
+              cmake_option: -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF
+                -DNRN_ENABLE_RX3D=OFF -DNMODL_SANITIZERS=address
+              sanitizer: thread
       fail-fast: false
 
     steps:
@@ -113,14 +120,18 @@ jobs:
           brew unlink mpich
           brew install openmpi
           brew install --cask xquartz
+          if [[ "${{matrix.os}}" == "macOS-14" ]]; then
+            brew install cmake
+            echo "$(brew --prefix)/opt/cmake/bin" >> $GITHUB_PATH
+          fi
           echo "$(brew --prefix)/opt/flex/bin:$(brew --prefix)/opt/bison/bin" >> $GITHUB_PATH
           # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
           if [[ "${{matrix.os}}" == "macOS-13" ]]; then
-              echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV
-              echo CTEST_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+            echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+            echo CTEST_PARALLEL_LEVEL=4 >> $GITHUB_ENV
           else
-              echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV
-              echo CTEST_PARALLEL_LEVEL=3 >> $GITHUB_ENV
+            echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV
+            echo CTEST_PARALLEL_LEVEL=3 >> $GITHUB_ENV
           fi
           echo CI_OS_NAME=osx >> $GITHUB_ENV
         shell: bash
@@ -130,7 +141,7 @@ jobs:
         run: |
           sudo apt-get install build-essential ccache libopenmpi-dev \
             libmpich-dev libx11-dev libxcomposite-dev mpich ninja-build \
-            openmpi-bin flex libfl-dev bison
+            openmpi-bin flex libfl-dev bison libreadline-dev
           # The sanitizer builds use ubuntu 22.04
           if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then
             sudo apt-get install g++-7 g++-8
@@ -160,9 +171,9 @@ jobs:
         if: ${{ matrix.config.python_dynamic == 'ON' }}
         working-directory: ${{runner.workspace}}/nrn
         run: |
-          python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
           python -m pip install --upgrade -r ci_requirements.txt
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
       - name: Set up Python@${{ env.PY_MAX_VERSION }}
         uses: actions/setup-python@v5
@@ -172,9 +183,9 @@ jobs:
       - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies
         working-directory: ${{runner.workspace}}/nrn
         run: |
-          python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
           python -m pip install --upgrade -r ci_requirements.txt
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
       - name: Install a new automake
         # A new automake is needed for python 3.12 because it generate a python script
@@ -196,7 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" numpy setuptools
+          python3 -m pip install 'mpi4py<4' cython numpy setuptools
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
           curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip

.gitlab-ci.yml

@@ -53,9 +53,9 @@ mac_m1_cmake_build:
     - echo "python3=$(command -v python3) is really ${real_python}"
     - PYTHONEXECUTABLE=${real_python} ${real_python} -mvenv venv
     - venv/bin/python3 -m ensurepip --upgrade --default-pip
-    - venv/bin/pip install --upgrade pip -r nrn_requirements.txt
     - git submodule update --init --recursive --force --depth 1 -- external/nmodl
     - venv/bin/pip install --upgrade -r external/nmodl/requirements.txt
+    - venv/bin/pip install --upgrade pip -r nrn_requirements.txt
     - source ./venv/bin/activate
     - export PYTHON=${PWD}/venv/bin/python
     - ${PYTHON} --version

.gitmodules

@@ -25,3 +25,9 @@
 [submodule "external/eigen"]
 	path = external/eigen
 	url = https://gitlab.com/libeigen/eigen.git
+[submodule "external/nanobind"]
+	path = external/nanobind
+	url = https://github.com/wjakob/nanobind
+[submodule "external/fmt"]
+	path = external/fmt
+	url = https://github.com/fmtlib/fmt

.sanitizers/undefined.supp

@@ -31,6 +31,7 @@ unsigned-integer-overflow:_philox4x32bumpkey(r123array2x32)
 unsigned-integer-overflow:coreneuron::nrnran123_deletestream(coreneuron::nrnran123_State*, bool)
 unsigned-integer-overflow:coreneuron::nrnran123_newstream3(unsigned int, unsigned int, unsigned int, bool)
 unsigned-integer-overflow:Py_INCREF(_object*)
+unsigned-integer-overflow:fmt::*
 vptr:NetCon::disconnect(ivObservable*)
 vptr:ObjObservable::object()
-vptr:PreSyn::disconnect(ivObservable*)
+vptr:PreSyn::disconnect(ivObservable*)

CMakeLists.txt

@@ -246,6 +246,13 @@ endif()
 include("${CODING_CONV_CMAKE}/3rdparty.cmake")
 cpp_cc_git_submodule(Random123)
 cpp_cc_git_submodule(eigen)
+nrn_add_external_project(fmt)
+set_property(TARGET fmt PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+file(COPY "${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/")
 
 # =================================================================================================
 # Enable sanitizer support if the NRN_SANITIZERS variable is set. Comes befores PythonHelper.cmake.
@@ -318,9 +325,6 @@ if(NRN_ENABLE_RX3D)
     message(SEND_ERROR "NRN_ENABLE_RX3D requires NRN_ENABLE_PYTHON feature.")
   else()
     find_package(Cython REQUIRED)
-    if(CYTHON_VERSION VERSION_GREATER_EQUAL 3)
-      message(FATAL_ERROR "Cython 3+ is not supported")
-    endif()
   endif()
 endif()
 if(MINGW)
@@ -375,9 +379,6 @@ if(NRN_ENABLE_MUSIC)
     message(FATAL "MUSIC requires -DNRN_ENABLE_PYTHON=ON")
   endif()
   find_package(Cython REQUIRED)
-  if(CYTHON_VERSION VERSION_GREATER_EQUAL 3)
-    message(FATAL_ERROR "Cython 3+ is not supported")
-  endif()
   find_package(MUSIC REQUIRED)
   set(NRN_MUSIC 1)
 endif()
@@ -432,6 +433,9 @@ endif()
 if(NRN_ENABLE_PYTHON)
   # Make sure the USE_PYTHON macro is defined in the C++ code
   list(APPEND NRN_COMPILE_DEFS USE_PYTHON)
+  # Ensure nanobind is there, but dont import, we don't want its CMake
+  nrn_add_external_project(nanobind DISABLE_ADD RECURSIVE SHALLOW)
+  include(NanoBindMinimal)
 endif()
 
 # =============================================================================
@@ -572,6 +576,10 @@ endif()
 # =============================================================================
 add_subdirectory(src/sparse13)
 add_subdirectory(src/gnu)
+if(NRN_ENABLE_PYTHON)
+  add_subdirectory(src/nrnpython)
+endif()
+
 add_subdirectory(src/nrniv)
 
 # Collect the environment variables that are needed to execute NEURON from the build directory. This
@@ -590,7 +598,11 @@ endfunction()
 set(NRN_RUN_FROM_BUILD_DIR_ENV "NEURONHOME=${PROJECT_BINARY_DIR}/share/nrn"
                                "NRNHOME=${PROJECT_BINARY_DIR}")
 prepend_to_var(PATH "${PROJECT_BINARY_DIR}/bin")
-prepend_to_var(LD_LIBRARY_PATH "${PROJECT_BINARY_DIR}/lib")
+if(APPLE)
+  prepend_to_var(DYLD_LIBRARY_PATH "${PROJECT_BINARY_DIR}/lib")
+else()
+  prepend_to_var(LD_LIBRARY_PATH "${PROJECT_BINARY_DIR}/lib")
+endif()
 if(NRN_ENABLE_CORENEURON)
   list(APPEND NRN_RUN_FROM_BUILD_DIR_ENV "CORENRNHOME=${PROJECT_BINARY_DIR}")
 endif()
@@ -599,10 +611,6 @@ if(NRN_ENABLE_PYTHON)
 endif()
 add_subdirectory(bin)
 
-if(NRN_ENABLE_PYTHON)
-  add_subdirectory(src/nrnpython)
-endif()
-
 if(NRN_MACOS_BUILD)
   add_subdirectory(src/mac)
 endif()
@@ -739,22 +747,17 @@ add_custom_target(
 # =============================================================================
 if(NRN_ENABLE_CORENEURON OR NRN_ENABLE_MOD_COMPATIBILITY)
   set(GLOBAL_VAR_TOGGLE_COMMAND "'s/ GLOBAL minf/ RANGE minf/'")
-  set(TABLE_VAR_TOGGLE_COMMAND "'s/ TABLE minf/ :TABLE minf/'")
 else()
   set(GLOBAL_VAR_TOGGLE_COMMAND "'s/ RANGE minf/ GLOBAL minf/'")
-  set(TABLE_VAR_TOGGLE_COMMAND "'s/ :TABLE minf/ TABLE minf/'")
 endif()
 separate_arguments(GLOBAL_VAR_TOGGLE_COMMAND UNIX_COMMAND "${GLOBAL_VAR_TOGGLE_COMMAND}")
-separate_arguments(TABLE_VAR_TOGGLE_COMMAND UNIX_COMMAND "${TABLE_VAR_TOGGLE_COMMAND}")
 add_custom_target(
   hh_update
   COMMAND sed ${GLOBAL_VAR_TOGGLE_COMMAND} ${CMAKE_SOURCE_DIR}/src/nrnoc/hh.mod >
           ${CMAKE_BINARY_DIR}/hh.mod.1
-  COMMAND sed ${TABLE_VAR_TOGGLE_COMMAND} ${CMAKE_BINARY_DIR}/hh.mod.1 >
-          ${CMAKE_BINARY_DIR}/hh.mod.2
-  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/hh.mod.2
+  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/hh.mod.1
           ${CMAKE_SOURCE_DIR}/src/nrnoc/hh.mod
-  COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_BINARY_DIR}/hh.mod.1 ${CMAKE_BINARY_DIR}/hh.mod.2
+  COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_BINARY_DIR}/hh.mod.1
   COMMENT "Update hh.mod for CoreNEURON compatibility"
   VERBATIM)
 add_dependencies(nrniv_lib hh_update)

azure-pipelines.yml

@@ -148,8 +148,8 @@ stages:
           export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH
           export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
           export NRN_BUILD_FOR_UPLOAD=1
-          sudo mkdir /opt/nrnwheel
-          sudo tar -zxf $(readlineSF.secureFilePath) --directory /opt/nrnwheel/
+          sudo mkdir -p /opt/nrnwheel/$(uname -m)
+          sudo tar -zxf $(readlineSF.secureFilePath) --directory /opt/nrnwheel/$(uname -m)
           packaging/python/build_wheels.bash osx $(python.version) coreneuron
         displayName: 'Build MacOS Wheel'
 

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.in

@@ -81,8 +81,19 @@ while [ "$1" ] ; do
         UserNMODLFLAGS="$UserNMODLFLAGS $2"
         shift
         shift;;
+    -h|--help)
+        echo "Usage: nrnivmodl [options] [mod files or directories with mod files]"
+        echo "Options:"
+        echo "  -coreneuron                      Compile MOD files for CoreNEURON using nrnivmodl-core."
+        echo "  -incflags    \"include flags\"     Extra include flags and paths when MOD (C++) files are compiled."
+        echo "  -loadflags   \"link flags\"        Extra link flags, paths, and libraries when MOD (C++) files are linked."
+        echo "  -nmodl /path/to/nmodl            Path to the new NMODL transpiler for MOD files (pre-alpha, development use only)."
+        echo "  -nmodlflags  \"CLI flags\"         Additional CLI flags for new NMODL transpiler"
+        echo "  -h, --help                       Show this help message and exit."
+        echo "If no MOD files or directories provided then MOD files from current directory are used."
+        exit 0;;
     -*)
-        echo "$1 unrecognized"
+        echo "$1 unrecognized, check available CLI options with --help"
         exit 1;;
     *)
         break;;