Merge branch 'master' into cornu/sparse13_treeset

.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
@@ -141,7 +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
@@ -171,9 +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@${{ env.PY_MAX_VERSION }}
         uses: actions/setup-python@v5
@@ -183,17 +183,17 @@ jobs:
       - name: Install Python@${{ 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
+        # A automake >= 1.16.5 is needed for python 3.12 because it generates a python script
         # called py-compile and the original one is not supporting this version of python
         # Once ubuntu got a newer version of automake we can remove this part.
         if: matrix.config.music == 'ON' && startsWith(matrix.os, 'ubuntu')
         run: |
-          curl -L -o automake.tar.xz https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.xz
+          curl -L -o automake.tar.xz https://ftpmirror.gnu.org/gnu/automake/automake-1.16.5.tar.xz
           tar -xf automake.tar.xz
           cd automake-1.16.5/
           ./configure --prefix=/usr/
@@ -207,7 +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
@@ -237,10 +237,10 @@ jobs:
           echo -----
 
       - name: Restore compiler cache
-        uses: actions/cache@v4
+        uses: actions/cache/restore@v4
+        id: restore-compiler-cache
         with:
           path: ${{runner.workspace}}/ccache
-          save-always: true
           key: ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}}
           restore-keys: |
             ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-
@@ -441,6 +441,15 @@ jobs:
           INSTALL_DIR : ${{ runner.workspace }}/install
           MATRIX_EVAL: ${{ matrix.config.matrix_eval }}
 
+      - name: Save compiler cache
+        uses: actions/cache/save@v4
+        if: always() && steps.restore-compiler-cache.outputs.cache-hit != 'true'
+        with:
+          path: ${{runner.workspace}}/ccache
+          key: |
+            ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-
+            ${{matrix.os}}-${{hashfiles('matrix.json')}}-
+
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To enable it, you have to:
       #   * add 'live-debug-ci' to your PR title

.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
@@ -148,19 +148,6 @@ spack_setup:
     # BLUECONFIGS_BRANCH does not correspond to a Spack package called blueconfigs
     SPACK_SETUP_IGNORE_PACKAGE_VARIABLES: BLUECONFIGS
 
-simulation_stack:
-  stage: .pre
-  # Take advantage of GitHub PR description parsing in the spack_setup job.
-  needs: [spack_setup]
-  trigger:
-    branch: $BLUECONFIGS_BRANCH
-    project: hpc/sim/blueconfigs
-    # NEURON CI status depends on the BlueConfigs CI status.
-    strategy: depend
-  variables:
-    GITLAB_PIPELINES_BRANCH: $GITLAB_PIPELINES_BRANCH
-    SPACK_ENV_FILE_URL: $SPACK_SETUP_COMMIT_MAPPING_URL
-
 # Performance seems to be terrible when we get too many jobs on a single node.
 .build:
   extends: [.spack_build]

.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

@@ -85,6 +85,13 @@ option(
   NRN_ENABLE_PERFORMANCE_TESTS
   "Enable tests that measure performance. These are known to be unreliable when run on busy/oversubscribed machines such as CI runners."
   ${NRN_ENABLE_PERFORMANCE_TESTS_DEFAULT})
+option(NRN_ENABLE_DIGEST
+       "Provides nrn_digest function for debugging cross platform floating result differences."
+       ${NRN_ENABLE_DIGEST_DEFAULT})
+option(
+  NRN_ENABLE_ARCH_INDEP_EXP_POW
+  "Provides use_exp_pow_precision(style) function so that exp and pow produce same results on all platforms"
+  ${NRN_ENABLE_ARCH_INDEP_EXP_POW_DEFAULT})
 # This can be helpful in very specific CI build configurations, where ccache is used *and* different
 # CI builds are built under different directories.
 option(NRN_AVOID_ABSOLUTE_PATHS
@@ -246,6 +253,13 @@ endif()
 include("${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 +332,6 @@ 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 +386,6 @@ 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 +440,9 @@ 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 +583,10 @@ 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
@@ -603,10 +618,6 @@ 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()
@@ -743,22 +754,17 @@ 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)
@@ -1057,6 +1063,10 @@ if(NRN_ENABLE_PROFILING)
     message(STATUS "  Caliper     | ${caliper_DIR}")
   endif()
 endif()
+if(NRN_ENABLE_DIGEST OR NRN_ARCH_INDEP_EXP_POW)
+  message(STATUS "NRN_ENABLE_DIGEST | ${NRN_ENABLE_DIGEST}")
+  message(STATUS "NRN_ENABLE_ARCH_INDEP_EXP_POW | ${NRN_ENABLE_ARCH_INDEP_EXP_POW}")
+endif()
 message(STATUS "--------------+--------------------------------------------------------------")
 message(STATUS " See documentation : https://www.neuron.yale.edu/neuron/")
 message(STATUS "--------------+--------------------------------------------------------------")

README.md

@@ -14,11 +14,16 @@ Linux and Mac you can install the official Python 3 wheel with:
 pip3 install neuron
 ```
 
-If you want to build the latest version from source, we support **CMake** as build system. **Autotools** build system has been removed after 8.0 release.
+If you want to build the latest version from source, we support **CMake** as build system.
 See detailed installation instructions: [docs/install/install_instructions.md](docs/install/install_instructions.md).
 
 It is possible to install the Linux Python wheels on Windows via the Windows Subsystem for Linux (WSL) - check the installation instructions above.
 
+> [!NOTE]
+> **About NEURON >= 9.0**: If you are experiencing compilation errors while using
+> `nrnivmodl` with NEURON >=9.0, but not with previous 8.x releases, see
+> [Adapting MOD files for C++ with NEURON >= 9.0](docs/guide/porting_mechanisms_to_cpp.rst).
+
 ## Documentation
 
 * See documentation section of the [NEURON website](https://neuron.yale.edu/neuron/docs)

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