Merge branch 'master' into flense-DOS

.github/workflows/coverage.yml

@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.8'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.11'
+  PY_MAX_VERSION: '3.12'
 
 jobs:
   coverage:
@@ -58,7 +58,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" numpy
+          python3 -m pip install mpi4py "cython<3" 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

.github/workflows/docs.yml

@@ -17,7 +17,7 @@ on:
       - release/**
 
 env:
-  DEFAULT_PY_VERSION: '3.11'
+  DEFAULT_PY_VERSION: '3.12'
 
 jobs:
   documentation:

.github/workflows/neuron-ci.yml

@@ -39,7 +39,7 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.11' }}
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
       MUSIC_VERSION: 1.2.1
 
@@ -49,7 +49,7 @@ jobs:
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", music: ON}
-          - { matrix_eval : "CC=gcc-10 CXX=g++-10",   build_mode: "cmake", python_dynamic: ON}
+          - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", python_dynamic: ON}
           - { matrix_eval : "CC=gcc-9 CXX=g++-9" ,  build_mode: "cmake", cmake_option: "-DNRN_ENABLE_CORENEURON=ON"}
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "cmake", cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON"}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", cmake_option: "-DNRN_ENABLE_PYTHON=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_CORENEURON=ON"}
@@ -114,9 +114,14 @@ jobs:
           brew install openmpi
           brew install --cask xquartz
           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#supported-runners-and-hardware-resources
-          echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV
-          echo CTEST_PARALLEL_LEVEL=3 >> $GITHUB_ENV
+          # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
+          if [[ "${{matrix.os}}" == "macOS-13" ]]; then
+              echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+              echo CTEST_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+          else
+              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
 
@@ -130,9 +135,9 @@ jobs:
           if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then
             sudo apt-get install g++-7 g++-8
           fi
-          # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
-          echo CMAKE_BUILD_PARALLEL_LEVEL=2 >> $GITHUB_ENV
-          echo CTEST_PARALLEL_LEVEL=2 >> $GITHUB_ENV
+          # 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
+          echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV
+          echo CTEST_PARALLEL_LEVEL=4 >> $GITHUB_ENV
           echo CI_OS_NAME=linux >> $GITHUB_ENV
         shell: bash
 
@@ -171,12 +176,27 @@ jobs:
           python -m pip install --upgrade -r external/nmodl/requirements.txt
           python -m pip install --upgrade -r ci_requirements.txt
 
+      - name: Install a new automake
+        # A new automake is needed for python 3.12 because it generate 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
+          tar -xf automake.tar.xz
+          cd automake-1.16.5/
+          ./configure --prefix=/usr/
+          make -j
+          sudo make -j install
+          automake --version
+        working-directory: ${{runner.temp}}
+
       - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
         if: matrix.config.music == 'ON'
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" numpy
+          python3 -m pip install mpi4py "cython<3" 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

.github/workflows/windows.yml

@@ -49,7 +49,7 @@ jobs:
     - name: Set up Python3
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Download Dependencies
       run: |

.sanitizers/undefined.supp

@@ -30,6 +30,7 @@ shift-base:nrnRan4int
 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*)
 vptr:NetCon::disconnect(ivObservable*)
 vptr:ObjObservable::object()
 vptr:PreSyn::disconnect(ivObservable*)

cmake/MacroHelper.cmake

@@ -164,6 +164,7 @@ macro(nocmodl_mod_to_cpp modfile_basename)
     COMMAND ${CMAKE_COMMAND} -E ${REMOVE_CMAKE_COMMAND}
             ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp
     DEPENDS nocmodl ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
+            ${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/src/nrniv)
 endmacro()
 

nrn_requirements.txt

@@ -8,7 +8,7 @@ bokeh<3
 ipython
 cython<3
 packaging
-pytest
+pytest<=8.1.1 # potential bug from 8.2.0 due to parallelism?
 pytest-cov
 mpi4py
 numpy

share/lib/python/neuron/rxd/region.py

@@ -344,8 +344,14 @@ def __repr__(self):
     def _short_repr(self):
         return "Extracellular"
 
-    def volume(self, index):
+    def volume(self, index=None):
         """Returns the volume of the voxel at a given index"""
+        if index is None:
+            if numpy.isscalar(self.alpha):
+                vol = self._nx * self._ny * self._nz * numpy.prod(self._dx) * self.alpha
+            else:
+                vol = numpy.sum(self.alpha) * numpy.prod(self._dx)
+            return vol
         if numpy.isscalar(self.alpha):
             return numpy.prod(self._dx) * self.alpha
         return numpy.prod(self._dx) * self.alpha[index]
@@ -1000,6 +1006,16 @@ def secs(self, value):
         else:
             raise RxDException("Cannot set secs now; model already instantiated")
 
-    def volume(self, index):
+    def volume(self, index=None):
         """Returns the volume of the voxel at a given index"""
+        initializer._do_init()
+        if index is None:
+            vol = 0
+            if hasattr(self, "_vol") and any(self._secs3d):
+                vol += numpy.sum(self._vol)
+            if hasattr(self, "_geometry") and any(self._secs1d):
+                vol += numpy.sum(
+                    [self._geometry.volumes1d(sec) for sec in self._secs1d]
+                )
+            return vol
         return self._vol[index]

share/lib/python/neuron/rxd/rxd.py

@@ -905,25 +905,27 @@ def _setup_matrices():
             num_3d_indices_per_1d_seg = numpy.asarray(
                 num_3d_indices_per_1d_seg, dtype=numpy.int64
             )
+            hybrid_grid_ids.append(-1)
             hybrid_grid_ids = numpy.asarray(hybrid_grid_ids, dtype=numpy.int64)
 
             hybrid_indices3d = numpy.asarray(hybrid_indices3d, dtype=numpy.int64)
             rates = numpy.asarray(rates, dtype=float)
             volumes1d = numpy.asarray(volumes1d, dtype=float)
             volumes3d = numpy.asarray(volumes3d, dtype=float)
             dxs = numpy.asarray(grids_dx, dtype=float)
-            set_hybrid_data(
-                num_1d_indices_per_grid,
-                num_3d_indices_per_grid,
-                hybrid_indices1d,
-                hybrid_indices3d,
-                num_3d_indices_per_1d_seg,
-                hybrid_grid_ids,
-                rates,
-                volumes1d,
-                volumes3d,
-                dxs,
-            )
+            if hybrid_grid_ids.size > 1:
+                set_hybrid_data(
+                    num_1d_indices_per_grid,
+                    num_3d_indices_per_grid,
+                    hybrid_indices1d,
+                    hybrid_indices3d,
+                    num_3d_indices_per_1d_seg,
+                    hybrid_grid_ids,
+                    rates,
+                    volumes1d,
+                    volumes3d,
+                    dxs,
+                )
 
         # TODO: Replace this this to handle 1d/3d hybrid models
         """

src/nrniv/nrnpy.h

@@ -1,5 +1,6 @@
 #pragma once
 #include <string_view>
+#include <vector>
 /**
  * Declarations of global symbols in NEURON that have to be populated with python-version-specific
  * values when dynamic Python is enabled. These are set by the nrnpython_reg_real function, and
@@ -24,7 +25,7 @@ namespace neuron::python {
 struct impl_ptrs {
     Object* (*callable_with_args)(Object*, int narg){};
     double (*call_func)(Object*, int, int*){};
-    char* (*call_picklef)(char*, std::size_t size, int narg, std::size_t* retsize){};
+    std::vector<char> (*call_picklef)(const std::vector<char>&, int narg){};
     void (*call_python_with_section)(Object*, Section*){};
     void (*cmdtool)(Object*, int type, double x, double y, int kd){};
     int (*guigetstr)(Object*, char**){};
@@ -43,9 +44,9 @@ struct impl_ptrs {
     Object* (*mpi_alltoall_type)(int, int){};
     double (*object_to_double)(Object*){};
     void* (*opaque_obj2pyobj)(Object*){};
-    Object* (*pickle2po)(char*, std::size_t size){};
+    Object* (*pickle2po)(const std::vector<char>&){};
     Object* (*po2ho)(PyObject*){};
-    char* (*po2pickle)(Object*, std::size_t* size){};
+    std::vector<char> (*po2pickle)(Object*){};
     double (*praxis_efun)(Object* pycallable, Object* hvec){};
     int (*pysame)(Object* o1, Object* o2){};
     void (*py2n_component)(Object*, Symbol*, int, int){};