Merge branch 'master' into header-hygiene-cabcode

.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<2' 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

.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
@@ -207,7 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" 'numpy<2' 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

CMakeLists.txt

@@ -325,9 +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)
@@ -382,9 +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()

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.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;;

ci/win_build_cmake.sh

@@ -10,7 +10,7 @@ export MSYSTEM_PREFIX=/mingw64
 export PATH=/mingw64/bin:$PATH
 
 # have compatible cython3
-python3 -m pip install "cython<3"
+python3 -m pip install "cython"
 
 # if BUILD_SOURCESDIRECTORY not available, use te root of the repo
 if [ -z "$BUILD_SOURCESDIRECTORY" ]; then
@@ -30,7 +30,7 @@ cd $BUILD_SOURCESDIRECTORY/build
 	-DNRN_ENABLE_RX3D=ON  \
 	-DNRN_RX3D_OPT_LEVEL=2 \
 	-DNRN_BINARY_DIST_BUILD=ON \
-	-DPYTHON_EXECUTABLE=/c/Python38/python.exe \
+	-DPYTHON_EXECUTABLE=/c/Python39/python.exe \
 	-DNRN_ENABLE_PYTHON_DYNAMIC=ON  \
 	-DNRN_PYTHON_DYNAMIC='c:/Python38/python.exe;c:/Python39/python.exe;c:/Python310/python.exe;c:/Python311/python.exe;c:/Python312/python.exe'  \
 	-DCMAKE_INSTALL_PREFIX='/c/nrn-install' \

ci/win_install_deps.cmd

@@ -23,11 +23,11 @@ pwsh -command "(Get-Content C:\Python310\Lib\distutils\cygwinccompiler.py) -repl
 pwsh -command "(Get-Content C:\Python311\Lib\distutils\cygwinccompiler.py) -replace 'msvcr100', 'msvcrt' | Out-File C:\Python311\Lib\distutils\cygwinccompiler.py"
 
 :: install numpy
-C:\Python38\python.exe -m pip install  numpy==1.17.5 "cython < 3" || goto :error
-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:\Python38\python.exe -m pip install  numpy cython || goto :error
+C:\Python39\python.exe -m pip install  numpy cython || goto :error
+C:\Python310\python.exe -m pip install numpy cython || goto :error
+C:\Python311\python.exe -m pip install numpy cython || goto :error
+C:\Python312\python.exe -m pip install numpy cython || goto :error
 :: setuptools 70.2 leads to an error
 C:\Python312\python.exe -m pip install setuptools==70.1.1 || goto :error
 

ci/win_test_installer.cmd

@@ -21,9 +21,24 @@ C:\Python38\python -c "import neuron; neuron.test(); quit()" || set "errorfound=
 C:\Python39\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
 C:\Python310\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
 C:\Python311\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
-:: install numpy dependency
-python -m pip install "numpy<2"
+C:\Python312\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+
+:: install oldest supported numpy
+C:\Python38\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+C:\Python39\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+C:\Python310\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+C:\Python311\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+C:\Python312\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+
+:: test all pythons again
+C:\Python38\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+C:\Python39\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+C:\Python310\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+C:\Python311\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+C:\Python312\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+
 :: run also using whatever is system python
+python -m pip install numpy
 python --version
 python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
 

cmake/ExternalProjectHelper.cmake

@@ -29,7 +29,11 @@ function(nrn_initialize_submodule path)
     list(APPEND UPDATE_OPTIONS --recursive)
   endif()
   if(opt_SHALLOW)
-    list(APPEND UPDATE_OPTIONS --depth 1)
+    # RHEL7-family distributions ship with an old git that does not support the --depth argument to
+    # git submodule update
+    if(GIT_VERSION_STRING VERSION_GREATER_EQUAL "1.8.4")
+      list(APPEND UPDATE_OPTIONS --depth 1)
+    endif()
   endif()
   if(NOT ${GIT_FOUND})
     message(

cmake/NeuronFileLists.cmake

@@ -127,7 +127,6 @@ set(NRNOC_FILE_LIST
     ldifus.cpp
     membfunc.cpp
     memblist.cpp
-    nrnnemo.cpp
     nrntimeout.cpp
     nrnversion.cpp
     passive0.cpp

cmake/coreneuron/MakefileBuildOptions.cmake

@@ -73,13 +73,19 @@ function(coreneuron_process_target target)
       if(target_imported)
         # In this case we can extract the full path to the library
         get_target_property(target_location ${target} LOCATION)
-        coreneuron_process_library_path(${target_location})
+        if(target_location)
+          coreneuron_process_library_path(${target_location})
+        endif()
       else()
         # This is probably another of our libraries, like -lcoreneuron-cuda. We might need to add -L
         # and an RPATH later.
         set_property(GLOBAL APPEND_STRING PROPERTY CORENRN_LIB_LINK_DEP_FLAGS " -l${target}")
       endif()
     endif()
+    get_target_property(target_flags ${target} INTERFACE_COMPILE_OPTIONS)
+    if(target_flags)
+      set_property(GLOBAL APPEND_STRING PROPERTY CORENRN_EXTRA_COMPILE_FLAGS " ${target_flags}")
+    endif()
     get_target_property(target_libraries ${target} LINK_LIBRARIES)
     if(target_libraries)
       foreach(child_target ${target_libraries})

docs/changelog.md

@@ -1,5 +1,21 @@
 # NEURON 8.2
 
+## 8.2.6
+_Release Date_ : 24-07-2024
+
+This release pins numpy to <2 and includes backports for several fixes.
+
+### Bug Fixes
+- Informative error when cannot import hoc module
+- ParallelContext: hoc_ac_ encodes global id of submitted process.
+- Python 3.12 compatibility with Windows installer (#2963)
+- Windows 11 fix for nrniv -python (#2946)
+- Fix for dynamic ECS diffusion characteristics.
+- python38 is back. For testing can use rx3doptlevel=0 bash bldnrnmacpkgcmake.sh
+- Fix cvode.use_fast_imem(1) error with electrode time varying conductance.
+- Apple M1 cmake failure in cloning subrepository. See #2326.
+- Update iv
+
 ## 8.2.4
 _Release Date_ : 08-02-2024
 

docs/conda_environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - cmake
   - xorg-libxcomposite
   - ffmpeg
-  - cython<3
+  - cython
   - pandoc
   - mpich
   - pip

docs/dev/setuptools/setuptools.md

@@ -15,20 +15,64 @@ We use [setup.py](../../../setup.py) in two operational modes
 :
 
 1) **wheel building**
-    It boils down to 
+    It boils down to
 
         setup.py build_ext bdist_wheel
-    
+
     We configure the HOC extension along with a CMake configure, build all extensios and collect them for the wheel. This is called via [build_wheels.bash](../../../packaging/python/build_wheels.bash).
 
 2) **CMake build**
     It boils down to
-
-        setup.py build_ext build  
 
-    We provide the cmake build folder, in this mode we do not run CMake configure, we build all extensions and make sure they are integrated into the CMake build and install. This is called via CMake in [src/nrnpython/CMakeLists.txt](../../../src/nrnpython/CMakeLists.txt) by passing **--cmake-build-dir** (the folder where we configured NEURON with CMake), along with other CMake options. 
+        setup.py build_ext build
+
+    We provide the cmake build folder, in this mode we do not run CMake configure, we build all extensions and make sure they are integrated into the CMake build and install. This is called via CMake in [src/nrnpython/CMakeLists.txt](../../../src/nrnpython/CMakeLists.txt) by passing **--cmake-build-dir** (the folder where we configured NEURON with CMake), along with other CMake options.
 
 
 ## **Activity Diagram**
 
-![](images/setup-py.png)
+![](images/setup-py.png)
+
+
+## Creating a Development Python Package
+
+`setup.py` can be lanched manually as well to create a dev build package, which can be tested
+immediately. It supports several arguments to that the build can be tuned:
+
+```
+ --disable-rx3d       Disables Rx3d. Implies CMake -DNRN_ENABLE_RX3D=OFF
+ --disable-iv         Disables IV. Implies CMake -DNRN_ENABLE_INTERVIEWS=OFF
+ --disable-mpi        Disables MPI. Implies -DNRN_ENABLE_MPI=OFF and disabling of neuronmusic
+ --enable-music       Enables neuronmusic
+ --enable-coreneuron  Enables experimental CorenNeuron support
+ --rx3d-opt-level     Sets the rx3d optimization level. Default: 0 (-O0)
+ --cmake-build-dir    Declares one wants to use a specic NEURON build (with CMake), instead
+                      of creating one behind the scenes. Only builds extensions and package.
+```
+
+A quick build for testing a change to a core component could therefore be:
+```
+python setup.py build --disable-rx3d --disable-iv --disable-mpi
+```
+
+---
+**Mac Note**
+
+Since the introduction of Mac with Apple silicon, with an Official Python distribution, extension are simultaneously built for arm64 and x86_64. Besides not required for a dev build, it may fail
+on older SDKs with `Unsupported architecture` errors.
+
+To skip that you may set the ARCHFLAGS environment var. Set it to "" (empty) for default architecture: `ARCHFLAGS='' python setup.py ...`
+
+---
+
+### Testing
+
+Once built, the package may be imported and used normally. You might, however, need to set up
+PYTHONPATH accordingly for the import to work:
+
+```
+export PYTHONPATH="<NRNDIR>/build/lib.macosx-10.9-x86_64-3.9/:$PYTHONPATH"
+
+# Run Neuron base tests
+python -c "import neuron; neuron.test()"
+```

docs/guide/hoc_chapter_11_old_reference.rst

@@ -338,7 +338,7 @@ Names introduced by nrnoc
 .. code::
     c++
 
-    node_data	disconnect	batch_run	batch_save
+    disconnect	batch_run	batch_save
 	pt3dclear	pt3dadd	n3d	x3d	y3d	z3d	diam3d	arc3d
 	define_shape	p3dconst	spine3d	setSpineArea	getSpineArea
 	area	ri	initnrn	topology	fadvance	distance

docs/hoc/compilationoptions.rst

@@ -3,8 +3,7 @@ Rarely Used Compilation Options
 
 The following definitions are found in nrnoc/SRC/options.h and add extra 
 functionality which not everyone may need. The extras come at the cost 
-of larger memory requirements for node and section structures. METHOD3 is too large 
-and obscure to benefit most users. 
+of larger memory requirements for node and section structures.
 
 .. code-block::
     none
@@ -27,29 +26,3 @@ and obscure to benefit most users.
     				 * of spine. setSpineArea() tells how much 
     				 * area/spine to add to the segment. */ 
     #endif 
-     
-    #define METHOD3		1	/* third order spatially correct method */ 
-    				/* testing only, not completely implemented */ 
-    				/* not working at this time */ 
-     
-    #if METHOD3 
-     spatial_method(i) 
-    	no arg, returns current method 
-    	i=0 The standard NEURON method with zero area nodes at the ends 
-    		of sections. 
-    	i=1 conventional method with 1/2 area end nodes 
-    	i=2 modified second order method 
-    	i=3 third order correct spatial method 
-    	Note: i=1-3 don't work under all circumstances. They have been 
-    	insufficiently tested and the correctness must be established for 
-    	each simulation. 
-    #endif 
-     
-    #if NEMO 
-    neuron2nemo("filename") Beginning of translator between John Millers 
-    		nemosys program	and NEURON. Probably out of date. 
-    nemo2neuron("filename") 
-    #endif 
-
-
-

docs/index.rst

@@ -98,7 +98,7 @@ Installation
 
          pip3 install neuron
 
-      Alternatively, you can use the `PKG installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.4/nrn-8.2.4-macosx-10.9-universal2-py-38-39-310-311.pkg>`_.
+      Alternatively, you can use the `PKG installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.6/nrn-8.2.6-macosx-10.9-universal2-py-38-39-310-311-312.pkg>`_.
 
       For troubleshooting, see the `detailed installation instructions <install/install_instructions.md>`_.
 
@@ -115,7 +115,7 @@ Installation
 
    .. tab-item:: Windows
 
-      `Download the Windows Installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.4/nrn-8.2.4.w64-mingw-py-37-38-39-310-311-setup.exe>`_.
+      `Download the Windows Installer <https://github.com/neuronsimulator/nrn/releases/download/8.2.6/nrn-8.2.6.w64-mingw-py-38-39-310-311-312-setup.exe>`_.
 
       You can also install the Linux wheel via the Windows Subsystem for Linux (WSL). See `instructions <install/install_instructions.html#windows-subsystem-for-linux-wsl-python-wheel>`_.