release/8.2 can use Python 3.13

.circleci/config.yml

@@ -54,6 +54,8 @@ jobs:
               39) pyenv_py_ver="3.9.1" ;;
               310) pyenv_py_ver="3.10.1" ;;
               311) pyenv_py_ver="3.11.0" ;;
+              312) pyenv_py_ver="3.12.0" ;;
+              313) pyenv_py_ver="3.13.1" ;;
               *) echo "Error: pyenv python version not specified!" && exit 1;;
             esac
 
@@ -110,5 +112,5 @@ workflows:
       - manylinux2014-aarch64:
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["37", "38", "39", "310", "311"]
+              NRN_PYTHON_VERSION: ["37", "38", "39", "310", "311", "312", "313"]
               NRN_NIGHTLY_UPLOAD: ["true"]

.github/workflows/coverage.yml

@@ -21,7 +21,7 @@ on:
 
 env:
   PY_MIN_VERSION: '3.7'
-  PY_MAX_VERSION: '3.11'
+  PY_MAX_VERSION: '3.13'
 
 jobs:
   coverage:

.github/workflows/neuron-ci.yml

@@ -22,8 +22,8 @@ on:
 env:
   BUILD_TYPE: Release
   DESIRED_CMAKE_VERSION: 3.15.0
-  PY_MIN_VERSION: '3.7'
-  PY_MAX_VERSION: '3.11'
+  PY_MIN_VERSION: '3.9'
+  PY_MAX_VERSION: '3.13'
 
 jobs:
   ci:
@@ -40,12 +40,12 @@ jobs:
       BUILD_TYPE: Release
       DESIRED_CMAKE_VERSION: 3.15.0
       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
 
     strategy:
       matrix:
-        os: [ macOS-12, ubuntu-20.04]
+        os: [ macOS-13, ubuntu-20.04]
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
           - { matrix_eval : "CC=gcc-8 CXX=g++-8",   build_mode: "cmake", music: ON}
@@ -148,15 +148,15 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install mpi4py "cython<3" "numpy<2"
+          python3 -m pip install mpi4py "cython>=3" "numpy>=2"
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
           # Stable build: https://github.com/INCF/MUSIC/archive/refs/heads/switch-to-MPI-C-interface.zip  @ f33b66ea9348888eed1761738ab48c23ffc8a0d0
           curl -L -o MUSIC.zip https://codeload.github.com/INCF/MUSIC/zip/f33b66ea9348888eed1761738ab48c23ffc8a0d0
           unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
           ./autogen.sh
           # workaround for MUSIC on MacOS 12
-          if [[ "${{matrix.os}}" == "macOS-12" ]]; then
+          if [[ "${{matrix.os}}" == "macOS-13" ]]; then
             MPI_CXXFLAGS="-g" MPI_CFLAGS="-g" MPI_LDFLAGS="-g" CC=mpicc CXX=mpicxx ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource
           else
             ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource

.gitmodules

@@ -3,7 +3,7 @@
 	url = https://github.com/neuronsimulator/iv.git
 [submodule "external/coreneuron"]
 	path = external/coreneuron
-	url = https://github.com/BlueBrain/CoreNeuron.git
+	url = https://github.com/neuronsimulator/CoreNeuron.git
 [submodule "external/catch2"]
 	path = external/catch2
 	url = https://github.com/catchorg/Catch2.git

azure-pipelines.yml

@@ -46,6 +46,8 @@ stages:
             python.version: '3.11'
           Python312:
             python.version: '3.12'
+          Python313:
+            python.version: '3.13'
       steps:
 
       # Secure files documentation:
@@ -86,7 +88,7 @@ stages:
     - job: 'MacOSWheels'
       timeoutInMinutes: 40
       pool:
-        vmImage: 'macOS-12'
+        vmImage: 'macOS-13'
       strategy:
         matrix:
           Python37:
@@ -113,6 +115,10 @@ stages:
             python.version: '3.12'
             python.org.version: '3.12.2'
             python.installer.name: 'macos11.pkg'
+          Python313:
+            python.version: '3.13'
+            python.org.version: '3.13.1'
+            python.installer.name: 'macos11.pkg'
 
       steps:
 

bldnrnmacpkgcmake.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -ex
 
-default_pythons="python3.8 python3.9 python3.10 python3.11 python3.12"
+default_pythons="python3.8 python3.9 python3.10 python3.11 python3.12 python3.13"
 # distribution built with
 # bash bldnrnmacpkgcmake.sh
 # without args, default are the pythons above.

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>=3"
 
 # if BUILD_SOURCESDIRECTORY not available, use te root of the repo
 if [ -z "$BUILD_SOURCESDIRECTORY" ]; then
@@ -29,9 +29,9 @@ cd $BUILD_SOURCESDIRECTORY/build
 	-DNRN_ENABLE_PYTHON=ON  \
 	-DNRN_ENABLE_RX3D=ON  \
 	-DNRN_RX3D_OPT_LEVEL=2 \
-	-DPYTHON_EXECUTABLE=/c/Python37/python.exe \
+	-DPYTHON_EXECUTABLE=/c/Python311/python.exe \
 	-DNRN_ENABLE_PYTHON_DYNAMIC=ON  \
-	-DNRN_PYTHON_DYNAMIC='c:/Python37/python.exe;c:/Python38/python.exe;c:/Python39/python.exe;c:/Python310/python.exe;c:/Python311/python.exe;c:/Python312/python.exe'  \
+	-DNRN_PYTHON_DYNAMIC='c:/Python39/python.exe;c:/Python310/python.exe;c:/Python311/python.exe;c:/Python312/python.exe;c:/Python313/python.exe'  \
 	-DCMAKE_INSTALL_PREFIX='/c/nrn-install' \
 	-DMPI_CXX_LIB_NAMES:STRING=msmpi \
 	-DMPI_C_LIB_NAMES:STRING=msmpi \

ci/win_download_deps.cmd

@@ -9,6 +9,7 @@ pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.9.exe htt
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.10.exe https://www.python.org/ftp/python/3.10.0/python-3.10.0-amd64.exe || goto :error
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.11.exe https://www.python.org/ftp/python/3.11.1/python-3.11.1-amd64.exe || goto :error
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.12.exe https://www.python.org/ftp/python/3.12.1/python-3.12.1-amd64.exe || goto :error
+pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.13.exe https://www.python.org/ftp/python/3.13.1/python-3.13.1-amd64.exe || goto :error
 
 :: mpi
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile msmpisetup.exe https://download.microsoft.com/download/a/5/2/a5207ca5-1203-491a-8fb8-906fd68ae623/msmpisetup.exe || goto :error

ci/win_install_deps.cmd

@@ -3,35 +3,29 @@
 :: install all dependencies
 
 :: install python
-python-3.7.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python37 || goto :error
-python-3.8.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python38 || goto :error
 python-3.9.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python39 || goto :error
 python-3.10.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python310 || goto :error
 python-3.11.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python311 || goto :error
 python-3.12.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python312 || goto :error
+python-3.13.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustForMeTargetDir=C:\Python313 || goto :error
 
 :: fix msvcc version for all python3
-pwsh -command "(Get-Content C:\Python37\Lib\distutils\cygwinccompiler.py) -replace 'elif msc_ver == ''1600'':', 'elif msc_ver == ''1900'':' | Out-File C:\Python37\Lib\distutils\cygwinccompiler.py"
-pwsh -command "(Get-Content C:\Python38\Lib\distutils\cygwinccompiler.py) -replace 'elif msc_ver == ''1600'':', 'elif msc_ver == ''1916'':' | Out-File C:\Python38\Lib\distutils\cygwinccompiler.py"
 pwsh -command "(Get-Content C:\Python39\Lib\distutils\cygwinccompiler.py) -replace 'elif msc_ver == ''1600'':', 'elif msc_ver == ''1927'':' | Out-File C:\Python39\Lib\distutils\cygwinccompiler.py"
 pwsh -command "(Get-Content C:\Python310\Lib\distutils\cygwinccompiler.py) -replace 'elif msc_ver == ''1600'':', 'elif msc_ver == ''1929'':' | Out-File C:\Python310\Lib\distutils\cygwinccompiler.py"
 pwsh -command "(Get-Content C:\Python311\Lib\distutils\cygwinccompiler.py) -replace 'elif msc_ver == ''1600'':', 'elif msc_ver == ''1934'':' | Out-File C:\Python311\Lib\distutils\cygwinccompiler.py"
 
 
 :: fix msvc runtime library for all python
-pwsh -command "(Get-Content C:\Python37\Lib\distutils\cygwinccompiler.py) -replace 'msvcr100', 'msvcrt' | Out-File C:\Python37\Lib\distutils\cygwinccompiler.py"
-pwsh -command "(Get-Content C:\Python38\Lib\distutils\cygwinccompiler.py) -replace 'msvcr100', 'msvcrt' | Out-File C:\Python38\Lib\distutils\cygwinccompiler.py"
 pwsh -command "(Get-Content C:\Python39\Lib\distutils\cygwinccompiler.py) -replace 'msvcr100', 'msvcrt' | Out-File C:\Python39\Lib\distutils\cygwinccompiler.py"
 pwsh -command "(Get-Content C:\Python310\Lib\distutils\cygwinccompiler.py) -replace 'msvcr100', 'msvcrt' | Out-File C:\Python310\Lib\distutils\cygwinccompiler.py"
 pwsh -command "(Get-Content C:\Python311\Lib\distutils\cygwinccompiler.py) -replace 'msvcr100', 'msvcrt' | Out-File C:\Python311\Lib\distutils\cygwinccompiler.py"
 
 :: install numpy
-C:\Python37\python.exe -m pip install numpy==1.14.6 "cython < 3" || goto :error
-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:\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
+C:\Python313\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

@@ -23,8 +23,9 @@ C:\Python39\python -c "import neuron; neuron.test(); quit()" || set "errorfound=
 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"
+C:\Python313\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
 :: install numpy dependency
-python -m pip install "numpy<2"
+python -m pip install "numpy"
 :: run also using whatever is system python
 python --version
 python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"

ci/win_test_installer_wo_rxd.cmd

@@ -26,9 +26,10 @@ C:\Python39\python -c "import neuron; neuron.test(); quit()" || set "errorfound=
 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"
+C:\Python313\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
 
 :: install numpy dependency
-python -m pip install "numpy<2"
+python -m pip install "numpy"
 :: run also using whatever is system python
 python --version
 python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"

docs/changelog.md

@@ -1,5 +1,10 @@
 # NEURON 8.2
 
+## 8.2.7
+_Release Date_ : 01-02-2025
+
+This release allows use of Python 3.13
+
 ## 8.2.6
 _Release Date_ : 24-07-2024
 

docs/docs_requirements.txt

@@ -9,7 +9,7 @@ bokeh<3
 # do not check import of next line
 ipython
 plotnine
-numpy<2
+numpy
 plotly
 nbsphinx
 jinja2

docs/index.rst

@@ -88,7 +88,7 @@ Installation
 
          pip3 install neuron
 
-      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>`_.
+      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-38-39-310-311-312-313.pkg>`_.
 
       For troubleshooting, see the `detailed installation instructions <install/install_instructions.html>`_.
 

docs/install/mac_pkg.md

@@ -55,7 +55,7 @@ cmake .. -DCMAKE_INSTALL_PREFIX=$NRN_INSTALL \
 
 The default variables above will be
 ```
-pythons="python3.9;python3.10;python3.11;python3.12"
+pythons="python3.9;python3.10;python3.11;python3.12;python3.13"
 archs_cmake='-DCMAKE_OSX_ARCHITECTURES=arm64;x86_64'
 ```
 

nrn_requirements.txt

@@ -5,9 +5,9 @@ matplotlib
 # bokeh 3 seems to break docs notebooks
 bokeh<3
 ipython
-cython<3
+cython
 packaging
 pytest
 pytest-cov
 mpi4py
-numpy<2
+numpy

packaging/python/build_requirements.txt

@@ -1,2 +1,2 @@
-cython<3
+cython
 packaging

packaging/python/build_wheels.bash

@@ -49,19 +49,17 @@ pip_numpy_install() {
     # numpy is special as we want the minimum wheel version
     numpy_ver="numpy"
     case "$py_ver" in
-      36) numpy_ver="numpy==1.12.1" ;;
-      37) numpy_ver="numpy==1.14.6" ;;
-      38) numpy_ver="numpy==1.17.5" ;;
-      39) numpy_ver="numpy==1.19.3" ;;
-      310) numpy_ver="numpy==1.21.3" ;;
-      311) numpy_ver="numpy==1.23.5" ;;
-      312) numpy_ver="numpy==1.26.0" ;;
+      39) numpy_ver="numpy>=2" ;;
+      310) numpy_ver="numpy>=2" ;;
+      311) numpy_ver="numpy>=2" ;;
+      312) numpy_ver="numpy>=2" ;;
+      313) numpy_ver="numpy>=2" ;;
       *) echo "Error: numpy version not specified for this python!" && exit 1;;
     esac
 
     # older version for apple m1 as building from source fails
-    if [[ `uname -m` == 'arm64' ]] && [[ $py_ver != 311 ]] && [[ $py_ver != 312 ]]; then
-      numpy_ver="numpy==1.21.3"
+    if [[ `uname -m` == 'arm64' ]] && [[ $py_ver -le 311 ]] ; then
+      numpy_ver="numpy>=2"
     fi
 
     echo " - pip install $numpy_ver"

packaging/python/test_wheels.sh

@@ -300,7 +300,7 @@ $python_exe -m pip install --upgrade setuptools
 # install numpy, pytest and neuron
 # we install setuptools because since python 3.12 it is no more installed
 # by default
-$python_exe -m pip install "numpy<2" pytest setuptools
+$python_exe -m pip install "numpy" pytest setuptools
 $python_exe -m pip install $python_wheel
 $python_exe -m pip show neuron \
     || $python_exe -m pip show neuron-nightly \

setup.py

@@ -410,7 +410,12 @@ def setup_package():
     NRN_COLLECT_DIRS = ["bin", "lib", "include", "share"]
 
     docs_require = []  # sphinx, themes, etc
-    maybe_rxd_reqs = ["numpy<2", "Cython<3"] if Components.RX3D else []
+    ver_lt_313 = sys.version_info[0] == 3 and sys.version_info[1] < 13
+    if Components.RX3D:
+        if ver_lt_313:
+            maybe_rxd_reqs = ["numpy", "Cython"]
+        else:
+            maybe_rxd_reqs = ["numpy", "Cython"]
     maybe_docs = docs_require if "docs" in sys.argv else []
     maybe_test_runner = ["pytest-runner"] if "test" in sys.argv else []
 
@@ -574,7 +579,7 @@ def setup_package():
         ],
         cmdclass=dict(build_ext=CMakeAugmentedBuilder, docs=Docs),
         install_requires=[
-            "numpy>=1.9.3,<2",
+            "numpy",
             "packaging",
             "find_libpython",
             "setuptools",
@@ -608,18 +613,21 @@ def mac_osx_setenv():
     def fmt(version):
         return ".".join(str(x) for x in version)
 
+    # Match Python OSX framework
+    py_osx_framework = extract_macosx_min_system_version(sys.executable)
+
     if "MACOSX_DEPLOYMENT_TARGET" in os.environ:
         # Don't override the value if it is set explicitly, but try and print a
         # helpful message
         explicit_target = tuple(
             int(x) for x in os.environ["MACOSX_DEPLOYMENT_TARGET"].split(".")
         )
+    else:
+        explicit_target = (10, 9)
 
-    # Match Python OSX framework
-    py_osx_framework = extract_macosx_min_system_version(sys.executable)
     if py_osx_framework is None:
-        py_osx_framework = [10, 9]
-    if py_osx_framework[1] > 9:
+        py_osx_framework = (10, 9)
+    if py_osx_framework > (10, 9):
         logging.warning(
             "[ WARNING ] You are building a wheel with a Python built"
             " for a recent MACOS version (from brew?). Your wheel won't be portable."
@@ -636,14 +644,14 @@ def fmt(version):
         # Python framework, or 10.9 if the version targeted by the framework
         # cannot be determined
         if py_osx_framework is None:
-            py_osx_framework = (10, 15)
-        if py_osx_framework < (10, 15):
+            py_osx_framework = (10, 9)
+        if py_osx_framework < (10, 9):
             logging.warning(
-                "C++17 support is required to build NEURON on macOS, "
-                "therefore minimum MACOSX_DEPLOYMENT_TARGET version is 10.15."
+                "C++11 support is required to build NEURON on macOS, "
+                "therefore minimum MACOSX_DEPLOYMENT_TARGET version is 10.9."
             )
-            py_osx_framework = (10, 15)
-        if py_osx_framework > (10, 15):
+            py_osx_framework = (10, 9)
+        if py_osx_framework > (10, 9):
             logging.warning(
                 "You are building a wheel with a Python built for macOS >={}. "
                 "Your wheel won't run on older versions, consider using an "

src/nrnpython/nrnpy_hoc.cpp

@@ -1596,13 +1596,16 @@ PyObject* nrnpy_forall(PyObject* self, PyObject* args) {
 static PyObject* hocobj_iter(PyObject* self) {
     //	printf("hocobj_iter %p\n", self);
     PyHocObject* po = (PyHocObject*) self;
-    if (po->type_ == PyHoc::HocObject) {
+    if (po->type_ == PyHoc::HocObject || po->type_ == PyHoc::HocSectionListIterator) {
         if (po->ho_->ctemplate == hoc_vec_template_) {
             return PySeqIter_New(self);
         } else if (po->ho_->ctemplate == hoc_list_template_) {
             return PySeqIter_New(self);
         } else if (po->ho_->ctemplate == hoc_sectionlist_template_) {
             // need a clone of self so nested loops do not share iteritem_
+            // The HocSectionListIter arm of the outer 'if' became necessary
+            // at Python-3.13.1 upon which the following body is executed
+            // twice. See https://github.com/python/cpython/issues/127682
             PyObject* po2 = nrnpy_ho2po(po->ho_);
             PyHocObject* pho2 = (PyHocObject*) po2;
             pho2->type_ = PyHoc::HocSectionListIterator;