[WIP] Backport 8.2: Python 3.13 support

.circleci/config.yml

@@ -31,7 +31,7 @@ jobs:
                 -e NRN_RELEASE_UPLOAD \
                 -e NEURON_WHEEL_VERSION \
                 -e NRN_BUILD_FOR_UPLOAD=1 \
-                'neuronsimulator/neuron_wheel:latest-gcc9-aarch64' \
+                'neuronsimulator/neuron_wheel:latest-aarch64' \
                 packaging/python/build_wheels.bash linux << parameters.NRN_PYTHON_VERSION >> coreneuron
 
       - store_artifacts:
@@ -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

@@ -23,7 +23,7 @@ env:
   BUILD_TYPE: Release
   DESIRED_CMAKE_VERSION: 3.15.0
   PY_MIN_VERSION: '3.7'
-  PY_MAX_VERSION: '3.11'
+  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}
@@ -120,6 +120,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 2
+          submodules: recursive
 
       - name: Set up Python@${{ env.PY_MIN_VERSION }}
         if: ${{matrix.config.python_dynamic == 'ON'}}
@@ -148,15 +149,15 @@ 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 numpy
           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

azure-pipelines.yml

@@ -46,7 +46,13 @@ stages:
             python.version: '3.11'
           Python312:
             python.version: '3.12'
+          Python313:
+            python.version: '3.13'
+
       steps:
+      - script: |
+          git submodule update --init --recursive
+        displayName: Init submodules
 
       # Secure files documentation:
       #   https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=azure-devops
@@ -71,7 +77,7 @@ stages:
             -e NRN_RELEASE_UPLOAD \
             -e NEURON_WHEEL_VERSION \
             -e NRN_BUILD_FOR_UPLOAD=1 \
-            'neuronsimulator/neuron_wheel:latest-gcc9-x86_64' \
+            'neuronsimulator/neuron_wheel:latest-x86_64' \
             packaging/python/build_wheels.bash linux $(python.version) coreneuron
         displayName: 'Building ManyLinux Wheel'
 
@@ -86,7 +92,7 @@ stages:
     - job: 'MacOSWheels'
       timeoutInMinutes: 40
       pool:
-        vmImage: 'macOS-12'
+        vmImage: 'macOS-13'
       strategy:
         matrix:
           Python37:
@@ -113,8 +119,15 @@ 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:
+      - script: |
+          git submodule update --init --recursive
+        displayName: Init submodules
 
       - script: |
           installer=python-$(python.org.version)-$(python.installer.name)

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

@@ -9,8 +9,9 @@ export MINGW_CHOST=x86_64-w64-mingw32
 export MSYSTEM_PREFIX=/mingw64
 export PATH=/mingw64/bin:$PATH
 
-# have compatible cython3
-python3 -m pip install "cython<3"
+
+# have compatible cython and setuptools
+python3 -m pip install cython setuptools
 
 # if BUILD_SOURCESDIRECTORY not available, use te root of the repo
 if [ -z "$BUILD_SOURCESDIRECTORY" ]; then
@@ -31,7 +32,7 @@ cd $BUILD_SOURCESDIRECTORY/build
 	-DNRN_RX3D_OPT_LEVEL=2 \
 	-DPYTHON_EXECUTABLE=/c/Python37/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:/Python37/python.exe;c:/Python38/python.exe;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

@@ -9,6 +9,7 @@ python-3.9.exe /passive Include_pip=1 Include_test=0 PrependPath=1 DefaultJustFo
 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"
@@ -26,14 +27,16 @@ 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:\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:\Python37\python.exe -m pip install numpy==1.14.6 cython || goto :error
+C:\Python38\python.exe -m pip install  numpy==1.17.5 cython || goto :error
+C:\Python39\python.exe -m pip install  numpy==1.19.3 cython || goto :error
+C:\Python310\python.exe -m pip install numpy==1.21.3 cython || goto :error
+C:\Python311\python.exe -m pip install numpy==1.23.5 cython || goto :error
+C:\Python312\python.exe -m pip install numpy==1.26.3 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
+C:\Python313\python.exe -m pip install setuptools==70.1.1 || goto :error
 
 :: install nsis
 nsis-3.05-setup.exe /S || goto :error
@@ -67,11 +70,11 @@ base-devel ^
 mingw-w64-x86_64-cmake ^
 mingw-w64-x86_64-ncurses ^
 mingw-w64-x86_64-readline ^
-mingw-w64-x86_64-python3 ^
+mingw-w64-x86_64-python ^
 mingw64/mingw-w64-x86_64-cython ^
-mingw-w64-x86_64-python3-setuptools ^
-mingw-w64-x86_64-python3-packaging ^
-mingw-w64-x86_64-python3-pip ^
+mingw-w64-x86_64-python-setuptools ^
+mingw-w64-x86_64-python-packaging ^
+mingw-w64-x86_64-python-pip ^
 mingw64/mingw-w64-x86_64-dlfcn ^
 mingw-w64-x86_64-toolchain || goto :error
 

ci/win_test_installer.cmd

@@ -23,8 +23,28 @@ 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 oldest supported numpy
+C:\Python37\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+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
+C:\Python313\python.exe -m pip install -r packaging/python/oldest_numpy_requirements.txt || goto :error
+
+:: test all pythons again
+C:\Python37\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
+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"
+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/conda_environment.yml

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

docs/domains/hocdomain.py

@@ -1617,7 +1617,6 @@ def resolve_any_xref(
         multiple_matches = len(matches) > 1
 
         for name, obj in matches:
-
             if multiple_matches and obj.aliased:
                 # Skip duplicated matches
                 continue

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/install_instructions.md

@@ -205,7 +205,7 @@ In order to build NEURON from source, the following packages must be available:
 The following packages are optional (see build options):
 
 - Python >=3.7 (for Python interface)
-- Cython < 3 (for RXD)
+- Cython (for RXD)
 - MPI (for parallel)
 - X11 (Linux) or XQuartz (MacOS) (for GUI)
 

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'
 ```
 

docs/parse_rst.py

@@ -10,7 +10,6 @@
 
 
 class ParseRst(object):
-
     help_dictionary = {}
 
     def __init__(self, rst_path, out_file):

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

@@ -52,15 +52,16 @@ pip_numpy_install() {
       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
+    if [[ `uname -m` == 'arm64' ]] && [[ $py_ver -le 311 ]] ; then
       numpy_ver="numpy==1.21.3"
     fi
 

packaging/python/oldest_numpy_requirements.txt

@@ -0,0 +1,8 @@
+numpy==1.14.6;python_version=='3.7'
+numpy==1.17.5;python_version=='3.8'
+numpy==1.20.3;python_version=='3.9' and platform_machine!='arm64'
+numpy==1.21.6;python_version=='3.9' and platform_machine=='arm64'
+numpy==1.21.6;python_version=='3.10'
+numpy==1.23.5;python_version=='3.11'
+numpy==1.26.4;python_version=='3.12'
+numpy>=2;python_version=='3.13'

packaging/python/test_requirements.txt

@@ -0,0 +1,2 @@
+pytest
+setuptools;python_version>='3.12' # From 3.12, no longer installed by default