Merge branch 'master' into leite/dat_files_use_vec

.circleci/config.yml

@@ -1,13 +1,13 @@
 version: 2.1
 
 orbs:
-  python: circleci/python@2.1.1
+  python: circleci/python@3.0.0
 
 jobs:
   manylinux2014-aarch64:
 
     parameters:
-      NRN_PYTHON_VERSION:
+      NRN_PYTHON_VERSION_MINOR:
         type: string
       NRN_NIGHTLY_UPLOAD:
         type: string
@@ -31,8 +31,8 @@ jobs:
                 -e NRN_RELEASE_UPLOAD \
                 -e SETUPTOOLS_SCM_PRETEND_VERSION \
                 -e NRN_BUILD_FOR_UPLOAD=1 \
-                'neuronsimulator/neuron_wheel:latest-gcc9-aarch64' \
-                packaging/python/build_wheels.bash linux << parameters.NRN_PYTHON_VERSION >> coreneuron
+                'neuronsimulator/neuron_wheel:latest-aarch64' \
+                packaging/python/build_wheels.bash linux 3<< parameters.NRN_PYTHON_VERSION_MINOR >> coreneuron
 
       - store_artifacts:
           path: ./wheelhouse
@@ -41,24 +41,16 @@ jobs:
       - run:
           name: Test manylinux AArch64 wheel
           command: |
-
-            # install mpi dependencies
             sudo apt update
+            echo "deb http://ppa.launchpad.net/deadsnakes/ppa/ubuntu jammy main" | sudo tee /etc/apt/sources.list.d/deadsnakes-ppa.list && sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys F23C5A6CF475977595C89F51BA6932366A755776 && sudo apt update
+            sudo apt update
+            # install mpi dependencies
             sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
+            version=3.<< parameters.NRN_PYTHON_VERSION_MINOR >>
+            # install Python from deadsnakes
+            sudo apt install -y python${version}-venv libpython${version}-dev g++ make
 
-            # choose available python versions from pyenv
-            pyenv_py_ver=""
-            case << parameters.NRN_PYTHON_VERSION >> in
-              39) pyenv_py_ver="3.9" ;;
-              310) pyenv_py_ver="3.10" ;;
-              311) pyenv_py_ver="3.11" ;;
-              312) pyenv_py_ver="3.12" ;;
-              *) echo "Error: pyenv python version not specified or not supported." && exit 1;;
-            esac
-
-            env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install $pyenv_py_ver --force
-            pyenv global $pyenv_py_ver
-            export PYTHON_EXE=$(which python)
+            export PYTHON_EXE=$(which python3.<< parameters.NRN_PYTHON_VERSION_MINOR >>)
 
             # test wheel
             packaging/python/test_wheels.sh $PYTHON_EXE $(ls -t wheelhouse/*.whl)
@@ -86,7 +78,7 @@ workflows:
                 - /circleci\/.*/
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["312"]
+              NRN_PYTHON_VERSION_MINOR: ["13"]
               NRN_NIGHTLY_UPLOAD: ["false"]
 
   nightly:
@@ -101,5 +93,5 @@ workflows:
       - manylinux2014-aarch64:
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["39", "310", "311", "312"]
+              NRN_PYTHON_VERSION_MINOR: ["9", "10", "11", "12", "13"]
               NRN_NIGHTLY_UPLOAD: ["true"]

.github/workflows/coverage.yml

@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.9'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.12'
+  PY_MAX_VERSION: '3.13'
 
 jobs:
   coverage:

.github/workflows/docs.yml

@@ -17,7 +17,7 @@ on:
       - release/**
 
 env:
-  DEFAULT_PY_VERSION: '3.12'
+  DEFAULT_PY_VERSION: '3.13'
 
 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 || '3.9' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }}
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
       # hash of commit containing mpi4py 4 fix
       MUSIC_VERSION: '13f312338dcccebfe74d391b1b24f1b6d816ac6c'

azure-pipelines.yml

@@ -42,6 +42,9 @@ stages:
             python.version: '3.11'
           Python312:
             python.version: '3.12'
+          Python313:
+            python.version: '3.13'
+
       steps:
 
       # Secure files documentation:
@@ -74,7 +77,7 @@ stages:
       - script: |
           sudo apt update
           sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
-        displayName: 'Install Test System Depdendencies'
+        displayName: 'Install Test System Dependencies'
 
       - template: ci/azure-wheel-test-upload.yml
 
@@ -102,6 +105,10 @@ stages:
             python.version: '3.12'
             python.org.version: '3.12.0'
             python.installer.name: 'macos11.pkg'
+          Python313:
+            python.version: '3.13'
+            python.org.version: '3.13.0'
+            python.installer.name: 'macos11.pkg'
 
       steps:
 

bldnrnmacpkgcmake.sh → bldnrnmacpkg.sh

@@ -1,19 +1,29 @@
 #!/usr/bin/env bash
 set -ex
 
-default_pythons="python3.8 python3.9 python3.10 python3.11"
+default_pythons="python3.9 python3.10 python3.11 python3.12 python3.13"
 # distribution built with
 # bash bldnrnmacpkgcmake.sh
 # without args, default are the pythons above.
 
+if test "$RX3D_OPT" = "" ; then
+  RX3D_OPT=1 # a value of 2 takes much longer to build
+fi
+
 # If all the pythons are universal, then so is NEURON.
 # Otherwise $CPU
-# All pythons must have the same macos version and that will become
-# the MACOSX_DEPLOYMENT_TARGET
 
+# Now obsolete...
 # On my machine, to build nrn-x.x.x-macosx-10.9-universal2-py-38-39-310-311.pkg
 # I built my own versions of 3.8 in $HOME/soft/python3.8, and
-export PATH=$HOME/soft/python3.8/bin:$PATH
+# export PATH=$HOME/soft/python3.8/bin:$PATH
+# All other python versions installed from python.org universal2 installers.
+
+# As of Python-3.13.0, we configure to link universal2 static readline
+# (and ncurses) into libnrniv.dylib.
+# The packages were downloade and the universal libraries were built with
+# nrn/packaging/python/build_static_readline_osx.bash
+READLINE_LIST="/opt/nrnwheel/arm64/readline;/opt/nrnwheel/arm64/ncurses"
 
 CPU=`uname -m`
 
@@ -24,10 +34,15 @@ if test "$args" = "" ; then
   args="$default_pythons"
 fi
 
+MPI_LIST="/opt/homebrew/opt/openmpi/include;/opt/homebrew/opt/mpich/include"
 
 # sysconfig.get_platform() looks like, e.g. "macosx-12.2-arm64" or
 # "macosx-11-universal2". I.e. encodes MACOSX_DEPLOYMENT_TARGET and archs.
 # Demand all pythons we are building against have same platform.
+# Update: nrn software now requires at least 10.15. All the python's on this
+# machine are 10.9, except python 3.13 is 10.13. The substantive aspect of
+# the following fragment (exit 1 if not all the same platform), has been
+# commented out.
 mac_platform=""
 for i in $args ; do
   last_py=$i
@@ -38,7 +53,7 @@ for i in $args ; do
   fi
   if test "$mac_platform" != "$mplat" ; then
     echo "$i platform \"$mplat\" differs from previous python \"$mac_platform\"."
-    exit 1
+#    exit 1
   fi
 done
 
@@ -93,13 +108,15 @@ fi
 
 cmake .. -G Ninja -DCMAKE_INSTALL_PREFIX=$NRN_INSTALL \
   -DNRN_ENABLE_MPI_DYNAMIC=ON \
+  -DNRN_MPI_DYNAMIC="$MPI_LIST" \
   -DPYTHON_EXECUTABLE=`which python3` -DNRN_ENABLE_PYTHON_DYNAMIC=ON \
   -DNRN_PYTHON_DYNAMIC="$pythons" \
   -DIV_ENABLE_X11_DYNAMIC=ON \
   -DNRN_ENABLE_CORENEURON=OFF \
-  -DNRN_RX3D_OPT_LEVEL=2 \
+  -DNRN_RX3D_OPT_LEVEL=$RX3D_OPT \
+  -DNRN_WHEEL_STATIC_READLINE=ON \
   $archs_cmake \
-  -DCMAKE_PREFIX_PATH=/usr/X11 \
+  -DCMAKE_PREFIX_PATH="/usr/X11;$READLINE_LIST" \
   -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
 
 ninja install
@@ -134,22 +151,29 @@ for i in $args ; do
   chk $i
 done
 
+describe="`sh $NRN_SRC/nrnversion.sh describe`"
+macos=macos${MACOSX_DEPLOYMENT_TARGET}
+PACKAGE_FULL_NAME=nrn-${describe}-${mac_platform}-${PYVS}.pkg
+PACKAGE_FILE_NAME=$NRN_BLD/src/mac/build/NEURON.pkg
+
 #/Applications/Packages.app from
 # http://s.sudre.free.fr/Software/Packages/about.html
 # For mac to do a productsign, need my developerID_installer.cer
 # and Neurondev.p12 file. To add to the keychain, double click each
 # of those files. By default, I added my certificates to the login keychain.
-ninja macpkg # will sign the binaries, construct below
-            # mentioned PACKAGE_FILE_NAME, request notarization from
-            # Apple, and staple the package.
+
+# Will sign the binaries, construct above
+# mentioned PACKAGE_FILE_NAME, request notarization from
+# Apple, and staple the package.
+if ! ninja macpkg ; then 
+  echo "ninja macpkg failed. (because of notification failure?)"
+  echo "Not creating $PACKAGE_FULL_NAME"
+  echo "  from $PACKAGE_FILE_NAME"
+  exit 1
+fi
 
 # Copy the package to $HOME/$PACKAGE_FULL_NAME
 # You should then manually upload that to github.
-describe="`sh $NRN_SRC/nrnversion.sh describe`"
-macos=macos${MACOSX_DEPLOYMENT_TARGET}
-PACKAGE_FULL_NAME=nrn-${describe}-${mac_platform}-${PYVS}.pkg
-PACKAGE_FILE_NAME=$NRN_BLD/src/mac/build/NEURON.pkg
-
 cp $PACKAGE_FILE_NAME $HOME/$PACKAGE_FULL_NAME
 
 echo "

ci/win_build_cmake.sh

@@ -32,7 +32,7 @@ cd $BUILD_SOURCESDIRECTORY/build
 	-DNRN_BINARY_DIST_BUILD=ON \
 	-DPYTHON_EXECUTABLE=/c/Python39/python.exe \
 	-DNRN_ENABLE_PYTHON_DYNAMIC=ON  \
-	-DNRN_PYTHON_DYNAMIC='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

@@ -7,6 +7,7 @@ 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/3.13.0/python-3.13.0-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

@@ -7,6 +7,7 @@ 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:\Python39\Lib\distutils\cygwinccompiler.py) -replace 'elif msc_ver == ''1600'':', 'elif msc_ver == ''1927'':' | Out-File C:\Python39\Lib\distutils\cygwinccompiler.py"
@@ -24,8 +25,10 @@ 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
+C:\Python313\python.exe -m pip install setuptools==70.1.1 || goto :error
 
 :: install nsis
 nsis-3.05-setup.exe /S || goto :error

ci/win_test_installer.cmd

@@ -21,18 +21,21 @@ 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:\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:\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"
 
 :: run also using whatever is system python
 python -m pip install numpy

docs/python/modelspec/programmatic/topology/seclist.rst

@@ -31,6 +31,10 @@ SectionList
             for sec in python_iterable_of_sections:
                 sl.append(sec)
 
+        ``len(sl)`` returns the number of sections in the SectionList.
+
+        ``list(sl)`` and ``[s for s in sl]`` generate equivalent lists.
+
     .. seealso::
         :class:`SectionBrowser`, :class:`Shape`, :meth:`RangeVarPlot.list`
 

packaging/python/Dockerfile

@@ -93,4 +93,7 @@ COPY Dockerfile .
 # build wheels from there
 WORKDIR /root
 
+# remove Python 3.13t since we do not support the free-threaded build yet
+RUN rm -fr /opt/python/cp313-cp313t
+
 ENV NMODL_PYLIB=/nrnwheel/python/lib/libpython3.10.so.1.0

packaging/python/oldest_numpy_requirements.txt

@@ -3,3 +3,4 @@ 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==2.1.0;python_version=='3.13'

setup.py

@@ -4,6 +4,7 @@
 import sys
 from collections import defaultdict
 import logging
+import platform
 
 logging.basicConfig(level=logging.INFO)
 from shutil import copytree, which
@@ -461,6 +462,8 @@ def setup_package():
                 + ["-Wl,-rpath,{}".format(REL_RPATH + "/../../.data/lib/")],
             )
         )
+        if platform.system() == "Darwin":
+            rxd_params["extra_link_args"] += ["-headerpad_max_install_names"]
 
         logging.info("RX3D compile flags %s" % str(rxd_params))
 

src/coreneuron/io/nrn_setup.cpp

@@ -220,6 +220,12 @@ std::vector<int> nrn_read_filesdat(const char* filesdat) {
         int iFile;
         nrn_assert(fscanf(fp, "%d\n", &iFile) == 1);
         if ((iNum % nrnmpi_numprocs) == nrnmpi_myid) {
+            // A "-1" entry means that this rank should not be assigned further gid groups.
+            // It is a way to create files.dat files which deterministically assign gid groups to
+            // ranks, particularly useful for very large simulations which required load balancing.
+            if (iFile == -1) {
+                break;
+            }
             rank_cell_groups.push_back(iFile);
         }
     }

src/mac/nrn_productsign.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+set -ex
 
 # Signing the package with an identified developer certificate means the
 # installer does not have to lower the security settings on their machine.