Merge branch 'master' into hines/soma-center

.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<4' "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

@@ -188,12 +188,12 @@ jobs:
           python -m pip install --upgrade pip -r nrn_requirements.txt
 
       - name: Install a new automake
-        # A new automake is needed for python 3.12 because it generate a python script
+        # A automake >= 1.16.5 is needed for python 3.12 because it generates 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
+          curl -L -o automake.tar.xz https://ftpmirror.gnu.org/gnu/automake/automake-1.16.5.tar.xz
           tar -xf automake.tar.xz
           cd automake-1.16.5/
           ./configure --prefix=/usr/
@@ -207,7 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' "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
@@ -237,10 +237,10 @@ jobs:
           echo -----
 
       - name: Restore compiler cache
-        uses: actions/cache@v4
+        uses: actions/cache/restore@v4
+        id: restore-compiler-cache
         with:
           path: ${{runner.workspace}}/ccache
-          save-always: true
           key: ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}}
           restore-keys: |
             ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-
@@ -441,6 +441,15 @@ jobs:
           INSTALL_DIR : ${{ runner.workspace }}/install
           MATRIX_EVAL: ${{ matrix.config.matrix_eval }}
 
+      - name: Save compiler cache
+        uses: actions/cache/save@v4
+        if: always() && steps.restore-compiler-cache.outputs.cache-hit != 'true'
+        with:
+          path: ${{runner.workspace}}/ccache
+          key: |
+            ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-
+            ${{matrix.os}}-${{hashfiles('matrix.json')}}-
+
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To enable it, you have to:
       #   * add 'live-debug-ci' to your PR title

.gitlab-ci.yml

@@ -148,19 +148,6 @@ spack_setup:
     # BLUECONFIGS_BRANCH does not correspond to a Spack package called blueconfigs
     SPACK_SETUP_IGNORE_PACKAGE_VARIABLES: BLUECONFIGS
 
-simulation_stack:
-  stage: .pre
-  # Take advantage of GitHub PR description parsing in the spack_setup job.
-  needs: [spack_setup]
-  trigger:
-    branch: $BLUECONFIGS_BRANCH
-    project: hpc/sim/blueconfigs
-    # NEURON CI status depends on the BlueConfigs CI status.
-    strategy: depend
-  variables:
-    GITLAB_PIPELINES_BRANCH: $GITLAB_PIPELINES_BRANCH
-    SPACK_ENV_FILE_URL: $SPACK_SETUP_COMMIT_MAPPING_URL
-
 # Performance seems to be terrible when we get too many jobs on a single node.
 .build:
   extends: [.spack_build]

.sanitizers/undefined.supp

@@ -31,6 +31,7 @@ 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*)
+unsigned-integer-overflow:fmt::*
 vptr:NetCon::disconnect(ivObservable*)
 vptr:ObjObservable::object()
-vptr:PreSyn::disconnect(ivObservable*)
+vptr:PreSyn::disconnect(ivObservable*)

CMakeLists.txt

@@ -85,6 +85,13 @@ option(
   NRN_ENABLE_PERFORMANCE_TESTS
   "Enable tests that measure performance. These are known to be unreliable when run on busy/oversubscribed machines such as CI runners."
   ${NRN_ENABLE_PERFORMANCE_TESTS_DEFAULT})
+option(NRN_ENABLE_DIGEST
+       "Provides nrn_digest function for debugging cross platform floating result differences."
+       ${NRN_ENABLE_DIGEST_DEFAULT})
+option(
+  NRN_ENABLE_ARCH_INDEP_EXP_POW
+  "Provides use_exp_pow_precision(style) function so that exp and pow produce same results on all platforms"
+  ${NRN_ENABLE_ARCH_INDEP_EXP_POW_DEFAULT})
 # This can be helpful in very specific CI build configurations, where ccache is used *and* different
 # CI builds are built under different directories.
 option(NRN_AVOID_ABSOLUTE_PATHS
@@ -325,9 +332,6 @@ if(NRN_ENABLE_RX3D)
     message(SEND_ERROR "NRN_ENABLE_RX3D requires NRN_ENABLE_PYTHON feature.")
   else()
     find_package(Cython REQUIRED)
-    if(CYTHON_VERSION VERSION_GREATER_EQUAL 3)
-      message(FATAL_ERROR "Cython 3+ is not supported")
-    endif()
   endif()
 endif()
 if(MINGW)
@@ -382,9 +386,6 @@ if(NRN_ENABLE_MUSIC)
     message(FATAL "MUSIC requires -DNRN_ENABLE_PYTHON=ON")
   endif()
   find_package(Cython REQUIRED)
-  if(CYTHON_VERSION VERSION_GREATER_EQUAL 3)
-    message(FATAL_ERROR "Cython 3+ is not supported")
-  endif()
   find_package(MUSIC REQUIRED)
   set(NRN_MUSIC 1)
 endif()
@@ -753,22 +754,17 @@ add_custom_target(
 # =============================================================================
 if(NRN_ENABLE_CORENEURON OR NRN_ENABLE_MOD_COMPATIBILITY)
   set(GLOBAL_VAR_TOGGLE_COMMAND "'s/ GLOBAL minf/ RANGE minf/'")
-  set(TABLE_VAR_TOGGLE_COMMAND "'s/ TABLE minf/ :TABLE minf/'")
 else()
   set(GLOBAL_VAR_TOGGLE_COMMAND "'s/ RANGE minf/ GLOBAL minf/'")
-  set(TABLE_VAR_TOGGLE_COMMAND "'s/ :TABLE minf/ TABLE minf/'")
 endif()
 separate_arguments(GLOBAL_VAR_TOGGLE_COMMAND UNIX_COMMAND "${GLOBAL_VAR_TOGGLE_COMMAND}")
-separate_arguments(TABLE_VAR_TOGGLE_COMMAND UNIX_COMMAND "${TABLE_VAR_TOGGLE_COMMAND}")
 add_custom_target(
   hh_update
   COMMAND sed ${GLOBAL_VAR_TOGGLE_COMMAND} ${CMAKE_SOURCE_DIR}/src/nrnoc/hh.mod >
           ${CMAKE_BINARY_DIR}/hh.mod.1
-  COMMAND sed ${TABLE_VAR_TOGGLE_COMMAND} ${CMAKE_BINARY_DIR}/hh.mod.1 >
-          ${CMAKE_BINARY_DIR}/hh.mod.2
-  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/hh.mod.2
+  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/hh.mod.1
           ${CMAKE_SOURCE_DIR}/src/nrnoc/hh.mod
-  COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_BINARY_DIR}/hh.mod.1 ${CMAKE_BINARY_DIR}/hh.mod.2
+  COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_BINARY_DIR}/hh.mod.1
   COMMENT "Update hh.mod for CoreNEURON compatibility"
   VERBATIM)
 add_dependencies(nrniv_lib hh_update)
@@ -1067,6 +1063,10 @@ if(NRN_ENABLE_PROFILING)
     message(STATUS "  Caliper     | ${caliper_DIR}")
   endif()
 endif()
+if(NRN_ENABLE_DIGEST OR NRN_ARCH_INDEP_EXP_POW)
+  message(STATUS "NRN_ENABLE_DIGEST | ${NRN_ENABLE_DIGEST}")
+  message(STATUS "NRN_ENABLE_ARCH_INDEP_EXP_POW | ${NRN_ENABLE_ARCH_INDEP_EXP_POW}")
+endif()
 message(STATUS "--------------+--------------------------------------------------------------")
 message(STATUS " See documentation : https://www.neuron.yale.edu/neuron/")
 message(STATUS "--------------+--------------------------------------------------------------")

README.md

@@ -14,11 +14,16 @@ Linux and Mac you can install the official Python 3 wheel with:
 pip3 install neuron
 ```
 
-If you want to build the latest version from source, we support **CMake** as build system. **Autotools** build system has been removed after 8.0 release.
+If you want to build the latest version from source, we support **CMake** as build system.
 See detailed installation instructions: [docs/install/install_instructions.md](docs/install/install_instructions.md).
 
 It is possible to install the Linux Python wheels on Windows via the Windows Subsystem for Linux (WSL) - check the installation instructions above.
 
+> [!NOTE]
+> **About NEURON >= 9.0**: If you are experiencing compilation errors while using
+> `nrnivmodl` with NEURON >=9.0, but not with previous 8.x releases, see
+> [Adapting MOD files for C++ with NEURON >= 9.0](docs/guide/porting_mechanisms_to_cpp.rst).
+
 ## Documentation
 
 * See documentation section of the [NEURON website](https://neuron.yale.edu/neuron/docs)

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

@@ -274,5 +274,15 @@ if [ "$LinkCoreNEURON" = true ] ; then
   fi
 fi
 
-make -j 4 -f "${bindir}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" "UserNMODLBIN=$UserNMODLBIN" "UserNMODLFLAGS=$UserNMODLFLAGS" special &&
-echo "Successfully created $MODSUBDIR/special"
+set +e
+
+make -j 4 -f "${bindir}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" "UserNMODLBIN=$UserNMODLBIN" "UserNMODLFLAGS=$UserNMODLFLAGS" special
+
+ MAKE_STATUS=$?
+
+ if [ $MAKE_STATUS -eq 0 ]; then
+     echo "Successfully created $MODSUBDIR/special"
+ else
+     printf "\nNOTE: If you are encountering MOD file compilation errors only with NEURON version 9.0 or later\n"
+     printf "refer to the C++ migration guide at https://nrn.readthedocs.io/en/9.0.0/guide/porting_mechanisms_to_cpp.html\n\n"
+ fi

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/BuildOptionDefaults.cmake

@@ -29,6 +29,8 @@ set(NRN_AVOID_ABSOLUTE_PATHS_DEFAULT OFF)
 set(NRN_NMODL_CXX_FLAGS_DEFAULT "-O0")
 set(NRN_SANITIZERS_DEFAULT "")
 set(NRN_ENABLE_MATH_OPT_DEFAULT OFF)
+set(NRN_ENABLE_DIGEST_DEFAULT OFF)
+set(NRN_ENABLE_ARCH_INDEP_EXP_POW_DEFAULT OFF)
 
 # Some distributions may set the prefix. To avoid errors, unset it
 set(NRN_PYTHON_DYNAMIC_DEFAULT "")

cmake/Coverage.cmake

@@ -34,7 +34,7 @@ if(NRN_ENABLE_COVERAGE)
   if(NOT BUILD_TYPE_UPPER STREQUAL "DEBUG")
     message(WARNING "Using CMAKE_BUILD_TYPE=Debug is recommended with NRN_ENABLE_COVERAGE")
   endif()
-  set(NRN_COVERAGE_FLAGS_UNQUOTED --coverage -fno-inline)
+  set(NRN_COVERAGE_FLAGS_UNQUOTED --coverage -fno-inline -fprofile-update=atomic)
   string(JOIN " " NRN_COVERAGE_FLAGS ${NRN_COVERAGE_FLAGS_UNQUOTED})
   set(NRN_COVERAGE_LINK_FLAGS --coverage)