Merge branch 'master' into jelic/test_313

.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/

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)

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

cmake/NeuronFileLists.cmake

@@ -385,7 +385,7 @@ set(MODLUNIT_FILES_LIST
     units1.cpp
     version.cpp)
 
-set(NMODL_FILES_LIST
+set(NOCMODL_FILES_LIST
     consist.cpp
     deriv.cpp
     discrete.cpp
@@ -430,7 +430,7 @@ set(NRN_NODEORDEROPTIM_SRC_DIR ${PROJECT_SOURCE_DIR}/src/coreneuron/permute)
 set(NRN_NRNCVODE_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nrncvode)
 set(NRN_NRNIV_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nrniv)
 set(NRN_MODLUNIT_SRC_DIR ${PROJECT_SOURCE_DIR}/src/modlunit)
-set(NRN_NMODL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nmodl)
+set(NRN_NOCMODL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nocmodl)
 set(NRN_IVOS_SRC_DIR ${PROJECT_SOURCE_DIR}/src/ivos)
 set(NRN_MUSIC_SRC_DIR ${PROJECT_SOURCE_DIR}/src/neuronmusic)
 set(NRN_PARALLEL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/parallel)
@@ -462,13 +462,13 @@ nrn_create_file_list(NRN_MODFILE_BASE_NAMES src/nrnoc ${MODFILE_BASE_NAMES})
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/ivoc/ nrnmain.cpp)
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/oc/ ockludge.cpp modlreg.cpp)
 nrn_create_file_list(NRN_MODLUNIT_SRC_FILES ${NRN_MODLUNIT_SRC_DIR} ${MODLUNIT_FILES_LIST})
-nrn_create_file_list(NRN_NMODL_SRC_FILES ${NRN_NMODL_SRC_DIR} ${NMODL_FILES_LIST})
+nrn_create_file_list(NRN_NOCMODL_SRC_FILES ${NRN_NOCMODL_SRC_DIR} ${NOCMODL_FILES_LIST})
 nrn_create_file_list(NRNMPI_DYNAMIC_INCLUDE_FILE ${PROJECT_SOURCE_DIR}/src/nrnmpi
                      ${MPI_DYNAMIC_INCLUDE})
 nrn_create_file_list(NRN_IVOS_SRC_FILES ${NRN_IVOS_SRC_DIR} ${IVOS_FILES_LIST})
 nrn_create_file_list(NRN_MUSIC_SRC_FILES ${NRN_MUSIC_SRC_DIR} ${NRN_MUSIC_FILES_LIST})
 list(APPEND NRN_OC_SRC_FILES ${PROJECT_BINARY_DIR}/src/oc/hocusr.h)
-list(APPEND NRN_NMODL_SRC_FILES ${NRN_MODLUNIT_SRC_DIR}/units.cpp)
+list(APPEND NRN_NOCMODL_SRC_FILES ${NRN_MODLUNIT_SRC_DIR}/units.cpp)
 
 # =============================================================================
 # Create mswin install lists needed for setup_exe target
@@ -480,7 +480,7 @@ if(MINGW)
   list(APPEND MSWIN_FILES ${MSWIN_SRC_DIR}/notes.txt)
 
   list(APPEND NRN_MODLUNIT_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
-  list(APPEND NRN_NMODL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
+  list(APPEND NRN_NOCMODL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
   list(APPEND NRN_OC_SRC_FILES ${PROJECT_SOURCE_DIR}/src/mswin/extra/d2upath.cpp)
 
   nrn_create_file_list(MSWIN_BIN_FILES ${MSWIN_SRC_DIR} nrniv.ico nrniv10.ico nmodl2a.ico)

cmake/NeuronTestHelper.cmake

@@ -282,7 +282,6 @@ function(nrn_add_test)
     set(feature_mod_compatibility_enabled OFF)
   endif()
   set(feature_gpu_enabled ${CORENRN_ENABLE_GPU})
-  set(feature_nmodl_enabled ${CORENRN_ENABLE_NMODL})
   # Check REQUIRES
   set(requires_coreneuron OFF)
   foreach(required_feature ${NRN_ADD_TEST_REQUIRES})

cmake/SanitizerHelper.cmake

@@ -10,6 +10,12 @@ set(${CODING_CONV_PREFIX}_SANITIZERS_UNDEFINED_EXCLUSIONS
 include("${CODING_CONV_CMAKE}/sanitizers.cmake")
 include(${CODING_CONV_CMAKE}/build-time-copy.cmake)
 
+# If there is an issue with the automatically determined LD_PRELOAD then force with an environment
+# variable when running cmake.
+if(DEFINED ENV{NRN_OVERRIDE_LD_PRELOAD})
+  set(NRN_SANITIZER_LIBRARY_PATH "$ENV{NRN_OVERRIDE_LD_PRELOAD}")
+endif()
+
 # Propagate the sanitizer flags to the NEURON sources
 list(APPEND NRN_COMPILE_FLAGS ${NRN_SANITIZER_COMPILER_FLAGS})
 list(APPEND NRN_LINK_FLAGS ${NRN_SANITIZER_COMPILER_FLAGS})

docs/cmake_doc/options.rst

@@ -396,8 +396,8 @@ Other CoreNEURON options:
 -------------------------
   There are 20 or so cmake arguments specific to a CoreNEURON
   build that are listed in https://github.com/neuronsimulator/nrn/blob/master/src/coreneuron/CMakeLists.txt.
-  The ones of particular interest that can be used on the NEURON
-  CMake configure line are `CORENRN_ENABLE_NMODL` and `CORENRN_ENABLE_GPU`.
+  The one of particular interest that can be used on the NEURON
+  CMake configure line is `CORENRN_ENABLE_GPU`.
 
 NMODL options
 =============

docs/docs_requirements.txt

@@ -5,12 +5,11 @@ jupyter
 nbconvert
 myst_parser
 matplotlib
-# bokeh 3 seems to break docs notebooks
-bokeh<3
+bokeh
 # do not check import of next line
 ipython
 plotnine
-numpy<2
+numpy
 plotly
 nbsphinx
 jinja2