CI test with cython<3

CMakeLists.txt

@@ -98,9 +98,8 @@ mark_as_advanced(NRN_WHEEL_BUILD)
 # ~~~
 # NEURON module installation:
 #   - OFF       : do not install
-#   - ON        : install with --home in ${CMAKE_INSTALL_PREFIX}
-#   - <string>  : install using other modes or locations using an appropriate
-#                 string that goes after python setup.py install
+#   - ON        : install in ${CMAKE_INSTALL_PREFIX} (default)
+#   NOTE: When building the wheel, this is set to OFF.
 # Dynamic Python version support:
 #   - OFF       : nrnpython interface is linked into libnrniv.so
 #   - ON        : nrnpython interface consistent with default python3 (falling back to python)
@@ -124,7 +123,8 @@ mark_as_advanced(NRN_WHEEL_BUILD)
 #   - ON        : Collect code coverage for files (default all).
 #   - <string>  : semicolon (;) separated list of files to collect coverage.
 # ~~~
-option(NRN_ENABLE_MODULE_INSTALL "Enable installation of NEURON Python module"
+option(NRN_ENABLE_MODULE_INSTALL
+       "Enable installation of NEURON Python module for regular CMake builds"
        ${NRN_ENABLE_MODULE_INSTALL_DEFAULT})
 set(NRN_MODULE_INSTALL_OPTIONS
     "${NRN_MODULE_INSTALL_OPTIONS_DEFAULT}"
@@ -586,14 +586,6 @@ if(NRN_ENABLE_PYTHON)
   add_subdirectory(src/nrnpython)
 endif()
 
-if(NRN_ENABLE_RX3D)
-  add_subdirectory(share/lib/python/neuron/rxd/geometry3d)
-endif()
-
-if(NRN_ENABLE_MUSIC)
-  add_subdirectory(src/neuronmusic)
-endif()
-
 if(NRN_MACOS_BUILD)
   add_subdirectory(src/mac)
 endif()

ci/win_install_deps.cmd

@@ -25,11 +25,10 @@ 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 || goto :error
-C:\Python38\python.exe -m pip install numpy==1.17.5 || goto :error
-C:\Python39\python.exe -m pip install numpy==1.19.3 || goto :error
-C:\Python310\python.exe -m pip install numpy==1.21.3 || goto :error
-C:\Python311\python.exe -m pip install numpy==1.23.5 || 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
 
 :: install nsis
 nsis-3.05-setup.exe /S || goto :error
@@ -66,6 +65,7 @@ mingw-w64-x86_64-readline ^
 mingw-w64-x86_64-python3 ^
 mingw64/mingw-w64-x86_64-cython ^
 mingw-w64-x86_64-python3-setuptools ^
+mingw-w64-x86_64-python3-packaging ^
 mingw-w64-x86_64-python3-pip ^
 mingw64/mingw-w64-x86_64-dlfcn ^
 mingw-w64-x86_64-toolchain || goto :error

cmake/CompilerHelper.cmake

@@ -11,8 +11,6 @@ endif()
 
 if(CMAKE_C_COMPILER_ID MATCHES "PGI" OR CMAKE_C_COMPILER_ID MATCHES "NVHPC")
   set(NRN_HAVE_NVHPC_COMPILER ON)
-  set(USING_PGI_COMPILER_TRUE "")
-  set(USING_PGI_COMPILER_FALSE "#")
   # See https://gitlab.kitware.com/cmake/cmake/-/issues/22168, upper limit of 3.20.3 is based on the
   # current assigned milestone there.
   if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.20" AND ${CMAKE_VERSION} VERSION_LESS "3.20.3")
@@ -43,6 +41,8 @@ if(CMAKE_C_COMPILER_ID MATCHES "PGI" OR CMAKE_C_COMPILER_ID MATCHES "NVHPC")
     list(APPEND NRN_COMPILE_FLAGS
          --diag_suppress=1,47,111,128,170,174,177,180,186,301,541,550,816,941,2465)
   endif()
+  list(APPEND NRN_COMPILE_FLAGS -noswitcherror)
+  list(APPEND NRN_LINK_FLAGS -noswitcherror)
   if(${CMAKE_C_COMPILER_VERSION} VERSION_GREATER_EQUAL 21.11)
     # Random123 does not play nicely with NVHPC 21.11+'s detection of ABM features, see:
     # https://github.com/BlueBrain/CoreNeuron/issues/724 and
@@ -51,8 +51,6 @@ if(CMAKE_C_COMPILER_ID MATCHES "PGI" OR CMAKE_C_COMPILER_ID MATCHES "NVHPC")
   endif()
 else()
   set(NRN_HAVE_NVHPC_COMPILER OFF)
-  set(USING_PGI_COMPILER_TRUE "#")
-  set(USING_PGI_COMPILER_FALSE "")
 endif()
 
 if(CMAKE_CXX_COMPILER_ID MATCHES "PGI")

cmake/ConfigFileSetting.cmake

@@ -310,12 +310,6 @@ else()
   file(REMOVE "${PROJECT_BINARY_DIR}/config.h")
 endif()
 
-# Prepare some variables for @VAR@ expansion in setup.py.in (nrnpython and rx3d)
-set(NRN_COMPILE_FLAGS_QUOTED ${NRN_COMPILE_FLAGS})
-set(NRN_LINK_FLAGS_QUOTED ${NRN_LINK_FLAGS})
-list(TRANSFORM NRN_COMPILE_FLAGS_QUOTED APPEND "'")
-list(TRANSFORM NRN_COMPILE_FLAGS_QUOTED PREPEND "'")
-list(TRANSFORM NRN_LINK_FLAGS_QUOTED APPEND "'")
-list(TRANSFORM NRN_LINK_FLAGS_QUOTED PREPEND "'")
-string(JOIN ", " NRN_COMPILE_FLAGS_COMMA_SEPARATED_STRINGS ${NRN_COMPILE_FLAGS_QUOTED})
-string(JOIN ", " NRN_LINK_FLAGS_COMMA_SEPARATED_STRINGS ${NRN_LINK_FLAGS_QUOTED})
+# Prepare some variables for setup.py extension building (hoc_module, rx3d and music)
+string(JOIN " " NRN_COMPILE_FLAGS_STRING ${NRN_COMPILE_FLAGS})
+string(JOIN " " NRN_LINK_FLAGS_STRING ${NRN_LINK_FLAGS})

packaging/python/build_requirements.txt

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

setup.cfg

@@ -2,7 +2,7 @@
 name = NEURON
 description = Empirically-based simulator for modeling neurons and networks of neurons
 author = Michael Hines, Yale, Blue Brain Project
-author-email = michael.hines@yale.edu
+author_email = michael.hines@yale.edu
 license = Copyright (c) Michael Hines (BSD compatible)
 url = https://neuron.yale.edu/neuron/
 project_urls =