Merge branch 'master' into cornu/use_fmt

.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<2' 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

@@ -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<2' 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

CMakeLists.txt

@@ -325,9 +325,6 @@ 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 +379,6 @@ 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()

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

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==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
 :: setuptools 70.2 leads to an error
 C:\Python312\python.exe -m pip install setuptools==70.1.1 || goto :error
 

docs/conda_environment.yml

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

docs/dev/setuptools/setuptools.md

@@ -15,20 +15,64 @@ We use [setup.py](../../../setup.py) in two operational modes
 :
 
 1) **wheel building**
-    It boils down to 
+    It boils down to
 
         setup.py build_ext bdist_wheel
-    
+
     We configure the HOC extension along with a CMake configure, build all extensios and collect them for the wheel. This is called via [build_wheels.bash](../../../packaging/python/build_wheels.bash).
 
 2) **CMake build**
     It boils down to
-
-        setup.py build_ext build  
 
-    We provide the cmake build folder, in this mode we do not run CMake configure, we build all extensions and make sure they are integrated into the CMake build and install. This is called via CMake in [src/nrnpython/CMakeLists.txt](../../../src/nrnpython/CMakeLists.txt) by passing **--cmake-build-dir** (the folder where we configured NEURON with CMake), along with other CMake options. 
+        setup.py build_ext build
+
+    We provide the cmake build folder, in this mode we do not run CMake configure, we build all extensions and make sure they are integrated into the CMake build and install. This is called via CMake in [src/nrnpython/CMakeLists.txt](../../../src/nrnpython/CMakeLists.txt) by passing **--cmake-build-dir** (the folder where we configured NEURON with CMake), along with other CMake options.
 
 
 ## **Activity Diagram**
 
-![](images/setup-py.png)
+![](images/setup-py.png)
+
+
+## Creating a Development Python Package
+
+`setup.py` can be lanched manually as well to create a dev build package, which can be tested
+immediately. It supports several arguments to that the build can be tuned:
+
+```
+ --disable-rx3d       Disables Rx3d. Implies CMake -DNRN_ENABLE_RX3D=OFF
+ --disable-iv         Disables IV. Implies CMake -DNRN_ENABLE_INTERVIEWS=OFF
+ --disable-mpi        Disables MPI. Implies -DNRN_ENABLE_MPI=OFF and disabling of neuronmusic
+ --enable-music       Enables neuronmusic
+ --enable-coreneuron  Enables experimental CorenNeuron support
+ --rx3d-opt-level     Sets the rx3d optimization level. Default: 0 (-O0)
+ --cmake-build-dir    Declares one wants to use a specic NEURON build (with CMake), instead
+                      of creating one behind the scenes. Only builds extensions and package.
+```
+
+A quick build for testing a change to a core component could therefore be:
+```
+python setup.py build --disable-rx3d --disable-iv --disable-mpi
+```
+
+---
+**Mac Note**
+
+Since the introduction of Mac with Apple silicon, with an Official Python distribution, extension are simultaneously built for arm64 and x86_64. Besides not required for a dev build, it may fail
+on older SDKs with `Unsupported architecture` errors.
+
+To skip that you may set the ARCHFLAGS environment var. Set it to "" (empty) for default architecture: `ARCHFLAGS='' python setup.py ...`
+
+---
+
+### Testing
+
+Once built, the package may be imported and used normally. You might, however, need to set up
+PYTHONPATH accordingly for the import to work:
+
+```
+export PYTHONPATH="<NRNDIR>/build/lib.macosx-10.9-x86_64-3.9/:$PYTHONPATH"
+
+# Run Neuron base tests
+python -c "import neuron; neuron.test()"
+```

docs/install/install_instructions.md

@@ -207,7 +207,7 @@ In order to build NEURON from source, the following packages must be available:
 The following packages are optional (see build options):
 
 - Python >=3.8 (for Python interface)
-- Cython < 3 (for RXD)
+- Cython (for RXD)
 - MPI (for parallel)
 - X11 (Linux) or XQuartz (MacOS) (for GUI)
 

nrn_requirements.txt

@@ -6,7 +6,7 @@ matplotlib
 # bokeh 3 seems to break docs notebooks
 bokeh<3
 ipython
-cython<3
+cython
 packaging
 pytest<=8.1.1 # potential bug from 8.2.0 due to parallelism?
 pytest-cov

packaging/python/build_requirements.txt

@@ -1,4 +1,4 @@
-cython<3
+cython
 packaging
 numpy==1.17.5;python_version=='3.8'
 numpy==1.19.3;python_version=='3.9' and platform_machine!='arm64'

setup.py

@@ -354,7 +354,7 @@ def setup_package():
     NRN_COLLECT_DIRS = ["bin", "lib", "include", "share"]
 
     docs_require = []  # sphinx, themes, etc
-    maybe_rxd_reqs = ["numpy<2", "Cython<3"] if Components.RX3D else []
+    maybe_rxd_reqs = ["numpy<2", "Cython"] if Components.RX3D else []
     maybe_docs = docs_require if "docs" in sys.argv else []
     maybe_test_runner = ["pytest-runner"] if "test" in sys.argv else []
 
@@ -379,7 +379,6 @@ def setup_package():
         list,
         library_dirs=[os.path.join(cmake_build_dir, "lib")],
         libraries=ext_common_libraries,
-        language="c++",
     )
 
     logging.info("Extension common compile flags %s" % str(extension_common_params))
@@ -436,6 +435,7 @@ def setup_package():
                 "neuronmusic",
                 ["src/neuronmusic/neuronmusic.pyx"],
                 include_dirs=["src/nrnpython", "src/nrnmusic"],
+                language="c++",
                 **extension_common_params,
             )
         ]

share/lib/python/neuron/rxd/geometry3d/surfaces.pyx

@@ -1,13 +1,11 @@
 import os
 import numpy
-import graphicsPrimitives
-import neuron
-import numpy
 cimport numpy
 import itertools
 import bisect
 cimport cython
 
+from neuron.rxd.geometry3d import graphicsPrimitives
 
 """
 The surfaces module