Support numpy>=2 and remove numpy<2 pin

.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" '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

@@ -207,7 +207,7 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' "cython" '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

ci/win_build_cmake.sh

@@ -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" || 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
+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 +21,23 @@ 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:\Python39\python.exe -m pip install numpy==1.20.3 || goto :error
+C:\Python310\python.exe -m pip install numpy==1.21.6 || goto :error
+C:\Python311\python.exe -m pip install numpy==1.23.5 || goto :error
+C:\Python312\python.exe -m pip install numpy==1.26.4 || 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"
 

docs/install/install_instructions.md

@@ -472,24 +472,3 @@ export CFLAGS="-fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -DMACOSX -
 ```
 
 If you see any other issues, please open [an issue here](https://github.com/neuronsimulator/nrn/issues/new/choose).
-
-* **I'm seeing compiler errors related to Python and RXD.***
-The error can manifest as follows:
-```
-share/lib/python/neuron/rxd/geometry3d/surfaces.cpp:14605:41: error: no member named 'subarray' in '_PyArray_Descr'
-    __Pyx_INCREF(((PyObject*)__pyx_v_d->subarray->shape));
-                             ~~~~~~~~~  ^
-```
-often there's something related to NumPy nearby, e.g. `npy`.
-
-The issue is that certain versions of NEURON (9.0 and earlier) are not
-compatible with `numpy>=2`. Check the numpy version, e.g.,
-```
-python -c "import numpy; print(numpy.__version__)"
-```
-
-If it prints `2.0` or higher, try installing an older version:
-```
-pip install "numpy<2"
-```
-(mind the quotes.) Then delete the build directory, reconfigure and compile. If the error persists, carefully check which version of Python NEURON picked up by checking the output of the CMake configure command and make sure that that exact version of Python doesn't pick up an incompatible version of Numpy.

nrn_requirements.txt

@@ -11,5 +11,5 @@ packaging
 pytest<=8.1.1 # potential bug from 8.2.0 due to parallelism?
 pytest-cov
 mpi4py<4 # MUSIC not compatible with MPI 4
-numpy<2
+numpy
 find_libpython

packaging/python/build_requirements.txt

@@ -1,8 +1,3 @@
 cython
 packaging
-numpy==1.17.5;python_version=='3.8'
-numpy==1.19.3;python_version=='3.9' and platform_machine!='arm64'
-numpy==1.21.3;python_version=='3.9' and platform_machine=='arm64'
-numpy==1.21.4;python_version=='3.10'
-numpy==1.23.5;python_version=='3.11'
-numpy==1.26.0;python_version=='3.12'
+numpy

packaging/python/test_requirements.txt

@@ -0,0 +1,10 @@
+# General test requirements
+pytest
+setuptools;python_version>='3.12' # From 3.12, no longer installed by default
+
+# Oldest supported numpy versions
+numpy==1.20.3;python_version=='3.9' and platform_machine!='arm64'
+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'

packaging/python/test_wheels.sh

@@ -257,10 +257,8 @@ fi
 $python_exe -m pip install --upgrade pip
 
 
-# install numpy, pytest and neuron
-# we install setuptools because since python 3.12 it is no more installed
-# by default
-$python_exe -m pip install "numpy<2" pytest setuptools
+# install test requirements
+$python_exe -m pip install -r packaging/python/test_requirements.txt
 $python_exe -m pip install $python_wheel
 $python_exe -m pip show neuron || $python_exe -m pip show neuron-nightly
 

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"] if Components.RX3D else []
+    maybe_rxd_reqs = ["numpy", "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 []
 
@@ -510,7 +510,7 @@ def setup_package():
         },
         cmdclass=dict(build_ext=CMakeAugmentedBuilder, docs=Docs),
         install_requires=[
-            "numpy>=1.9.3,<2",
+            "numpy>=1.9.3",
             "packaging",
             "find_libpython",
             "setuptools<=70.3.0",

share/lib/python/neuron/rxd/rxd.py

@@ -61,7 +61,7 @@
 setup_solver.argtypes = [
     ndpointer(ctypes.c_double),
     ctypes.c_int,
-    numpy.ctypeslib.ndpointer(numpy.int_, flags="contiguous"),
+    numpy.ctypeslib.ndpointer(ctypes.c_long, flags="contiguous"),
     ctypes.c_int,
 ]
 
@@ -630,8 +630,8 @@ def _matrix_to_rxd_sparse(m):
     return (
         n,
         len(nonzero_i),
-        numpy.ascontiguousarray(nonzero_i, dtype=numpy.int_),
-        numpy.ascontiguousarray(nonzero_j, dtype=numpy.int_),
+        numpy.ascontiguousarray(nonzero_i, dtype=ctypes.c_long),
+        numpy.ascontiguousarray(nonzero_j, dtype=ctypes.c_long),
         nonzero_values,
     )
 
@@ -709,7 +709,7 @@ def _setup_matrices():
         n = len(_node_get_states())
 
         volumes = node._get_data()[0]
-        zero_volume_indices = (numpy.where(volumes == 0)[0]).astype(numpy.int_)
+        zero_volume_indices = (numpy.where(volumes == 0)[0]).astype(ctypes.c_long)
         if species._has_1d:
             # TODO: initialization is slow. track down why
             for sr in _species_get_all_species():
@@ -1896,7 +1896,7 @@ def _init():
     _setup_matrices()
     # if species._has_1d and species._1d_submatrix_n():
     # volumes = node._get_data()[0]
-    # zero_volume_indices = (numpy.where(volumes == 0)[0]).astype(numpy.int_)
+    # zero_volume_indices = (numpy.where(volumes == 0)[0]).astype(ctypes.c_long)
     # setup_solver(_node_get_states(), len(_node_get_states()), zero_volume_indices, len(zero_volume_indices), h._ref_t, h._ref_dt)
     clear_rates()
     _setup_memb_currents()

share/lib/python/neuron/rxd/species.py

@@ -60,12 +60,12 @@
     ctypes.c_int,
     ctypes.py_object,
     ctypes.c_long,
-    numpy.ctypeslib.ndpointer(dtype=int),
-    numpy.ctypeslib.ndpointer(dtype=int),
+    numpy.ctypeslib.ndpointer(dtype=ctypes.c_long),
+    numpy.ctypeslib.ndpointer(dtype=ctypes.c_long),
     ctypes.c_long,
-    numpy.ctypeslib.ndpointer(dtype=int),
+    numpy.ctypeslib.ndpointer(dtype=ctypes.c_long),
     ctypes.c_long,
-    numpy.ctypeslib.ndpointer(dtype=int),
+    numpy.ctypeslib.ndpointer(dtype=ctypes.c_long),
     ctypes.c_long,
     numpy.ctypeslib.ndpointer(dtype=float),
     ctypes.c_double,
@@ -842,7 +842,7 @@ def line_defs(self, nodes, direction, nodes_length):
 
         # sort list for parallelization
         line_defs.sort(key=lambda x: x[1], reverse=True)
-        line_defs = numpy.asarray(line_defs, dtype=int)
+        line_defs = numpy.asarray(line_defs, dtype=ctypes.c_long)
         line_defs = line_defs.reshape(2 * len(line_defs))
         return line_defs
 
@@ -862,7 +862,7 @@ def ordered_nodes(self, p_line_defs, direction, neighbors):
 
     def create_neighbors_array(self, nodes, nodes_length):
         self._isalive()
-        my_array = numpy.zeros((nodes_length, 3), dtype=int)
+        my_array = numpy.zeros((nodes_length, 3), dtype=ctypes.c_long)
         for n in nodes:
             for i, ele in enumerate(n.neighbors[::2]):
                 my_array[n._index, i] = ele if ele is not None else -1

test/rxd/conftest.py

@@ -1,5 +1,6 @@
 import os.path as osp
 import numpy
+import ctypes
 import pytest
 import gc
 
@@ -81,7 +82,7 @@ def neuron_nosave_instance(neuron_import):
     rxd.rxd.rxd_include_node_flux1D(0, None, None, None)
     rxd.species._has_1d = False
     rxd.species._has_3d = False
-    rxd.rxd._zero_volume_indices = numpy.ndarray(0, dtype=numpy.int_)
+    rxd.rxd._zero_volume_indices = numpy.ndarray(0, dtype=ctypes.c_long)
     rxd.set_solve_type(dimension=1)