From a7b601146264e43b635d7ee9bb02e2eddbee3189 Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Tue, 13 Aug 2024 12:01:39 +0200
Subject: [PATCH 01/12] Remove numpy<2 pins

---
 .github/workflows/coverage.yml       |  2 +-
 .github/workflows/neuron-ci.yml      |  2 +-
 ci/win_test_installer.cmd            |  2 +-
 docs/docs_requirements.txt           |  2 +-
 docs/install/install_instructions.md | 21 ---------------------
 nrn_requirements.txt                 |  2 +-
 packaging/python/test_wheels.sh      |  2 +-
 setup.py                             |  4 ++--
 8 files changed, 8 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 96ee062936..ce0bb21bae 100644
--- a/.github/workflows/coverage.yml
+++ b/.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
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
index abd42d2873..e3ca977eb4 100644
--- a/.github/workflows/neuron-ci.yml
+++ b/.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
diff --git a/ci/win_test_installer.cmd b/ci/win_test_installer.cmd
index 85255af463..ce34887d35 100644
--- a/ci/win_test_installer.cmd
+++ b/ci/win_test_installer.cmd
@@ -22,7 +22,7 @@ C:\Python39\python -c "import neuron; neuron.test(); quit()" || set "errorfound=
 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"
+python -m pip install "numpy"
 :: run also using whatever is system python
 python --version
 python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
index 6571d22ac2..db118e9f1b 100644
--- a/docs/docs_requirements.txt
+++ b/docs/docs_requirements.txt
@@ -10,7 +10,7 @@ bokeh<3
 # do not check import of next line
 ipython
 plotnine
-numpy<2
+numpy
 plotly
 nbsphinx
 jinja2
diff --git a/docs/install/install_instructions.md b/docs/install/install_instructions.md
index af7a86583f..17405175a0 100644
--- a/docs/install/install_instructions.md
+++ b/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.
diff --git a/nrn_requirements.txt b/nrn_requirements.txt
index c28bc995bb..f049602b4e 100644
--- a/nrn_requirements.txt
+++ b/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
diff --git a/packaging/python/test_wheels.sh b/packaging/python/test_wheels.sh
index 1234d57c2d..fbbe2c73c1 100755
--- a/packaging/python/test_wheels.sh
+++ b/packaging/python/test_wheels.sh
@@ -260,7 +260,7 @@ $python_exe -m pip install --upgrade pip
 # install numpy, pytest and neuron
 # we install setuptools because since python 3.12 it is no more installed
 # by default
-$python_exe -m pip install "numpy<2" pytest setuptools
+$python_exe -m pip install "numpy" pytest setuptools
 $python_exe -m pip install $python_wheel
 $python_exe -m pip show neuron || $python_exe -m pip show neuron-nightly
 
diff --git a/setup.py b/setup.py
index d27d995c11..977f04aea9 100644
--- a/setup.py
+++ b/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",

From e953fa490534d7f04e94a633aba3cbdd22e5fe18 Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Tue, 13 Aug 2024 16:42:36 +0200
Subject: [PATCH 02/12] Build wheels with latest numpy and test them with
 oldest supported numpy

---
 packaging/python/build_requirements.txt |  7 +------
 packaging/python/test_requirements.txt  | 11 +++++++++++
 packaging/python/test_wheels.sh         |  6 ++----
 3 files changed, 14 insertions(+), 10 deletions(-)
 create mode 100644 packaging/python/test_requirements.txt

diff --git a/packaging/python/build_requirements.txt b/packaging/python/build_requirements.txt
index 29d2c1b080..71fe06794e 100644
--- a/packaging/python/build_requirements.txt
+++ b/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
diff --git a/packaging/python/test_requirements.txt b/packaging/python/test_requirements.txt
new file mode 100644
index 0000000000..8d7b6fa197
--- /dev/null
+++ b/packaging/python/test_requirements.txt
@@ -0,0 +1,11 @@
+# General test requirements
+pytest
+setuptools;python_version>='3.12' # From 3.12, no longer installed by default
+
+# Oldest supported numpy versions
+numpy==1.19.5;python_version=='3.8'
+numpy==1.19.5;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'
diff --git a/packaging/python/test_wheels.sh b/packaging/python/test_wheels.sh
index fbbe2c73c1..ac0cfab918 100755
--- a/packaging/python/test_wheels.sh
+++ b/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
-$python_exe -m pip install "numpy" pytest setuptools
+# install test requirements
+$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
 

From 03e1d0e1dbb952096fcff2ee1bf88b08330d606b Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Wed, 14 Aug 2024 11:10:22 +0200
Subject: [PATCH 03/12] Build with latest numpy on Windows and test with oldest
 supported numpy

---
 ci/win_install_deps.cmd   | 10 +++++-----
 ci/win_test_installer.cmd | 10 ++++++++--
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/ci/win_install_deps.cmd b/ci/win_install_deps.cmd
index b27cfba3af..b30c41c733 100644
--- a/ci/win_install_deps.cmd
+++ b/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
 
diff --git a/ci/win_test_installer.cmd b/ci/win_test_installer.cmd
index ce34887d35..262928b1cf 100644
--- a/ci/win_test_installer.cmd
+++ b/ci/win_test_installer.cmd
@@ -16,13 +16,19 @@ echo %NEURONHOME%
 :: If so, try again to generate it. No wait required like previous strategies, we rely on testing entropy from this point on.
 if not exist association.hoc.out (start /wait /REALTIME %cd%\ci\association.hoc)
 
+:: install oldest supported numpy
+C:\Python38\python.exe -m pip install numpy==1.19.5 || goto :error
+C:\Python39\python.exe -m pip install numpy==1.19.5 || 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
 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"
-:: install numpy dependency
-python -m pip install "numpy"
+C:\Python312\python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"
 :: run also using whatever is system python
 python --version
 python -c "import neuron; neuron.test(); quit()" || set "errorfound=y"

From 119c946f16b900d0180170b2d4c33ca3d3c80e77 Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Fri, 16 Aug 2024 09:48:28 +0200
Subject: [PATCH 04/12] Update oldest supported Python and Numpy versions

---
 ci/win_build_cmake.sh                  | 2 +-
 ci/win_test_installer.cmd              | 4 ++--
 packaging/python/test_requirements.txt | 3 +--
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/ci/win_build_cmake.sh b/ci/win_build_cmake.sh
index fcf5fe419c..ca610acea3 100755
--- a/ci/win_build_cmake.sh
+++ b/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' \
diff --git a/ci/win_test_installer.cmd b/ci/win_test_installer.cmd
index 262928b1cf..22621d4a81 100644
--- a/ci/win_test_installer.cmd
+++ b/ci/win_test_installer.cmd
@@ -17,8 +17,7 @@ echo %NEURONHOME%
 if not exist association.hoc.out (start /wait /REALTIME %cd%\ci\association.hoc)
 
 :: install oldest supported numpy
-C:\Python38\python.exe -m pip install numpy==1.19.5 || goto :error
-C:\Python39\python.exe -m pip install numpy==1.19.5 || goto :error
+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
@@ -30,6 +29,7 @@ C:\Python310\python -c "import neuron; neuron.test(); quit()" || set "errorfound
 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"
 
diff --git a/packaging/python/test_requirements.txt b/packaging/python/test_requirements.txt
index 8d7b6fa197..06e85a5d63 100644
--- a/packaging/python/test_requirements.txt
+++ b/packaging/python/test_requirements.txt
@@ -3,8 +3,7 @@ pytest
 setuptools;python_version>='3.12' # From 3.12, no longer installed by default
 
 # Oldest supported numpy versions
-numpy==1.19.5;python_version=='3.8'
-numpy==1.19.5;python_version=='3.9' and platform_machine!='arm64'
+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'

From 10cf8b589a7a0b1abad72388af42b15d8d67642f Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Mon, 19 Aug 2024 09:08:23 +0200
Subject: [PATCH 05/12] Pin `numpy<2` for documentation only

---
 docs/docs_requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
index db118e9f1b..6571d22ac2 100644
--- a/docs/docs_requirements.txt
+++ b/docs/docs_requirements.txt
@@ -10,7 +10,7 @@ bokeh<3
 # do not check import of next line
 ipython
 plotnine
-numpy
+numpy<2
 plotly
 nbsphinx
 jinja2

From 879d2e441418d2baaa7994ebbdf42e2017df8d1e Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Mon, 19 Aug 2024 10:37:04 +0200
Subject: [PATCH 06/12] Test Windows build with both latest and oldest
 supported Numpy

---
 ci/win_test_installer.cmd | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/ci/win_test_installer.cmd b/ci/win_test_installer.cmd
index 22621d4a81..35c69c2e85 100644
--- a/ci/win_test_installer.cmd
+++ b/ci/win_test_installer.cmd
@@ -16,18 +16,26 @@ echo %NEURONHOME%
 :: If so, try again to generate it. No wait required like previous strategies, we rely on testing entropy from this point on.
 if not exist association.hoc.out (start /wait /REALTIME %cd%\ci\association.hoc)
 
+:: test all pythons
+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"
+
 :: 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
+:: 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

From 7b9e1be83f16e36ec5e60d3da0cda1731938ae17 Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Wed, 21 Aug 2024 11:12:29 +0200
Subject: [PATCH 07/12] Cast to `c_long` in RxD on Python side before passing
 to C++

---
 share/lib/python/neuron/rxd/rxd.py     | 10 +++++-----
 share/lib/python/neuron/rxd/species.py | 12 ++++++------
 test/rxd/conftest.py                   |  3 ++-
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/share/lib/python/neuron/rxd/rxd.py b/share/lib/python/neuron/rxd/rxd.py
index 0ac5249684..3c0fd18a8e 100644
--- a/share/lib/python/neuron/rxd/rxd.py
+++ b/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()
diff --git a/share/lib/python/neuron/rxd/species.py b/share/lib/python/neuron/rxd/species.py
index de8a3095b2..bd6e59f610 100644
--- a/share/lib/python/neuron/rxd/species.py
+++ b/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
diff --git a/test/rxd/conftest.py b/test/rxd/conftest.py
index 1fbe8ee0cc..2a98c9d3f9 100644
--- a/test/rxd/conftest.py
+++ b/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)
 
 

From b62426773c2d570c53d2db7e7e8a670005e2a43b Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Fri, 23 Aug 2024 14:52:34 +0200
Subject: [PATCH 08/12] Test wheels with both latest and oldest NumPy

---
 packaging/python/oldest_numpy_requirements.txt |  5 +++++
 packaging/python/test_requirements.txt         |  9 +--------
 packaging/python/test_wheels.sh                | 10 ++++++++--
 3 files changed, 14 insertions(+), 10 deletions(-)
 create mode 100644 packaging/python/oldest_numpy_requirements.txt

diff --git a/packaging/python/oldest_numpy_requirements.txt b/packaging/python/oldest_numpy_requirements.txt
new file mode 100644
index 0000000000..4a77e64c2b
--- /dev/null
+++ b/packaging/python/oldest_numpy_requirements.txt
@@ -0,0 +1,5 @@
+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'
diff --git a/packaging/python/test_requirements.txt b/packaging/python/test_requirements.txt
index 06e85a5d63..e92c3c1a67 100644
--- a/packaging/python/test_requirements.txt
+++ b/packaging/python/test_requirements.txt
@@ -1,10 +1,3 @@
-# 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'
+numpy
diff --git a/packaging/python/test_wheels.sh b/packaging/python/test_wheels.sh
index ac0cfab918..2c4aab6816 100755
--- a/packaging/python/test_wheels.sh
+++ b/packaging/python/test_wheels.sh
@@ -269,8 +269,14 @@ if echo $compile_options | grep "NRN_ENABLE_CORENEURON=ON" > /dev/null ; then
   has_coreneuron=true
 fi
 
-# run tests
-test_wheel "${python_exe}"
+# run tests with latest NumPy
+echo " == Running tests with latest NumPy == "
+time test_wheel "${python_exe}"
+
+# run tests with oldest supported NumPy
+echo " == Running tests with oldest supported NumPy == "
+$python_exe -m pip install -r packaging/python/oldest_numpy_requirements.txt
+time test_wheel "${python_exe}"
 
 # cleanup
 if [[ "$use_venv" != "false" ]]; then

From 44527d33d65f29dcca6e7588c2e484221d3b4fca Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Tue, 27 Aug 2024 14:23:13 +0200
Subject: [PATCH 09/12] Only basic python wheel tests with oldest NumPy

---
 packaging/python/test_wheels.sh | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/packaging/python/test_wheels.sh b/packaging/python/test_wheels.sh
index 2c4aab6816..853d7cbd7e 100755
--- a/packaging/python/test_wheels.sh
+++ b/packaging/python/test_wheels.sh
@@ -237,6 +237,12 @@ test_wheel () {
 }
 
 
+test_wheel_basic_python () {
+    echo "=========== BASIC PYTHON TESTS ==========="
+    $python_exe -c "import neuron; neuron.test(); neuron.test_rxd()"
+}
+
+
 echo "== Testing $python_wheel using $python_exe ($python_ver) =="
 
 
@@ -271,12 +277,12 @@ fi
 
 # run tests with latest NumPy
 echo " == Running tests with latest NumPy == "
-time test_wheel "${python_exe}"
+test_wheel
 
-# run tests with oldest supported NumPy
-echo " == Running tests with oldest supported NumPy == "
+# run basic python tests with oldest supported NumPy
+echo " == Running basic python tests with oldest supported NumPy == "
 $python_exe -m pip install -r packaging/python/oldest_numpy_requirements.txt
-time test_wheel "${python_exe}"
+test_wheel_basic_python
 
 # cleanup
 if [[ "$use_venv" != "false" ]]; then

From 23ba9675f0a49741df302106c68185910fb2642d Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Wed, 28 Aug 2024 12:02:07 +0200
Subject: [PATCH 10/12] Take oldest NumPy versions in Windows CI from
 requirements file

---
 ci/win_test_installer.cmd | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/ci/win_test_installer.cmd b/ci/win_test_installer.cmd
index 35c69c2e85..0bf68842ab 100644
--- a/ci/win_test_installer.cmd
+++ b/ci/win_test_installer.cmd
@@ -24,10 +24,11 @@ C:\Python311\python -c "import neuron; neuron.test(); quit()" || set "errorfound
 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
+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"

From 5a460bb2cd9d04f0969f38718f9a6260712ce39c Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Wed, 28 Aug 2024 12:07:43 +0200
Subject: [PATCH 11/12] Remove numpy from wheel test requirements

---
 packaging/python/test_requirements.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/packaging/python/test_requirements.txt b/packaging/python/test_requirements.txt
index e92c3c1a67..6dbabce060 100644
--- a/packaging/python/test_requirements.txt
+++ b/packaging/python/test_requirements.txt
@@ -1,3 +1,2 @@
 pytest
 setuptools;python_version>='3.12' # From 3.12, no longer installed by default
-numpy

From 9fb93ec0a121a17c09f0bb5df11ea8fc438b3295 Mon Sep 17 00:00:00 2001
From: Koen van Walstijn <kbvw@pm.me>
Date: Wed, 28 Aug 2024 13:14:40 +0200
Subject: [PATCH 12/12] Revert and update troubleshooting message in install
 instructions

---
 docs/install/install_instructions.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/docs/install/install_instructions.md b/docs/install/install_instructions.md
index 17405175a0..dcce802840 100644
--- a/docs/install/install_instructions.md
+++ b/docs/install/install_instructions.md
@@ -472,3 +472,24 @@ 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 (below 9.0) 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.