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Do not link to libpython on MacOS with Anaconda Python #3088

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Sep 23, 2024
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Do not link to libpython on MacOS with Anaconda Python #3088

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9 changes: 9 additions & 0 deletions cmake/PythonHelper.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,15 @@ function(nrn_find_python)
PARENT_SCOPE)
endfunction()

# Check if Python from Conda is being used on MacOS
if(NRN_MACOS_BUILD)
string(FIND "${PYTHON_EXECUTABLE}" "/anaconda" anaconda_found)
string(FIND "${PYTHON_EXECUTABLE}" "/miniconda" miniconda_found)
if(anaconda_found GREATER -1 OR miniconda_found GREATER -1)
set(NRN_WITH_MACOS_CONDA_PYTHON TRUE)
endif()
endif()

# For each Python in NRN_PYTHON_EXECUTABLES, find its version number, its include directory, and its
# library path. Store those in the new lists NRN_PYTHON_VERSIONS, NRN_PYTHON_INCLUDES and
# NRN_PYTHON_LIBRARIES. Set NRN_PYTHON_COUNT to be the length of those lists, and
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10 changes: 10 additions & 0 deletions docs/install/install_instructions.md
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Expand Up @@ -493,3 +493,13 @@ 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.


* **NEURON segfaults when using the Anaconda Python distribution. What can I do?**

Some Anaconda distributions (e.g., macOS) ship Python binaries with `libpython` statically linked,
which has caused issues in NEURON and other packages (see discussion [here](https://github.com/neuronsimulator/nrn/issues/2358)).

On the macOS platform, NEURON attempts to detect the use of Anaconda Python by checking for the `/anaconda`
prefix in the Python binary path. An alternative solution is to build NEURON with the dynamic Python
option enabled, using the CMake flag `-DNRN_ENABLE_PYTHON_DYNAMIC=ON`.
5 changes: 4 additions & 1 deletion src/nrnpython/CMakeLists.txt
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Expand Up @@ -69,7 +69,10 @@ else()
set_property(TARGET nrnpython PROPERTY POSITION_INDEPENDENT_CODE ON)
target_include_directories(nrnpython PUBLIC ${INCLUDE_DIRS})
target_include_directories(nrnpython PUBLIC "${NRN_DEFAULT_PYTHON_INCLUDES}")
target_link_libraries(nrnpython ${NRN_DEFAULT_PYTHON_LIBRARIES})
# see nrn/issues/2358
if(NOT NRN_WITH_MACOS_CONDA_PYTHON)
target_link_libraries(nrnpython ${NRN_DEFAULT_PYTHON_LIBRARIES})
endif()
target_link_libraries(nrnpython fmt::fmt)
target_include_directories(nrnpython PUBLIC ${PROJECT_SOURCE_DIR}/${NRN_3RDPARTY_DIR}/eigen)
target_include_directories(nrnpython PUBLIC ${PROJECT_BINARY_DIR}/src/nrniv/oc_generated)
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