Bug 2254189 - neuron fails to build with Python 3.13: error: implicit declaration of function ‘Py_SetPythonHome’, ‘PySys_SetArgv’
Summary: neuron fails to build with Python 3.13: error: implicit declaration of functi...
Keywords:
Status: CLOSED WORKSFORME
Alias: None
Product: Fedora
Classification: Fedora
Component: neuron
Version: 40
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON3.13
TreeView+ depends on / blocked
 
Reported: 2023-12-12 15:10 UTC by Karolina Surma
Modified: 2024-05-31 10:09 UTC (History)
5 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2024-05-31 10:09:39 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)


Links
System ID Private Priority Status Summary Last Updated
Github neuronsimulator nrn issues 2629 0 None open Releases with Python 3.12 support 2023-12-12 15:27:24 UTC
Github neuronsimulator nrn issues 2640 0 None open Python 3.13 support 2023-12-12 15:27:24 UTC

Description Karolina Surma 2023-12-12 15:10:25 UTC
neuron fails to build with Python 3.13.0a2.

/builddir/build/BUILD/nrn-8.2.2/src/nrnpython/nrnpython.cpp:157:13: error: ‘Py_SetPythonHome’ was not declared in this scope; did you mean ‘Py_GetPythonHome’?
  157 |             Py_SetPythonHome(mywstrdup(_p_pyhome));
      |             ^~~~~~~~~~~~~~~~
      |             Py_GetPythonHome
/builddir/build/BUILD/nrn-8.2.2/src/nrnpython/nrnpython.cpp:165:9: error: ‘PySys_SetArgv’ was not declared in this scope
  165 |         PySys_SetArgv(nrn_global_argc, wcargv);
      |         ^~~~~~~~~~~~~

According to https://docs.python.org/3.13/whatsnew/3.13.html:
Remove the following old functions to configure the Python initialization, deprecated in Python 3.11:
    PySys_AddWarnOptionUnicode(): use PyConfig.warnoptions instead.
    PySys_AddWarnOption(): use PyConfig.warnoptions instead.
    PySys_AddXOption(): use PyConfig.xoptions instead.
    PySys_HasWarnOptions(): use PyConfig.xoptions instead.
    PySys_SetArgvEx(): set PyConfig.argv instead.
    PySys_SetArgv(): set PyConfig.argv instead.
    PySys_SetPath(): set PyConfig.module_search_paths instead.
    Py_SetPath(): set PyConfig.module_search_paths instead.
    Py_SetProgramName(): set PyConfig.program_name instead.
    Py_SetPythonHome(): set PyConfig.home instead.
    Py_SetStandardStreamEncoding(): set PyConfig.stdio_encoding instead, and set also maybe PyConfig.legacy_windows_stdio (on Windows).
    _Py_SetProgramFullPath(): set PyConfig.executable instead.


https://docs.python.org/3.13/whatsnew/3.13.html

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.13/fedora-rawhide-x86_64/06712032-neuron/

For all our attempts to build neuron with Python 3.13, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.13/package/neuron/

Testing and mass rebuild of packages is happening in copr.
You can follow these instructions to test locally in mock if your package builds with Python 3.13:
https://copr.fedorainfracloud.org/coprs/g/python/python3.13/

Let us know here if you have any questions.

Python 3.13 is planned to be included in Fedora 41.
To make that update smoother, we're building Fedora packages with all pre-releases of Python 3.13.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires),
so if this package is required a lot, it's important for us to get it fixed soon.

We'd appreciate help from the people who know this package best,
but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 Ankur Sinha (FranciscoD) 2023-12-12 15:27:25 UTC
Upstream is only now working on 3.12 support, so it'll be sometime before they do 3.13. I've filed an issue upstream anyway.

Comment 2 Aoife Moloney 2024-02-15 23:07:45 UTC
This bug appears to have been reported against 'rawhide' during the Fedora Linux 40 development cycle.
Changing version to 40.

Comment 3 Sandro 2024-05-31 10:09:39 UTC
Builds fine now with Python 3.13. Latest build in Python 3.13 Copr also succeeded.


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