Python 3.14 install fails and outdated pypi metainfo

[Christian-B]

We run github actions to test Spynnaker

These install PyNN which in turn installs morphio

This works fine in Python 3.8 to python 3.13 but with 3.14 we get

× Building wheel for morphio (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [105 lines of output]
toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section
toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-314/morphio
copying morphio/init.py -> build/lib.linux-x86_64-cpython-314/morphio
creating build/lib.linux-x86_64-cpython-314/morphio/mut
copying morphio/mut/init.py -> build/lib.linux-x86_64-cpython-314/morphio/mut
creating build/lib.linux-x86_64-cpython-314/morphio/vasculature
copying morphio/vasculature/init.py -> build/lib.linux-x86_64-cpython-314/morphio/vasculature
running build_ext
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 has been removed from CMake.

      Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
      to tell CMake that the project requires at least <min> but has been updated
      to work with policies introduced by <max> or earlier.
    
      Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.
    
    
    -- Configuring incomplete, errors occurred!
    Traceback (most recent call last):
      File "/opt/hostedtoolcache/Python/3.14.0/x64/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
        main()
        ~~~~^^
      File "/opt/hostedtoolcache/Python/3.14.0/x64/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
        json_out["return_val"] = hook(**hook_input["kwargs"])
                                 ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.14.0/x64/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
        return _build_backend().build_wheel(
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
            wheel_directory, config_settings, metadata_directory
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        )
        ^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 435, in build_wheel
        return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 423, in _build
        return self._build_with_temp_dir(
               ~~~~~~~~~~~~~~~~~~~~~~~~~^
            cmd,
            ^^^^
        ...<3 lines>...
            self._arbitrary_args(config_settings),
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        )
        ^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir
        self.run_setup()
        ~~~~~~~~~~~~~~^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 512, in run_setup
        super().run_setup(setup_script=setup_script)
        ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 317, in run_setup
        exec(code, locals())
        ~~~~^^^^^^^^^^^^^^^^
      File "<string>", line 72, in <module>
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/__init__.py", line 115, in setup
        return distutils.core.setup(**attrs)
               ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/core.py", line 186, in setup
        return run_commands(dist)
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
        dist.run_commands()
        ~~~~~~~~~~~~~~~~~^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
        self.run_command(cmd)
        ~~~~~~~~~~~~~~~~^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/dist.py", line 1102, in run_command
        super().run_command(command)
        ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
        cmd_obj.run()
        ~~~~~~~~~~~^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
        self.run_command("build")
        ~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
        self.distribution.run_command(command)
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/dist.py", line 1102, in run_command
        super().run_command(command)
        ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
        cmd_obj.run()
        ~~~~~~~~~~~^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
        ~~~~~~~~~~~~~~~~^^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
        self.distribution.run_command(command)
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/dist.py", line 1102, in run_command
        super().run_command(command)
        ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
      File "/tmp/pip-build-env-hsmd7r8f/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
        cmd_obj.run()
        ~~~~~~~~~~~^^
      File "<string>", line 28, in run
      File "<string>", line 59, in build_extension
      File "/opt/hostedtoolcache/Python/3.14.0/x64/lib/python3.14/subprocess.py", line 419, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-vuecvv0u/morphio_189b6ac851964136b0c94c2a44e7ee5f', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-vuecvv0u/morphio_189b6ac851964136b0c94c2a44e7ee5f/build/lib.linux-x86_64-cpython-314/morphio', '-DMORPHIO_VERSION_STRING=3.4.0', '-DMORPHIO_TESTS=OFF', '-DPYTHON_EXECUTABLE=/opt/hostedtoolcache/Python/3.14.0/x64/bin/python', '-DHIGHFIVE_EXAMPLES=OFF', '-DHIGHFIVE_UNIT_TESTS=OFF', '-DCMAKE_BUILD_TYPE=Release', '-DMorphIO_CXX_WARNINGS=OFF', '-GNinja']' returned non-zero exit status 1.

---

Also the metadata on pypi still points to a githuib which is listed as archived.

[Christian-B]

This issue causes NeuralEnsemble/PyNN#823

[mgeplf]

Looks like we haven't tested compatibility with the newer CMakes.

We haven't made a wheel release yet for python 3.14, which was just released, so you're likely picking up the wheels for the old version, and that's why it works.

Also the metadata on pypi still points to a githuib which is listed as archived.

I will fix that as well.

I'm not sure when I'll get a chance to do all this, though, so it might be a while.

[cattabiani]

I have the same problem. Maybe time to make a new release?

[mgeplf]

@Christian-B Sorry about the delay, as expected, many other things have come up.

@cattabiani > I have the same problem. Maybe time to make a new release?

I think I should be able to cut one, can you check that wheels in https://github.com/openbraininstitute/MorphIO/actions/runs/22565801944 work how you expect?

[Christian-B]

The parts of https://github.com/NeuralEnsemble/PyNN that we use do not depend on MorphIO.

We only need pip install morphio to not raise an error when using python 3.14

This because PyNN currently lists morphio in https://github.com/NeuralEnsemble/PyNN/blob/master/pyproject.toml

so pip install pynn
will work.

[cattabiani]

wheel checked. To me it works. I hope this issue will be closed soon

[mgeplf]

The new wheels have been released on pypi, and I checked that pynn installs with python 3.14:

$ uv venv -p cpython-3.14 pynn
Using CPython 3.14.0
Creating virtual environment at: pynn
Activate with: source pynn/bin/activate
$ . ./pynn/bin/activate
$ uv pip install pynn
Using Python 3.14.0 environment at: pynn
Resolved 7 packages in 1.08s
Prepared 4 packages in 536ms
Installed 7 packages in 53ms
 + lazyarray==0.7.0
 + morphio==3.4.1
 + neo==0.14.3
 + numpy==2.4.2
 + packaging==26.0
 + pynn==0.12.4
 + quantities==0.16.4

@Christian-B let me know if that works for you?

[Christian-B]

Thank you are github actions using python 31.4 now work.

[mgeplf]

Thank you are github actions using python 31.4 now work.

Great; sorry again for the delay.