Debian 12 install fail

[SoftwareLiteracy]

Hi, I tried both a pypi and github install, both fail. The install commands are:

python -m pip install pycortex --target=$PYTHON_SITE_PACKAGES/ --upgrade

python -m pip install git+https://github.com/gallantlab/pycortex.git --target=$PYTHON_SITE_PACKAGES/ --upgrade

The system is:

Linux xxx 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
No LSB modules are available.
Distributor ID:	Debian
Description:	Debian GNU/Linux 12 (bookworm)
Release:	12
Codename:	bookworm

> python --version
Python 3.13.1

Excerpt of the error:

  Building wheel for pycortex (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for pycortex (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [593 lines of output]
      running bdist_wheel

...

      /home/xxx/apps/Python-3.13.1/include/python3.13/cpython/longobject.h:111:17: note: declared here
        111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
            |                 ^~~~~~~~~~~~~~~~~~~
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pycortex
Failed to build pycortex

Thank you.

[mvdoc]

This is probably caused by the interaction between gcc, cython, and the most recent python version. Specifically, I'm not sure if we support python 3.13 yet. Or it could be that debian 12 has a gcc version that is "too modern" and we haven't modified the cython code. Would you be able to test the installation in python 3.12?

…

On Wed, Jan 29, 2025 at 12:07 PM Software Literacy Foundation < ***@***.***> wrote: Hi, I tried both a pypi and github install, both fail. The install commands are: python -m pip install pycortex --target=$PYTHON_SITE_PACKAGES/ --upgrade python -m pip install git+https://github.com/gallantlab/pycortex.git --target=$PYTHON_SITE_PACKAGES/ --upgrade The system is: Linux xxx 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux No LSB modules are available. Distributor ID: Debian Description: Debian GNU/Linux 12 (bookworm) Release: 12 Codename: bookworm > python --version Python 3.13.1 Excerpt of the error: Building wheel for pycortex (pyproject.toml) ... error error: subprocess-exited-with-error × Building wheel for pycortex (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [593 lines of output] running bdist_wheel ... /home/xxx/apps/Python-3.13.1/include/python3.13/cpython/longobject.h:111:17: note: declared here 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, | ^~~~~~~~~~~~~~~~~~~ error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pycortex Failed to build pycortex Thank you. — Reply to this email directly, view it on GitHub <#563>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO5TGV543HG75Q5ZA64RVT2NEDEFAVCNFSM6AAAAABWDLGNPSVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAYTQNZXGQ2TGMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Matteo Visconti di Oleggio Castello, Ph.D. Assistant Project Scientist Department of Neuroscience, UC Berkeley MatteoVisconti.com <http://matteovisconti.com> || github.com/mvdoc || linkedin.com/in/matteovisconti

[SoftwareLiteracy]

Thanks for the feedback.

Downgrading is a step back I'm not invested in for a single dependency. Please let us know when you feel these are supported. Thank you.

> gcc --version
gcc (Debian 12.2.0-14) 12.2.0

> python --version
Python 3.13.1

[kroq-gar78]

This looks like a Python 3.13 problem. I think we'll need to update to Cython 3.x to solve this, since I don't see the relevant commit on the 0.29.x branch that we're still using. cython/cython#5997

Log with the specific error:

| Building wheels for collected packages: pycortex
|   Building editable for pycortex (pyproject.toml) ... error
|   error: subprocess-exited-with-error
|
|   × Building editable for pycortex (pyproject.toml) did not run successfully.
|   │ exit code: 1

[...]

|       cortex/openctm.c: In function ‘__Pyx_PyInt_As_int’:
|       cortex/openctm.c:12029:27: error: too few arguments to function ‘_PyLong_AsByteArray’
|       12029 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
|             |                           ^~~~~~~~~~~~~~~~~~~
|       In file included from /usr/local/include/python3.13/longobject.h:107,
|                        from /usr/local/include/python3.13/Python.h:81,
|                        from cortex/openctm.c:54:
|       /usr/local/include/python3.13/cpython/longobject.h:111:17: note: declared here
|         111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
|             |                 ^~~~~~~~~~~~~~~~~~~
|       cortex/openctm.c: In function ‘__Pyx_PyInt_As_CTMenum’:
|       cortex/openctm.c:12225:27: error: too few arguments to function ‘_PyLong_AsByteArray’
|       12225 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
|             |                           ^~~~~~~~~~~~~~~~~~~
|       /usr/local/include/python3.13/cpython/longobject.h:111:17: note: declared here
|         111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
|             |                 ^~~~~~~~~~~~~~~~~~~
|       cortex/openctm.c: In function ‘__Pyx_PyInt_As_unsigned_int’:
|       cortex/openctm.c:12497:27: error: too few arguments to function ‘_PyLong_AsByteArray’
|       12497 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
|             |                           ^~~~~~~~~~~~~~~~~~~
|       /usr/local/include/python3.13/cpython/longobject.h:111:17: note: declared here
|         111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
|             |                 ^~~~~~~~~~~~~~~~~~~
|       cortex/openctm.c: In function ‘__Pyx_PyInt_As_long’:
|       cortex/openctm.c:12693:27: error: too few arguments to function ‘_PyLong_AsByteArray’
|       12693 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
|             |                           ^~~~~~~~~~~~~~~~~~~
|       /usr/local/include/python3.13/cpython/longobject.h:111:17: note: declared here
|         111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
|             |                 ^~~~~~~~~~~~~~~~~~~

[...]

|       error: command '/usr/bin/gcc' failed with exit code 1
|       [end of output]

[mvdoc]

@SoftwareLiteracy , thanks to @kroq-gar78's fixes you should be able to install pycortex in Python 3.13. I will release a new pycortex version on pypi soon, but in the meanwhile you can try installing directly from the repo on github. Please feel free to reopen this issue if there are still issues.