pip install using Cython 3.0.0 fails with "Function signature does not match previous declaration" error

[patkaehuaea]

A few previous issues reference pip install from master to resolve errors. I'm installing from master, but seeing a new error since Cython 3.0.0 was released on July 17th - _javabridge_mac.pyx:34:5: Function signature does not match previous declaration.

Attempting the same install using Cython 0.29.36 works as expected.

environment details

$ python --version
Python 3.10.12

$ java -version
openjdk version "20.0.1" 2023-04-18
OpenJDK Runtime Environment Homebrew (build 20.0.1)
OpenJDK 64-Bit Server VM Homebrew (build 20.0.1, mixed mode, sharing)

$ echo $JAVA_HOME
/opt/homebrew/Cellar/openjdk/20.0.1/libexec/openjdk.jdk/Contents/Home

$ sw_vers -productVersion 
13.4.1

$ system_profiler SPSoftwareDataType
Software:

    System Software Overview:

      System Version: macOS 13.4.1 (c) (22F770820d)
      Kernel Version: Darwin 22.5.0
      Boot Volume: Macintosh HD
      Boot Mode: Normal
      Computer Name: MacBook Pro
      User Name: pat
      Secure Virtual Memory: Enabled
      System Integrity Protection: Enabled
      Time since boot: 2 days, 10 hours, 7 minutes

steps to reproduce

show cython version

$ pip show cython
Name: Cython
Version: 3.0.0
Summary: The Cython compiler for writing C extensions in the Python language.
Home-page: https://cython.org/
Author: Robert Bradshaw, Stefan Behnel, Dag Seljebotn, Greg Ewing, et al.
Author-email: [email protected]
License: Apache-2.0
Location: /Users/pat/temp/foo/.venv/lib/python3.10/site-packages
Requires: 
Required-by: 

attempt javabridge install from master

$ pip install https://github.com/LeeKamentsky/python-javabridge/archive/master.zip#egg=javabridge

...

Error compiling Cython file:
      ------------------------------------------------------------
      ...
          void MacRunLoopStop() nogil
          void MacRunLoopReset() nogil
          int MacIsMainThread() nogil
          void MacRunLoopRunInMode(double) nogil
      
      cdef void StopVM(JavaVM *vm):
           ^
      ------------------------------------------------------------
      
      _javabridge_mac.pyx:34:5: Function signature does not match previous declaration

...

subprocess.CalledProcessError: Command '['/Users/pat/temp/foo/.venv/bin/python3.10', '-m', 'cython', '-3', '/private/var/folders/zp/yc7pxt6x7zj01_vr01sqznx00000gp/T/pip-install-h8pjccy7/javabridge_fc0d7b9f2f59493a8e3e5116191f8cb4/_javabridge.pyx', '/private/var/folders/zp/yc7pxt6x7zj01_vr01sqznx00000gp/T/pip-install-h8pjccy7/javabridge_fc0d7b9f2f59493a8e3e5116191f8cb4/_javabridge_mac.pyx', '/private/var/folders/zp/yc7pxt6x7zj01_vr01sqznx00000gp/T/pip-install-h8pjccy7/javabridge_fc0d7b9f2f59493a8e3e5116191f8cb4/_javabridge_nomac.pyx']' returned non-zero exit status 1.

install cython 0.29.36

$ pip uninstall cython
Found existing installation: Cython 3.0.0
Uninstalling Cython-3.0.0:
  Would remove:
    /Users/pat/temp/foo/.venv/bin/cygdb
    /Users/pat/temp/foo/.venv/bin/cython
    /Users/pat/temp/foo/.venv/bin/cythonize
    /Users/pat/temp/foo/.venv/lib/python3.10/site-packages/Cython-3.0.0.dist-info/*
    /Users/pat/temp/foo/.venv/lib/python3.10/site-packages/Cython/*
    /Users/pat/temp/foo/.venv/lib/python3.10/site-packages/cython.py
    /Users/pat/temp/foo/.venv/lib/python3.10/site-packages/pyximport/*
Proceed (Y/n)? y
  Successfully uninstalled Cython-3.0.0

$ pip install Cython==0.29.36
Collecting Cython==0.29.36
  Obtaining dependency information for Cython==0.29.36 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata
  Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB)
Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB)
Installing collected packages: Cython

attempt javabridge install from master again - SUCCESS

$ pip install https://github.com/LeeKamentsky/python-javabridge/archive/master.zip#egg=javabridge
Collecting javabridge
  Using cached https://github.com/LeeKamentsky/python-javabridge/archive/master.zip
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in ./.venv/lib/python3.10/site-packages (from javabridge) (1.25.1)
Installing collected packages: javabridge
  DEPRECATION: javabridge is being installed using the legacy 'setup.py install' method, because it does not have a 'pyproject.toml' and the 'wheel' package is not installed. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at https://github.com/pypa/pip/issues/8559
  Running setup.py install for javabridge ... done
Successfully installed javabridge-0.0.0

[notice] A new release of pip is available: 23.0.1 -> 23.2.1
[notice] To update, run: pip install --upgrade pip

run test

$ cat test_javabridge.py 
#!/Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8
import os
import javabridge

javabridge.start_vm(run_headless=True)
try:
        print(javabridge.run_script('java.lang.String.format("Hello, %s!", greetee);', dict(greetee='world')))
finally:
        javabridge.kill_vm()

$ python test_javabridge.py 
Hello, world!

[LeeKamentsky]

Hi Pat, thanks for reporting this. I'll put together the environment today to reproduce the problem and see what the fix is. Usually these things are a warning in a previous version that's become an error in the current and are easy to fix. Will reference this issue with the check in.

[benjamin-asdf]

HI, I am trying

pip3 install https://github.com/LeeKamentsky/python-javabridge/archive/master.zip#egg=javabridge

to get around #209 and get the error reported here.

Is there perhaps a working version other than master? Cheers.