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[BUG] Weird cython/pythran related bug when building PyME from source (not really a PyME bug; solution provided) #1677

Description

@csoeller

Describe the bug

Note: this is not a PYME bug per se but a build issue that seems to result from some weird cython and pythran components (within cython) interactions. Noting this here in case somebody runs into it

Came across a very weird issue when trying to build PyME from source on a co-workers computer. After spinning up a new build with a new conda environment using the PYME-test-env build scripts the actual PYME build failed with a cyton related error:

[15 lines of output]
  + meson setup C:\pyt\pte\build-test-py3.11-mamba_nopip\python-microscopy-master C:\pyt\pte\build-test-py3.11-mamba_nopip\python-microscopy-master\build\cp311 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:\pyt\pte\build-test-py3.11-mamba_nopip\python-microscopy-master\build\cp311\meson-python-native-file.ini
  The Meson build system
  Version: 1.11.1
  Source dir: C:\pyt\pte\build-test-py3.11-mamba_nopip\python-microscopy-master
  Build dir: C:\pyt\pte\build-test-py3.11-mamba_nopip\python-microscopy-master\build\cp311
  Build type: native build
  Activating VS 17.6.5
  Project name: python-microscopy
  Project version:
  C compiler for the host machine: cl (msvc 19.36.32537 "Microsoft (R) C/C++ Optimizing Compiler Version 19.36.32537 for x64")
  C linker for the host machine: link link 14.36.32537.0
  
  ..\..\meson.build:1:0: ERROR: Compiler cython cannot transpile programs.

See below for the possible cause and a workaround.

To Reproduce
Steps to reproduce the behavior (only an issue on windows, macOS is ok):

  1. Try building PYME from source using python>=3.11 (3.10 is ok in my tests)
  2. Possibly dependent on a conda environment build and/or conda based dependency packages install.
  3. Try building with python -m pip install --no-deps --no-build-isolation --editable . (the issue likely does not depend on an editable install)
  4. See error

Cause of the issue and workaround

In the next comment below I provide the cause and a workaround.

Platform (please complete the following information - or copy-paste from error dialog if shown):

  • OS: Windows
  • Python version: Python>=3.11
  • numpy version: not sure this matters
  • wxpython version [if a UI bug]: neither matters (I think)

Activity

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