Error Installing czitools on Python 3.12 Due to scikit-image Dependency

[bryanbarcelona]

I encountered an error while trying to install czitools using pip on Python 3.12. The installation process fails due to an issue with the scikit-image dependency. The error does not occur when installing in a virtual environment with Python 3.11.9.

Steps performed:
Set up a virtual environment with Python 3.12.
Attempt to install czitools using the command: pip install czitools

Error Message:
INFO: pip is looking at multiple versions of scikit-image to determine which version is compatible with other requirements. This could take a while.
Collecting scikit-image (from czitools)
Using cached scikit_image-0.23.2-cp312-cp312-win_amd64.whl.metadata (14 kB)
Using cached scikit_image-0.23.1-cp312-cp312-win_amd64.whl.metadata (14 kB)
Using cached scikit_image-0.22.0-cp312-cp312-win_amd64.whl.metadata (13 kB)
Using cached scikit_image-0.21.0.tar.gz (22.7 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [12 lines of output]
+ meson setup C:\Users\Bryan\AppData\Local\Temp\pip-install-_tvihm_p\scikit-image_ba7c7e00d0b94ee6a922f2ea55a85f8a C:\Users\Bryan\AppData\Local\Temp\pip-install-_tvihm_p\scikit-image_ba7c7e00d0b94ee6a922f2ea55a85f8a.mesonpy-vi4vx85a -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:\Users\Bryan\AppData\Local\Temp\pip-install-_tvihm_p\scikit-image_ba7c7e00d0b94ee6a922f2ea55a85f8a.mesonpy-vi4vx85a\meson-python-native-file.ini
The Meson build system
Version: 1.5.0
Source dir: C:\Users\Bryan\AppData\Local\Temp\pip-install-_tvihm_p\scikit-image_ba7c7e00d0b94ee6a922f2ea55a85f8a
Build dir: C:\Users\Bryan\AppData\Local\Temp\pip-install-_tvihm_p\scikit-image_ba7c7e00d0b94ee6a922f2ea55a85f8a.mesonpy-vi4vx85a
Build type: native build
Project name: scikit-image
Project version: 0.21.0

  ..\meson.build:1:0: ERROR: Compiler cl cannot compile programs.

  A full log can be found at C:\Users\Bryan\AppData\Local\Temp\pip-install-_tvihm_p\scikit-image_ba7c7e00d0b94ee6a922f2ea55a85f8a\.mesonpy-vi4vx85a\meson-logs\meson-log.txt
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

Environment:
Operating System: Windows
Python Version: 3.12
czitools Version: Latest (attempted to install via pip)
Virtual Environment: Yes

Additional Information:
The installation works fine in a virtual environment with Python 3.11.9.
The issue appears to be related to the scikit-image package and its dependencies when used with Python 3.12.
Request:
Could you please look into this compatibility issue with Python 3.12? Any guidance on resolving this error or recommended steps to make czitools compatible with Python 3.12 would be greatly appreciated.

Thank you!

[acorbat]

I am having the same issue. Once the installation finishes, you can still import czitools, but almost none of the modules are there (for example read_tools is missing).

[sebi06]

Hi all,

actually scikit-image is not a direct dependency of czitools 0.7.0 anymore (I need to check again, but see: https://github.com/sebi06/czitools/blob/main/setup.cfg), so I also do not really know why this happens.

Another maybe related topic is that czitools is obviously having a dependecy to pylibCZIrw which does not support Python 3.12 yet. The same is true for czitools. If once scrolls down a bit you will see, that only Python 3.11 is listed. Sorry for not specifying this correctly under the "Requires" section.

But as I said I do not really know if those this are related. The wish for Python 3.12 support is understood and I will check how quickly this can be added to pylibCZIrw.