Ants version crash kernel on python 3.9

[EnriqueFV]

Describe the bug

I have create an enviroment with antspyx from the binaries antspyx-0.5.4-cp39-cp39-win_amd64. I have to stay on pyhton 3.9 because I want to use pyradiomics package, and the latest version I could install it was on python 3.9. every time I tried to read an image with the ants package, the kernel crashes.

To reproduce

This is my toml config file. I am using uv to manage the packages. Just running ants.image_read crashes the kernel.

[project] name = "clamp-precised" version = "0.1.0" description = "Add your description here" readme = "README.md" requires-python = "==3.9.*" dependencies = [ "altair", "ipykernel", "ipywidgets", "itk", "marimo", "matplotlib", "medvae @ https://github.com/EnriqueFV/MedVAE.git", "modin[dask]", "monai[all]", "numpy", "openpyxl", "pandarallel", "pandas", "phate", "pyradiomics", "pingouin", "plotly", "pydicom", "scikit-image", "scikit-learn", "scipy", "seaborn", "shap", "simpleitk", "statsmodels", "torch", "torchvision", "totalsegmentator", "uv", "antspyx @ https://github.com/ANTsX/ANTsPy/releases/download/v0.5.4/antspyx-0.5.4-cp39-cp39-win_amd64.whl", "blosc2>=2.5.1", "polars>=1.34.0", ] [tool.uv.sources] torch = [ { index = "pytorch-cu129", marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] torchvision = [ { index = "pytorch-cu129", marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] [[tool.uv.index]] name = "pytorch-cu129" url = "https://download.pytorch.org/whl/cu129" explicit = true

for example, running ants.image_read(ants.get_data('mni')) downloads the MNI test file but crashes when it reads it.

[cookpa]

I think Python 3.9 stopped working on Windows and that's why we stopped building those wheels (#837).

You might have more success if you can build from source. I believe the issue was that the Github runner we use was newer, and didn't build correct binaries for older python

[EnriqueFV]

I tried building from source, specifying the tar release file on my toml and got the following when I run uv sync:

(clamp-precised) PS D:\VHIR-IMM\CLAMP-PRECISED> uv sync Updated https://github.com/openai/CLIP.git (dcba3cb2e2827b402d2701e7e1c7d9fed8a20ef1) Resolved 309 packages in 10.93s × Failed to build antspyx @ https://github.com/ANTsX/ANTsPy/archive/refs/tags/v0.5.4.tar.gz`
├─▶ The build backend returned an error
╰─▶ Call to scikit_build_core.build.build_wheel failed (exit code: 1)

  [stdout]
  *** scikit-build-core 0.11.6 using CMake 4.2.0 (wheel)
  *** Configuring CMake...
  loading initial cache file build\cp39-cp39-win_amd64\CMakeInit.txt
  -- Building for: Visual Studio 17 2022
  -- Selecting Windows SDK version 10.0.26100.0 to target Windows 10.0.26200.
  -- The CXX compiler identification is MSVC 19.44.35209.0
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: D:/Microsoft Visual Studio/2022/Community/VC/Tools/MSVC/14.44.35207/bin/Hostx64/x64/cl.exe - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Found Python: C:/Users/Usuario/AppData/Local/uv/cache/builds-v0/.tmpmbskwB/Scripts/python.exe (found suitable version "3.9.23", minimum required is "3.8") found components:`

...

" HEAD is now at 4535548a85 STYLE: Declare local radius, center variables in Filtering constexpr
Acceso denegado.
Acceso denegado.
Acceso denegado.
CMake Error at CMakeLists.txt:46 (project):
No CMAKE_CXX_COMPILER could be found.

    Tell CMake where to find the compiler by setting either the environment
    variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
    to the compiler, or to the compiler name if it is in the PATH.


  CMake Error at CMakeLists.txt:46 (project):
    No CMAKE_C_COMPILER could be found.

    Tell CMake where to find the compiler by setting either the environment
    variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
    the compiler, or to the compiler name if it is in the PATH.


  ninja: error: loading 'build.ninja': The system cannot find the file specified.

  Cloning into 'antsrepo'...
  Already on 'master'
  Note: switching to '35d9381721b143c7bbd9d5f7f4ad853406351c1c'.

  You are in 'detached HEAD' state. You can look around, make experimental
  changes and commit them, and you can discard any commits you make in this
  state without impacting any branches by switching back to a branch.

  If you want to create a new branch to retain commits you create, you may
  do so (now or later) by using -c with the switch command. Example:

    git switch -c <new-branch-name>

  Or undo this operation with:

    git switch -

  Turn off this advice by setting config variable advice.detachedHead to false

  HEAD is now at 35d93817 Merge pull request #1710 from ANTsX/iMath_truncate_mask_range
  El sistema no puede encontrar el controlador especificado.
  CMake Error at CMakeLists.txt:25 (find_package):
    By not providing "FindITK.cmake" in CMAKE_MODULE_PATH this project has
    asked CMake to find a package configuration file provided by "ITK", but
    CMake did not find one.

    Could not find a package configuration file provided by "ITK" with any of
    the following names:

      ITKConfig.cmake
      itk-config.cmake

    Add the installation prefix of "ITK" to CMAKE_PREFIX_PATH or set "ITK_DIR"
    to a directory containing one of the above files.  If "ITK" provides a
    separate development package or SDK, be sure it has been installed.



  *** CMake configuration failed"

What does this means? I retried it after cleaning my cache, but still fails. Am I missing some steps?

[cookpa]

I'm not very familiar with windows or uv, sorry.

Tagging in case others can help.

Maybe an older ANTspy can work, like in the issue I linked above?

[EnriqueFV]

I solve it by initializing the visual code (and its terminal) from the developer command promp terminal, that specifies the cmake path. Now, I fall into the same problem I have had in other situation trying to install antspyx, the lenght path of the ITK directory :
CMake Error at CMakeLists.txt:105 (message): ITK source code directory path length is too long (106 > 50).Please move the ITK source code directory to a directory with a shorter path.
And this is something I didn't know how to solve before.

[cookpa]

I am just guessing on a fix from reading this SimpleITK page:

https://simpleitk.readthedocs.io/en/master/windowsPathLength.html

Enable Long Paths in Windows 10, Version 1607, and Later

Set the ITK_SKIP_PATH_LENGTH_CHECKS cmake variable to ON, ie edit

[ANTsPy](https://github.com/ANTsX/ANTsPy/tree/master)/[scripts](https://github.com/ANTsX/ANTsPy/tree/master/scripts) /configure_ITK.bat

and add to the cmake command -DITK_SKIP_PATH_LENGTH_CHECKS=ON

then try building

[EnriqueFV]

I have done it already. I made this branch to set the flag "ON" in Configure_ITK.bat. Setting the variable ITK_SKIP_PATH_LENGTH_CHECKS at local or global level didn't work, as it appeard overwritten on the compilation file (CMAKEcache in the itk build). Now it seems that the building process advance and almost finalizes, since it updates all the files of ants build. I print the log of the terminal when I execute uv sync (with uv cache clean). From what i could understand, it says that it can't find pearl (¿?) and a python package is missing. I dont know really know how to debug, since I am not used to compile packages from source. Another possible problem is the version of Cmake, or the acces to the .gits it needs (since is on the branch I made for this). I hope this is easier to solve, since It looks is almost ready to build and I think is more related to my system.

full_build_log.txt

[EnriqueFV]

As you said, from the issue you linked above the wheels of Antspyx 0.5.2 works fine!