Installing with uv complains about Python version missmatch

[jo-mueller]

Hi @anwai98 ,

I just wanted to test some things with micro-sam and noticed that it doesn't support Python > 3.10. Is that bound informed by critical dependencies? Python 3.10 is EOL in fall 2026, and many applications (critically, zarr-python for zarr v3) already now require Python>3.12.

Is relaxing this constraint a possibility?

[constantinpape]

Hi @jo-mueller ,

I just wanted to test some things with micro-sam and noticed that it doesn't support Python > 3.10.

This is not correct. We support any python version from 3.10 - 3.14. (Though 3.10 may actually not work well due to zarr dependencies). See https://github.com/computational-cell-analytics/micro-sam/blob/main/setup.cfg#L20-L24 and https://github.com/computational-cell-analytics/micro-sam/blob/main/.github/workflows/test.yaml#L22 (tests only run for 3.12 to keep the matrix limited).

It is of course entirely possible that there are some dependency issues etc. that prevent installation for other python versions --- but these are much more likely due to napari than due to micro_sam itself. Can you please let us know how exactly you tried to install it and which issues you ran into with other python versions? Then we can see how to resolve this.

[jo-mueller]

Hi Constantin, thanks for chiming in. I think I was looking in the wrong file here (mea culpa), but I do get a dependency conflict if I do a uv pip install micro_sam:

(microsam) C:\Users\johan\Documents\GitHub\ngff-spec>uv pip install micro-sam
Using Python 3.12.13 environment at: C:\Users\johan\miniforge3\envs\microsam
Resolved 176 packages in 4.94s
  x Failed to build `llvmlite==0.36.0`
  |-> The build backend returned an error
  `-> Call to `setuptools.build_meta:__legacy__.build_wheel` failed (exit code: 1)

      [stderr]
      C:\Users\johan\AppData\Local\uv\cache\builds-v0\.tmpFp5K7q\Lib\site-packages\setuptools\_vendor\wheel\bdist_wheel.py:4:
      FutureWarning: The 'wheel' package is no longer the canonical location of the 'bdist_wheel' command, and will be
      removed in a future release. Please update to setuptools v70.1 or later which contains an integrated version of
      this command.
        warn(
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
        File "C:\Users\johan\AppData\Local\uv\cache\builds-v0\.tmpFp5K7q\Lib\site-packages\setuptools\build_meta.py",
      line 333, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\johan\AppData\Local\uv\cache\builds-v0\.tmpFp5K7q\Lib\site-packages\setuptools\build_meta.py",
      line 301, in _get_build_requires
          self.run_setup()
        File "C:\Users\johan\AppData\Local\uv\cache\builds-v0\.tmpFp5K7q\Lib\site-packages\setuptools\build_meta.py",
      line 520, in run_setup
          super().run_setup(setup_script=setup_script)
        File "C:\Users\johan\AppData\Local\uv\cache\builds-v0\.tmpFp5K7q\Lib\site-packages\setuptools\build_meta.py",
      line 317, in run_setup
          exec(code, locals())
        File "<string>", line 55, in <module>
        File "<string>", line 52, in _guard_py_ver
      RuntimeError: Cannot install on Python version 3.12.13; only versions >=3.6,<3.10 are supported.

      hint: This usually indicates a problem with the package or the build environment.
  help: `llvmlite` (v0.36.0) was included because `micro-sam` (v1.8.4) depends on `trackastra` (v0.5.3) which depends
        on `numba` (v0.53.1) which depends on `llvmlite`

Maybe that's just the dependency resolution of uv pip install though? Will check...

[jo-mueller]

Ok, update: uv pip install complains, pip install doesn't. The problem would then probably need to be solved somewhere upstream 🤔

[anwai98]

Thanks for the detailed report @jo-mueller. We'll look into this and see what's going on! (good to confirm that pip works -- would be unexpected otherwise) ;)

[anwai98]

Hi @jo-mueller,

Could you quickly try pinning numba range like: uv pip install micro-sam "numba>=0.59" -- and tell me if this works for you?

(uv reads like it somehow backtracks numba to fall too old for weird numpy and llvmlite conflicts)

[jo-mueller]

@anwai98 can confirm, works here :)

[anwai98]

Awesome, I think I know what it means (numba needs to have a range pin to avoid all the fuss -- and the source should be trackastra). I'll come back to this in a few days and leave this issue open for now!