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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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starfish is incompatible with Python 3.9 #1950

Closed ora-lv closed 2 years ago

ora-lv commented 3 years ago

Description

We have not been able to get starfish to work in Python 3.9

Steps/Code to Reproduce

Currently the latest version of skimage that starfish is compatible with is 0.15.0 (or 0.15.x) The oldest version of skimage we were able to pip install on Python 3.9 is 0.16.2

Expected Results

We can run starfish on Python 3.9 with a compatible version of skimage (more recent than 0.15.0)

Actual Results

We can install skimage 0.18.0 and starfish 0.2.2 on Python 3.9.2, but they are not compatible (running into this issue https://github.com/spacetx/starfish/issues/1887 when running the quick start guide)

Note that there was no actual fix for the issue mentioned, only flagging that the scikit-image version is incompatible with starfish (but now 0.18.0 is available and back to the same issue)

Versions

Linux-5.4.89+-x86_64-with-glibc2.31 Python 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46) [GCC 9.3.0] NumPy 1.19.5 SciPy 1.6.3 scikit-image 0.18.0 pandas 1.2.4 sklearn 0.24.2 xarray 0.18.2 sympy 1.5.1 starfish 0.2.2

neuromusic commented 2 years ago

this should be fixed with #1963