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MacOS installation issues #14

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schoinh opened this issue Feb 13, 2021 · 0 comments
Open

MacOS installation issues #14

schoinh opened this issue Feb 13, 2021 · 0 comments

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@schoinh
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schoinh commented Feb 13, 2021

Description

The installation instructions for MacOS fails at step 3.2, specifically at pip install -e .[all].

Building wheels for collected packages: scikit-image, numba, llvmlite, scikit-fmm
  Building wheel for scikit-image (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/nahyung.choi/opt/anaconda3/envs/segmenter/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fc/6dkngtd52rg1m5mjnwq9krxh0000gp/T/pip-install-3nxi1pk7/scikit-image_9643b29650014f62bf9ee746d7a1304b/setup.py'"'"'; __file__='"'"'/private/var/folders/fc/6dkngtd52rg1m5mjnwq9krxh0000gp/T/pip-install-3nxi1pk7/scikit-image_9643b29650014f62bf9ee746d7a1304b/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/fc/6dkngtd52rg1m5mjnwq9krxh0000gp/T/pip-wheel-3jzv7uph
       cwd: /private/var/folders/fc/6dkngtd52rg1m5mjnwq9krxh0000gp/T/pip-install-3nxi1pk7/scikit-image_9643b29650014f62bf9ee746d7a1304b/

Simply running pip install aicssegmentation in a Python 3.7 environment worked, but the PyPI link is buried towards the bottom of the instructions in this note: "Note 4: For advanced user to deploy segmenter on cluster, our package is also available on PyPi"

Expected Behavior

Either the instructions for installing from source should be updated or the link to the PyPI page should be moved up to the top of the instructions. Probably both.

Reproduction

Follow the instructions in this repo for MacOS installation.

Environment

MacOS Big Sur v11.2
conda environment -- tried with Python 3.6, 3.8, and 3.9

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