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macronucleus / Chromagnon

Image correction software for chromatic shifts in fluorescence microscopic images
GNU General Public License v2.0
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arrayIO missing? #28

Open tschoonj opened 2 years ago

tschoonj commented 2 years ago

Hi,

I am trying to create a conda package out of Chromagnon, but I keep running into trouble with arrayIO, which appears to be missing?

I keep seeing errors like:

$ chromagnon
 * couldn't load module(s):    P
Traceback (most recent call last):
  File "/usr/local/Caskroom/miniconda/base/bin/chromagnon", line 6, in <module>
    from Chromagnon.chromagnon import command_line
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/Chromagnon/__init__.py", line 12, in <module>
    from . import version, cutoutAlign, alignfuncs, chromformat, aligner, threads, chromagnon
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/Chromagnon/alignfuncs.py", line 7, in <module>
    from Chromagnon import imgio
  File "/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/Chromagnon/imgio/__init__.py", line 8, in <module>
    from . import generalIO, mrcIO, imgSeqIO, multitifIO, bioformatsIO, arrayIO
ImportError: cannot import name 'arrayIO' from partially initialized module 'Chromagnon.imgio' (most likely due to a circular import) (/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/Chromagnon/imgio/__init__.py)

Any thoughts?

Thanks!

macronucleus commented 2 years ago

I am sorry for getting this error. This is because I did not update setup.py for long time. I have updated setup.py and some files in imgio. Please try v0.90. If this version did not work for you, please feel free to post here again.