Bug 1852635 - python-scikit-image is broken with Python 3.9
Summary: python-scikit-image is broken with Python 3.9
Keywords:
Status: CLOSED NOTABUG
Alias: None
Product: Fedora
Classification: Fedora
Component: python-scikit-image
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Sergio Pascual
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-07-01 00:19 UTC by Elliott Sales de Andrade
Modified: 2020-07-08 13:50 UTC (History)
4 users (show)

Fixed In Version: python3.9-3.9.0~b4-1.fc33
Doc Type: If docs needed, set a value
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Clone Of:
Environment:
Last Closed: 2020-07-08 13:50:23 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Elliott Sales de Andrade 2020-07-01 00:19:13 UTC
All tests fail like so:
____________ ERROR collecting segmentation/tests/test_boundaries.py ____________
ImportError while importing test module '/builddir/build/BUILDROOT/python-scikit-image-0.16.2-4.fc33.x86_64/usr/lib64/python3.9/site-packages/skimage/segmentation/tests/test_boundaries.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
skimage/segmentation/tests/__init__.py:1: in <module>
    from ..._shared.testing import setup_test, teardown_test
skimage/_shared/testing.py:22: in <module>
    from .. import data, io
skimage/io/__init__.py:7: in <module>
    from .manage_plugins import *
skimage/io/manage_plugins.py:24: in <module>
    from .collection import imread_collection_wrapper
skimage/io/collection.py:13: in <module>
    from ..external.tifffile import TiffFile
skimage/external/tifffile/__init__.py:1: in <module>
    from .tifffile import imsave, imread, imshow, TiffFile, TiffWriter, \
skimage/external/tifffile/tifffile.py:285: in <module>
    from xml.etree import cElementTree as etree
E   ImportError: cannot import name 'cElementTree' from 'xml.etree' (/usr/lib64/python3.9/xml/etree/__init__.py)

except test failures are ignored, so the build is 'fine'.


Version-Release number of selected component (if applicable):
python-scikit-image-0.16.2-4.fc33


Steps to Reproduce:
1. fedpkg clone python-scikit-image
2. fedpkg mockbuild

Or

1. mock -r fedora-rawhide-x86_64 --install python3-scikit-image
2. mock -r fedora-rawhide-x86_64 --shell
3. python3 -c 'import skimage.io'

Actual results:
See above.


Expected results:
Imports and tests work.

Comment 1 Miro Hrončok 2020-07-01 00:35:45 UTC
"The xml.etree.cElementTree module has been removed, use the xml.etree.ElementTree module instead. Since Python 3.3 the xml.etree.cElementTree module has been deprecated, the xml.etree.ElementTree module uses a fast implementation whenever available."

However, this change in Python was recently reverted and will be gone in next beta (scheduled for 2020-06-29 but not yet released).

Comment 2 Charalampos Stratakis 2020-07-07 16:04:20 UTC
There is a new version out (17.2) now which might be fixing some of the issues, however it requires a new dependency to be packaged which was bundled before (tifffile).


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