Bug 1808737 - python-biopython fails to build with Python 3.9: Element.getiterator() is gone
Summary: python-biopython fails to build with Python 3.9: Element.getiterator() is gone
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: python-biopython
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Antonio T. (sagitter)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-02-29 19:46 UTC by Miro Hrončok
Modified: 2020-03-02 13:40 UTC (History)
10 users (show)

Fixed In Version:
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Environment:
Last Closed: 2020-03-02 13:40:04 UTC
Type: Bug
Embargoed:


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System ID Private Priority Status Summary Last Updated
Github biopython biopython pull 2774 0 None open Use iter instead of getiterator for Python 3.9 compatibility. 2020-03-01 10:56:14 UTC

Description Miro Hrončok 2020-02-29 19:46:36 UTC
python-biopython fails to build with Python 3.9.0a4.

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Traceback (most recent call last):
  File "/builddir/build/BUILD/python-biopython-1.76/python3/Tests/common_BioSQL.py", line 1226, in test_ambiguous_location
    self.assertTrue(self.db.load(seqiter) == 1)
  File "/builddir/build/BUILD/python-biopython-1.76/python3/build/lib.linux-x86_64-3.9/BioSQL/BioSeqDatabase.py", line 936, in load
    for cur_record in record_iterator:
  File "/builddir/build/BUILD/python-biopython-1.76/python3/build/lib.linux-x86_64-3.9/Bio/SeqIO/UniprotIO.py", line 96, in UniprotIterator
    yield Parser(
  File "/builddir/build/BUILD/python-biopython-1.76/python3/build/lib.linux-x86_64-3.9/Bio/SeqIO/UniprotIO.py", line 584, in parse
    _parse_comment(element)
  File "/builddir/build/BUILD/python-biopython-1.76/python3/build/lib.linux-x86_64-3.9/Bio/SeqIO/UniprotIO.py", line 289, in _parse_comment
    for text_element in element.getiterator(NS + "text"):
AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getiterator'
----------------------------------------------------------------------

See https://docs.python.org/3.9/whatsnew/3.9.html#removed

"Methods getchildren() and getiterator() in the ElementTree module have been removed. They were deprecated in Python 3.2. Use functions list() and iter() instead. The xml.etree.cElementTree module has been removed." 


For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01266452-python-biopython/

For all our attempts to build python-biopython with Python 3.9, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/python-biopython/

Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.9:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/

Let us know here if you have any questions.

Python 3.9 will be included in Fedora 33. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.9.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon.
We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 Karthikeyan Singaravelan 2020-03-01 05:30:52 UTC
Upstream PR : https://github.com/biopython/biopython/pull/2774

Comment 2 Antonio T. (sagitter) 2020-03-01 16:00:25 UTC
Fixed on Rawhide with current release 1.76-3


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