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'
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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 1Karthikeyan Singaravelan
2020-03-01 05:30:52 UTC
python-biopython fails to build with Python 3.9.0a4. ---------------------------------------------------------------------- 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.