[Debian-med-packaging] Bug#1064147: ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO

[Étienne Mollier]

Source: python-biopython
Version: 1.81+dfsg-3
Severity: serious
Tags: ftbfs
Justification: ftbfs

While trying to pinpoint the root cause of test failures in the
packaging attempt of Biopython 1.83, I eventually realized that
the version 1.81 of Biopython is also affected by the same
issues.  The relevant part of the test log looks like:

	======================================================================
	ERROR: test_embl7 (test_SeqIO.TestSeqIO.test_embl7)
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 3388, in test_embl7
	    self.perform_test(
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626, in perform_test
	    self.check_simple_write_read(
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363, in check_simple_write_read
	    records2 = list(SeqIO.parse(handle=handle, format=fmt))
	               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line 72, in __next__
	    return next(self.records)
	           ^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 447, in iterate
	    parser.close()
	  File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
	    self.feed(b"", isFinal=True)
	  File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
	    self._parser.Parse(data, isFinal)
	  File "../Modules/pyexpat.c", line 416, in StartElement
	  File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in start_element_ns
	    self._cont_handler.startElementNS(pair, None,
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 163, in startEntryFieldElement
	    return self.startPropertyElement(attrs)
	           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 339, in startPropertyElement
	    record = self.records[-1]
	             ~~~~~~~~~~~~^^^^
	IndexError: list index out of range
	
	======================================================================
	ERROR: test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8)
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 2785, in test_genbank8
	    self.perform_test(
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 626, in perform_test
	    self.check_simple_write_read(
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 363, in check_simple_write_read
	    records2 = list(SeqIO.parse(handle=handle, format=fmt))
	               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line 72, in __next__
	    return next(self.records)
	           ^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 447, in iterate
	    parser.close()
	  File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
	    self.feed(b"", isFinal=True)
	  File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
	    self._parser.Parse(data, isFinal)
	  File "../Modules/pyexpat.c", line 416, in StartElement
	  File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in start_element_ns
	    self._cont_handler.startElementNS(pair, None,
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 163, in startEntryFieldElement
	    return self.startPropertyElement(attrs)
	           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 339, in startPropertyElement
	    record = self.records[-1]
	             ~~~~~~~~~~~~^^^^
	IndexError: list index out of range

I haven't checked but I heavily suspect that this is causing
also autopkgtest failures.

For information,
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/0, please excuse my verbosity
   `-
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