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@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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Processing control commands:

forwarded -1 https://github.com/biopython/biopython/issues/4640

Bug #1064147 [src:python-biopython] ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
Set Bug forwarded-to-address to 'https://github.com/biopython/biopython/issues/4640'.

tags -1 + sid

Bug #1064147 [src:python-biopython] ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
Added tag(s) sid.

tags -1 - testing

Unknown tag/s: testing.
Recognized are: patch wontfix moreinfo unreproducible help security upstream pending confirmed ipv6 lfs d-i l10n newcomer a11y ftbfs fixed-upstream fixed fixed-in-experimental sid experimental potato woody sarge sarge-ignore etch etch-ignore lenny lenny-
ignore squeeze squeeze-ignore wheezy wheezy-ignore jessie jessie-ignore stretch stretch-ignore buster buster-ignore bullseye bullseye-ignore bookworm bookworm-ignore trixie trixie-ignore forky forky-ignore.

Bug #1064147 [src:python-biopython] ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
Requested to remove no tags; doing nothing.

--
1064147: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064147
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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So, following discutions with upstream, and quite some
investigation, this turned out to be caused by the migration of
expat from version 2.5 to 2.6. The newer version looks to have
had to introduce breaking changes in order to be able to fix a
security vulnerability.

When looking into expat migration excuses[1], I noted that there
were also test failures affecting Python's xml module[2]. Then,
I had a lookup at open CPython issues, which suggest a change to
address the build failure has landed[3] and will be ready for
upcoming interpreter versions. That being said, looking closely
at the patch, it seems the direction taken was to adjust the
test suite to ignore the affected cases. There don't seem to
have been any changes to the core logic of the xml module. This
suggests it may be necessary to skip the affected tests, at
least for now. Those are only two failures among dozens of
tests, which suggest the SeqXmlIO is in otherwise mostly working
conditions.

[1]: https://qa.debian.org/excuses.php?package=expat
[2]: https://ci.debian.net/packages/p/python3.12/testing/amd64/43764480/
[3]: https://github.com/python/cpython/pull/115289/files

Now pondering a version that has a chance to migrate,
--
.''`. Étienne Mollier <emollier@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/2, please excuse my verbosity
`- on air: Genesis - Turn It on Again

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Processing control commands:

severity -1 normal

Bug #1064147 [src:python-biopython] ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO
Severity set to 'normal' from 'serious'

--
1064147: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064147
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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