Control: tags -1 + upstream patch Hi Santiago,
Thanks for your report! Concerning the main issue of the entry,
it looks to be caused by a change in bwa 0.7.19, uploaded in sid
last month. I managed to get somewhere with this workaround:
-------8<--------------8<--------------8<--------------8<-------
--- python-biopython.orig/Tests/test_BWA_tool.py
+++ python-biopython/Tests/test_BWA_tool.py
@@ -161,7 +161,7 @@
with open(self.samfile1) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput
starts:{headline}",
)
@@ -184,7 +184,7 @@
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput
starts:{headline}",
)
@@ -201,7 +201,7 @@
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ" or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput
starts:{headline}",
)
-------8<--------------8<--------------8<--------------8<-------
Regarding your secondary remark:
> Note: In addition to this package failing to build in unstable six
> days ago, it also fails to build in bookworm right now.
the relevant part of the symptoms is different:
self.perform_test(
File
"/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py",
line 631, in perform_test
self.check_simple_write_read(
File
"/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py",
line 367, in check_simple_write_read
records2 = list(SeqIO.parse(handle=handle, format=fmt))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py",
line 72, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py",
line 448, 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
"/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py",
line 164, in startEntryFieldElement
return self.startPropertyElement(attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py",
line 340, in startPropertyElement
record = self.records[-1]
~~~~~~~~~~~~^^^^
IndexError: list index out of range
The issue does ring a bell though and I believe it stems from
Debian 12.12's libxml2 upgrade to address a few CVEs, as
documented in the official announcement[1].
[1]: https://lists.debian.org/debian-stable-announce/2025/09/msg00001.html
Have a nice day, :)
--
.''`. Étienne Mollier <[email protected]>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/3, please excuse my verbosity
`-
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