Your message dated Sun, 04 Dec 2022 20:41:50 +0000
with message-id <[email protected]>
and subject line Bug#1009118: fixed in python-biopython 1.80+dfsg-2
has caused the Debian Bug report #1009118,
regarding python3-biopython: incompatible with muscle >= 5
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1009118: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009118
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: python3-biopython
Severity: important
Tags: upstream
Hello,
python3-biopython is incompatible with muscle >= 5. Upstream tests
detect this incompatibility:
======================================================================
ERROR: test_Muscle_profile_simple (test_Muscle_tool.MuscleApplication)
Simple round-trip through app doing a profile alignment.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_Muscle_tool.py",
line 133, in test_Muscle_profile_simple
output, error = cmdline()
File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py",
line 574, in __call__
raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
Bio.Application.ApplicationError: Non-zero return code 1 from 'muscle
-out Fasta/temp_align_out3.fa -profile -in1 Fasta/fa01 -in2 Fasta/f001',
message 'Invalid command line'
(only one failing test is shown for brevity)
However, tests with muscle are skipped as the build system is unable to
detect newer muscle. I attach a patch prodding the build system to run
muscle tests. Normally I would push such patch to cause FTBFS for
package, but now I think failures of integration with muscle should not
cause AUTORM for Biopython. Nevertheless, I think this should be fixed
for bookworm.
Andrius--- a/Tests/test_Muscle_tool.py
+++ b/Tests/test_Muscle_tool.py
@@ -49,14 +49,13 @@
if muscle_exe:
break
else:
- from subprocess import getoutput
+ from subprocess import getstatusoutput
- output = getoutput("muscle -version")
+ exitcode, _ = getstatusoutput("muscle -version")
# Since "not found" may be in another language, try and be sure this is
# really the MUSCLE tool's output
- if "not found" not in output and "not recognized" not in output:
- if "MUSCLE" in output and "Edgar" in output:
- muscle_exe = "muscle"
+ if exitcode == 0:
+ muscle_exe = "muscle"
if not muscle_exe:
raise MissingExternalDependencyError(
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.80+dfsg-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated python-biopython
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 04 Dec 2022 19:15:42 +0100
Source: python-biopython
Architecture: source
Version: 1.80+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1009118 1022307
Changes:
python-biopython (1.80+dfsg-2) unstable; urgency=medium
.
* d/NEWS: fix typo in news item.
* d/control: bring back t_coffee tests since upstream version revert.
Closes: #1022307
* d/control: restore muscle3 instead of plain muscle (version 5).
Closes: #1009118
* port_tutorial_to_muscle3.patch: add; fix doctest failures.
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