Source: umis
Version: 1.0.9-1
Severity: serious
Justification: superficial-autopkgtest
Hi,
While looking at umis to tackle Python SyntaxWarnings, I ended
up realizing that it is affected by a couple of tracebacks which
should normally be fatal:
Traceback (most recent call last):
File "/usr/bin/umis", line 33, in <module>
sys.exit(load_entry_point('umis==1.0.9', 'console_scripts', 'umis')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/umis/umis.py", line 299, in fastqtransform
read1_dict['MB'] = read1_dict['MB1'] + read1_dict['MB2']
~~~~~~~~~~^^^^^^^
KeyError: 'MB1'
and:
Traceback (most recent call last):
File "/usr/bin/umis", line 33, in <module>
sys.exit(load_entry_point('umis==1.0.9', 'console_scripts', 'umis')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/umis/umis.py", line 502, in tagcount
cb_hist = pd.read_csv(cb_histogram, index_col=0, header=None, squeeze=True, sep="\t")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: read_csv() got an unexpected keyword argument 'squeeze'
autopkgtest is currently passing though, because due to missing
option -e, the test unfolds despite errors, and a scripting bug
in the data consistency check at the end of the script gets it
to be routed straight through the "Tests passed" code path:
test.sh: 198: [: Files: unexpected operator
Tests passed.
autopkgtest [20:07:46]: test run-unit-test: -----------------------]
I may have a closer look at this in the upcoming weekend, but if
not, at least let's leave a target open for the ongoing Advent
Calendar Bug Squashing Party. ;)
Have a nice day, :)
The issues was reported upstream two years ago and I have pinged the issue. (No response so far.)
We believe that the bug you reported is fixed in the latest version of
umis, 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 1089115@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated umis 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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Tue, 20 Oct 2026 14:22:30 +0200
Source: umis
Architecture: source
Version: 1.0.9-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1089115 1134417
Changes:
umis (1.0.9-3) unstable; urgency=medium
.
* d/watch: version=5
* Standards-Version: 4.7.4 (routine-update)
* Reformat the Last-Update date as ISO YYYY-MM-DD.
* Remove redundant Priority: optional from source stanza.
* Remove Rules-Requires-Root: no
* Fix dual index and dual UMI support (KeyError: 'MB1' in fastqtransform)
* Make test script fail on errors and fix result comparison
Closes: #1089115, #1134417
Checksums-Sha1:
44edc25d790e507be9b9a84bae631f97e54154bc 2110 umis_1.0.9-3.dsc
eb36b72143c76a0560e5fe1e229e2a910ac9c63d 7040 umis_1.0.9-3.debian.tar.xz
134fdbc591e4cf9899cad789b25c4b4400adaf5b 7936 umis_1.0.9-3_amd64.buildinfo
Checksums-Sha256:
284f0d8b057dbfcb25f64510f3b9b1f885438a725a75a15eacefad8290e855bb 2110 umis_1.0.9-3.dsc
e9e5464704719decac8923f29efc2aa0e771df28b2ba51437e46e81903d3b77c 7040 umis_1.0.9-3.debian.tar.xz
25abe3c0e1e6eb03f173628efc288562b652aeb44ef585141eee7551fb039bb3 7936 umis_1.0.9-3_amd64.buildinfo
Files:
b8c4df159c6af3ea62caf81c99c6f1e3 2110 science optional umis_1.0.9-3.dsc
f5ff98de1cbd58cfd23913f759ae5723 7040 science optional umis_1.0.9-3.debian.tar.xz
2d4191a45b72b46c1b81d7d47da317d7 7936 science optional umis_1.0.9-3_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=01Vv
-----END PGP SIGNATURE-----