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, :)
--
.''`. Étienne Mollier <[email protected]>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/2, please excuse my verbosity
`- on air: Cloverseeds - Avalon
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