[Debian-med-packaging] Bug#1089115: umis: tracebacks normally fatal during autopkgtest runs

[Étienne Mollier]

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 <emollier at debian.org>
 : :' :  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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