I decided to try patching the test but I now realise that test_Wise.py
is not actually the problem. In fact since I don't have the WISE2
software installed that test is skipped. The actual test is in the doc
string of the module.
"""
>>> os.environ["WISE_KBYTE"]="300000"
>>> _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), "/tmp/
output", kbyte=100000)
'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output'
>>> _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), "/tmp/
output_aa")
'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa'
"""
I could change the doc string but that doesn't make sense as it is
correct in the expected context. Which brings me back to ignoring the
test. I could make the message clear about what the test should give.
The downside is that it requires a person to check it. On the other
hand, I would guess that the optional package is normally installed
manually and so would be seen. BTW the test does not throw a signal
that the bash script is looking for and so the install proceeds in any
case.
Adam
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