There is an #optional directive one can pyt on doctests so they get
run (and output tested) only if the user has installed the package.
Sounds like that's what we should be using here.
- Robert
On Oct 10, 2009, at 6:20 AM, MaxTheMouse wrote:
> 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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