One alternative would be to patch the test_Wise.py file so that
instead of
self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000
seq1.fna seq2.fna"))
within test_dnal we'd have
self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000")
and similarly for test_psw. That would have the advantage of actually
testing those functions instead of always ignoring problems with
them. But perhaps there is a more sophisticated solution without
patching; unfortunately I'm not a bash expert either.
-Marshall
On Oct 9, 10:05 am, MaxTheMouse <maxthemo...@googlemail.com> wrote:
> Hi all,
>
> I am playing around with the new biopython spkg (1.52). In particular,
> I would like to have a spkg-check script to run the included tests.
> This mostly works and the test skips testing modules that are not
> installed. I am having one problem however. I get a failure with one
> test.
>
> ======================================================================
> FAIL: Doctest: Bio.Wise._build_align_cmdline
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File ".../download/sage-4.1.2.rc0/local/lib/python/doctest.py", line
> 2145, in runTest
> raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for Bio.Wise._build_align_cmdline
> File ".../download/sage-4.1.2.rc0/spkg/build/biopython-1.52/src/
> build/lib.linux-i686-2.6/Bio/Wise/__init__.py", line 23, in
> _build_align_cmdline
>
> ----------------------------------------------------------------------
> File ".../download/sage-4.1.2.rc0/spkg/build/biopython-1.52/src/build/
> lib.linux-i686-2.6/Bio/Wise/__init__.py", line 26, in
> Bio.Wise._build_align_cmdline
> Failed example:
> _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), "/tmp/
> output", kbyte=100000)
> Expected:
> 'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output'
> Got:
> 'dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/output'
> ----------------------------------------------------------------------
> File ".../download/sage-4.1.2.rc0/spkg/build/biopython-1.52/src/build/
> lib.linux-i686-2.6/Bio/Wise/__init__.py", line 28, in
> Bio.Wise._build_align_cmdline
> Failed example:
> _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), "/tmp/
> output_aa")
> Expected:
> 'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa'
> Got:
> 'psw -kbyte 300000 -quiet seq1.faa seq2.faa > /tmp/output_aa'
>
> ----------------------------------------------------------------------
>
> The reason is that there is an "if not os.isatty(sys.stderr.fileno
> ()):" test in the function that adds a -quiet to the string. This test
> passes if the script runs directly from the command line but fails
> when using 'sage -f'.
>
> I am not sure what can be done to change this as I am not a bash
> expert. My simple solution would be to just add a message like "Note:
> There is one expected failure with Doctest:
> Bio.Wise._build_align_cmdline. Other test failures should be
> examined." and continue. This fail is purely an artifact of how the
> testing takes place. However, if there is a better solution than I
> would like to do that.
>
> Cheers,
> Adam
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