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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