[Biopython-dev] [Bug 2469] New: requires_wise.py fails on Windows (test suite)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2469

           Summary: requires_wise.py fails on Windows (test suite)
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


On my Windows XP machine, I don't have wise installed, so the dnal command
doesn't work:

C:\TEMP\>dnal
'dnal' is not recognized as an internal or external command,
operable program or batch file.

When running the unit test suite, test_Wise.py SHOULD fail with a missing
external dependency error - instead it tries to run with a failed assertion
error.  The problem is requires_wise.py fails... which seems to be an issue
with the commands.getoutput() function not working on Windows, its unix only
according to:

http://www.python.org/doc/current/lib/module-commands.html

Annoyingly, the commands module is present on Windows (or at least Python 2.3)
but simply doesn't work due to calling this:

os.popen('{ ' + cmd + '; } 2>&1', 'r')

As a result,

>>> commands.getoutput("xyz")
"'{' is not recognized as an internal or external command,\noperable program or
batch file."

Assuming wise/dnal actually works on Windows, we need to use something other
than commands.getoutput("dnal") to check for it.


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