[Biopython-dev] docstring tests

[Bruce Southey]

Michiel de Hoon wrote:
> Thanks for the patch. I've updated run_tests.py along these lines, and I added an option "doctest" to specify running the doctests:
>
> $ python run_tests.py doctest
> Bio.Seq docstring test ... ok
> Bio.SeqRecord docstring test ... ok
> Bio.SeqIO docstring test ... ok
> Bio.Align.Generic docstring test ... ok
> Bio.AlignIO docstring test ... ok
> Bio.KEGG.Compound docstring test ... ok
> Bio.KEGG.Enzyme docstring test ... ok
> Bio.Wise docstring test ... ok
> Bio.Wise.psw docstring test ... ok
> Bio.Statistics.lowess docstring test ... ok
> ----------------------------------------------------------------------
> Ran 10 tests in 0.726 seconds
>
>
>
>
> --- On Thu, 2/12/09, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
>   
>> From: Peter <biopython at maubp.freeserve.co.uk>
>> Subject: Re: [Biopython-dev] docstring tests
>> To: mjldehoon at yahoo.com
>> Cc: biopython-dev at biopython.org
>> Date: Thursday, February 12, 2009, 6:49 AM
>> Hi Michiel (and everyone else),
>>
>> I was wondering about how the doctests are currently
>> integrated into
>> run_tests.py, and wondered if this patch makes things more
>> concise?
>> This patch is against run_tests.py CVS revision 1.22,
>> essentially it
>> adds the doctest modules to the list of tests - rather than
>> as a
>> separate list.  The code becomes slightly shorter, but I am
>> not sure
>> if this is actually clearer or not.
>>
>> Note - this does not address the issue of how to run just
>> the doctests
>> - something I think is very useful when working on them.
>>
>> Peter
>>
>> $ diff run_tests.py run_tests2.py
>> 209,211c209
>> <         if self.tests:
>> <             self.doctest_modules = []
>> <         else:
>> ---
>>     
>>>         if not self.tests:
>>>       
>> 218c216,222
>> <             self.doctest_modules = DOCTEST_MODULES
>> ---
>>     
>>>             if sys.version_info[:2] < (2, 4):
>>>                 #On python 2.3, doctest uses slightly
>>>       
>> different formatting
>>     
>>>                 #which would be a problem as the
>>>       
>> expected output won't match.
>>     
>>>                 #Also, it can't cope with
>>>       
>> <BLANKLINE> in a doctest string.
>>     
>>>                 sys.stderr.write("Skipping
>>>       
>> doctests which require Python 2.4+\n")
>>     
>>>             else :
>>>                 self.tests.extend(DOCTEST_MODULES)
>>>       
>> 234,240c238,253
>> <                 module = __import__(name)
>> <                 suite =
>> unittest.TestLoader().loadTestsFromModule(module)
>> <                 if suite.countTestCases()==0:
>> <                     # This is a print-and-compare test
>> instead of a unittest-
>> <                     # type test.
>> <                     test = ComparisonTestCase(name,
>> output)
>> <                     suite = unittest.TestSuite([test])
>> ---
>>     
>>>                 if "." in name :
>>>                     #Its a doc test
>>>                     #Can't use
>>>       
>> fromlist=name.split(".") until python 2.5+
>>     
>>>                     module = __import__(name, None,
>>>       
>> None, name.split("."))
>>     
>>>                     suite =
>>>       
>> doctest.DocTestSuite(module)
>>     
>>>                     del module
>>>                 else :
>>>                     #Its a unittest (or a
>>>       
>> print-and-compare test)
>>     
>>>                     suite =
>>>       
>> unittest.TestLoader().loadTestsFromName(name)
>>     
>>>                     if suite.countTestCases()==0:
>>>                         # This is a print-and-compare
>>>       
>> test instead of a
>>     
>>>                         # unittest-type test.
>>>                         test =
>>>       
>> ComparisonTestCase(name, output)
>>     
>>>                         suite =
>>>       
>> unittest.TestSuite([test])
>> 263,277d275
>> <     def runDocTest(self, name):
>> <         #Can't use
>> fromlist=name.split(".") until python 2.5+
>> <         module = __import__(name, None, None,
>> name.split("."))
>> <         sys.stderr.write("%s docstring test ...
>> " % module.__name__)
>> <         suite = doctest.DocTestSuite(module)
>> <         result = self._makeResult()
>> <         suite.run(result)
>> <         if result.wasSuccessful():
>> <             sys.stderr.write("ok\n")
>> <             return True
>> <         else:
>> <             sys.stderr.write("FAIL\n")
>> <             result.printErrors()
>> <             return False
>> <
>> 287,297d284
>> <         if sys.version_info[:2] < (2, 4):
>> <             #On python 2.3, doctest uses slightly
>> different formatting
>> <             #which would be a problem as the expected
>> output won't match.
>> <             #Also, it can't cope with
>> <BLANKLINE> in a doctest string.
>> <             sys.stderr.write("Docstring tests
>> require Python 2.4 or
>> later; skipping\n")
>> <         else:
>> <             for test in self.doctest_modules:
>> <                 ok = self.runDocTest(test)
>> <                 if not ok:
>> <                     failures += 1
>> <                 total += 1
>>     
>
>
>       
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>   
Hi,
At present 'python setup.py test'  does do all the tests including the 
doctests. Just curious, will you also add the ability to select the 
doctests there as well?

Bruce