[Biopython-dev] Re: Post Biopython 1.62 release, clean-up after dropping Python 2.5

Sergei Lebedev superbobry at gmail.com
Fri Aug 30 13:28:50 UTC 2013

Sure, a common pattern for a lot of BioPython modules seems to be:

    # +from __future__ import print_function

    def foo():
        """A docstring with print statement.

        >>> print "foo"
        print "Running foo ..."
        # +print("Running foo ...")

    if __name__ == "__main__":
        import doctest

where foo is some function, which uses print statement in its body. Since we want to switch from print statements to print function we replace print "Running foo ..." with a print() call and add from __future__ import ... to the beginning of the module. 

What happens if we try to run the doctests after we've switched to print_function?

    $ python /tmp/foo.py
    File "/tmp/foo.py", line 7, in __main__.foo
    Failed example:
        print "foo"
    Exception raised:
        Traceback (most recent call last):
          File ".../doctest.py", line 1254, in __run
            compileflags, 1) in test.globs
          File "<doctest __main__.foo[0]>", line 1
            print "foo"
        SyntaxError: invalid syntax
    1 items had failures:
       1 of   1 in __main__.foo
    ***Test Failed*** 1 failures.

So, enabling print_function makes doctests using print statement fail with a SyntaxError, as shown by the example above. Thus, if we want to get rid of print statement in the code we have no other choice but to do the same it in the doctests.


On August 30, 2013 at 5:14:14 PM, Peter Cock (p.j.a.cock at googlemail.com) wrote:

On Fri, Aug 30, 2013 at 1:58 PM, Sergei Lebedev <superbobry at gmail.com> wrote:  
>> (8) Excluding doctests and the Tutorial, use print function  
>> rather than print statement. e.g. replace this:  
> Unfortunately we cannot exclude doctests, because 'from __future__' import  
> is module wide, thus the 'doctest.testmod()' will raise a SyntaxError on  
> docstrings with print statement.  
> Sergei  

Could you clarify this? Does this cause a problem via:  

[Tests]$ python run_tests.py doctest  

If you have a small example, copy & paste the "git diff" output here.  

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