[Biopython] BioPython unit tests: Tutorial

[Peter Cock]

Hi Andreas,

Python doctests are fragile because the do exact string
matching of the command and its output. Normally the
docstrings live inside the Python source code within the
module comments as documentation. Here the doctests
are embedded within our LaTeX tutorial.

To get more information, try - probably after installing
Biopython:

$ cd Tests/
$ python test_Tutorial.py

Peter



On Wed, Sep 23, 2015 at 1:42 PM, Andreas Tille <andreas at an3as.eu> wrote:
> Hi,
>
> I try to activate all possible tests of BioPython at Debian package
> build time but I found some issues.  I will discuss these in separate
> mails, starting with test_Tutorial and python2.7:
>
> ======================================================================
> ERROR: test_doctests (test_Tutorial.TutorialTestCase)
> Run tutorial doctests.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Tutorial.py", line 175, in test_doctests
>     (len(failures), ", ".join(failures)))
> ValueError: 23 Tutorial doctests failed: test_chapter_align_line_00074, test_chapter_align_line_00097, test_chapter_align_line_00645, test_chapter_align_line_00814, test_chapter_align_line_00976, test_chapter_align_line_00996, test_chapter_align_line_01240, test_chapter_cookbook_line_01492, test_chapter_phylo_line_00040, test_chapter_phylo_line_00074, test_chapter_searchio_line_00126, test_chapter_searchio_line_00485, test_chapter_searchio_line_00642, test_chapter_searchio_line_00928, test_chapter_seqio_line_00289, test_chapter_seqio_line_00300, test_chapter_seqio_line_00311, test_chapter_seqio_line_00522, test_chapter_seqio_line_00641, test_chapter_seqio_line_00674, test_chapter_seqio_line_00864, test_chapter_seqio_line_00883, test_chapter_seqio_line_01124
>
> ----------------------------------------------------------------------
>
> Unfortunately I have no idea how to deal with this.  Any hint?
>
> Kind regards
>
>         Andreas.
>
> --
> http://fam-tille.de