[Debian-med-packaging] Bug#944242: Test issues with BioPython 1.75

[Peter Cock]

It seems we have some invalid doctests in the C code (which might
reveal a bug or two, but are mostly likely harmless oversights).
There is some key difference in your build setup and our continuous
integration which is not looking at the C code's docstests:

https://github.com/biopython/biopython/issues/2350

Peter


Peter

On Tue, Nov 19, 2019 at 10:25 PM Andreas Tille <andreas at fam-tille.de> wrote:
>
> On Tue, Nov 19, 2019 at 10:03:25AM +0000, Peter Cock wrote:
> >
> > Do you have a list of things still depending on Biopython & Python 2.7
> > handy? We're discussing when exactly to drop Python 2.7 support -
> > with a final compatible release in December 2019 or January 2020
> > looking most likely.
>
> Speaking about droping Python2 and just running tests with Python3
> I was running into other errors:
>
> ======================================================================
> FAIL: kmedoids (Bio.Cluster._cluster)
> Doctest: Bio.Cluster._cluster.kmedoids
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python3.8/doctest.py", line 2196, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for Bio.Cluster._cluster.kmedoids
>   File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line unknown line number, in kmedoids
>
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.kmedoids
> Failed example:
>     distance = array([[0.0, 1.1, 2.3],
>                       [1.1, 0.0, 4.5],
>                       [2.3, 4.5, 0.0]])
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.kmedoids[0]>", line 1, in <module>
>         distance = array([[0.0, 1.1, 2.3],
>     NameError: name 'array' is not defined
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.kmedoids
> Failed example:
>     distance = array([1.1, 2.3, 4.5])
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.kmedoids[1]>", line 1, in <module>
>         distance = array([1.1, 2.3, 4.5])
>     NameError: name 'array' is not defined
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.kmedoids
> Failed example:
>     distance = [array([]),
>                 array([1.1]),
>                 array([2.3, 4.5])]
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.kmedoids[2]>", line 1, in <module>
>         distance = [array([]),
>     NameError: name 'array' is not defined
>
>
> ======================================================================
> FAIL: pca (Bio.Cluster._cluster)
> Doctest: Bio.Cluster._cluster.pca
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python3.8/doctest.py", line 2196, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for Bio.Cluster._cluster.pca
>   File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line unknown line number, in pca
>
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.pca
> Failed example:
>     columnmean + dot(coordinates, pc)
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.pca[0]>", line 1, in <module>
>         columnmean + dot(coordinates, pc)
>     NameError: name 'columnmean' is not defined
>
>
> ======================================================================
> FAIL: treecluster (Bio.Cluster._cluster)
> Doctest: Bio.Cluster._cluster.treecluster
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python3.8/doctest.py", line 2196, in runTest
>     raise self.failureException(self.format_failure(new.getvalue()))
> AssertionError: Failed doctest test for Bio.Cluster._cluster.treecluster
>   File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line unknown line number, in treecluster
>
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.treecluster
> Failed example:
>     distance = array([[0.0, 1.1, 2.3],
>                       [1.1, 0.0, 4.5],
>                       [2.3, 4.5, 0.0]])
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.treecluster[0]>", line 1, in <module>
>         distance = array([[0.0, 1.1, 2.3],
>     NameError: name 'array' is not defined
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.treecluster
> Failed example:
>     distance = array([1.1, 2.3, 4.5])
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.treecluster[1]>", line 1, in <module>
>         distance = array([1.1, 2.3, 4.5])
>     NameError: name 'array' is not defined
> ----------------------------------------------------------------------
> File "/build/python-biopython-1.75+dfsg/.pybuild/cpython3_3.8/build/Bio/Cluster/_cluster.cpython-38-x86_64-linux-gnu.so", line ?, in Bio.Cluster._cluster.treecluster
> Failed example:
>     distance = [array([]),
>                 array([1.1]),
>                 array([2.3, 4.5])]
> Exception raised:
>     Traceback (most recent call last):
>       File "/usr/lib/python3.8/doctest.py", line 1328, in __run
>         exec(compile(example.source, filename, "single",
>       File "<doctest Bio.Cluster._cluster.treecluster[2]>", line 1, in <module>
>         distance = [array([]),
>     NameError: name 'array' is not defined
>
>
> ----------------------------------------------------------------------
> Ran 521 tests in 210.480 seconds
>
> FAILED (failures = 1)
>
>
> Kind regards
>
>       Andreas.
>
> --
> http://fam-tille.de