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

[Andreas Tille]

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