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