[Debian-med-packaging] Bug#943622: some python-biom-format tests fail with python3.8

[Matthias Klose]

Package: src:python-biom-format
Version: 2.1.7+dfsg-3
Severity: important
Tags: sid bullseye
User: debian-python at lists.debian.org
Usertags: python3.8

======================================================================
ERROR: Test an invalid HDF5 table
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py", 
line 155, in skipper_func
     return f(*args, **kwargs)
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py", 
line 88, in test_invalid_hdf5
     copy(self.hdf5_file_valid, 'invalid.hdf5')
   File "/usr/lib/python3.8/shutil.py", line 409, in copy
     copyfile(src, dst, follow_symlinks=follow_symlinks)
   File "/usr/lib/python3.8/shutil.py", line 259, in copyfile
     with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: 
'/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom'

======================================================================
ERROR: Test a valid HDF5 table
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py", 
line 155, in skipper_func
     return f(*args, **kwargs)
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py", 
line 79, in test_valid_hdf5
     obs = self.cmd(table=self.hdf5_file_valid)
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", 
line 112, in __call__
     return self.run(table=table, format_version=format_version,
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", 
line 78, in run
     is_json = not is_hdf5_file(kwargs['table'])
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/util.py", 
line 518, in is_hdf5_file
     with open(fp, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory: 
'/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom'

======================================================================
ERROR: test_valid_hdf5_metadata_v210 
(biom.tests.test_cli.test_validate_table.TableValidatorTests)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python3/dist-packages/numpy/testing/_private/decorators.py", 
line 155, in skipper_func
     return f(*args, **kwargs)
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_validate_table.py", 
line 62, in test_valid_hdf5_metadata_v210
     obs = self.cmd(table=self.hdf5_file_valid,
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", 
line 112, in __call__
     return self.run(table=table, format_version=format_version,
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/cli/table_validator.py", 
line 78, in run
     is_json = not is_hdf5_file(kwargs['table'])
   File 
"/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/util.py", 
line 518, in is_hdf5_file
     with open(fp, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory: 
'/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build/examples/min_sparse_otu_table_hdf5.biom'

----------------------------------------------------------------------
Ran 336 tests in 4.624s

FAILED (SKIP=1, errors=3)
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd 
/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.8_biom-format/build; 
python3.8 -m nose -v
dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.8 3.7" 
returned exit code 13