[Debian-med-packaging] Bug#977067: igdiscover FTBFS with pytest 6

[Christian Kastner]

Source: igdiscover
Version: 0.11-3
Severity: important
User: pytest at packages.debian.org
Usertags: pytest-v6

Hi,

igdiscover FTBFS with pytest 6 in experimental.

The error log below has more details.

> I: pybuild base:232: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_igdiscover/build; python3.9 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.9.1, pytest-6.0.2, py-1.9.0, pluggy-0.13.0
> rootdir: /<<PKGBUILDDIR>>, configfile: setup.cfg
> collected 36 items
> 
> tests/test_cluster.py ..                                                 [  5%]
> tests/test_commands.py .....                                             [ 19%]
> tests/test_merger.py ............                                        [ 52%]
> tests/test_parse.py .                                                    [ 55%]
> tests/test_species.py FFF                                                [ 63%]
> tests/test_trie.py .....                                                 [ 77%]
> tests/test_utils.py F.......                                             [100%]
> 
> =================================== FAILURES ===================================
> __________________________ test_cdr3_detection_heavy ___________________________
> 
>     def test_cdr3_detection_heavy():
>     	heavy = """
>     	ARRLHSGSYILFDY CAGGTGACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGTATGGGTGTGGGCTGGATCCGTCAGCCCTCACGGAAGACCCTGGAGTGGCTTGCACACATTTATTGGAATGATGATAAATACTACAGCACATCGCTGAAGAGCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTTCTAACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACGGAGACTTCATAGTGGGAGCTACATTCTCTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGA
>     
>     	ARIKWLRSPGYGYFDF CAGGTGACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAGACCCACACAGACCCTCACTCTGACCTGCACCTTCTCTGGGTTCTCAATCAGCACCTCTGGAACAGGTGTGGGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAATGGCTTGCAAGCATTTATTGGACTGATGCTAAATACTATAGCACATCGCAGAAGAGCAGGCTCACCATCTCCAAGGACACCTCCAGAAACCAGGTGATTCTAACAATGACCAACATGGAGCCTGTGGACATAGCCACATATTTCTGTGCACGGATAAAGTGGCTGCGGTCCCCAGGCTATGGATACTTCGATTTCTGGGGCCCTGGCACCCCAATCACCATCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGA
>     
>     	ARHGIAAAGTHNWFDP TCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGGATTACTGTGCGAGACATGGGATAGCAGCAGCTGGTACCCACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGCAGGTTGTT
>     	"""
>>   	assert_cdr3_detection('VH', heavy)
> 
> tests/test_species.py:30: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> 
> chain = 'VH'
> s = '\n\tARRLHSGSYILFDY CAGGTGACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGG...ACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGCAGGTTGTT\n\t'
> 
>     def assert_cdr3_detection(chain, s):
>     	for amino_acids, sequence in split(s):
>     		for offset in range(3):
>     			target = sequence[offset:]
>     			match = find_cdr3(target, chain)
>>   			assert match is not None
> E      assert None is not None
> 
> tests/test_species.py:18: AssertionError
> __________________________ test_cdr3_detection_kappa ___________________________
> 
>     def test_cdr3_detection_kappa():
>     	kappa = """
>     QQYDSSPRT TTCAGTGGCAGTGGAGCAGGGACAGATTTCACTCTCACCATCAGCAGTCTGGAACCTGAGGATGTCGCAACTTACTACTGTCAGCAGTATGATAGCAGCCCCCGGACGTTCGGCGCTGGGACCAAGCTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>     
>     QQYSSYPYT GAGCTGGCCTCGGGAGTCCCAGCTCGCTTCAGTGGGAGTGGGTCAGGGACTTCTTTCTCTCTCACAATCAGCAACGTGGAGGCTGAAGATGTTGCAACCTATTACTGTCAGCAGTATAGCAGTTATCCGTACACGTTCGGCGCAGGGACCAAGCTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>     
>     LQYDSSPYT ATTCTCACCATCAGCAGCCTGCAGCCTGAAGACTTTGCAACTTACTACTGTCTACAGTATGATAGTTCCCCGTACACGTTCGGCGCAGGGACCAAGCTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>     
>     FQYYSGRLT ACAGACTTCACTCTCACCATCAGCAGCCTGCAGCCTGAGGACATTGCAGTTTATTACTGTTTCCAGTATTACAGCGGGAGACTCACGTTCGGAGGAGGGACCCGCTTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>     	"""
>>   	assert_cdr3_detection('VK', kappa)
> 
> tests/test_species.py:43: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> 
> chain = 'VK'
> s = '\nQQYDSSPRT TTCAGTGGCAGTGGAGCAGGGACAGATTTCACTCTCACCATCAGCAGTCTGGAACCTGAGGATGTCGCAACTTACTACTGTCAGCAGTATGATAGCAGCCCCCGG...ACTGTTTCCAGTATTACAGCGGGAGACTCACGTTCGGAGGAGGGACCCGCTTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG\n\t'
> 
>     def assert_cdr3_detection(chain, s):
>     	for amino_acids, sequence in split(s):
>     		for offset in range(3):
>     			target = sequence[offset:]
>     			match = find_cdr3(target, chain)
>>   			assert match is not None
> E      assert None is not None
> 
> tests/test_species.py:18: AssertionError
> __________________________ test_cdr3_detection_lambda __________________________
> 
>     def test_cdr3_detection_lambda():
>     	lambda_ = """
>     LTYHGNSGTFV GGATCCAAAAACCCCTCAGCCAATGCAGGAATTTTGCTCATCTCTGAACTCCAGAATGAGGATGAGGCTGACTATTACTGTCTGACATATCATGGTAATAGTGGTACTTTTGTATTCGGTGGAGGAACCAAGCTGACCGTCCTAGGTCAGCCCAAGTCTGCCCCCACAGTCAGCCTGTTCC
>     
>     QLWDANSTV ATGGCCACACTGACCATCACTGGCGCCCAGGGTGAGGACGAGGCCGACTATTGCTGTCAGTTGTGGGATGCTAACAGTACTGTGTTCGGTGGAGGAACCACGCTGACCGTCCTAGGTCAGCCCAAGTCTGCCCCCACAGTCAGCCTGTTCCCGCCCTCCTC
>     
>     GVGYSGGYV GATCGCTACTTAACCATCTCCAACATCCAGCCTGAAGACGAGGCTGACTATTTCTGTGGTGTGGGTTATAGCGGTGGTTATGTATTCGGTGGAGGAACCAAGTTGACCGTCCTAGGTCAGCCCAAGTCTGCTCCCACAGTCAGCCTGTTCCCGCCCTCCTC
>     	"""
>>   	assert_cdr3_detection('VL', lambda_)
> 
> tests/test_species.py:54: 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> 
> chain = 'VL'
> s = '\nLTYHGNSGTFV GGATCCAAAAACCCCTCAGCCAATGCAGGAATTTTGCTCATCTCTGAACTCCAGAATGAGGATGAGGCTGACTATTACTGTCTGACATATCATGGTAATAGTG...CTATTTCTGTGGTGTGGGTTATAGCGGTGGTTATGTATTCGGTGGAGGAACCAAGTTGACCGTCCTAGGTCAGCCCAAGTCTGCTCCCACAGTCAGCCTGTTCCCGCCCTCCTC\n\t'
> 
>     def assert_cdr3_detection(chain, s):
>     	for amino_acids, sequence in split(s):
>     		for offset in range(3):
>     			target = sequence[offset:]
>     			match = find_cdr3(target, chain)
>>   			assert match is not None
> E      assert None is not None
> 
> tests/test_species.py:18: AssertionError
> ________________________________ test_has_stop _________________________________
> 
>     def test_has_stop():
>>   	assert has_stop('TAA')
> E    AssertionError: assert False
> E     +  where False = has_stop('TAA')
> 
> tests/test_utils.py:11: AssertionError
> =========================== short test summary info ============================
> FAILED tests/test_species.py::test_cdr3_detection_heavy - assert None is not ...
> FAILED tests/test_species.py::test_cdr3_detection_kappa - assert None is not ...
> FAILED tests/test_species.py::test_cdr3_detection_lambda - assert None is not...
> FAILED tests/test_utils.py::test_has_stop - AssertionError: assert False
> ========================= 4 failed, 32 passed in 2.21s =========================
> E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_igdiscover/build; python3.9 -m pytest tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13
> make: *** [debian/rules:8: build] Error 25
> dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2