Source: igdiscover
Version: 0.11-3
Severity: important
User: [email protected]
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
