Source: ncbi-acc-download Version: 0.2.8-1 Severity: serious Tags: sid bookworm User: debian...@lists.debian.org Usertags: needs-update User: debian-pyt...@lists.debian.org Usertags: python3.11 Control: affects -1 src:python3-defaults
Dear maintainer(s),We are in the transition of adding python3.11 as a supported Python version [0]. With a recent upload of python3-defaults the autopkgtest of ncbi-acc-download fails in testing when that autopkgtest is run with the binary packages of python3-defaults from unstable. It passes when run with only packages from testing. In tabular form:
pass fail
python3-defaults from testing 3.10.6-3
ncbi-acc-download from testing 0.2.8-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of python3-defaults
to testing [1]. https://docs.python.org/3/whatsnew/3.11.html lists
what's new in Python3.11, it may help to identify what needs to be updated.
More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [0] https://bugs.debian.org/1021984 [1] https://qa.debian.org/excuses.php?package=python3-defaults https://ci.debian.net/data/autopkgtest/testing/amd64/n/ncbi-acc-download/28727754/log.gz=================================== FAILURES =================================== __________________________ test_config_have_biopython __________________________
def test_config_have_biopython():
"""Test we detect Biopython."""
assert core.HAVE_BIOPYTHON
E assert False E + where False = core.HAVE_BIOPYTHON test_core.py:46: AssertionError_________________ test_validate_and_write_extended_validation __________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58de410>
def test_validate_and_write_extended_validation(req):
"""Test extended validation before writing."""
handle = StringIO()
req.get('http://fake/', text=u'>foo\nMAGIC')
r = requests.get('http://fake/')
config = core.Config(extended_validation='loads', molecule='protein')
test_core.py:226: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__
self.extended_validation = extended_validation
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
self = <ncbi_acc_download.core.Config object at 0x7f09f5d73ec0>, value =
'loads'
@extended_validation.setter
def extended_validation(self, value):
if value != 'none' and not HAVE_BIOPYTHON:
raise ValueError("Asked for extended validation, but Biopython not
available")
/usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError____________________ test_download_and_validate_partial_wgs ____________________
req = <requests_mock.mocker.Mocker object at 0x7f09f5933610>
def test_download_and_validate_partial_wgs(req):
handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read())
assert validate.run_extended_validation(handle, 'genbank', 'loads')
E AssertionError: assert FalseE + where False = <function run_extended_validation at 0x7f09f5882c00>(<_io.StringIO object at 0x7f09f5a3e710>, 'genbank', 'loads') E + where <function run_extended_validation at 0x7f09f5882c00> = validate.run_extended_validation
test_correct.py:15: AssertionError_____________________ test_run_extended_validation_raises ______________________
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7f09f5767850>
mocker = <pytest_mock.plugin.MockerFixture object at 0x7f09f5767910>
def test_run_extended_validation_raises(monkeypatch, mocker):
"""Test the "seqence loads" validator catches exceptions in
SeqIO.parse()."""
seqio_mock = mocker.MagicMock()
seqio_mock.parse = mocker.MagicMock(side_effect=ValueError)
monkeypatch.setattr(validate, 'SeqIO', seqio_mock)
test_validate.py:19: AttributeError______________________ test_run_extended_validation_loads ______________________
def test_run_extended_validation_loads():
"""Test the "sequence loads" validator."""
handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n')
assert validate.run_extended_validation(handle, 'fasta', 'loads')
E AssertionError: assert FalseE + where False = <function run_extended_validation at 0x7f09f5882c00>(<_io.StringIO object at 0x7f09f5a3ecb0>, 'fasta', 'loads') E + where <function run_extended_validation at 0x7f09f5882c00> = validate.run_extended_validation
test_validate.py:29: AssertionError_________________________ test_download_wgs_parts_wgs __________________________
req = <requests_mock.mocker.Mocker object at 0x7f09f5761990>
def test_download_wgs_parts_wgs(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs.gbk'), 'rt')
req.get(ENTREZ_URL, body=open(full_path('wgs_full.gbk'), 'rt'))
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
wgs_full = open(full_path('wgs_full.gbk'), 'rt')
assert outhandle.getvalue() == wgs_full.read()
test_wgs.py:91: AttributeError______________________ test_download_wgs_parts_wgs_retry _______________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58fee90>
def test_download_wgs_parts_wgs_retry(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs.gbk'), 'rt')
req.get(ENTREZ_URL, response_list=[
{"text": u'Whoa, slow down', "status_code": 429, "headers":
{"Retry-After": "0"}},
{"body": open(full_path('wgs_full.gbk'), 'rt')},
])
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
wgs_full = open(full_path('wgs_full.gbk'), 'rt')
assert outhandle.getvalue() == wgs_full.read()
test_wgs.py:106: AttributeError______________________ test_download_wgs_parts_wgs_scafld ______________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58aad10>
def test_download_wgs_parts_wgs_scafld(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt')
with open(full_path('wgs_full.gbk'), 'rt') as handle:
full_file = handle.read()
req.get(ENTREZ_URL, text=full_file)
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
assert outhandle.getvalue() == full_file
test_wgs.py:119: AttributeError_____________________ test_download_wgs_parts_supercontig ______________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58f1990>
def test_download_wgs_parts_supercontig(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig.gbk'), 'rt')
req.get(ENTREZ_URL,
body=open(full_path('supercontig_full.gbk'), 'rt'))
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
assert outhandle.getvalue() == supercontig_full.read()
test_wgs.py:130: AttributeError__________________ test_download_wgs_parts_supercontig_retry ___________________
req = <requests_mock.mocker.Mocker object at 0x7f09f5933110>
def test_download_wgs_parts_supercontig_retry(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig.gbk'), 'rt')
req.get(ENTREZ_URL, response_list=[
{"text": u'Whoa, slow down', "status_code": 429, "headers":
{"Retry-After": "0"}},
{"body": open(full_path('supercontig_full.gbk'), 'rt')}
])
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
assert outhandle.getvalue() == supercontig_full.read()
test_wgs.py:145: AttributeError__________________________ test_download_wgs_no_parts __________________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58791d0>
def test_download_wgs_no_parts(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig_full.gbk'), 'rt')
req.get(ENTREZ_URL, status_code=404)
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
assert outhandle.getvalue() == supercontig_full.read()
test_wgs.py:157: AttributeError=========================== short test summary info ============================
FAILED test_core.py::test_config_have_biopython - assert FalseFAILED test_core.py::test_validate_and_write_extended_validation - ValueError... FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... =================== 11 failed, 20 passed, 1 xfailed in 0.15s ===================
autopkgtest [20:14:21]: test run-param-test
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