Package: python3-pychopper
Version: 2.5.0-1
Severity: normal
X-Debbugs-Cc: ple...@debian.org
Hi all, I just tried to routine-update python3-pychopper but it failed.
I do not have time to troubleshoot further. I am pasting the error so
that you can prepare before picking the ball.
Cheers,
-- Charles
dh_auto_test -- --system=custom --test-args="PYTHONPATH={build_dir}
{interpreter} -m pytest -v"
pybuild --test --test-pytest -i python{version} -p 3.10 --system=custom
"--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest -v"
I: pybuild base:240:
PYTHONPATH=/home/charles-plessy/Debian/python3-pychopper/.pybuild/cpython3_3.10_pychopper/build
python3.10 -m pytest -v
= test session starts ==
platform linux -- Python 3.10.7, pytest-7.1.2, pluggy-1.0.0+repack --
/usr/bin/python3.10
cachedir: .pytest_cache
hypothesis profile 'default' ->
database=DirectoryBasedExampleDatabase('/home/charles-plessy/Debian/python3-pychopper/.hypothesis/examples')
rootdir: /home/charles-plessy/Debian/python3-pychopper, configfile: pytest.ini,
testpaths: pychopper
plugins: openfiles-0.5.0, remotedata-0.3.3, arraydiff-0.5.0, cov-4.0.0,
xonsh-0.13.3, hypothesis-6.36.0, timeout-2.1.0, xdist-2.5.0, mock-3.8.2,
forked-1.4.0, doctestplus-0.12.1
collecting ... collected 4 items
pychopper/tests/test_detector.py::TestDetector::testPairAlign PASSED [ 25%]
pychopper/tests/test_detector.py::TestDetector::testScoreCutoff PASSED [ 50%]
pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration
FAILED [ 75%]
pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration_umi
FAILED [100%]
=== FAILURES ===
___ TestIntegration.testIntegration
self =
def testIntegration(self):
""" Integration test. """
base = path.dirname(__file__)
test_base = path.join(base, 'data')
barcodes = path.join(test_base, 'barcodes.fas')
input_fasta = path.join(test_base, 'ref.fq.gz')
output_fasta = path.join(test_base, 'test_output.fq.gz')
expected_output = path.join(test_base, 'expected_output.fas')
subprocess.call("{} {} {} {} {}".format('pychopper', "-Y 0 -B 3 -q 0.5
-m edlib -b", barcodes, input_fasta, output_fasta), shell=True)
retval = subprocess.call(['cmp', output_fasta, expected_output])
> self.assertEqual(retval, 0)
E AssertionError: 2 != 0
pychopper/tests/test_regression_simple.py:21: AssertionError
- Captured stderr call -
/bin/sh: 1: pychopper: not found
cmp:
/home/charles-plessy/Debian/python3-pychopper/pychopper/tests/data/test_output.fq.gz:
No such file or directory
_ TestIntegration.testIntegration_umi __
self =
def testIntegration_umi(self):
""" Integration test. """
base = path.dirname(__file__)
test_base = path.join(base, 'data')
input_fasta = path.join(test_base, 'PCS111_umi_test_reads.fastq.gz')
output_fasta = path.join(test_base, 'test_output_umi.fq.gz')
expected_output = path.join(test_base,
'PCS111_umi_test_reads_expected.fastq')
subprocess.call("{} {} {} {}".format('pychopper', "-U -m edlib -k
PCS111", input_fasta, output_fasta), shell=True)
retval = subprocess.call(['cmp', output_fasta, expected_output])
> self.assertEqual(retval, 0)
E AssertionError: 2 != 0
pychopper/tests/test_regression_simple.py:35: AssertionError
- Captured stderr call -
/bin/sh: 1: pychopper: not found
cmp:
/home/charles-plessy/Debian/python3-pychopper/pychopper/tests/data/test_output_umi.fq.gz:
No such file or directory
=== short test summary info
FAILED
pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration
FAILED
pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration_umi
= 2 failed, 2 passed in 0.10s ==
E: pybuild pybuild:379: test: plugin custom failed with: exit code=1:
PYTHONPATH=/home/charles-plessy/Debian/python3-pychopper/.pybuild/cpython3_3.10_pychopper/build
python3.10 -m pytest -v
rm -fr -- /tmp/dh-xdg-rundir-MUPdeGOd
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10
--system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest -v"
returned exit code 13
make[1]: *** [debian/rules:29: override_dh_auto_test] Error 25
make[1]: Leaving directory '/home/charles-plessy/Debian/python3-pychopper'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
-- System Information:
Debian Release: 11.5
APT prefers stable-updates
APT policy:
