[Debian-med-packaging] Bug#1021971: python3-pychopper: New upstream release available, but routine-update fails.

[Charles Plessy]

Package: python3-pychopper
Version: 2.5.0-1
Severity: normal
X-Debbugs-Cc: plessy at 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 = <pychopper.tests.test_regression_simple.TestIntegration testMethod=testIntegration>

    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 = <pychopper.tests.test_regression_simple.TestIntegration testMethod=testIntegration_umi>

    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: (500, 'stable-updates'), (500, 'stable-security'), (500, 'unstable'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 5.10.0-17-amd64 (SMP w/8 CPU threads)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages python3-pychopper depends on:
ii  python3                   3.10.6-1
ii  python3-edlib             1.2.7-3+b1
ii  python3-matplotlib        3.5.2-2
ii  python3-pandas            1.3.5+dfsg-5
ii  python3-parasail          1.2.3-1
ii  python3-pytest            7.1.2-3
ii  python3-seaborn           0.12.0-1
ii  python3-six               1.16.0-2
ii  python3-sphinx            4.5.0-4
ii  python3-sphinx-rtd-theme  1.0.0+dfsg-1
ii  python3-tqdm              4.64.0-2

python3-pychopper recommends no packages.

python3-pychopper suggests no packages.

-- no debconf information