Package: src:propka Version: 3.5.1-2 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202512/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:propka, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem pybuild --with python3 dh_auto_clean -O--buildsystem=pybuild I: pybuild base:317: python3.14 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2) [... snipped ...] with open(pdb_path, 'r') as writer: filestream = StringIO(writer.read()) with tmpdir.as_cwd(): > run_propka_stream(options, filestream, filename) tests/test_streamio.py:84: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_streamio.py:36: in run_propka_stream parameters = read_parameter_file(args.parameters, Parameters()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ propka/input.py:153: in read_parameter_file parameters.parse_line(line) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Parameters(interaction_matrix=<propka.parameters.InteractionMatrix object at 0x7f69359c8c00>, sidechain_cutoffs=<propk...on_energy=0.5, max_free_energy_diff=1.0, min_swap_pka_shift=1.0, min_pka=0.0, max_pka=10.0, sidechain_interaction=0.85) line = 'version VersionA\n' def parse_line(self, line): """Parse parameter file line.""" # first, remove comments comment_pos = line.find('#') if comment_pos != -1: line = line[:comment_pos] # split the line into words words = line.split() if len(words) == 0: return # parse the words > typeannotation = self.__annotations__.get(words[0]) ^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? propka/parameters.py:148: AttributeError ________________ test_stringio_filestream[3SGB: --titrate_only] ________________ tmpdir = local('/tmp/pytest-of-sbuild/pytest-0/test_stringio_filestream_3SGB_0') pdb = '3SGB-subset' options = ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139', '3SGB-subset.pdb'] @pytest.mark.parametrize("pdb, options", [ pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), pytest.param('3SGB-subset', [ "--titrate_only", "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], id="3SGB: --titrate_only"), pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), ]) def test_stringio_filestream(tmpdir, pdb, options): """Basic regression test using StringIO streams for the input PDB file""" # Get the relevant paths ref_path, pdb_path = get_paths(pdb) filename = f"{pdb}.pdb" with open(pdb_path, 'r') as writer: filestream = StringIO(writer.read()) with tmpdir.as_cwd(): > run_propka_stream(options, filestream, filename) tests/test_streamio.py:84: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_streamio.py:36: in run_propka_stream parameters = read_parameter_file(args.parameters, Parameters()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ propka/input.py:153: in read_parameter_file parameters.parse_line(line) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Parameters(interaction_matrix=<propka.parameters.InteractionMatrix object at 0x7f69359cd270>, sidechain_cutoffs=<propk...on_energy=0.5, max_free_energy_diff=1.0, min_swap_pka_shift=1.0, min_pka=0.0, max_pka=10.0, sidechain_interaction=0.85) line = 'version VersionA\n' def parse_line(self, line): """Parse parameter file line.""" # first, remove comments comment_pos = line.find('#') if comment_pos != -1: line = line[:comment_pos] # split the line into words words = line.split() if len(words) == 0: return # parse the words > typeannotation = self.__annotations__.get(words[0]) ^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? propka/parameters.py:148: AttributeError _________________ test_stringio_filestream[1HPX-warn: --quiet] _________________ tmpdir = local('/tmp/pytest-of-sbuild/pytest-0/test_stringio_filestream_1HPX_0') pdb = '1HPX-warn', options = ['--quiet', '1HPX-warn.pdb'] @pytest.mark.parametrize("pdb, options", [ pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"), pytest.param('3SGB-subset', [ "--titrate_only", "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"], id="3SGB: --titrate_only"), pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"), ]) def test_stringio_filestream(tmpdir, pdb, options): """Basic regression test using StringIO streams for the input PDB file""" # Get the relevant paths ref_path, pdb_path = get_paths(pdb) filename = f"{pdb}.pdb" with open(pdb_path, 'r') as writer: filestream = StringIO(writer.read()) with tmpdir.as_cwd(): > run_propka_stream(options, filestream, filename) tests/test_streamio.py:84: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_streamio.py:36: in run_propka_stream parameters = read_parameter_file(args.parameters, Parameters()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ propka/input.py:153: in read_parameter_file parameters.parse_line(line) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Parameters(interaction_matrix=<propka.parameters.InteractionMatrix object at 0x7f69359cd6d0>, sidechain_cutoffs=<propk...on_energy=0.5, max_free_energy_diff=1.0, min_swap_pka_shift=1.0, min_pka=0.0, max_pka=10.0, sidechain_interaction=0.85) line = 'version VersionA\n' def parse_line(self, line): """Parse parameter file line.""" # first, remove comments comment_pos = line.find('#') if comment_pos != -1: line = line[:comment_pos] # split the line into words words = line.split() if len(words) == 0: return # parse the words > typeannotation = self.__annotations__.get(words[0]) ^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? propka/parameters.py:148: AttributeError __________________________ test_valuerror_nofiletype ___________________________ def test_valuerror_nofiletype(): """Tests for raised ValueError when an unknown filename is passed to read_molecule_file""" pdb = "1FTJ-Chain-A" options = [] ref_path, pdb_path = get_paths(pdb) with open(pdb_path, 'r') as writer: filestream = StringIO(writer.read()) errmsg = "Unknown input file type" with pytest.raises(ValueError, match=errmsg): > run_propka_stream(options, filestream, filename="test.dat") tests/test_streamio.py:103: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_streamio.py:36: in run_propka_stream parameters = read_parameter_file(args.parameters, Parameters()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ propka/input.py:153: in read_parameter_file parameters.parse_line(line) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Parameters(interaction_matrix=<propka.parameters.InteractionMatrix object at 0x7f6935b792e0>, sidechain_cutoffs=<propk...on_energy=0.5, max_free_energy_diff=1.0, min_swap_pka_shift=1.0, min_pka=0.0, max_pka=10.0, sidechain_interaction=0.85) line = 'version VersionA\n' def parse_line(self, line): """Parse parameter file line.""" # first, remove comments comment_pos = line.find('#') if comment_pos != -1: line = line[:comment_pos] # split the line into words words = line.split() if len(words) == 0: return # parse the words > typeannotation = self.__annotations__.get(words[0]) ^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? propka/parameters.py:148: AttributeError ____________________________ test_valuerror_notpdb _____________________________ def test_valuerror_notpdb(): """Tests for raised ValueError when a stream object that isn't a PDB is passed to read_molecule_file""" pdb = "1FTJ-Chain-A" options = [] ref_path, pdb_path = get_paths(pdb) filestream = StringIO() errmsg = "The pdb file does not seem to contain any " with pytest.raises(ValueError, match=errmsg): > run_propka_stream(options, filestream, filename="test.pdb") tests/test_streamio.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_streamio.py:36: in run_propka_stream parameters = read_parameter_file(args.parameters, Parameters()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ propka/input.py:153: in read_parameter_file parameters.parse_line(line) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Parameters(interaction_matrix=<propka.parameters.InteractionMatrix object at 0x7f6935ae9cd0>, sidechain_cutoffs=<propk...on_energy=0.5, max_free_energy_diff=1.0, min_swap_pka_shift=1.0, min_pka=0.0, max_pka=10.0, sidechain_interaction=0.85) line = 'version VersionA\n' def parse_line(self, line): """Parse parameter file line.""" # first, remove comments comment_pos = line.find('#') if comment_pos != -1: line = line[:comment_pos] # split the line into words words = line.split() if len(words) == 0: return # parse the words > typeannotation = self.__annotations__.get(words[0]) ^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'Parameters' object has no attribute '__annotations__'. Did you mean: '__annotate_func__'? propka/parameters.py:148: AttributeError =========================== short test summary info ============================ FAILED tests/test_basic_regression.py::test_regression[sample-issue-140: no options] FAILED tests/test_basic_regression.py::test_regression[1FTJ-Chain-A: no options] FAILED tests/test_basic_regression.py::test_regression[1HPX: no options] - At... FAILED tests/test_basic_regression.py::test_regression[4DFR: no options] - At... FAILED tests/test_basic_regression.py::test_regression[3SGB: no options] - At... FAILED tests/test_basic_regression.py::test_regression[3SGB: --titrate_only] FAILED tests/test_basic_regression.py::test_regression[1HPX-warn: --quiet] - ... FAILED tests/test_run.py::test_single_file[1FTJ-Chain-A: no options] - Attrib... FAILED tests/test_run.py::test_single_file[3SGB: --titrate_only] - AttributeE... FAILED tests/test_run.py::test_single_file[1HPX-warn: --quiet] - AttributeErr... FAILED tests/test_run.py::test_single_filestream[1FTJ-Chain-A: no options] - ... FAILED tests/test_run.py::test_single_filestream[3SGB: --titrate_only] - Attr... FAILED tests/test_run.py::test_single_filestream[1HPX-warn: --quiet] - Attrib... FAILED tests/test_run.py::test_single_nopka - AttributeError: 'Parameters' ob... FAILED tests/test_run.py::test_single_extra_files_logwarn - AttributeError: '... FAILED tests/test_streamio.py::test_textio_filestream[1FTJ-Chain-A: no options] FAILED tests/test_streamio.py::test_textio_filestream[3SGB: --titrate_only] FAILED tests/test_streamio.py::test_textio_filestream[1HPX-warn: --quiet] - A... FAILED tests/test_streamio.py::test_stringio_filestream[1FTJ-Chain-A: no options] FAILED tests/test_streamio.py::test_stringio_filestream[3SGB: --titrate_only] FAILED tests/test_streamio.py::test_stringio_filestream[1HPX-warn: --quiet] FAILED tests/test_streamio.py::test_valuerror_nofiletype - AttributeError: 'P... FAILED tests/test_streamio.py::test_valuerror_notpdb - AttributeError: 'Param... ================= 23 failed, 24 passed, 2 deselected in 0.35s ================== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_propka/build; python3.14 -m pytest -k 'not test_molecular_container' I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_propka/build; python3.13 -m pytest -k 'not test_molecular_container' ============================= test session starts ============================== platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 rootdir: /<<PKGBUILDDIR>> plugins: typeguard-4.4.4 collected 49 items / 2 deselected / 47 selected tests/test_basic_regression.py ....... [ 14%] tests/test_hybrid36.py .. [ 19%] tests/test_input.py .. [ 23%] tests/test_lib.py .. [ 27%] tests/test_protonate.py . [ 29%] tests/test_run.py ........ [ 46%] tests/test_streamio.py ........ [ 63%] tests/test_vector_algebra.py ............... [ 95%] tests/test_version.py .. [100%] ======================= 47 passed, 2 deselected in 3.01s ======================= dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 make: *** [debian/rules:12: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
