--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
pgp0CkS5FwF8y.pgp
