[Debichem-devel] Bug#1081680: FTBFS with Python 3.13
Stefano Rivera
stefanor at debian.org
Fri Sep 13 19:03:54 BST 2024
Source: pymatgen
Version: 2024.6.10+dfsg1-8
Severity: normal
User: debian-python at lists.debian.org
Usertags: python3.13
Forwarded: https://github.com/materialsproject/pymatgen/pull/3923
This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.
To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.
What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html
Log snippet:
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
py=`py3versions --default -v`; \
pybuilddir=`pybuild --pyver $py --print build_dir | awk '{print $3}'`; \
testdir=/<<PKGBUILDDIR>>/.pybuild/test_python$py; \
cp -a $pybuilddir $testdir; \
cp -a tests $testdir; \
SKIP_TESTS=""; \
list_initialised=0; \
for t in test_matproj TestGenKpt TestHighSymmetryPoint test_from_multi_jobs_file test_from_string test_read_molecule test_read_nbo test_read_negative test_read_plots test_read_write_nbo7 test_all test_custom_smd_write test_sets test_CifWriter test_read_write test_init test_get_site_symmetries BSDOSPlotterTest test_cdft_dc_parsing test_get_structure_by_id test_babel_PC_with_RO_depth_0_vs_depth_10 test_fit test_get_parchg "(TestAnharmonicQuasiharmociDebyeApprox and test_gruneisen_parameter)"; do \
if [ ${list_initialised} = 0 ]; then \
SKIP_TESTS=$t; \
list_initialised=1; \
else \
SKIP_TESTS="${SKIP_TESTS} or $t"; \
fi; \
done; \
if [ "x${SKIP_TESTS}" != "x" ]; then \
SKIP_TESTS="not ( ${SKIP_TESTS} )"; \
fi; \
echo "skipping tests: ${SKIP_TESTS}"; \
PMG_TEST_FILES_DIR=/usr/share/doc/pymatgen-test-files/examples/files \
PYTHONPATH=$testdir PATH=$pybuilddir/../scripts:$PATH \
pytest-3 -v --import-mode=prepend --color=no -k "${SKIP_TESTS}" $testdir; \
skipping tests: not ( test_matproj or TestGenKpt or TestHighSymmetryPoint or test_from_multi_jobs_file or test_from_string or test_read_molecule or test_read_nbo or test_read_negative or test_read_plots or test_read_write_nbo7 or test_all or test_custom_smd_write or test_sets or test_CifWriter or test_read_write or test_init or test_get_site_symmetries or BSDOSPlotterTest or test_cdft_dc_parsing or test_get_structure_by_id or test_babel_PC_with_RO_depth_0_vs_depth_10 or test_fit or test_get_parchg or (TestAnharmonicQuasiharmociDebyeApprox and test_gruneisen_parameter) )
============================= test session starts ==============================
platform linux -- Python 3.12.6, pytest-8.3.2, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
configfile: pyproject.toml
plugins: typeguard-4.3.0
collected 2924 items / 337 deselected / 2 skipped / 2587 selected
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=================================== FAILURES ===================================
________________ TestSpacegroupAnalyzer.test_get_crystal_system ________________
self = <tests.symmetry.test_analyzer.TestSpacegroupAnalyzer testMethod=test_get_crystal_system>
def test_get_crystal_system(self):
crystal_system = self.sg.get_crystal_system()
assert crystal_system == "orthorhombic"
assert self.disordered_sg.get_crystal_system() == "tetragonal"
orig_spg = self.sg._space_group_data["number"]
> self.sg._space_group_data["number"] = 0
E TypeError: 'SpglibDataset' object does not support item assignment
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/tests/symmetry/test_analyzer.py:175: TypeError
----------------------------- Captured stderr call -----------------------------
/usr/lib/python3/dist-packages/spglib/spglib.py:115: DeprecationWarning:
dict interface (SpglibDataset['number']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead
/usr/lib/python3/dist-packages/spglib/spglib.py:115: DeprecationWarning:
dict interface (SpglibDataset['number']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead
/usr/lib/python3/dist-packages/spglib/spglib.py:115: DeprecationWarning:
dict interface (SpglibDataset['number']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead
============================= slowest 30 durations =============================
35.82s call .pybuild/test_python3.12/tests/electronic_structure/test_plotter.py::TestBSPlotterProjected::test_methods
32.79s call .pybuild/test_python3.12/tests/symmetry/test_kpath_lm.py::TestKPathLatimerMunro::test_kpath_generation
27.38s call .pybuild/test_python3.12/tests/analysis/test_fragmenter.py::TestFragmentMolecule::test_pc_then_ec_depth_10
21.35s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_plot
18.67s call .pybuild/test_python3.12/tests/io/vasp/test_optics.py::TestVasprun::test_optics
17.96s call .pybuild/test_python3.12/tests/analysis/elasticity/test_elastic.py::TestElasticTensorExpansion::test_get_yield_stress
15.73s call .pybuild/test_python3.12/tests/analysis/test_structure_analyzer.py::TestMiscFunction::test_average_coordination_number
15.12s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_thermal_conductivity_slack
15.06s call .pybuild/test_python3.12/tests/core/test_surface.py::TestSlabGenerator::test_non_stoichiometric_symmetrized_slab
15.03s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_average_gruneisen
14.86s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_as_from_dict
14.74s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_tdos
14.66s call .pybuild/test_python3.12/tests/io/test_phonopy.py::TestGruneisen::test_gruneisen_parameter
14.64s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_frequencies
14.63s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_acoustic_debye_temp
14.58s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_phdos
14.52s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_multi
14.35s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_gruneisen
14.30s call .pybuild/test_python3.12/tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
14.28s call .pybuild/test_python3.12/tests/symmetry/test_kpath_sc.py::TestBandStructureSC::test_kpath_generation
14.18s call .pybuild/test_python3.12/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_debye_temp_phonopy
13.63s call .pybuild/test_python3.12/tests/analysis/test_prototypes.py::TestAflowPrototypeMatcher::test_prototype_matching
13.43s call .pybuild/test_python3.12/tests/symmetry/test_groups.py::TestSpaceGroup::test_order_symm_ops
11.41s call .pybuild/test_python3.12/tests/io/test_packmol.py::TestPackmolSet::test_chdir_behavior
11.17s call .pybuild/test_python3.12/tests/io/lobster/test_lobsterenv.py::TestLobsterNeighbors::test_get_info_cohps_to_neighbors
11.16s call .pybuild/test_python3.12/tests/entries/test_entry_tools.py::TestEntrySet::test_ground_states
11.04s call .pybuild/test_python3.12/tests/analysis/topological/test_spillage.py::TestSolar::test_spillage_from_vasprun
10.83s call .pybuild/test_python3.12/tests/core/test_surface.py::TestSlab::test_symmetrization
10.16s call .pybuild/test_python3.12/tests/core/test_trajectory.py::TestTrajectory::test_xdatcar_write
9.96s call .pybuild/test_python3.12/tests/core/test_trajectory.py::TestTrajectory::test_extend
=========================== short test summary info ============================
SKIPPED [1] .pybuild/test_python3.12/tests/io/test_openff.py:25: could not import 'openff.toolkit': No module named 'openff'
SKIPPED [1] .pybuild/test_python3.12/tests/io/test_shengbte.py:11: could not import 'f90nml': No module named 'f90nml'
SKIPPED [1] .pybuild/test_python3.12/tests/analysis/magnetism/test_analyzer.py:255: enumlib not present
SKIPPED [1] .pybuild/test_python3.12/tests/analysis/test_graphs.py:341: graphviz executables not present
SKIPPED [1] .pybuild/test_python3.12/tests/analysis/test_local_env.py:1333: critic2 executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_bader_caller.py:118: bader executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_bader_caller.py:86: bader executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_bader_caller.py:68: bader executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_bader_caller.py:133: bader executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_critic2_caller.py:26: critic2 executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_critic2_caller.py:62: critic2 executable not present
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_enumlib_caller.py:92: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_enumlib_caller.py:80: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_enumlib_caller.py:122: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_gulp_caller.py:41: gulp not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_gulp_caller.py:68: gulp not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_gulp_caller.py:169: gulp not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_gulp_caller.py:142: gulp not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_gulp_caller.py:212: gulp not present.
SKIPPED [1] .pybuild/test_python3.12/tests/command_line/test_gulp_caller.py:248: gulp not present.
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SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:1696: could not import 'chgnet': No module named 'chgnet'
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:1761: TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:1673: could not import 'chgnet': No module named 'chgnet'
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:1773: TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:1784: TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:1793: TODO remove skip once https://github.com/materialsvirtuallab/matgl/issues/238 is resolved
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:2400: Pytorch and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_structure.py:2410: Pytorch and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060
SKIPPED [1] .pybuild/test_python3.12/tests/core/test_surface.py:667: This test relies on neighbor orders and is hard coded. Disable temporarily
SKIPPED [1] .pybuild/test_python3.12/tests/electronic_structure/test_boltztrap.py:244: No x_trans.
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SKIPPED [1] .pybuild/test_python3.12/tests/transformations/test_standard_transformations.py:246: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.12/tests/transformations/test_standard_transformations.py:252: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.12/tests/util/test_graph_hashing.py:44: could not import 'emmet.core.graph_hashing': No module named 'emmet.core.graph_hashing'
SKIPPED [1] .pybuild/test_python3.12/tests/util/test_graph_hashing.py:61: could not import 'emmet.core.graph_hashing': No module named 'emmet.core.graph_hashing'
=== 1 failed, 2430 passed, 158 skipped, 337 deselected in 1202.75s (0:20:02) ===
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/712485/
This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.
Thanks,
Stefano
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