Package: src:pymatgen
Version: 2025.2.18+dfsg1-4
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f pymatgen/optimization/linear_assignment.c pymatgen/optimization/neighbors.c pymatgen/util/coord_cython.c
rm -rf pd.json .hypothesis tmp_dir
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild

[... snipped ...]

/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/elasticity/stress.py:101: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/interfaces/test_coherent_interface.py: 81 warnings
.pybuild/test_python3.13/tests/analysis/interfaces/test_substrate_analyzer.py: 296 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/elasticity/strain.py:235: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/interfaces/test_coherent_interface.py: 81 warnings
.pybuild/test_python3.13/tests/analysis/interfaces/test_substrate_analyzer.py: 296 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/elasticity/strain.py:237: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/interfaces/test_coherent_interface.py: 78 warnings
.pybuild/test_python3.13/tests/analysis/interfaces/test_substrate_analyzer.py: 592 warnings
.pybuild/test_python3.13/tests/core/test_tensors.py: 82 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/core/tensors.py:1021: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/interfaces/test_coherent_interface.py: 78 warnings
.pybuild/test_python3.13/tests/analysis/interfaces/test_substrate_analyzer.py: 592 warnings
.pybuild/test_python3.13/tests/core/test_tensors.py: 82 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/core/tensors.py:992: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_graphs.py: 17 warnings .pybuild/test_python3.13/tests/command_line/test_critic2_caller.py: 5 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/command_line/critic2_caller.py:490: DeprecationWarning:

Parsing critic2 standard output is deprecated and will not be maintained, please use the native JSON output in the future.

.pybuild/test_python3.13/tests/analysis/test_interface_reactions.py: 24 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/analysis/test_interface_reactions.py:368: DeprecationWarning:

Arrays of 2-dimensional vectors are deprecated. Use arrays of 3-dimensional vectors instead. (deprecated in NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_nmr.py::TestChemicalShieldingNotation::test_notations
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/nmr.py:91: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_nmr.py::TestChemicalShieldingNotation::test_notations
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/nmr.py:104: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_nmr.py::TestChemicalShieldingNotation::test_notations
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/nmr.py:112: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_nmr.py::TestChemicalShieldingNotation::test_principal_axis_system
.pybuild/test_python3.13/tests/analysis/test_nmr.py::TestElectricFieldGradient::test_principal_axis_system
/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py:851: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 120 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:385: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 590 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:387: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 120 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:388: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 60 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:396: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 1040 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:393: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 10620 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:568: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 2160 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:571: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 1080 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:581: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 18720 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:578: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 708 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:437: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 144 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:439: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 72 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:449: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 1248 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:446: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 88 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:126: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 88 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:145: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 84 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:243: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_piezo_sensitivity.py: 98 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/piezo_sensitivity.py:244: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/analysis/test_pourbaix_diagram.py::TestPourbaixDiagram::test_multielement_parallel
.pybuild/test_python3.13/tests/analysis/test_pourbaix_diagram.py::TestPourbaixDiagram::test_multielement_parallel
/usr/lib/python3.13/multiprocessing/popen_fork.py:67: DeprecationWarning:

This process (pid=10651) is multi-threaded, use of fork() may lead to deadlocks in the child.

.pybuild/test_python3.13/tests/analysis/test_quasirrho.py::TestQuasiRRHO::test_extreme_temperature_and_pressure
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/quasirrho.py:243: RuntimeWarning:

overflow encountered in exp

.pybuild/test_python3.13/tests/analysis/test_quasirrho.py::TestQuasiRRHO::test_extreme_temperature_and_pressure
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/quasirrho.py:244: RuntimeWarning:

overflow encountered in exp

.pybuild/test_python3.13/tests/analysis/test_reaction_calculator.py::TestComputedReaction::test_calculated_reaction_energy_uncertainty
.pybuild/test_python3.13/tests/analysis/test_reaction_calculator.py::TestComputedReaction::test_calculated_reaction_energy_uncertainty_for_nan
.pybuild/test_python3.13/tests/analysis/test_reaction_calculator.py::TestComputedReaction::test_calculated_reaction_energy_uncertainty_for_no_uncertainty
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/analysis/reaction_calculator.py:489: FutureWarning:

AffineScalarFunc.__lt__() is deprecated. It will be removed in a future release.

.pybuild/test_python3.13/tests/core/test_structure.py::TestStructure::test_rotate_sites
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/core/structure.py:4699: RuntimeWarning:

invalid value encountered in divide

.pybuild/test_python3.13/tests/core/test_tensors.py: 18 warnings
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/core/test_tensors.py:207: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_convert_to_ieee
/usr/lib/python3/dist-packages/numpy/_core/_methods.py:44: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_round
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/core/test_tensors.py:376: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensor::test_round
/usr/lib/python3/dist-packages/numpy/_core/fromnumeric.py:48: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestTensorCollection::test_list_based_functions
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/core/test_tensors.py:409: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestSquareTensor::test_get_scaled
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/core/tensors.py:1003: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestSquareTensor::test_properties
.pybuild/test_python3.13/tests/core/test_tensors.py::TestSquareTensor::test_properties
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/core/test_tensors.py:524: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/core/test_tensors.py::TestSquareTensor::test_refine_rotation
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/core/test_tensors.py:556: DeprecationWarning:

__array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

.pybuild/test_python3.13/tests/electronic_structure/test_bandstructure.py::TestLobsterBandStructureSymmLine::test_proj_bandstructure_plot
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/electronic_structure/plotter.py:1119: RuntimeWarning:

More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
Consider using `matplotlib.pyplot.close()`.

.pybuild/test_python3.13/tests/electronic_structure/test_dos.py::TestFermiDos::test_doping_fermi
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/electronic_structure/dos.py:527: RuntimeWarning:

divide by zero encountered in divide

.pybuild/test_python3.13/tests/entries/test_compatibility.py::TestMaterialsProjectCompatibility::test_parallel_process_entries
.pybuild/test_python3.13/tests/entries/test_compatibility.py::TestMaterialsProjectCompatibility::test_parallel_process_entries
.pybuild/test_python3.13/tests/entries/test_compatibility.py::TestMaterialsProjectCompatibility::test_parallel_process_entries
/usr/lib/python3/dist-packages/joblib/externals/loky/backend/fork_exec.py:38: DeprecationWarning:

This process (pid=10651) is multi-threaded, use of fork() may lead to deadlocks in the child.

.pybuild/test_python3.13/tests/io/lammps/test_data.py::TestLammpsData::test_get_str
.pybuild/test_python3.13/tests/io/lammps/test_data.py::TestLammpsData::test_write_file
.pybuild/test_python3.13/tests/io/lammps/test_data.py::TestLammpsData::test_write_file
.pybuild/test_python3.13/tests/io/lammps/test_data.py::TestCombinedData::test_as_lammpsdata
.pybuild/test_python3.13/tests/io/lammps/test_data.py::TestCombinedData::test_get_str
/usr/lib/python3/dist-packages/numpy/_core/fromnumeric.py:57: FutureWarning:

'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.

.pybuild/test_python3.13/tests/io/test_cif.py::TestCifIO::test_cif_writer_write_file
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/io/cif.py:1767: FutureWarning:

We strongly discourage using implicit binary/text `mode`, and this would not be allowed after 2025-06-01. I.e. you should pass t/b in `mode`.

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_dfpt_ionic
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:366: UnconvergedVASPWarning:

/usr/share/doc/pymatgen-test-files/examples/files/io/vasp/outputs/vasprun.dfpt.ionic.xml.gz is an unconverged VASP run.
Electronic convergence reached: True.
Ionic convergence reached: False.

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_dfpt_unconverged
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:373: UnconvergedVASPWarning:

/usr/share/doc/pymatgen-test-files/examples/files/io/vasp/outputs/vasprun.dfpt.unconverged.xml.gz is an unconverged VASP run.
Electronic convergence reached: False.
Ionic convergence reached: True.

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:159: UnconvergedVASPWarning:

/usr/share/doc/pymatgen-test-files/examples/files/io/vasp/outputs/vasprun.hse06.xml.gz is an unconverged VASP run.
Electronic convergence reached: False.
Ionic convergence reached: True.

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:165: UnconvergedVASPWarning:

/usr/share/doc/pymatgen-test-files/examples/files/io/vasp/outputs/vasprun.dfpt.ionic.xml.gz is an unconverged VASP run.
Electronic convergence reached: True.
Ionic convergence reached: False.

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_standard
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:238: RuntimeWarning:

invalid value encountered in divide

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_standard
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:243: RuntimeWarning:

invalid value encountered in divide

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_standard
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:248: RuntimeWarning:

invalid value encountered in divide

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_standard
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/tests/io/vasp/test_outputs.py:256: RuntimeWarning:

invalid value encountered in divide

.pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestWavecar::test_standard
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/io/vasp/outputs.py:5008: RuntimeWarning:

invalid value encountered in cast

.pybuild/test_python3.13/tests/phonon/test_plotter.py::TestPhononBSPlotter::test_proj_plot
/<<PKGBUILDDIR>>/.pybuild/test_python3.13/pymatgen/phonon/plotter.py:514: RuntimeWarning:

More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
Consider using `matplotlib.pyplot.close()`.

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ============================= slowest 30 durations =============================
27.04s call .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py::TestCubicSupercellTransformation::test_apply_transformation_orthorhombic_supercell
20.68s call .pybuild/test_python3.13/tests/electronic_structure/test_plotter.py::TestBSPlotterProjected::test_methods
15.18s call .pybuild/test_python3.13/tests/analysis/test_fragmenter.py::TestFragmentMolecule::test_pc_then_ec_depth_10
13.98s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_plot
12.35s call .pybuild/test_python3.13/tests/ext/test_optimade.py::TestOptimade::test_update_aliases
11.36s call .pybuild/test_python3.13/tests/symmetry/test_kpath_lm.py::TestKPathLatimerMunro::test_kpath_generation
10.76s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_tdos
10.37s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_debye_temp_phonopy
10.01s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_average_gruneisen
9.86s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_acoustic_debye_temp
9.79s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_frequencies
9.73s call .pybuild/test_python3.13/tests/analysis/elasticity/test_elastic.py::TestElasticTensorExpansion::test_get_yield_stress
9.65s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_gruneisen
9.63s call .pybuild/test_python3.13/tests/io/test_phonopy.py::TestGruneisen::test_gruneisen_parameter
9.61s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_as_from_dict
9.54s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_multi
9.53s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_phdos
9.51s call .pybuild/test_python3.13/tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_thermal_conductivity_slack
8.68s call .pybuild/test_python3.13/tests/io/vasp/test_optics.py::TestVasprun::test_optics
8.39s call .pybuild/test_python3.13/tests/core/test_surface.py::TestSlabGenerator::test_non_stoichiometric_symmetrized_slab
8.26s call .pybuild/test_python3.13/tests/analysis/test_structure_analyzer.py::TestMiscFunction::test_average_coordination_number
8.03s call .pybuild/test_python3.13/tests/core/test_surface.py::TestSlab::test_symmetrization
7.85s call .pybuild/test_python3.13/tests/io/test_packmol.py::TestPackmolSet::test_chdir_behavior
7.75s call .pybuild/test_python3.13/tests/io/lobster/test_inputs.py::TestLobsterin::test_standard_with_energy_range_from_vasprun
7.62s call .pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
6.50s call .pybuild/test_python3.13/tests/io/vasp/test_outputs.py::TestVasprun::test_vasprun_soc
6.27s call .pybuild/test_python3.13/tests/io/lobster/test_lobsterenv.py::TestLobsterNeighbors::test_get_info_cohps_to_neighbors
6.03s call .pybuild/test_python3.13/tests/io/qchem/test_outputs.py::TestQCOutput::test_nbo_hyperbonds
5.99s call .pybuild/test_python3.13/tests/io/qchem/test_outputs.py::TestQCOutput::test_nbo7_infinite_e2pert
5.43s call .pybuild/test_python3.13/tests/cli/test_pmg_plot.py::test_plot_chgint
=========================== short test summary info ============================
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap2.py:27: No boltztrap2
SKIPPED [1] .pybuild/test_python3.13/tests/ext/test_matproj.py:44: MP API is down
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_openff.py:25: could not import 'openff.toolkit': No module named 'openff'
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_shengbte.py:10: could not import 'f90nml': No module named 'f90nml'
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_zeopp.py:20: zeo not installed
SKIPPED [1] .pybuild/test_python3.13/tests/performance/test_import_time.py:32: ref time only comparable in CI runner
SKIPPED [1] .pybuild/test_python3.13/tests/symmetry/test_kpath_hin.py:11: seekpath not installed
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py:174: TODO: need someone to fix this
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py:169: TODO: need someone to fix this
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SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_graphs.py:243: Need someone to fix this, see issue 4206
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SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_molecule_structure_comparator.py:144: TODO: need someone to fix this
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SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_surface_analysis.py:278: TODO: need someone to fix this
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_surface_analysis.py:256: TODO: need someone to fix this
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_surface_analysis.py:286: TODO: need someone to fix this
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_bader_caller.py:119: bader executable not present
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SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_vampire_caller.py:34: vampire executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:714: Only run this in CI tests
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:107: enumlib or mcsqs executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:988: could not import 'moyopy': No module named 'moyopy'
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:1931: chgnet is not built against NumPy 2.0
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2003: TODO: #3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:1021: PMG_MAPI_KEY environment variable not set or MP API is down. This is also the case in a PR.
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:1906: chgnet is not built against NumPy 2.0
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2015: TODO: #3958 wait for matgl resolve of torch dependency

[continued in next message]

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Source: pymatgen
Followup-For: Bug #1106436

Ah true, in this case the test failure is more specific.

uncertainties/3.2.3-2 was uploaded in the middle of the package freeze,
and seems to be triggering failure in pymatgen's TestInterfaceReaction.test_get_entry_energy

Should uncertainties/3.2.3-2 be reverted back to its previous version?

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

On 2025-05-30 23:23, Santiago Vila wrote:

El 30/5/25 a las 23:10, Drew Parsons escribió:

Source: pymatgen
Followup-For: Bug #1106436

Ah true, in this case the test failure is more specific.

uncertainties/3.2.3-2 was uploaded in the middle of the package
freeze,
and seems to be triggering failure in pymatgen's
TestInterfaceReaction.test_get_entry_energy

Should uncertainties/3.2.3-2 be reverted back to its previous version?

Now I remember... I talked with Colin about this a few days ago
(because of
two other packages also broken by the new "uncertainties") and we both believed
that doing nothing was the best course of action:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1106426;msg=21

(I agree that I could have made that more visible, sorry for that).

In this case "do nothing" = let all the involved packages in testing
to be the ones which we release with Debian 13.

That sounds fine.

To be honest, the failing test is a bit odd. It's expecting 1
UserWarning and getting upset that uncertainties/3.2.3 is giving it 3 UserWarnings. Seems a bit overzealous. pymatgen upstream is currently
working through a campaign of making their tests more rational. They'll upgrade their uncertainties and notice this bug before too long, well in
time for the forky release.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

tags 1106436 patch
thanks

Hi. I'm going to see if this upstream commit fixes the pymatgen issue.

https://github.com/materialsproject/pymatgen/commit/22834931904cfd138206a57684fff20ba0469580

If it does, we probably don't need to revert uncertainties.

Doing nothing and expect trixie to become stable "soon" is really no fix, and creates
extra work for the Release Managers.

Thanks.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)