Your message dated Sun, 08 Jun 2025 09:04:24 +0000
with message-id <e1uobx2-004pss...@fasolo.debian.org>
and subject line Bug#1106436: fixed in pymatgen 2025.2.18+dfsg1-5
has caused the Debian Bug report #1106436,
regarding pymatgen: FTBFS: TestInterfaceReaction.test_get_entry_energy fails
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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immediately.)
--
1106436: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1106436
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
SKIPPED [1]
.pybuild/test_python3.13/tests/analysis/magnetism/test_analyzer.py:264: enumlib
not present
SKIPPED [1]
.pybuild/test_python3.13/tests/analysis/magnetism/test_analyzer.py:300: enumlib
not present
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_graphs.py:351:
graphviz executables not present
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_graphs.py:243: Need
someone to fix this, see issue 4206
SKIPPED [1] .pybuild/test_python3.13/tests/analysis/test_local_env.py:1367:
critic2 executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/analysis/test_molecule_structure_comparator.py:144:
TODO: need someone to fix this
SKIPPED [1]
.pybuild/test_python3.13/tests/analysis/test_surface_analysis.py:263: TODO:
need someone to fix this
SKIPPED [1]
.pybuild/test_python3.13/tests/analysis/test_surface_analysis.py:270: TODO:
need someone to fix this
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
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_bader_caller.py:84: bader
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_bader_caller.py:66: bader
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_bader_caller.py:136: bader
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_critic2_caller.py:26: critic2
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_critic2_caller.py:62: critic2
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_enumlib_caller.py:93: enum_lib
not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_enumlib_caller.py:81: enum_lib
not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_enumlib_caller.py:123:
enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:41:
gulp not present.
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:74:
gulp not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:181: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:148: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:236: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:272: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:114: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:139: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:144: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:135: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:120: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:130: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:126: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:283: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:212: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:320: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:332: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:315: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:356: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:345: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:352: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:363: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:359: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:383: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:373: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:379: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_gulp_caller.py:386: gulp not
present.
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:67: mcsqs
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:101: mcsqs
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:28: mcsqs
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:51: mcsqs
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:59: mcsqs
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:77: mcsqs
executable not present
SKIPPED [1]
.pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:89: mcsqs
executable not present
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
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2026: TODO:
#3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2035: TODO:
#3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2668: could
not import 'tblite': No module named 'tblite'
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2676: Pytorch
and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_surface.py:700: This test
relies on neighbor orders and is hard coded. Disable temporarily
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_xcfunc.py:56: TODO:
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:254: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:221: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:241: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:169: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:199: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:232: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:101: No
FDINT
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:123: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:203: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:132: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:116: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:86: No
FDINT
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:207: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:141: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:157: No
x_trans.
SKIPPED [1]
.pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:43: No
x_trans.
SKIPPED [19]
.pybuild/test_python3.13/tests/electronic_structure/test_plotter.py: No x_trans
executable found
SKIPPED [1] .pybuild/test_python3.13/tests/io/exciting/test_inputs.py:137:
inconsistent data
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_cif.py:322: non-free PF*.cif
test files are not available
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_jarvis.py:12: JARVIS-tools
not loaded.
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_jarvis.py:20: JARVIS-tools
not loaded.
SKIPPED [1] .pybuild/test_python3.13/tests/io/vasp/test_inputs.py:1717: TODO:
need someone to fix this
SKIPPED [1] .pybuild/test_python3.13/tests/symmetry/test_kpaths.py:21: No seek
path present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:97:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:158:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:188:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:207:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:237:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:249:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:364:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:304:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:342:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:334:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:352:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:492:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:540:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:549:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:607:
mcsqs not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:617:
mcsqs not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:638:
mcsqs not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:670:
icet not installed.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:656:
icet not installed.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:681:
icet not installed.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:874:
hiphive not present
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_site_transformations.py:214:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:238:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:255:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:273:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:279:
enum_lib not present.
= 1 failed, 2686 passed, 145 skipped, 292 deselected, 291145 warnings in
713.83s (0:11:53) =
..tot conformations = 3
..tot confs tested = 3
..below energy threshold = 3
make[1]: *** [debian/rules:115: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:100: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202505/
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 could not 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:pymatgen, so that this is still
visible in the BTS web page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: pymatgen
Source-Version: 2025.2.18+dfsg1-5
Done: Santiago Vila <sanv...@debian.org>
We believe that the bug you reported is fixed in the latest version of
pymatgen, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1106...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <sanv...@debian.org> (supplier of updated pymatgen package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 08 Jun 2025 10:45:00 +0200
Source: pymatgen
Architecture: source
Version: 2025.2.18+dfsg1-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Santiago Vila <sanv...@debian.org>
Closes: 1106436 1107280
Changes:
pymatgen (2025.2.18+dfsg1-5) unstable; urgency=medium
.
* Team upload.
* Fix build with new uncertainties. Closes: #1106436.
* Do not try to access Internet during build. Closes: #1107280.
* Skip performance tests, as they fail in Salsa CI.
* Change BD from python3-numpy to python3-numpy-dev (lintian error).
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Files:
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pymatgen_2025.2.18+dfsg1-5.dsc
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pymatgen_2025.2.18+dfsg1-5.debian.tar.xz
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