Package: src:pymatgen
Version: 2024.6.10+dfsg1-8
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
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[...]
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
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I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build"
module
I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel
--outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pymatgen
* Building wheel...
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-312
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=================================== FAILURES ===================================
____________ TestQuasiHarmonicDebyeApprox.test_thermal_conductivity ____________
self =
<tests.analysis.test_quasi_harmonic_debye_approx.TestQuasiHarmonicDebyeApprox
testMethod=test_thermal_conductivity>
def test_thermal_conductivity(self):
kappa = self.qhda.thermal_conductivity(self.T, self.opt_vol)
assert_allclose(kappa, 131.736242, atol=1e-1)
.pybuild/test_python3.12/tests/analysis/test_quasi_harmonic_debye_approx.py:129:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
args = (<function assert_allclose.<locals>.compare at 0x7f51f791afc0>,
array(131.88900754), array(131.736242))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance
rtol=1e-07, atol=0.1', 'verbose': True}
@wraps(func)
def inner(*args, **kwds):
with self._recreate_cm():
return func(*args, **kwds)
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0.1
E
E Mismatched elements: 1 / 1 (100%)
E Max absolute difference: 0.15276554
E Max relative difference: 0.00115963
E x: array(131.889008)
E y: array(131.736242)
/usr/lib/python3.12/contextlib.py:81: AssertionError
----------------------------- Captured stderr call -----------------------------
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:264:
DeprecationWarning:
`scipy.integrate.quadrature` is deprecated as of SciPy 1.12.0and will be
removed in SciPy 1.15.0. Please use`scipy.integrate.quad` instead.
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:302:
DeprecationWarning:
scipy.misc.derivative is deprecated in SciPy v1.10.0; and will be completely
removed in SciPy v1.12.0. You may consider using findiff:
https://github.com/maroba/findiff or numdifftools:
https://github.com/pbrod/numdifftools
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:303:
DeprecationWarning:
scipy.misc.derivative is deprecated in SciPy v1.10.0; and will be completely
removed in SciPy v1.12.0. You may consider using findiff:
https://github.com/maroba/findiff or numdifftools:
https://github.com/pbrod/numdifftools
/<<PKGBUILDDIR>>/.pybuild/test_python3.12/pymatgen/analysis/quasiharmonic.py:304:
DeprecationWarning:
scipy.misc.derivative is deprecated in SciPy v1.10.0; and will be completely
removed in SciPy v1.12.0. You may consider using findiff:
https://github.com/maroba/findiff or numdifftools:
https://github.com/pbrod/numdifftools
________________ 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 =============================
23.87s call
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.pybuild/test_python3.12/tests/io/lobster/test_inputs.py::TestFatband::test_attributes
7.28s call
.pybuild/test_python3.12/tests/symmetry/test_groups.py::TestSpaceGroup::test_order_symm_ops
6.71s call
.pybuild/test_python3.12/tests/entries/test_entry_tools.py::TestEntrySet::test_ground_states
6.61s call
.pybuild/test_python3.12/tests/core/test_surface.py::TestSlab::test_symmetrization
6.03s call
.pybuild/test_python3.12/tests/io/lobster/test_lobsterenv.py::TestLobsterNeighbors::test_get_info_cohps_to_neighbors
5.83s 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
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.pybuild/test_python3.12/tests/command_line/test_bader_caller.py:118: bader
executable not present
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executable not present
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executable not present
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executable not present
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.pybuild/test_python3.12/tests/command_line/test_critic2_caller.py:26: critic2
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not present.
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not present.
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or mcsqs executable not present
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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
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relies on neighbor orders and is hard coded. Disable temporarily
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boltztrap2, skipping tests...
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test files are not available
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not loaded.
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free_sph.cif not present
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path present.
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enum_lib not present.
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mcsqs not present.
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mcsqs not present.
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.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:634:
mcsqs not present.
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.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:666:
icet not installed.
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.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:652:
icet not installed.
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.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:677:
icet not installed.
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.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:784:
hiphive not present
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.pybuild/test_python3.12/tests/transformations/test_site_transformations.py:213:
enum_lib not present.
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enum_lib not present.
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.pybuild/test_python3.12/tests/transformations/test_standard_transformations.py:235:
enum_lib not present.
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enum_lib not present.
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.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'
=== 2 failed, 2434 passed, 154 skipped, 336 deselected in 782.98s (0:13:02) ====
..tot conformations = 3
..tot confs tested = 3
..below energy threshold = 3
make[1]: *** [debian/rules:107: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:92: 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/202409/
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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
