Your message dated Fri, 08 Nov 2024 10:04:20 +0000
with message-id <[email protected]>
and subject line Bug#1081680: fixed in pymatgen 2024.10.29+dfsg1-1
has caused the Debian Bug report #1081680,
regarding FTBFS with Python 3.13
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.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1081680: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1081680
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pymatgen
Version: 2024.6.10+dfsg1-8
Severity: normal
User: [email protected]
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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.pybuild/test_python3.12/tests/util/test_string.py ........... [ 99%]
.pybuild/test_python3.12/tests/util/test_typing.py ..... [ 99%]
.pybuild/test_python3.12/tests/vis/test_plotters.py ... [100%]
=================================== 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
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enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:300:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:338:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:330:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:348:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:488:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:536:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:545:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:603:
mcsqs not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:613:
mcsqs not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:634:
mcsqs not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:666:
icet not installed.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:652:
icet not installed.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:677:
icet not installed.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_advanced_transformations.py:784:
hiphive not present
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_site_transformations.py:213:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_standard_transformations.py:221:
enum_lib not present.
SKIPPED [1]
.pybuild/test_python3.12/tests/transformations/test_standard_transformations.py:235:
enum_lib not present.
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
--- End Message ---
--- Begin Message ---
Source: pymatgen
Source-Version: 2024.10.29+dfsg1-1
Done: Drew Parsons <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 08 Nov 2024 10:46:09 +0100
Source: pymatgen
Architecture: source
Version: 2024.10.29+dfsg1-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1081680 1082571 1085812
Changes:
pymatgen (2024.10.29+dfsg1-1) unstable; urgency=medium
.
* New upstream release
- Build-Depends: pymatgen-test-files (>= 2024.10.29~)
- update versioned Build-Depends: python3-monty (>= 2024.7.29~),
python3-networkx (>= 3~), python3-palettable (>= 3.3.3~),
python3-spglib (>= 2.5.0~). Closes: #1081680, #1082571.
* update package Recommends: python3-ase (>= 3.23.0~)
to match Build-Depends.
* refresh debian patches: source moved to src subdir
* update debian patch test_lammps_regex_path.patch to use raw string
r"\+" to treat '+' in "+dfsg" as a literal plus. Closes: #1085812.
* Build-Depends: allow python3-paraview as an alternative to python3-vtk9.
python3-pymatgen Recommends: python3-vtk9 | python3-paraview
* Drop explicit Depends: python3-spglib from python3-pymatgen.
Dependency is automated by dh_python3.
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Files:
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pymatgen_2024.10.29+dfsg1-1.dsc
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pymatgen_2024.10.29+dfsg1-1.debian.tar.xz
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