pymatgen ftbfs with Python 3.12

[Benjamin Drung]

Imported from Debian bug http://bugs.debian.org/1069219:

Package: src:pymatgen
Version: 2024.1.27+dfsg1-7
Severity: important
Tags: sid trixie ftbfs
User: <email address hidden>
Usertags: python3.12

[...]
=================================== FAILURES
===================================
______________________ TestTransformedStructure.test_snl
_______________________

self = <tests.alchemy.test_materials.TestTransformedStructure
testMethod=test_snl>

     def test_snl(self):
         self.trans.set_parameter("author", "will")
         with pytest.warns(UserWarning) as warns:
             snl = self.trans.to_snl([("will", "<email address hidden>")])
 > assert len(warns) == 1, "Warning not raised on type conversion
with other_parameters"
E AssertionError: Warning not raised on type conversion with
other_parameters
E assert 2 == 1
E + where 2 = len(WarningsChecker(record=True))

/<<PKGBUILDDIR>>/.pybuild/test_python3.12/tests/alchemy/test_materials.py:107:
AssertionError
____________________ TestLobsterin.test_dict_functionality
_____________________

self = <tests.io.lobster.test_inputs.TestLobsterin
testMethod=test_dict_functionality>

     def test_dict_functionality(self):
 > assert self.Lobsterinfromfile.get("COHPstartEnergy") == -15.0
E AssertionError: assert None == -15.0
E + where None = <bound method UserDict.get of
{'cohpstartenergy': -15.0, 'cohpendenergy': 5.0, 'basisset':
'pbeVaspFit2015', 'gaussian...s'], 'skipdos': True, 'skipcohp': True,
'skipcoop': True, 'skippopulationanalysis': True, 'skipgrosspopulation':
True}>('COHPstartEnergy')
E + where <bound method UserDict.get of {'cohpstartenergy':
-15.0, 'cohpendenergy': 5.0, 'basisset': 'pbeVaspFit2015',
'gaussian...s'], 'skipdos': True, 'skipcohp': True, 'skipcoop': True,
'skippopulationanalysis': True, 'skipgrosspopulation': True}> =
{'cohpstartenergy': -15.0, 'cohpendenergy': 5.0, 'basisset':
'pbeVaspFit2015', 'gaussiansmearingwidth': 0.1, 'basisfun...4s'],
'skipdos': True, 'skipcohp': True, 'skipcoop': True,
'skippopulationanalysis': True, 'skipgrosspopulation': True}.get
E + where {'cohpstartenergy': -15.0, 'cohpendenergy': 5.0,
'basisset': 'pbeVaspFit2015', 'gaussiansmearingwidth': 0.1,
'basisfun...4s'], 'skipdos': True, 'skipcohp': True, 'skipcoop': True,
'skippopulationanalysis': True, 'skipgrosspopulation': True} =
<tests.io.lobster.test_inputs.TestLobsterin
testMethod=test_dict_functionality>.Lobsterinfromfile

.pybuild/test_python3.12/tests/io/lobster/test_inputs.py:1655:
AssertionError
______________________ TestVasprun.test_potcar_not_found
_______________________

self = <tests.io.vasp.test_outputs.TestVasprun
testMethod=test_potcar_not_found>

     def test_potcar_not_found(self):
         filepath = f"{TEST_FILES_DIR}/vasprun.xml"
         # Ensure no potcar is found and nothing is updated
         with pytest.warns(UserWarning, match="No POTCAR file with
matching TITEL fields was found in") as warns:
             vasp_run = Vasprun(filepath, parse_potcar_file=".")
 > assert len(warns) == 2
E assert 3 == 2
E + where 3 = len(WarningsChecker(record=True))

/<<PKGBUILDDIR>>/.pybuild/test_python3.12/tests/io/vasp/test_outputs.py:645:
AssertionError
_________________________ TestVasprun.test_unconverged
_________________________

self = <tests.io.vasp.test_outputs.TestVasprun testMethod=test_unconverged>

     def test_unconverged(self):
         filepath = f"{TEST_FILES_DIR}/vasprun.xml.unconverged"
         with pytest.warns(UnconvergedVASPWarning,
match="vasprun.xml.unconverged is an unconverged VASP run") as warns:
             vasprun_unconverged = Vasprun(filepath,
parse_potcar_file=False)
 > assert len(warns) == 1
E assert 2 == 1
E + where 2 = len(WarningsChecker(record=True))

/<<PKGBUILDDIR>>/.pybuild/test_python3.12/tests/io/vasp/test_outputs.py:298:
AssertionError

[Benjamin Drung (bdrung)]

Updating to pymatgen 2024.5.1 should fix that failure. That release contains commit c1a610c259620509d47ca60db11a4ad32d085994 that adds official support for Python 3.12.

[Vladimir Petko (vpa1977)]

I have prepared a patch for the current version that cherry-picks python 3.12 support.

PPA: ppa:vpa1977/pymatgen-update-existing [1]

Testing:
 - rebuild reverse dependencies[1]

[1] https://launchpad.net/~vpa1977/+archive/ubuntu/pymatgen-update-existing

[Vladimir Petko (vpa1977)]

python 3.12 patch

[Launchpad Janitor (janitor)]

This bug was fixed in the package pymatgen - 2024.1.27+dfsg1-7ubuntu1

---------------
pymatgen (2024.1.27+dfsg1-7ubuntu1) oracular; urgency=medium

  * d/p/python312.patch: cherry-pick upstream patch to resolve python
    3.12 ftbfs (LP: #2067725).

 -- Vladimir Petko <email address hidden> Wed, 10 Jul 2024 15:59:41 +1200