Your message dated Wed, 15 Jul 2026 23:49:03 +0000
with message-id <[email protected]>
and subject line Bug#1137479: fixed in pymatgen-core 2026.4.7+dfsg1-6
has caused the Debian Bug report #1137479,
regarding pymatgen-core: FTBFS: test_packmol test_atoms_constraints 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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--
1137479: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1137479
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pymatgen-core
Version: 2026.4.7+dfsg1-1
Severity: serious
Control: forwarded -1
https://github.com/materialsproject/pymatgen-core/issues/70
test_atoms_constraints in io/test_packmol.py is fragile with different
coordinates generated on different architectures
e.g.
https://buildd.debian.org/status/fetch.php?pkg=pymatgen-core&arch=arm64&ver=2026.4.7%2Bdfsg1-3&stamp=1779556969&raw=0
=================================== FAILURES ===================================
____________________ TestPackmolSet.test_atoms_constraints _____________________
[gw3] linux -- Python 3.14.5 /usr/bin/python3.14
self = <test_packmol.TestPackmolSet object at 0xffff67a1d0f0>
def test_atoms_constraints(self):
"""
Test individual constraints.
"""
pw = PackmolBoxGen(
inputfile="input.in",
outputfile=Path("output.xyz"),
stdoutfile=Path("stdout.txt"),
control_params={"precision": 0.001},
).get_input_set(
molecules=[
{
"name": "water",
"number": 5,
"coords": water,
"constraints": ["inside sphere 0 0 0 10"],
"atoms_constraints": [
{"indices": [2], "constraints": ["inside sphere 0 0 0
5"]},
{"indices": [0, 1], "constraints": ["outside sphere 0 0
0 5.5"]},
],
},
],
)
pw.write_input(f"{self.tmp_path}/with_atoms_constraints")
assert
os.path.isfile(f"{self.tmp_path}/with_atoms_constraints/input.in")
with open(f"{self.tmp_path}/with_atoms_constraints/input.in") as f:
inp = f.read()
assert ("\n atoms 3\n inside sphere 0 0 0 5\n end atoms\n") in inp
assert ("\n atoms 1 2\n outside sphere 0 0 0 5.5\n end atoms\n")
in inp
pw.run(f"{self.tmp_path}/with_atoms_constraints")
assert
os.path.isfile(f"{self.tmp_path}/with_atoms_constraints/output.xyz")
assert
os.path.isfile(f"{self.tmp_path}/with_atoms_constraints/stdout.txt")
out =
Molecule.from_file(f"{self.tmp_path}/with_atoms_constraints/output.xyz")
assert out.composition.num_atoms == 15
for site in out:
if site.specie.symbol == "H":
> assert np.linalg.norm(site.coords) >= 5.49
E AssertionError: assert np.float64(5.483361163873123) >= 5.49
E + where np.float64(5.483361163873123) = <function norm at
0xffff7ff909b0>(array([ 3.165768, 0.049572, -4.476908]))
E + where <function norm at 0xffff7ff909b0> = <module
'numpy.linalg' from
'/usr/lib/python3/dist-packages/numpy/linalg/__init__.py'>.norm
E + where <module 'numpy.linalg' from
'/usr/lib/python3/dist-packages/numpy/linalg/__init__.py'> = np.linalg
E + and array([ 3.165768, 0.049572, -4.476908]) = Site: H
(3.1658, 0.0496, -4.4769).coords
/build/reproducible-path/pymatgen-core-2026.4.7+dfsg1/.pybuild/test_python3.14/tests/io/test_packmol.py:427:
AssertionError
= 1 failed, 2507 passed, 124 skipped, 5 xfailed, 1 xpassed, 64 warnings in
251.16s (0:04:11) =
The non-H case fails similarly on i386, loong64, ppc64el.
Reported upstream
https://github.com/materialsproject/pymatgen-core/issues/70
Severity: serious since FTBFS
--- End Message ---
--- Begin Message ---
Source: pymatgen-core
Source-Version: 2026.4.7+dfsg1-6
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pymatgen-core, 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-core 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: Thu, 16 Jul 2026 01:08:31 +0200
Source: pymatgen-core
Architecture: source
Version: 2026.4.7+dfsg1-6
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1137479
Changes:
pymatgen-core (2026.4.7+dfsg1-6) unstable; urgency=medium
.
* debian patch relax_packmol_test_tol_cf32d2a.patch applies upstream
commit cf32d2a relaxing tolerances to allow packmol tests to pass
on all architectures. Closes: #1137479
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