Bug#1118027: pymatgen: test_packmol test_atoms_constraints fails on various architectures

Source: pymatgen
Version: 2025.10.7+dfsg1-1
Severity: serious
Justification: FTBFS
X-Debbugs-Cc: [email protected], [email protected], [email protected]
User: [email protected]
Usertags: arm64
User: [email protected]
Usertags: ppc64 ppc64el
User: [email protected]
Usertags: i386
User: [email protected]
Usertags: loong64
Control: forwarded -1 https://github.com/materialsproject/pymatgen/issues/4519

pymatgen 2025.10.7 FTBFS on arm64, ppc64el, i386, loong64, ppc64
in packmol tests

=================================== FAILURES ===================================
____________________ TestPackmolSet.test_atoms_constraints _____________________

self = <test_packmol.TestPackmolSet object at 0xffff7443e350>

    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 0xffff905acff0>(array([ 3.1658,  0.0496, -4.4769]))
E                +    where <function norm at 0xffff905acff0> = <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([ 3.1658,  0.0496, -4.4769]) = Site: H (3.1658, 0.0496, -4.4769).coords

/build/reproducible-path/pymatgen-2025.10.7+dfsg1/.pybuild/test_python3.13/tests/io/test_packmol.py:427: AssertionError
...
= 1 failed, 2689 passed, 159 skipped, 294 deselected, 10 xfailed, 2 xpassed, 77 warnings in 1227.19s (0:20:27) =