FAILED src/alchemlyb/tests/parsing/test_lammps.py::test_u_nk on Ubuntu runners

[orbeckst]

In PR #456 all ubuntu runners failed src/alchemlyb/tests/parsing/test_lammps.py::test_u_nk

https://github.com/alchemistry/alchemlyb/actions/runs/24628692124/job/72012085846?pr=456#step:5:1105

u_nk.shape is one larger than expected. Warnings indicate that the parser changed something

Number of energy values in file, /home/runner/micromamba/envs/test/lib/python3.13/site-packages/alchemtest/lammps/benzene/2_NPT_vdw/mbar_lj-cut-soft-lambda_0.65_0.7_charge--0.0_0.txt.bz2, N=3669, inconsistent with previous files of length, 3668. Adding NaN to row: [1394]

All our tests should pass the same on differen operating systems, so this is a bug of some kind.

It also seems to have come up recently so perhaps it's connected to a change in numpy or pandas.

Partial pytest output from run

_________________________________ test_u_nk ___________________________________
[gw3] linux -- Python 3.13.13 /home/runner/micromamba/envs/test/bin/python3.13
def test_u_nk():
    """Test that u_nk has the correct form when extracted from files."""
    dataset = load_benzene()

    for leg, filenames in dataset["data"]["mbar"].items():
        u_nk = lmp.extract_u_nk(filenames, 300, **kwargs_mbar[leg])

        assert u_nk.index.names == ["time", "fep-lambda"]
        if leg == "1_coul-off":
            assert u_nk.shape == (30006, 6)
        elif leg == "2_vdw":


          assert u_nk.shape == (78681, 16)


E               assert (78682, 16) == (78681, 16)

E

E                 At index 0 diff: 78682 != 78681

E

E                 Full diff:

E                   (

E                 -     78681,

E                 ?         ^

E                 +     78682,

E                 ?         ^

E                       16,

E                   )
src/alchemlyb/tests/parsing/test_lammps.py:127: AssertionError

=============================== warnings summary ===============================

src/alchemlyb/tests/parsing/test_lammps.py::test_u_nk

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_col_lambda2

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_col_lambda2

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_error_no_file

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_error_num_cols

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_error_duplicate_files

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_default_tolerance

src/alchemlyb/tests/parsing/test_lammps.py::TestLammpsMbar::test_u_nk_custom_tolerance

/home/runner/work/alchemlyb/alchemlyb/src/alchemlyb/parsing/lammps.py:987: UserWarning: Number of energy values in file, /home/runner/micromamba/envs/test/lib/python3.13/site-packages/alchemtest/lammps/benzene/2_NPT_vdw/mbar_lj-cut-soft-lambda_0.65_0.7_charge--0.0_0.txt.bz2, N=3669, inconsistent with previous files of length, 3668. Adding NaN to row: [1394]

warnings.warn(

...