CI broken for pandas 2.1

[IAlibay]

See #92

Looks like Pandas 2.1 has some compatibility issues with solvation-analysis.

[orbeckst]

From the failed CI run https://github.com/MDAnalysis/solvation-analysis/actions/runs/6185101020/job/16790038552

________________ ERROR at setup of test_residence_times[fec-10] ________________

solvation_data_sparse =                                                 distance  ... solvent_ix
frame solute_ix solute_atom_ix solvent_atom_i...9508  ...        150
                               4204             2.208404  ...        350

[13599 rows x 4 columns]

    @pytest.fixture(scope='module')
    def residence(solvation_data_sparse):
>       return Residence(solvation_data_sparse, step=10)

solvation_analysis/tests/conftest.py:322: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
solvation_analysis/residence.py:88: in __init__
    self._auto_covariances = self._calculate_auto_covariance_dict()
solvation_analysis/residence.py:123: in _calculate_auto_covariance_dict
    adjacency_df = adjacency_mini.reindex(frame_solute_index, fill_value=0)
/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/frame.py:5144: in reindex
    return super().reindex(
/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/generic.py:5521: in reindex
    return self._reindex_axes(
/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/generic.py:5544: in _reindex_axes
    new_index, indexer = ax.reindex(
/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/indexes/base.py:4426: in reindex
    indexer = self.get_indexer(
/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/indexes/base.py:3942: in get_indexer
    return self._get_indexer(target, method, limit, tolerance)
/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/indexes/base.py:3963: in _get_indexer
    tgt_values = engine._extract_level_codes(  # type: ignore[union-attr]
index.pyx:723: in pandas._libs.index.BaseMultiIndexCodesEngine._extract_level_codes
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = MultiIndex([(500, 650,  0),
            (500, 651,  1),
            (500, 652,  2),
            (500, 653,  3),
      ...   (990, 695, 45),
            (990, 696, 46)],
           names=['frame', 'solute_ix', 'solute_atom_ix'], length=2350)
new_levels = FrozenList([[500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, ...3, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696]])
copy = True

    def _recode_for_new_levels(
        self, new_levels, copy: bool = True
    ) -> Generator[np.ndarray, None, None]:
        if len(new_levels) != self.nlevels:
>           raise AssertionError(
                f"Length of new_levels ({len(new_levels)}) "
                f"must be same as self.nlevels ({self.nlevels})"
            )
E           AssertionError: Length of new_levels (2) must be same as self.nlevels (3)

/usr/local/miniconda/envs/test/lib/python3.11/site-packages/pandas/core/indexes/multi.py:2464: AssertionError

....
....
....


FAILED solvation_analysis/tests/test_plotting.py::test_compare_residence_times - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
FAILED solvation_analysis/tests/test_residence.py::test_residence_from_solute - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
FAILED solvation_analysis/tests/test_residence.py::test_residence_time_warning - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
FAILED solvation_analysis/tests/test_solute.py::test_run_w_all - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
FAILED solvation_analysis/tests/test_solute.py::test_iba_all_analysis - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
ERROR solvation_analysis/tests/test_residence.py::test_residence_times[fec-10] - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
ERROR solvation_analysis/tests/test_residence.py::test_residence_times[bn-80] - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
ERROR solvation_analysis/tests/test_residence.py::test_residence_times[pf6-nan] - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
ERROR solvation_analysis/tests/test_residence.py::test_plot_auto_covariance[fec] - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
ERROR solvation_analysis/tests/test_residence.py::test_plot_auto_covariance[bn] - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)
ERROR solvation_analysis/tests/test_residence.py::test_plot_auto_covariance[pf6] - AssertionError: Length of new_levels (2) must be same as self.nlevels (3)

[orbeckst]

Is it pandas >= 2.1 or is 2.0 also broken?

[orbeckst]

#92 answered my question: it is 2.1 so pandas<2.1 should work.

[hmacdope]

Fixed with pin in #98