Summary

This PR fixes an error that occurs when calling merge_sites on a structure with only one site. For example:

from pymatgen.core import Structure, Lattice
cu = Structure(Lattice.from_parameters(2.5, 2.5, 2.5, 60, 60, 60), species=["Cu"], coords=[[0.0, 0.0, 0.0]])
cu.merge_sites(mode="delete")

This currently raises the following error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mrok/work/pymatgen/.venv/lib/python3.11/site-packages/pymatgen/core/structure.py", line 4840, in merge_sites
    clusters = fcluster(linkage(squareform((dist_mat + dist_mat.T) / 2)), tol, "distance")
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mrok/work/pymatgen/.venv/lib/python3.11/site-packages/scipy/cluster/hierarchy.py", line 1033, in linkage
    n = int(distance.num_obs_y(y))
            ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mrok/work/pymatgen/.venv/lib/python3.11/site-packages/scipy/spatial/distance.py", line 2742, in num_obs_y
    raise ValueError("The number of observations cannot be determined on "
ValueError: The number of observations cannot be determined on an empty distance matrix.

The root cause is that the distance matrix is a 1×1 array [[0.0]], which leads to a failure in scipy.cluster.hierarchy.linkage.

This PR resolves the issue by skipping the merging step and returning the original structure unchanged when only one site is present.

A unit test is also added to verify this behavior and prevent regressions.

Todos

No more todos.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install