scikit-fem: DEBUG:skfem.mesh.mesh:Mesh contains duplicate vertices.

In jupyter notebook, after running

import logging
import meshio
import skfem.io

logging.basicConfig(level=logging.WARNING)
logging.getLogger('skfem').setLevel(logging.DEBUG)

mesh_ = meshio.read(tmp_mesh_file)
mesh_.remove_lower_dimensional_cells()
mesh_.remove_orphaned_nodes()
skfem.io.from_meshio(mesh_)

I still get a warning

DEBUG:skfem.mesh.mesh:Mesh contains duplicate vertices.

The gmsh code is fairly trivial:

    gmsh.initialize()
    try:
        gmsh.option.setNumber("Mesh.MeshSizeFactor", ...)
        gmsh.model.occ.add_rectangle(...)
        gmsh.model.occ.synchronize()
        ... # generate a background field for mesh element sizes
        gmsh.model.mesh.field.setAsBackgroundMesh(...)
        gmsh.model.mesh.generate(2)
        gmsh.write(tmp_mesh_file)
    finally:
        gmsh.clear()
        gmsh.finalize()