pygmsh/meshio: how to handle physical groups

[dajuno]

Hi all,

I want to create a mesh with physical groups using pygmsh and write it in XDMF format using meshio.
Is there a way to handle the mesh with meshio, without the intermediate step of writing and re-reading a .msh using gmsh?
Consider the following MWE with the flag gmsh_workaround = True|False:

import meshio
import numpy as np
import pygmsh

def create_mesh(mesh, cell_type):
    cells = mesh.get_cells_type(cell_type)
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
    out_mesh = meshio.Mesh(
        points=mesh.points, cells={cell_type: cells}, cell_data={"markers": [cell_data]}
    )
    return out_mesh


gmsh_workaround = True

with pygmsh.geo.Geometry() as geom:
    ny = 10
    cylinder = geom.add_circle((0.2, 0, 0), 0.05, mesh_size=np.pi / ny / 30)
    rectangle = geom.add_rectangle(
        0.0, 2.2, -0.2, 0.21, 0, mesh_size=0.41 / ny, holes=[cylinder]
    )

    geom.add_physical(rectangle.lines[3], "inlet")      # 1
    geom.add_physical(rectangle.lines[1], "outlet")     # 2
    geom.add_physical(rectangle.lines[0::2], "walls")   # 3
    geom.add_physical(cylinder.curve_loop.curves, "cylinder")   # 4
    geom.add_physical(rectangle.surface, "domain")      # 5
    mesh = geom.generate_mesh(dim=2, verbose=True)

    if gmsh_workaround:
        import gmsh

        gmsh.write("karm_test.msh")
        gmsh.clear()
        mesh = meshio.read("karm_test.msh")

    triangle_mesh = create_mesh(mesh, "triangle")
    line_mesh = create_mesh(mesh, "line")

    meshio.write("mesh_2d.xdmf", triangle_mesh)
    meshio.write("mesh_1d.xdmf", line_mesh)

Without writing the intermediary gmsh mesh (gmsh_workaround == False), I get this error:

Traceback (most recent call last):
  File "/home/david/work/FEniCS/NavierStokes/examples/scripts/test_genmesh.py", line 38, in <module>
    triangle_mesh = create_mesh(mesh, "triangle")
  File "/home/david/work/FEniCS/NavierStokes/examples/scripts/test_genmesh.py", line 8, in create_mesh
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
  File "/usr/lib/python3.10/site-packages/meshio/_mesh.py", line 250, in get_cell_data
    [d for c, d in zip(self.cells, self.cell_data[name]) if c.type == cell_type]
KeyError: 'gmsh:physical'

Thanks!

Bonus question: is there a way to force the integer IDs for physical groups? Some versions ago ints could be specified instead of string labels for add_physical().