add checks of cell tag consistency in gmshio

[pierricmora]

Relates to issue #3332

Add checks to the gmshio interface to ensure that all cells are tagged once, to avoid undesired behaviour or crashes.

Compared to the discussion in issue #3332, the impact on the code is slightly more as not only model_to_mesh but also extract_topology_and_markers have been modified. This is because storing entity_tags in extract_topology_and_markers enables to call the relatively expensive np.unique on a smaller array. Then, the overcost due to these checks is below 5%, compared to 15% - 10% reported before.

[jhale]

As these are user-facing errors they should raise Exceptions of the appropriate type directly, probably RuntimeError, rather than using assert.

[pierricmora]

Done.

Suggestion: could the first RuntimeError (no cell is tagged) be converted into a RuntimeWarning by defaulting a uniform tag for all cells?

[jorgensd]

Currently most warnings get swallowed by FFCx (FEniCS/ffcx#712) so I am not sure this is a good idea

[pierricmora]

I corrected two formatting errors but I still get Lint failed. This time the error is not very verbose... Any idea? When I do ruff check and ruff format in my computer I get no error.

[pierricmora]

Could be used to remove gdim from parameters. What about this simplification? @jorgensd

if comm.rank == rank:
    gdim = model.getDimension()
    gdim = comm.bcast(gdim, root=rank)

# ...

else:
    gdim = comm.bcast(None, root=rank)

[jorgensd]

Not sure that is safe, as you might want: A flat manifold in some plane, i.e.

In [1]: import gmsh

In [2]: gmsh.initialize()

In [3]: idx = gmsh.model.occ.add_rectangle(0,0,0.1,1,1)

In [4]: gmsh.model.occ.synchronize()

In [5]: gmsh.model.add_physical_group(2,[idx])
Out[5]: 1

In [6]: gmsh.model.mesh.generate(2)
Info    : Meshing 1D...
Info    : [  0%] Meshing curve 1 (Line)
Info    : [ 30%] Meshing curve 2 (Line)
Info    : [ 60%] Meshing curve 3 (Line)
Info    : [ 80%] Meshing curve 4 (Line)
Info    : Done meshing 1D (Wall 0.000247945s, CPU 0.000433s)
Info    : Meshing 2D...
Info    : Meshing surface 1 (Plane, Frontal-Delaunay)
Info    : Done meshing 2D (Wall 0.00361243s, CPU 0.003612s)
Info    : 98 nodes 198 elements

In [7]: gmsh.model.getDimension()
Out[7]: 2

In [8]: gmsh.model.mesh.generate(3)
Info    : Meshing 3D...
Info    : Done meshing 3D (Wall 2.2143e-05s, CPU 2.1e-05s)
Info    : 98 nodes 198 elements

In [9]: gmsh.model.getDimension()
Out[9]: 2

ref:

In [10]: gmsh.model.occ.add_rectangle?
Signature: gmsh.model.occ.add_rectangle(x, y, z, dx, dy, tag=-1, roundedRadius=0.0)
Docstring:
gmsh.model.occ.addRectangle(x, y, z, dx, dy, tag=-1, roundedRadius=0.)

Add a rectangle in the OpenCASCADE CAD representation, with lower left
corner at (`x', `y', `z') and upper right corner at (`x' + `dx', `y' +
`dy', `z'). If `tag' is positive, set the tag explicitly; otherwise a new
tag is selected automatically. Round the corners if `roundedRadius' is
nonzero. Return the tag of the rectangle.

Return an integer.

Types:
- `x': double
- `y': double
- `z': double
- `dx': double
- `dy': double
- `tag': integer
- `roundedRadius': double

[pierricmora]

Ok, good point. I'm not sure to understand in details what should be the desired behaviour here -- I guess you would expect 3 as output, and another method that does not exist but which could be named gmsh.model.getTopologicalDimension() to return 2, am I right?
I think I am done with my code. Could you have a review?