Support for XDMF export

[RemDelaporteMathurin]

Proposed changes

This PR adds a class to support XDMF export.

The XDMF format isn't maintained anymore so we may end up dropping support for it one day, but for now this is still a very valid option for exporting CG type functions.

Usage

    my_model = F.HydrogenTransportProblem()
    my_model.mesh = F.Mesh1D(vertices=np.linspace(0, 1))
    my_mat = F.Material(D_0=1.9e-7, E_D=0.2, name="my_mat")
    my_subdomain = F.VolumeSubdomain1D(id=1, borders=[0, 1], material=my_mat)
    my_model.subdomains = [my_subdomain]
    my_model.temperature = 500.0
    my_model.species = [F.Species("H")]

    my_model.exports = [F.XDMFExport(filename="test.xdmf", field=my_model.species)]

    my_model.initialise()
    my_model.run(1)

Other:

• slight refactoring of the VTX define

Types of changes

What types of changes does your code introduce to FESTIM?

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Code refactoring
• Documentation Update (if none of the other choices apply)
• New tests

Checklist

• Black formatted
• Unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)

[codecov]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (2b4b095) 96.68% compared to head (46103eb) 96.97%.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #613      +/-   ##
===========================================
+ Coverage    96.68%   96.97%   +0.29%     
===========================================
  Files           12       13       +1     
  Lines          362      397      +35     
===========================================
+ Hits           350      385      +35     
  Misses          12       12              

Files	Coverage Δ
festim/__init__.py	72.00% <100.00%> (+1.16%)	⬆️
festim/exports/vtx.py	100.00% <100.00%> (ø)
festim/exports/xdmf.py	100.00% <100.00%> (ø)
festim/hydrogen_transport_problem.py	97.76% <100.00%> (-0.04%)	⬇️

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[jhdark]

LGTM, the only thing is, its one thing verifying a file is created, but is there any way we can test the value in the output file to ensure its exporting correctly? Perhaps not

[RemDelaporteMathurin]

LGTM, the only thing is, its one thing verifying a file is created, but is there any way we can test the value in the output file to ensure its exporting correctly? Perhaps not

Yeah no it isn't possible to read the file (XDMF or VTX) programmatically right now.
We need to wait until checkpointing is added to dolfinx (it'll likely be added to VTX only).

The best we can do at the moment is checking the file is created and manual testing...