VTX export capability

[RemDelaporteMathurin]

Proposed changes

This implements a VTXExport class that exports fields as VTX.
It takes a filename and a species or list of species as argument.

VTX files are readable with the MPI version of paraview.
Note: I opened an issue on the VTK repo to track progress on the development of a non-MPI VTX writer.

Usage

import dolfinx
import festim

u = dolfinx.fem.Function(V)
my_export = festim.VTXExport("my_export.bp")
my_export.define_writer(mesh.comm, [u])
for t in range(10):
    u.interpolate(lambda x: t * (x[0] ** 2 + x[1] ** 2 + x[2] ** 2))
    my_export.write(t)

with HTransportProblem

my_model.species = [F.Species("H")]
my_model.exports = [F.VTXExport("my_new_export.bp", field=my_model.species[0])]

my_model.initialise()

Current limitations:

• the field argument takes only festim.Species of list of festim.Species

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 (2fc987a) 95.06% compared to head (c9bfbc0) 95.83%.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #603      +/-   ##
===========================================
+ Coverage    95.06%   95.83%   +0.76%     
===========================================
  Files            9       10       +1     
  Lines          223      264      +41     
===========================================
+ Hits           212      253      +41     
  Misses          11       11              

Files	Coverage Δ
festim/__init__.py	68.18% <100.00%> (+1.51%)	⬆️
festim/exports/vtx.py	100.00% <100.00%> (ø)
festim/hydrogen_transport_problem.py	97.52% <100.00%> (+0.10%)	⬆️

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[jhdark]

might be worth just updating the permeation tests to use this new vtx output too

[jhdark]

LGTM