Export average surface temperature

[kaelyndunnell]

Proposed changes

Adds export for average surface temperature.

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)

Further comments

If this is a relatively large or complex change, kick off the discussion by explaining why you chose the solution you did and what alternatives you considered, etc...

[codecov]

Codecov Report

Attention: Patch coverage is 93.33333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 95.98%. Comparing base (96d62ff) to head (e531a88).
Report is 48 commits behind head on fenicsx.

Files with missing lines	Patch %	Lines
src/festim/hydrogen_transport_problem.py	71.42%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #949      +/-   ##
===========================================
- Coverage    96.02%   95.98%   -0.04%     
===========================================
  Files           45       46       +1     
  Lines         2439     2517      +78     
===========================================
+ Hits          2342     2416      +74     
- Misses          97      101       +4     

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[RemDelaporteMathurin]

Hi @kaelyndunnell thanks for this, this is very much needed!

However I think it should be implemented differently:

• It doesn't make sense to ask users to provide temperature_field as an argument of SurfaceTemperature since they don't have access to the fenics object (fem.Constant or fem.Temperature) before calling initialise and since exports are defined before calling initialise. Instead, I believe the class should not have this argument at all, and temperature_field is set as an attribute only inside HTransportProblem

for export in self.exports:
    if isinstance(export, SurfaceTemperature):
        export.temperature_field = self.temperature_fenics

• SurfaceTemperature shares a lot of functionality with SurfaceQuantity: it should inherit from it
• I'm thinking by looking at this we should revisit the design of these quantities @JonathanGSDUFOUR , I'll open an issue to describe my idea but here's the rough pitch

class SurfaceQuantity:
    def __init__(self, surface, filename):
        self.surface = surface
        self.filename = filename

        self.field = None   # this is no longer a user argument but only an attribute
     
    ...

class AverageSurfaceConcentration(SurfaceQuantity):
    def __init__(self, species, surface, filename):
        self.species = species
        super.__init__(surface, filename)

Inside HTransportProblem

def initialise_exports(self):
    for export in self.exports:
        if not hasattr(export, "species"):  # appropriate fenics functions are already stored in F.Species objects
            export.field = self.temperature_fenics 

[RemDelaporteMathurin]

These lines are not tested. That's because by design, it's impossible to use SurfaceTemperature in combination with HTransportProblem