Reactions

[RemDelaporteMathurin]

Proposed changes

This is a first step towards #598

This PR implements a Reaction class and an ImplicitSpecies class.

For now the Reaction class just has a method called reaction_term that returns k * c1 * c2 - p * c3

This form will be used in the variational formulation later.

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 (4d4a65a) 96.97% compared to head (ec2d15e) 97.30%.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #614      +/-   ##
===========================================
+ Coverage    96.97%   97.30%   +0.32%     
===========================================
  Files           13       14       +1     
  Lines          397      445      +48     
===========================================
+ Hits           385      433      +48     
  Misses          12       12              

Files	Coverage Δ
festim/__init__.py	73.07% <100.00%> (+1.07%)	⬆️
festim/reaction.py	100.00% <100.00%> (ø)
festim/species.py	96.96% <100.00%> (+8.08%)	⬆️

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[jhdark]

Looks good otherwise