First look to the addition of derived quantities, Issue 638

[JonathanGSDUFOUR]

Proposed changes

A first look into what I have for now in trying to work on Issue #638 .

Types of changes

What types of changes does your code introduce to FESTIM?

• [ ] Bugfix (non-breaking change which fixes an issue)
• [x] 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

• [x] 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

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.95%. Comparing base (2f9f966) to head (dcccfc5). Report is 49 commits behind head on fenicsx.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx     #735      +/-   ##
===========================================
+ Coverage    98.90%   98.95%   +0.05%     
===========================================
  Files           28       35       +7     
  Lines         1550     1631      +81     
===========================================
+ Hits          1533     1614      +81     
  Misses          17       17              

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[RemDelaporteMathurin]

@JonathanGSDUFOUR glad to see progress on this! Have you tried testing your implementation on an example?

[JonathanGSDUFOUR]

@JonathanGSDUFOUR glad to see progress on this! Have you tried testing your implementation on an example?

Not yet, but it's a good next step indeed

[JonathanGSDUFOUR]

Would it be better to test each quantity separately or can we test them all in one case ?

[RemDelaporteMathurin]

Would it be better to test each quantity separately or can we test them all in one case ?

We want to test each quantity ensuring it computes the expected value. A way to do it would be to create a function, store it as the species.solution and then check that the value computed by the derived quantity is the expected one.

[RemDelaporteMathurin]

@JonathanGSDUFOUR I don't know if you are aware but:

• the tests don't pass with your changes. You can run the tests locally with python -m pytest .
• there are a couple of unadressed comments

[JonathanGSDUFOUR]

@JonathanGSDUFOUR I don't know if you are aware but:

• the tests don't pass with your changes. You can run the tests locally with python -m pytest .
• there are a couple of unadressed comments

Yeah I currently have an issue with the version of dolfinx on my environment so the test don't run correctly, so I'm a bit blind on that, I wanted to share some of the new additions on the PR. I will go back to the comment next

[RemDelaporteMathurin]

I currently have an issue with the version of dolfinx on my environment

What's the issue?

[JonathanGSDUFOUR]

I currently have an issue with the version of dolfinx on my environment

What's the issue?

I had the latest version of dolfinx in my conda env (0.8.0) but it's solved now (I have one with 0.7.3 that runs the test correctly)

[RemDelaporteMathurin]

@JonathanGSDUFOUR tests pass yay 🎉