Simplify custom tagging of meshes

RemDelaporteMathurin commented 5 months ago

Proposed changes

This PR brings some simplification in subdomains:

moved the meshtags creation from Mesh1D to Mesh to make it more generic
moved locate entities methods to base classes
added default behaviour of tagging all surfaces with 1 and all cells with 1 to SurfaceSubdomain and VolumeSubdomain respectively.

An example of how this simplifies a lot of things is the refactoring of the system tests!

@jhdark an additional simplification would be to enable users to provide a geometrical locator function when defining a subdomain (instead of creating a custom class). What do you think?

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

[ ] 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[bot] commented 5 months ago

Codecov Report

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

Project coverage is 98.90%. Comparing base (8d3ab7b) to head (072578b). Report is 72 commits behind head on fenicsx.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## fenicsx #755 +/- ## =========================================== + Coverage 98.39% 98.90% +0.51% =========================================== Files 28 28 Lines 1554 1550 -4 =========================================== + Hits 1529 1533 +4 + Misses 25 17 -8 ```

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RemDelaporteMathurin commented 3 months ago

@jhdark is this ok to be merged? I would like to merge it before #735 as it may bring some conflicts

festim-dev / FESTIM