refractoring neutronics (again)

[shimwell]

Proposed changes

This is a refactoring of the neutronics which tidies things up and. Features added include:

• ability to speed up graveyard_creation by specifying the graveyard_size
• ability to speed up mesh creation and extra control f the location of the regular mesh using mesh_2d_corners and mesh_3d_corners
• movement of export_h5m to Shape and Reactor classes
• ability to skip production of h5m files when simulating
• ability to use preexisting stp files instead of making them
• changed graveyard to a lower case (compatible with shift)
• reduced the complexity of methods by separating them and moving some methods to utils functions
• added support for sector models
• fixed a bug in the submersion reactor where the inner blanket overlapped the divertor

TODO
add tests

Types of changes

• 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

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code.

• Pep8 applied
• 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)

[shimwell]

Code coverage appears to be missing a few lines that are covered by the tests

[shimwell]

I think it might be time to merge this if there are no objections

[shimwell]

the tests cover-cov appears to be missing are covered by the
def test_find_materials_in_h5_file(self):
def test_make_watertight_cmd_with_example_dagmc_file(self):
in the test_neutronics_utils.py file

[RemDelaporteMathurin]

the tests cover-cov appears to be missing are covered by the
def test_find_materials_in_h5_file(self):
def test_make_watertight_cmd_with_example_dagmc_file(self):
in the test_neutronics_utils

How is that possible ? Seems weird

[shimwell]

the tests cover-cov appears to be missing are covered by the
def test_find_materials_in_h5_file(self):
def test_make_watertight_cmd_with_example_dagmc_file(self):
in the test_neutronics_utils

How is that possible ? Seems weird

Ah I might have found the problem. I thik it is missing a --cov append in the circle yml

[shimwell]

code coverage is +0.04% 🎉

That patch is still low but perhaps that is acceptable?

[billingsley-john]

All looks good!