Removing graveyards

[shimwell]

Proposed changes

graveyards are now automatic in openmc so we can remove a nice amount of code 🎉

[codecov]

Codecov Report

Merging #281 (1abfa40) into develop (15f7166) will increase coverage by 0.17%.
The diff coverage is 86.48%.

❗ Current head 1abfa40 differs from pull request most recent head 8fa8b28. Consider uploading reports for the commit 8fa8b28 to get more accurate results

@@             Coverage Diff             @@
##           develop     #281      +/-   ##
===========================================
+ Coverage    96.30%   96.48%   +0.17%     
===========================================
  Files           82       82              
  Lines         5524     5405     -119     
===========================================
- Hits          5320     5215     -105     
+ Misses         204      190      -14     

Impacted Files	Coverage Δ
src/paramak/shape.py	96.83% <76.92%> (-0.24%)	⬇️
src/paramak/reactor.py	84.65% <88.23%> (+4.73%)	⬆️
src/paramak/__init__.py	94.56% <100.00%> (+0.05%)	⬆️
...tric_components/toroidal_field_coil_princeton_d.py	100.00% <100.00%> (ø)
src/paramak/utils.py	90.85% <100.00%> (-1.87%)	⬇️

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[shimwell]

It looks like some of the numpy/scipy code used in the tf_coil_casing.py is no longer supported in the latest versions of numpy.

We had a DeprecationWarning message for a while (scipy 1.8.0 and numpy 1.22.2)

DeprecationWarning: setting an array element with a sequence. This was supported in some cases where the elements are arrays with a single element. For example `np.array([1, np.array([2])], dtype=int)`. In the future this will raise the same ValueError as `np.array([1, [2]], dtype=int)`.
    output = _odepack.odeint(func, y0, t, args, Dfun, col_deriv, ml, mu,

but now the code is failing (scipy 1.9.3 and numpy 1.24.1)

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part.

[shimwell]

Looks like the scipy odeint function no longer accepts numpy arrays of a particular shape, I think this is the line of code causing pytest tests/tests_units/test_parametric_components/test_test_tf_coil_casing.py to fail

paramak/src/paramak/parametric_components/toroidal_field_coil_princeton_d.py

Line 108 in 8e41bff

asol = integrate.odeint(solvr, [z_0, 0], a_R)