Avoid using full equality (`==`) to compare float, avoid `assert_array_equal` compare float array

[DanielYang59]

Summary

• Avoid using full equality == to compare float, to fix #4158
• Avoid assert_array_equal on int array:

  Assert fails with numerical imprecision with floats: Use assert_allclose or one of the nulp (number of floating point values) functions for these cases instead:

• Tweak _proj implementation, ~3x speedup
• (Partially) Replace sequence of float comparison with == (list/tuple/dict ...): https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/tests/core/test_bonds.py#L56
• Other type/comment tweaks