Add species to cloning of both beam classes

[jank324]

Description

Passes species in both beam classes clone method as well as to various track methods.

Motivation and Context

• I have raised an issue to propose this change (required for new features and bug fixes)

Fixes #368 and fixes #371.

Types of changes

• Bug fix (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 change)
• Documentation (update in the documentation)

Checklist

• I have updated the changelog accordingly (required).
• My change requires a change to the documentation.
• I have updated the tests accordingly (required for a bug fix or a new feature).
• I have updated the documentation accordingly.
• I have reformatted the code and checked that formatting passes (required).
• I have have fixed all issues found by flake8 (required).
• I have ensured that all pytest tests pass (required).
• I have run pytest on a machine with a CUDA GPU and made sure all tests pass (required).
• I have checked that the documentation builds (required).

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[Hespe]

Changes look mostly good to me, but there is one general thing we probably want to change before merging. Taking a deep copy of Species is likely problematic since its properties are stored as torch.Tensor which cannot be deepcopied if they are not leaf tensors. I assume this will work until we try to add gradients to any of the Species properties.