feat: Add 'add_leaf' and 'remove_leaf' methods

[ayushnag]

This pull request introduces several new features and improvements to the TreeVec struct in the phylo2vec library. The changes include new methods for manipulating the tree structure, additional documentation, and new tests to ensure functionality.

Enhancements to TreeVec struct:

• phylo2vec/src/tree_vec/mod.rs: Added new methods add_leaf, remove_leaf, and from_sample to the TreeVec struct, allowing for dynamic manipulation of the tree structure.
• phylo2vec/src/tree_vec/mod.rs: Implemented the to_newick method to convert the tree to Newick format and updated the get_ancestry method to return an Ancestry type.

Documentation improvements:

• phylo2vec/src/tree_vec/mod.rs: Added detailed documentation for the TreeVec struct and its methods, including new, from_sample, to_newick, get_ancestry, add_leaf, and remove_leaf. [1] [2]

Test additions:

• phylo2vec/src/tree_vec/mod.rs: Added new tests for creating trees from samples, converting trees to Newick format, retrieving ancestry matrices, and adding/removing leaves from the tree. [1] [2] [3] [4]

Utility functions:

• phylo2vec/src/tree_vec/ops/vector.rs: Added utility functions find_coords_of_first_leaf, order_cherries, order_cherries_no_parents, and build_vector to support the new TreeVec methods.

Code refactoring:

• phylo2vec/src/tree_vec/ops/vector.rs: Refactored the get_ancestry function to use usize::MAX instead of -1 for uninitialized parent values, improving type safety and clarity.

These changes collectively enhance the functionality, documentation, and test coverage of the TreeVec struct, making the library more robust and easier to use.

TODOs

• Add docs
• Tests added
• Tests passing

Related Issues

• Closes feat: Add 'add_leaf' function so user can add a leaf to the Vector #20
• Closes feat: Add 'remove_leaf' function for Vector #21

[lsetiawan]

@ayushnag I've fixed the bugs to add leaf method. looks like now there's a merge conflict. Could you please resolve this? Thanks!

[lsetiawan]

@ayushnag I went ahead and fixed the merge conflicts, now the only thing failing is the remove_leaf, which I think need to be updated.

[lsetiawan]

@ayushnag Thanks for the initial codebase, I was able to quickly update the code and make it work. 😄 I think this is good now.

[ayushnag]

Thanks @lsetiawan!