refactor: Perform codebase refactor to separate appropriate functions

[lsetiawan]

This pull request involves several changes to the phylo2vec library, focusing on code organization and refactoring. The primary changes include moving type definitions to a new types module, updating import paths, and refactoring functions to use the new module. Additionally, a new newick module has been introduced to handle Newick string construction.

Code Organization and Refactoring:

• phylo2vec/src/tree_vec/mod.rs: Introduced a new types module and updated type references to use this module. [1] [2] [3] [4] [5] [6]
• phylo2vec/src/tree_vec/ops/mod.rs: Added a new newick module and refactored the to_newick function to use this module.
• phylo2vec/src/tree_vec/ops/vector.rs: Removed type aliases and Newick string construction functions, which were moved to the new types and newick modules respectively. [1]R1, [2]
• phylo2vec/src/tree_vec/types.rs: Created a new types module to define type aliases for Pair, Ancestry, and PairsVec.

Function and Type Updates:

• phylo2vec/benches/benchmarks/get_ancestry_dtype.rs: Updated type references from ops::vector::PairsVec to PairsVec. [1] [2] [3] [4]
• py-phylo2vec/src/lib.rs: Updated the build_newick function to use the new ops::newick::build_newick function.

Related Issues

Closes #50

Copilot reviewed 5 out of 8 changed files in this pull request and generated no suggestions.

Files not reviewed (3)

• phylo2vec/benches/benchmarks/get_ancestry_dtype.rs: Evaluated as low risk
• phylo2vec/src/tree_vec/mod.rs: Evaluated as low risk
• phylo2vec/src/tree_vec/ops/avl.rs: Evaluated as low risk