…ests in python

refactor: unify newick --> matrix conversion in rust and tests in python

* feat: cophenetic distances from matrix format

* refactor: hardcode MAX_N_LEAVES_COPH to 50

* feat: add from_pairs (rust) and pairs conversion in python 
* refactor(rust): linter fixes in newick functions
* chore: bump versions and remove python Cargo.lock

* chore: bump python version

* style: pre-commit fixes

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* feat(r): add all vector operations in R

* fix(r): add ape dependency for cophenetic distan
ce tests

* feat: add v <--> pairs conversion

* chore: update name of sample to sample_vector in CD in README

* fix(pixi): add ape dependency to r-phylo2vec

* refactor: consistent output in order_cherries functions

* refactor: remove Ancestry type call in matrix mod

…s for cherry permutations and ladderization + minor fixes

fix(rust): make matrix formulation bijective

…ust (#44)

* refactor: move label_mapping functions to rust and make them more robust

* fix copilot warnings

* refactor(rust): simplify get cherries

* docs: add docs to get_cherries functions

* feat(r): add IO ops for R (+ minor touch to py reader)

* fix: check float subdtype in matrix (python) and export newick IO functions (R)