* feat: Add sample() functions

* fix: update sample ranges

* fix: update max vector capacity

* feat: Use default params for sample()

Co-authored-by: Don Setiawan <landungs@uw.edu>

* fix: remove extra function from API

Co-authored-by: Don Setiawan <landungs@uw.edu>

* feat: add sample() tests, check_v(), and docs

* test: use rtest for sample()

* test: rstest check_v()

---------

Co-authored-by: Don Setiawan <landungs@uw.edu>

* feat: add WIP AVL tree implementation

* fix: Fix issues with avl rotations

* chore: Clean up to_newick

* chore: Clean up some commented out code

---------

Co-authored-by: Landung 'Don' Setiawan <landungs@uw.edu>

* ci: Add CD for python builds with maturin

* ci: Tweak some triggers

* ci: Update default run working directory

* fix: Attempt to fix the CD for working-directory

* ci: Fix to use maturin manifest path

* fix: Add full path to Cargo.toml

* fix: Remove leftover defaults

* chore: Update package metadata files

* chore: Add updated root cargo metadata

* chore(deps): Add openssl to root cargo deps

* chore: Add LICENSE symlink and update manifest

* chore(deps): Remove openssl and git2 rust dependency

* chore: Add benchmarking for rust get_pairs

* chore: Add benchmark task to pixi

* ci: Add CI for Rust

* style: Perform linting

* style: Fix missed linting

* ci: Comment out the beta and nightly builds for now

* feat: Add is_unordered function and modify max validator

* style: Lint code

* fix: Fix python version to sync with Rust version

* chore: Remove notes about dynamic version

* feat: add get_common_ancestor between two nodes

Co-authored-by: molkjar <molkjara@gmail.com>

* bump numpy version; add integer conversion in get_common_ancestor for numba

* chore: Update dependencies to reflect main

---------

Co-authored-by: Neclow <neilclow24@gmail.com>
Co-authored-by: molkjar <molkjara@gmail.com>

…of arrays

* chore: setup ancestry_dtype comparison

* refactor: change Ancestry type to nested Vec

* style: format benchmarks

* initial implementation

* refactor: update ancestry dtype and add_leaf experiment

* fix: Fix bugs within add_leaf functions

* refactor: Update order cherries no parents to not clone

* fix: Fix remove_leaf implementation

* style: Run formatting

* docs: add initial docs

* style: Fix formatting

---------

Co-authored-by: Landung 'Don' Setiawan <landungs@uw.edu>

* docs: Add a small readme for rust directory

* Update phylo2vec/README.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update phylo2vec/README.md

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* feat: Add pre-commit configuration file

* chore: Add codespell words whitelists

* chore: Add pre-commit deps and bump down jupyterlab

* refactor: Skip prettier for yaml

* style: Perform style fixes with pre-commit

* chore: Remove R-CMD-check action for now

* ci: Change cargo-fmt to have language of rust

…#51)

* feat: Add from_newick function to parse newick string

* refactor: Revert back order_cherries to use simple vector, not hashmap

* refactor: Renamed v_res to v

* refactor: Revert back build_vector to use idxs temp array

* feat: Add newick string operation functions

* docs: Add docstrings for functions

* preliminary tests added

* merge

* tests

* clarified insert function names

* more tests

* style: pre-commit fixes

* revert renaming insert

* merge

* style: pre-commit fixes

* accidental comment

* corrected tests

---------

Co-authored-by: Madeline <madgord@Madelines-MacBook-Pro.local>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* chore: Update docs for R and fix binding

* chore: Run build

* test: Add R tests with testthat

* chore: Add easy R install

* ci: Add R ci test

* ci: Update to have args input for r tasks

* docs: Update phylo2vec misspelling

* Apply suggestions from code review

Co-authored-by: Maddie Gordon <50681653+madelinegordon@users.noreply.github.com>

---------

Co-authored-by: Maddie Gordon <50681653+madelinegordon@users.noreply.github.com>

* test: add initial benchmarking suite for rust bindings

* test: add python benchmark workflow

* test: update benchmark name

* refactor addleaf and removeleaf

* rust format

* decoupling

* style: pre-commit fixes

* python bindings

* remove using

* added pyo3 apis

* format nits

---------

Co-authored-by: Madeline <madgord@Madelines-MacBook-Pro.local>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* feat: io modules draft

* fix: update python API with correct function names

* docs: add docstrings and update API reference

* style: make io names clearer

* docs: update API reference

* fix: added file suffix validation on reading files

* style: rename supported file extension constants

* added matrix & parse newick with bls

* binding

* updates

* get cherries tests pass

* added sample_matrix

* added sample_matrix changes to the python side

* updates

* test cases

* rust analyzer fixes

* account for sample_vector name change in benchmarks

* rust formatting

* duplicate line

* python benchmarks sample_vector rename

* docstring and unused variable

---------

Co-authored-by: Madeline <madgord@Madelines-MacBook-Pro.local>

Co-authored-by: Madeline <madgord@Madelines-MacBook-Pro.local>

* ci: Add python version update script and update CD config

* feat: Enhance versioning logic in CI workflow for releases and test releases

* feat: Update version determination action and integrate into CI workflow

* feat: Use commit hash for version and fix semver

* feat: Modify the version to be distance from latest tag

* feat: Add fetch-depth 0 to get tags

* chore: Uncomment publish action

* fix: Fix return type hint

* feat: Remove unused import

* chore: Skip git cli call error

* refactor: added iterative get_cherries

* refactor: clean up newick API

* fix: use private stoi_substr

* ci: Add R CD workflow

* chore: Remove set version for now

* fix: Try to get r dependencies ahead of time

* fix: Fix argument variable for devtools build

* fix: Add dist mkdir step

* fix: Remove r deps to phylo2vec dir for build

* fix: Remove r-deps step

* fix: Make binary build instead of source code

* fix: Change macOS path to be .tgz

* feat: Add R version determination and update functionality

* fix: Set up Python environment with specified version in CI workflows

* fix: Update Python setup action to v5 and refine version regex patterns in update_r_version.py

* fix: Update R version determination to read from DESCRIPTION file in action.yml

* fix: Update Python version to 3.11 in CI workflows

* fix: Ensure pip is installed before installing dependencies in action.yml

* fix: Ensure bash shell is explicitly set for the 'Ensure pip is installed' step in action.yml

* fix: Update Python version to '3.x' in CI workflows and remove container image for build-linux

* fix: Set R version to 'release' in setup-r action for consistency

* fix: Remove macos-13 runner

* fix: Remove 'test-r-build' branch from workflow triggers

* refactor: Consolidate version update logic into a single script and remove obsolete files

* added to_newick_from_matrix and check_m

* style: pre-commit fixes

* comments

* style: pre-commit fixes

* rust linter

* rust test correction

* remove unnecessary doctest

* renamed existing to_newick for clarity

* style: pre-commit fixes

* name update

* missed naming updates

* r data structure

* input type

* typo

* fixed R datatype conversion

* deepsource ignore

* style: pre-commit fixes

* Update lib.rs

* style: pre-commit fixes

* deepsource comment

* chore: Ignore some anti-pattern and fix some

* chore: Remove comment, ignored in deepsource as intentional

---------

Co-authored-by: Madeline <madgord@Madelines-MacBook-Pro.local>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Landung 'Don' Setiawan <landungs@uw.edu>

* docs: add demo notebooks

* style: pre-commit fixes

* docs: add development guide

* docs: add profiling and benchmark sections

* style: pre-commit fixes

* docs: remove demo_matrix.ipynb for refactoring

* style: pre-commit fixes

* docs: remove demo_matrix from TOC

---------

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

* test: add code profiling

* chore: add rust profiling to workflow

* fix: update rust ci steps order

* fix: add checkout step to rust ci

* fix: add samply install to pixi workflow

* fix: add elevated perf_event permissions

* fix: no server start on samply record

* refactor: add rust benchmarks and profiling pixi task

* style: pre-commit fixes

---------

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

* chore: update profiling imports for CI

* refactor: switch to to_newick_from_vector

* Create CODE_OF_CONDUCT.md

* Create CONTRIBUTING.md

* style: pre-commit fixes

---------

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

* refactor: Update README and remove setup.py

* chore: Add badges and update couple of things