chore: Update docs for R, fix binding, test, and easy install

[lsetiawan]

This pull request includes several changes to add CI for R, improve the R package phylo2vec, and update documentation and testing. The most important changes include setting up a CI workflow for R, adding new tasks and dependencies in pixi.toml, exporting functions in the R package, and updating the README with installation and usage instructions.

CI Setup:

• .github/workflows/ci-R.yml: Added a new GitHub Actions workflow for CI with R to build and test the project on pushes and pull requests.

Package Configuration:

• pixi.toml: Added new tasks for installing and testing the R package, and specified the R version and dependencies.

R Package Improvements:

• r-phylo2vec/NAMESPACE: Exported new functions check_v, sample, to_newick, and to_vector to make them available for users.
• r-phylo2vec/R/extendr-wrappers.R: Added @export tags to functions to make them accessible from the R package.

Documentation Updates:

• r-phylo2vec/README.md: Updated README with quick installation and usage instructions, as well as a development guide for adding Rust bindings.

Testing:

• r-phylo2vec/tests/testthat.R: Added a setup file for testthat to configure testing for the R package.
• r-phylo2vec/tests/testthat/test_to_newick.R: Added a test file to verify the to_newick function.

Related Issues

Part of #4 and #5

[deepsource-io]

Here's the code health analysis summary for commits ef96fce..ef4860e. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Rust	✅ Success		View Check ↗
Python	✅ Success		View Check ↗

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Copilot reviewed 4 out of 11 changed files in this pull request and generated no comments.

Files not reviewed (7)

• r-phylo2vec/DESCRIPTION: Language not supported
• r-phylo2vec/NAMESPACE: Language not supported
• r-phylo2vec/R/extendr-wrappers.R: Language not supported
• r-phylo2vec/scripts/install-package.R: Language not supported
• r-phylo2vec/scripts/run-tests.R: Language not supported
• r-phylo2vec/tests/testthat.R: Language not supported
• r-phylo2vec/tests/testthat/test_to_newick.R: Language not supported

Comments suppressed due to low confidence (2)

r-phylo2vec/src/rust/src/lib.rs:17

• The function 'to_newick' does not have a corresponding test case to verify its behavior. Please add a test case for this function.

fn to_newick(input_integers: Vec<i32>) -> String {

r-phylo2vec/README.md:6

• The word 'pylo2vec' should be 'phylo2vec'.

This directory contains the pylo2vec R codebase, which includes Rust binding

[madelinegordon]

LGTM!

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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