Fix dependency issues

[EngineerDanny]

The animint package in the root DESCRIPTION file has been discontinued.
The Github CI test showed that it is not possible to install it because it could not recognize the package.
Fast forward, there is an updated version called the animint2 which comes with improved features and better syntax.

[EngineerDanny]

This PR changes the DESCRIPTION file by updating the animint2 package.
I have updated, checked and tested all the functions that depend on the animint2 package.

[EngineerDanny]

Github CI Test Before the PR :

Github CI Test After initial PR :

git2r package is the only package left to be updated.

[EngineerDanny]

git2r update PR #3 has been merged into this branch since they all address dependency conflicts.

[EngineerDanny]

This PR also focuses on updating the git2r package to support the latest features and improvements.
More specifically, git2r (>= 0.30.1)
However, updating the package came with a minor hurdle.
The package has transitioned from supporting S4 objects to S3 objects.
Hence, it has made some of the functions used with git2r (<= 0.21.0) obsolete.
Therefore, I have updated and tested all the git2r functions that we use to support S3 objects.

This PR fixes issues #44 and #45

[EngineerDanny]

Explicitly writing scripts to install dependencies is not widely accepted in the R community since it makes the DESCRIPTION file redundant.
Therefore, r-lib/actions/setup-r-dependencies is adopted to automatically install packages declared in DESCRIPTION.

The Github CI test is now successful ✅.

[tdhock]

binary files like .github/actions/.DS_Store should not be added to the github repo. please remove them from the PR and add .DS_Store to the .gitignore file.