Automate R File Formatting

[Sweetdevil144]

Description

Fixes #3280 (Styler Section)
This PR introduces a new script, format.sh, designed to automate the formatting of all .R files within the PEcAN repository using the styler package. The script performs the following functions:

1. Tracking Formatted Files:
   Maintains a formatted.csv file that logs each formatted R script's relative path, its MD5 hash, and the timestamp of the last formatting. This ensures that only new or modified files are formatted in subsequent runs.

2. Formatting Process:

   • Initial Run: Formats all existing .R files and records their hashes and timestamps.
   • Subsequent Runs:
     • New Files: Automatically formats and adds them to the tracking file.
     • Modified Files: Detects changes via MD5 hash comparison, re-formats them, and updates the tracking file.
     • Unchanged Files: Skips formatting to optimize performance.

3. Roxygen Documentation:
   After formatting, the script runs make document to update all roxygen-based documentation, ensuring that documentation remains consistent with the latest code changes.

Motivation and Context

I myself was frustrated a bit on discovering extended formatting issues while working on workflow.R.
Maintaining consistent code formatting across a large repository like PEcAN enhances readability, reduces merge conflicts, and enforces coding standards. Manually formatting and tracking changes in numerous .R files can be time-consuming and error-prone.

This automation facilitates a more streamlined development workflow, allowing contributors to focus on functionality rather than manual formatting tasks.

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• New feature (non-breaking change which adds functionality)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.