Add foodwebr article demonstrating package function dependencies

[Copilot]

Description

Adds documentation article using foodwebr to visualize package function dependencies and call graphs.

Changes

• Documentation: New article vignettes/articles/package-structure.qmd demonstrates:

  • Function dependency visualization with foodwebr
  • Architecture analysis (leaf/root/hub functions)
  • Integration with tidygraph for advanced graph operations
  • Practical workflows for code review and refactoring
  • Conditional rendering to support HTML, RevealJS, and DOCX output formats

• Demo functions: Created layered architecture for meaningful visualizations:

  # 3-layer hierarchy demonstrating clean separation
  validate_input() → clean_data() → calculate_statistic() → example_function()
                                                           ↘
                   → clean_data() ────────────────────────→ calculate_summary()

• Dependencies:

  • Added foodwebr to Suggests in DESCRIPTION
  • Added cli to Imports for improved error handling with cli::cli_abort()

• Tests: Added 11 tests for new calculate_summary() function and updated existing tests

• Website integration:

  • Added package-structure article to website navigation (navbar and sidebar)
  • Article accessible under "Articles" menu and "Advanced" section in sidebar

• Workflow fixes:

  • Incremented package version to 0.0.0.9011
  • Added NEWS.md entry documenting changes
  • Updated error handling to use cli::cli_abort() instead of stop() to satisfy linter requirements
  • Implemented conditional rendering with knitr::is_html_output() to suppress interactive plots in DOCX format while maintaining all output formats
  • Added foodwebr-related terms to spellcheck WORDLIST
  • Added tests/testthat/_snaps/ to .gitignore to prevent empty directory build issues

Example Output

Article renders in HTML, RevealJS, and DOCX formats:

---

Checklist

• The title of your PR should briefly describe the change.
• Commit/merge messages to be included in NEWS.md should begin with -.
• Code should follow the tidyverse style guide.
• Documentation should use roxygen2, with Markdown syntax.
• Contributions should include unit tests (using testthat).

For more information see Contributing.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>use https://lewinfox.com/foodwebr/</issue_title>
<issue_description>include graphs of the structure of the package functions in a dedicated article on the topic</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes use https://lewinfox.com/foodwebr/ #99

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

Files with missing lines	Coverage Δ
R/calculate_statistic.R	100.00% <100.00%> (ø)
R/calculate_summary.R	100.00% <100.00%> (ø)
R/clean_data.R	100.00% <100.00%> (ø)
R/example_function.R	100.00% <100.00%> (ø)
R/format_result.R	100.00% <100.00%> (ø)
R/validate_input.R	100.00% <100.00%> (ø)

[d-morrison]

@copilot fix issues in failing workflows

[Copilot]

@copilot fix issues in failing workflows

Fixed all failing workflows in commit b251d70:

1. lint-changed-files - Replaced stop() with cli::cli_abort() in validation functions
2. version-check - Incremented version from 0.0.0.9010 to 0.0.0.9011
3. Spellcheck - Added foodwebr-related terms to WORDLIST
4. docs - Added prefer-html: true to article YAML for DOCX compatibility
5. Check Changelog - Added NEWS.md entry describing the changes

[github-actions]

PR Preview Action v1.8.1
🚀 View preview at https://UCD-SERG.github.io/rpt/pr-preview/pr-100/
Built to branch gh-pages at 2026-02-03 19:02 UTC. Preview will be ready when the GitHub Pages deployment is complete.

[d-morrison]

@copilot fix https://github.com/UCD-SERG/rpt/actions/runs/21629385642/job/62389726217?pr=100

[Copilot]

@copilot fix https://github.com/UCD-SERG/rpt/actions/runs/21629385642/job/62389726217?pr=100

Fixed macOS build failure in commit 699e450. The issue was an empty tests/testthat/_snaps/ directory that was being created during testing but causing package build errors. Added this directory to .gitignore to prevent it from being included in the package build.