Add automated daily workflow for project status tracking

[Copilot]

This PR implements a comprehensive workflow that automatically tracks the progress of various EpiForeSITE projects with GitHub repositories.

Overview

The workflow reads project information from YAML files in the data/ directory, filters projects with GitHub repositories, and generates a daily status report with real-time metrics from the GitHub API.

Features Added

🔄 Daily Automated Workflow

• Runs every day at 6 AM UTC via GitHub Actions
• Manual trigger option available through GitHub Actions UI
• Also triggers on relevant file changes for testing

📊 Project Metrics Tracking

The system tracks 19 projects with GitHub repositories and extracts:

• Contributors with avatar images (up to 5 displayed per project)
• Open issues count with live GitHub badges
• Open pull requests count with live badges
• Last commit date and hash with links
• Total commits count per repository

📝 Generated Output

Creates project_status.md containing:

• Professional markdown table format
• Clickable project names linking to repositories
• Contributor avatars and counts
• Live GitHub badges for issues/PRs
• Commit history links
• Automatic timestamps

🛠 Technical Implementation

• R script (scripts/update_project_status.R) handles all processing
• GitHub API integration with proper rate limiting and error handling
• Robust YAML parsing processes all 57 project files
• Automatic git commits using existing stefanzweifel/git-auto-commit-action

Files Added

• .github/workflows/project-status-update.yml - Main workflow configuration
• scripts/update_project_status.R - Core processing script with GitHub API calls
• scripts/test_workflow.R - Testing/validation script
• scripts/README.md - Complete documentation
• EXAMPLE_project_status.md - Example of expected output format

Example Output

The generated dashboard includes projects like:

• EpiForeSITE/vaccine-equity-model
• Fernandez-Lab-WSU/quadkeyr
• UofUEpiBio/epiworldpy
• HopkinsIDD/COVIDScenarioPipeline
• And 15 others with real-time metrics

Dependencies

Uses existing R infrastructure with additional packages: yaml, data.table, httr, jsonlite

The implementation follows existing repository patterns and integrates seamlessly with the current Quarto + R workflow used for README generation.

Fixes #52.

Warning

Firewall rules blocked me from connecting to one or more addresses

I tried to connect to the following addresses, but was blocked by firewall rules:

• cloud.r-project.org
  • Triggering command: /usr/lib/R/bin/exec/R --no-echo --no-restore -e install.packages(c('writexl',~+~'rmarkdown',~+~'yaml',~+~'data.table',~+~'knitr',~+~'httr',~+~'jsonlite')) (dns block)
• cran.rstudio.com
  • Triggering command: /usr/lib/R/bin/exec/R --no-echo --no-restore -e install.packages(c('writexl',~+~'rmarkdown',~+~'yaml',~+~'data.table',~+~'knitr',~+~'httr',~+~'jsonlite'),~+~repos~+~=~+~'REDACTED') (dns block)
• esm.ubuntu.com
  • Triggering command: /usr/lib/apt/methods/https (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to my firewall allow list

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[gvegayon]

@copilot, I need this workflow to also be triggered when PR targets main.

[Copilot]

@copilot, I need this workflow to also be triggered when PR targets main.

Added pull request trigger to the workflow. Now the project status update will also run when PRs target the main branch (commit 830f682).