Project Setup Checklist

Complete the following steps after creating your project from this template to customize and finalize your project. Each item is designed to be clear and actionable for both human users and AI assistants.

Essential Setup Tasks

• Enable GitHub Security Alerts: Navigate to your repository’s “Security” tab on GitHub and enable Dependabot alerts and security updates to monitor vulnerabilities in dependencies.
• Protect the Main Branch: In repository settings under “Branches”, add a branch protection rule for main to require pull request reviews before merging and prevent force pushes.
• Update Project Details: Replace all placeholder values in the following files with your actual project information:
  • FULLNAME → Your full name (e.g., “Jane Doe”)
  • USERNAME → Your GitHub username (e.g., “janedoe”)
  • REPO_NAME → Your repository name (e.g., “my-research-data”)
  • SHORT_DESCRIPTION → Brief description of your project (e.g., “Analysis of climate data from 2020-2024”)
  • [INSERT CONTACT METHOD] → Your contact email or preferred method
  • GITHUB_REPO_ID → Your GitHub repository ID (e.g., “123456789”)
  • ZENODO_RECORD → Your Zenodo record number (e.g., “1234567”) after first release or manually create a Zenodo deposit
  • DOI → Your DOI after first release (e.g., “10.5281/zenodo.1234567”)
  • Files to update: .github/ISSUE_TEMPLATE/config.yml, _brand.yml, CODE_OF_CONDUCT.md, package.json, README.template.md, and SECURITY.md
• Set Up Zenodo Integration: Follow the GitHub guide for Zenodo integration to enable automatic archiving and obtain a DOI for your repository.
• Set Up Zenodo DOI Badge: Replace GITHUB_REPO_ID with the repository ID from https://api.github.com/repos/USERNAME/REPO_NAME (look for the id field in the JSON response). The badge will automatically display your Zenodo DOI after the first release.
• Add Zenodo DOI to README: After creating your first release and obtaining a Zenodo DOI, replace ZENODO_RECORD in README.md with your actual Zenodo record number (found in your Zenodo deposit URL).
• Add Favicons: Generate and add favicon files to the root directory using favicon.io or a similar service. Include favicon.ico, favicon-16x16.png, favicon-32x32.png, apple-touch-icon.png, and Android icons.
• Address TODO Comments: Search for TODO comments throughout all project files using grep -r "TODO" . and complete or remove each task as appropriate for your project.
• Finalize README: Once all customization is complete, delete the template README.md and rename README.template.md to README.md to make it your project’s main README.
• Format Files: Run npm run format to apply consistent formatting to all files using Prettier before committing changes.
• Commit Changes: Use npm run commit to create a properly formatted commit message following Conventional Commits standards (e.g., “chore: initial project setup”).
• Generate Changelog: Run npm run changelog to generate changelog entries from your commit history, then copy the output into CHANGELOG.md.
• Customize Documentation: Adapt the Quarto documentation to your project by editing .qmd files, adding your data analysis, visualizations, and narrative. See Quarto documentation for guidance.
• Enable GitHub Pages: In repository settings under “Pages”, set the source to “Deploy from a branch” and select the gh-pages branch and / (root) folder.
• Publish Documentation: Run quarto publish gh-pages to build and publish your documentation website to GitHub Pages.

Optional Enhancements

• Add Citation File: Create a CITATION.cff file with your project’s citation metadata using the Citation File Format guide. Include authors, title, version, DOI, and repository URL.
• Add Zenodo Metadata File: Create a .zenodo.json file to control metadata sent to Zenodo during archival. Include custom creators, contributors, keywords, and license information. See Zenodo developer documentation for schema details.

Verification Steps

After completing the checklist:

1. Run npm run check to verify all files are properly formatted
2. Run quarto preview to ensure documentation renders correctly
3. Review your GitHub Pages site to confirm it displays as expected
4. Test that all links in your README work correctly
5. Verify that security alerts and branch protection are active