Refactor CI workflow and update documentation on archiving and artifacts

Author: maehr

.github/workflows/quarto-publish.yml

@@ -85,12 +85,6 @@ jobs:
         run: |
           npx @divriots/jampack ./_site
 
-      - name: Upload Built Artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: built-site
-          path: _site
-
       - name: Upload static files as artifact
         id: deployment
         uses: actions/upload-pages-artifact@v4 # or specific "vX.X.X" version tag for this action

AGENTS.md

@@ -105,6 +105,8 @@ Place new files accordingly.
 - Run and validate scripts in `src/`, `build/`, and `analysis/`
 - Confirm `.github/workflows/` still pass for changes
 
+**Archiving note**: CI artifacts are short-lived and for debugging only. GitHub Pages is a delivery channel. Long-term preservation uses GitHub Releases (site archive) and Zenodo for DOI-backed archival.
+
 ## 9) GitHub Features and Security (Project instances)
 
 - **Enable GitHub Security Alerts** and Dependabot updates (Repository → Security).

README.md

@@ -38,6 +38,13 @@ Conventional data publication as static supplementary files offers limited repro
 - Licensed under [AGPL 3.0](https://www.gnu.org/licenses/agpl-3.0.html) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/deed) according to [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-sharing.html#step-3-choose-a-licence-and-link-to-your-paper-and-code)
 - Template for reporting data issues via `github/ISSUE_TEMPLATE/data_issue_report.yml`
 
+### Archiving and Artifacts
+
+- CI artifacts are short-lived and intended for debugging workflows, not preservation
+- GitHub Pages is a delivery channel for the site, not a long-term archive
+- Releases include a `site.tar.gz` build artifact for long-term access to the rendered site
+- Zenodo integration provides DOI-backed archival of releases
+
 ### Documentation
 
 - `README.md` following [www.makeareadme.com](https://www.makeareadme.com/) and [The Turing Way](https://book.the-turing-way.org/project-design/pd-overview/project-repo/project-repo-readme)

README.template.md

@@ -49,6 +49,13 @@ _Zenodo_ provides an [API (REST & OAI-PMH)](https://developers.zenodo.org/) to a
 curl -i https://zenodo.org/api/records/ZENODO_RECORD
 ```
 
+## Archiving and Artifacts
+
+- CI artifacts are short-lived and intended for debugging workflows, not preservation
+- GitHub Pages is a delivery channel for the site, not a long-term archive
+- Releases include a `site.tar.gz` build artifact for long-term access to the rendered site
+- Zenodo integration provides DOI-backed archival of releases
+
 ## Support
 
 This project is maintained by [@USERNAME](https://github.com/USERNAME). Please understand that we can't provide individual support via email. We also believe that help is much more valuable when it's shared publicly, so more people can benefit from it.

TODO.md

@@ -19,6 +19,7 @@ Complete the following steps after creating your project from this template to c
 - [ ] **Set Up Zenodo Integration**: Follow the [GitHub guide for Zenodo integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content) 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).
+- [ ] **Create a Release Archive**: Publish a GitHub Release so the workflow attaches `site.tar.gz` for long-term access to the rendered site.
 - [ ] **Add Favicons**: Generate and add favicon files to the root directory using [favicon.io](https://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.