ci: migrate Pages deploy to actions/deploy-pages by ShixiangWang · Pull Request #308 · openbiox/Bizard

ShixiangWang · 2026-10-09T04:10:50Z

Summary

Migrate GitHub Pages deployment from the legacy quarto publish gh-pages
target to the official actions/deploy-pages flow in both publish
workflows (issue #306, item A1).

Problem

The current deploy step (quarto-dev/quarto-actions/publish@v2 with
target gh-pages) force-pushes the entire rendered site (~493 MB) to the
gh-pages branch on every deploy. With 434 commits on gh-pages, this is
the single largest driver of repository growth tracked in issue #306.
Every deploy permanently appends a full site snapshot to git history.

Change

Replace the quarto publish action with the official three-step Pages
flow in both workflows (quarto-publish.yml, quarto-publish-update-cache.yml):

actions/upload-pages-artifact@v3 packages _site as the github-pages
artifact (keeps its original step conditions)
actions/configure-pages@v6 configures the Pages site
actions/deploy-pages@v5 deploys the artifact directly to the
github-pages environment

Configure/Deploy steps are skipped for pull_request events (same
conditions as the previous deploy step), so PR preview builds are
unaffected. Both workflows already declare the required pages write and
id-token write permissions, and the github-pages environment exists in
the repo.

Expected benefit

Repo growth stopped: deploys no longer append ~493 MB per push to git
history.
Follow-up enabled: once this is merged and verified live, the
gh-pages branch (434 commits, ~493 MB tip) can be deleted entirely.

Verification plan

CI on this PR renders the site and uploads the artifact (deploy steps
skip on PR).
After merge: verify the first deploy-pages run deploys the site
successfully and the live site works, then delete the gh-pages branch
in a follow-up step.

Refs: #306

🤖 Generated with Claude Code

Replace quarto publish --target gh-pages with the official actions/deploy-pages flow (upload-pages-artifact, configure-pages, deploy-pages) in both publish workflows. Motivation: the legacy gh-pages target force-pushes the entire rendered site (~493 MB) to the gh-pages branch on every deploy, growing the repository history indefinitely. This is the main driver of repository growth tracked in issue #306 (item A1). With this change the site is packaged as the github-pages artifact and deployed directly to the github-pages environment. The Upload Quarto artifacts step keeps its original conditions; Configure/Deploy are skipped for pull_request events (same conditions as the previous deploy step). Note: after this migration is verified live, the gh-pages branch can be deleted (Pages source switches from branch-based to workflow-based automatically on the first deploy-pages run). Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com>

github-actions · 2026-10-09T04:10:59Z

✅ QMD Format Check

No new QMD tutorial files to check.

Automated check by the PR Review workflow.
See contribution guidance for the expected tutorial format.

ShixiangWang · 2026-10-09T05:16:05Z

CI verification complete on this PR — all green ✅

Render the new Quarto files (pull_request_target): pass (5m8s) — Upload Quarto artifacts correctly skipped on PR, as designed
Github Page (pull_request, full render): pass (1h4m18s) — Upload Quarto artifacts completed/success; Configure/Deploy correctly skipped on PR
format-check: pass

Deploy path (Configure Pages → Deploy to Pages) will execute on the first merge push to main. After merge I will verify the first deploy-pages run and the live site before deleting the gh-pages branch.

The first deploy-pages run on main (merge of #308, run 37889595653) failed at "Deploy to GitHub Pages" with: HttpError: Missing environment. Ensure your workflow's deployment job has an environment. actions/deploy-pages requires the deployment job to target the github-pages environment; the legacy quarto publish gh-pages target never needed one, so neither workflow declared it. Add environment.name: github-pages to both build-deploy jobs. Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com>

* ci: upgrade workflow actions to Node24-compatible majors Resolve the "Node.js 20 is deprecated" runner annotations by bumping all GitHub Actions to their latest Node24-based majors: - actions/checkout v4 -> v7 - actions/setup-python v5 -> v7 - actions/github-script v7 -> v9 - actions/upload-pages-artifact v3 -> v5 (wraps upload-artifact v7) - actions/upload-artifact v4 -> v7 - actions/cache (incl. restore/save) v4 -> v6 - julia-actions/setup-julia v2 -> v3 - tj-actions/changed-files v46.0.5 -> v47.0.6 actions/configure-pages@v6 and actions/deploy-pages@v5 are already the latest majors. quarto-dev/quarto-actions@v2 and r-lib/actions@v2 track their latest majors (v2.2.0 / v2) and are kept. Version-only change: no step logic, inputs, or permissions modified. Verified all eight workflow YAML files still parse. Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com> * fix: require github-pages environment for deploy-pages job The first deploy-pages run on main (merge of #308, run 37889595653) failed at "Deploy to GitHub Pages" with: HttpError: Missing environment. Ensure your workflow's deployment job has an environment. actions/deploy-pages requires the deployment job to target the github-pages environment; the legacy quarto publish gh-pages target never needed one, so neither workflow declared it. Add environment.name: github-pages to both build-deploy jobs. Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com> * fix: move Pages deploy to dedicated job gated on non-PR events The github-pages environment protection rules only allow deployments from main (and legacy gh-pages), so a job targeting the environment fails on pull_request events (ref refs/pull/<n>/merge) before any step runs. Split the deploy steps into a separate deploy job with needs: build-deploy that only runs on push/schedule/dispatch. Co-Authored-By: Claude Code <noreply@anthropic.com> --------- Co-authored-by: Claude Code <noreply@anthropic.com>

The first deploy-pages run on main (merge of #308, run 37889595653) failed at "Deploy to GitHub Pages" with: HttpError: Missing environment. Ensure your workflow's deployment job has an environment. actions/deploy-pages requires the deployment job to target the github-pages environment; the legacy quarto publish gh-pages target never needed one, so neither workflow declared it. Add environment.name: github-pages to both build-deploy jobs. Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com>

* fix: require github-pages environment for deploy-pages job The first deploy-pages run on main (merge of #308, run 37889595653) failed at "Deploy to GitHub Pages" with: HttpError: Missing environment. Ensure your workflow's deployment job has an environment. actions/deploy-pages requires the deployment job to target the github-pages environment; the legacy quarto publish gh-pages target never needed one, so neither workflow declared it. Add environment.name: github-pages to both build-deploy jobs. Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com> * fix: move Pages deploy to dedicated job gated on non-PR events The github-pages environment protection rules only allow deployments from main (and legacy gh-pages), so a job targeting the environment fails on pull_request events (ref refs/pull/<n>/merge) before any step runs. Split the deploy steps into a separate deploy job with needs: build-deploy that only runs on push/schedule/dispatch. Co-Authored-By: Claude Code <noreply@anthropic.com> * fix: resolve build warnings from the website render pipeline - ManhattanPlot.qmd / ManhattanPlot.zh.qmd: restore the mangled opening fence of the {#fig-HistApplications} div (was a bare "fig-HistApplications}" line, leaking a literal closing ::: that triggered Quarto's fenced-div warning and rendered stray text on the page) - index.qmd: point template links at the rendered .html files; the .qmd hrefs produced "Unable to resolve link target" warnings on every render (rendered output is unchanged - Quarto rewrites both to the same URL) - workflows: drop the vestigial "Cache R packages" step; its renv paths never exist on the runner, so every run logged a cache path validation error and the cache was never saved. R packages are already cached by the r-lib/actions/setup-r-dependencies composite action - update-dependencies.R: print warnings as they occur (options(warn=1)) so the recurring "There were 13 warnings" session summary becomes actionable in CI logs Co-Authored-By: Claude Code <noreply@anthropic.com> --------- Co-authored-by: Claude Code <noreply@anthropic.com>

#311) * fix: require github-pages environment for deploy-pages job The first deploy-pages run on main (merge of #308, run 37889595653) failed at "Deploy to GitHub Pages" with: HttpError: Missing environment. Ensure your workflow's deployment job has an environment. actions/deploy-pages requires the deployment job to target the github-pages environment; the legacy quarto publish gh-pages target never needed one, so neither workflow declared it. Add environment.name: github-pages to both build-deploy jobs. Refs: #306 Co-Authored-By: Claude Code <noreply@anthropic.com> * fix: move Pages deploy to dedicated job gated on non-PR events The github-pages environment protection rules only allow deployments from main (and legacy gh-pages), so a job targeting the environment fails on pull_request events (ref refs/pull/<n>/merge) before any step runs. Split the deploy steps into a separate deploy job with needs: build-deploy that only runs on push/schedule/dispatch. Co-Authored-By: Claude Code <noreply@anthropic.com> * fix: resolve build warnings from the website render pipeline - ManhattanPlot.qmd / ManhattanPlot.zh.qmd: restore the mangled opening fence of the {#fig-HistApplications} div (was a bare "fig-HistApplications}" line, leaking a literal closing ::: that triggered Quarto's fenced-div warning and rendered stray text on the page) - index.qmd: point template links at the rendered .html files; the .qmd hrefs produced "Unable to resolve link target" warnings on every render (rendered output is unchanged - Quarto rewrites both to the same URL) - workflows: drop the vestigial "Cache R packages" step; its renv paths never exist on the runner, so every run logged a cache path validation error and the cache was never saved. R packages are already cached by the r-lib/actions/setup-r-dependencies composite action - update-dependencies.R: print warnings as they occur (options(warn=1)) so the recurring "There were 13 warnings" session summary becomes actionable in CI logs Co-Authored-By: Claude Code <noreply@anthropic.com> * perf: deduplicate zh figures and drop source maps from deploy artifact Phase 1 of issue #306: shrink the deployed site (current artifact ~318 MB) without touching rendered content. - Rewrite zh figure references to share the English figure trees (.github/scripts/rewrite-zh-figure-refs.py). The previous "Fix zh page figure files" step copied every English <name>_files/ tree into the zh output directory (~80 MB of duplicated PNGs in the artifact); the new step rewrites each *.zh_files/ reference to the relative path of the identical existing English figure. References without an English counterpart are left untouched and counted. - Delete *.map source maps from _site before upload. They are browser-devtools-only files and have no effect on the rendered site. Co-Authored-By: Claude Code <noreply@anthropic.com> --------- Co-authored-by: Claude Code <noreply@anthropic.com>

ShixiangWang merged commit 209c75f into main Oct 9, 2026
3 checks passed

ShixiangWang deleted the ci/deploy-pages-migration branch October 9, 2026 05:39

ShixiangWang mentioned this pull request Oct 9, 2026

ci: upgrade workflow actions to Node24-compatible majors #309

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ShixiangWang mentioned this pull request Oct 9, 2026

工程优化专项：站点存储瘦身 × CI 构建提速 × 工作流可扩展性（含实测数据与分阶段方案） #306

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ci: migrate Pages deploy to actions/deploy-pages - #308

ci: migrate Pages deploy to actions/deploy-pages#308
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