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75 changes: 75 additions & 0 deletions .github/workflows/docs.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,75 @@
# Build the Quarto docs site in docs/ and publish it to GitHub
# Pages. Same pattern as sciSpatialR's pkgdown workflow.
#
# The site is rebuilt from docs/ on every run and handed to Pages
# as a build artifact, so no rendered HTML is ever committed and
# there is no gh-pages branch to keep in sync. Pull requests build
# but do not publish, which surfaces a broken page during review
# rather than after merge.
#
# The pages are plain Markdown, so Quarto renders them without R.
# Which pages are built is set by `project: render` in
# docs/_quarto.yml.
#
# Repository prerequisite: Settings > Pages > Source = "GitHub
# Actions". Without that, the deploy job fails with a 404.

name: docs

on:
push:
branches: [main]
paths:
- "docs/**"
- ".github/workflows/docs.yaml"
pull_request:
paths:
- "docs/**"
- ".github/workflows/docs.yaml"
workflow_dispatch:

# Deny by default; each job requests only the scopes it needs.
permissions: {}

# Serialize publishing. Queued runs collapse to the newest, but an
# in-flight deployment is allowed to finish so the live site is
# never left half-written.
concurrency:
group: pages
cancel-in-progress: false

jobs:
build:
runs-on: ubuntu-latest
permissions:
contents: read
steps:
- uses: actions/checkout@v7

- uses: quarto-dev/quarto-actions/setup@v2

# Renders to docs/_site, as set in docs/_quarto.yml
- name: Build site
run: quarto render docs

# No configure-pages step: Quarto reads its base URL from
# `site-url` in docs/_quarto.yml, so this job stays on
# contents:read alone.
- uses: actions/upload-pages-artifact@v5
with:
path: docs/_site

deploy:
# Publishing is a main-branch-only consequence of a green build.
if: github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
needs: build
runs-on: ubuntu-latest
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
permissions:
pages: write
id-token: write
steps:
- id: deployment
uses: actions/deploy-pages@v5
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,7 @@ vignettes/*.pdf
!3_output/**/tables/parity_summary.csv
!3_output/**/tables/coverage.csv
!3_output/**/tables/metric_summary.csv
!3_output/**/tables/grid_summary.csv
!3_output/**/tables/v2_self_agreement_summary.csv

AGENTS.md
Expand Down
1 change: 0 additions & 1 deletion 1_code/.gitkeep

This file was deleted.

233 changes: 0 additions & 233 deletions 1_code/_deprecated/01_bootstrap_ids.R

This file was deleted.

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