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Adapt content to outbreak context and R packages #24

Adapt content to outbreak context and R packages

Adapt content to outbreak context and R packages #24

Workflow file for this run

name: "Receive Pull Request"
on:
pull_request:
types:
[opened, synchronize, reopened]
concurrency:
group: ${{ github.ref }}
cancel-in-progress: true
jobs:
test-pr:
name: "Record PR number"
if: ${{ github.event.action != 'closed' }}
runs-on: ubuntu-latest
outputs:
is_valid: ${{ steps.check-pr.outputs.VALID }}
steps:
- name: "Record PR number"
id: record
if: ${{ always() }}
run: |
echo ${{ github.event.number }} > ${{ github.workspace }}/NR # 2022-03-02: artifact name fixed to be NR
- name: "Upload PR number"
id: upload
if: ${{ always() }}
uses: actions/upload-artifact@v3
with:
name: pr
path: ${{ github.workspace }}/NR
- name: "Get Invalid Hashes File"
id: hash
run: |
echo "json<<EOF
$(curl -sL https://files.carpentries.org/invalid-hashes.json)
EOF" >> $GITHUB_OUTPUT
- name: "echo output"
run: |
echo "${{ steps.hash.outputs.json }}"
- name: "Check PR"
id: check-pr
uses: carpentries/actions/check-valid-pr@main
with:
pr: ${{ github.event.number }}
invalid: ${{ fromJSON(steps.hash.outputs.json)[github.repository] }}
build-md-source:
name: "Build markdown source files if valid"
needs: test-pr
runs-on: ubuntu-latest
if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RENV_PATHS_ROOT: ~/.local/share/renv/
CHIVE: ${{ github.workspace }}/site/chive
PR: ${{ github.workspace }}/site/pr
MD: ${{ github.workspace }}/site/built
steps:
- name: "Check Out Main Branch"
uses: actions/checkout@v3
- name: "Check Out Staging Branch"
uses: actions/checkout@v3
with:
ref: md-outputs
path: ${{ env.MD }}
- name: "Set up R"
uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
install-r: false
- name: "Set up Pandoc"
uses: r-lib/actions/setup-pandoc@v2
- name: "Setup Lesson Engine"
uses: carpentries/actions/setup-sandpaper@main
with:
cache-version: ${{ secrets.CACHE_VERSION }}
- name: "Setup Package Cache"
uses: carpentries/actions/setup-lesson-deps@main
with:
cache-version: ${{ secrets.CACHE_VERSION }}
- name: "Validate and Build Markdown"
id: build-site
run: |
sandpaper::package_cache_trigger(TRUE)
sandpaper::validate_lesson(path = '${{ github.workspace }}')
sandpaper:::build_markdown(path = '${{ github.workspace }}', quiet = FALSE)
shell: Rscript {0}
- name: "Generate Artifacts"
id: generate-artifacts
run: |
sandpaper:::ci_bundle_pr_artifacts(
repo = '${{ github.repository }}',
pr_number = '${{ github.event.number }}',
path_md = '${{ env.MD }}',
path_pr = '${{ env.PR }}',
path_archive = '${{ env.CHIVE }}',
branch = 'md-outputs'
)
shell: Rscript {0}
- name: "Upload PR"
uses: actions/upload-artifact@v3
with:
name: pr
path: ${{ env.PR }}
- name: "Upload Diff"
uses: actions/upload-artifact@v3
with:
name: diff
path: ${{ env.CHIVE }}
retention-days: 1
- name: "Upload Build"
uses: actions/upload-artifact@v3
with:
name: built
path: ${{ env.MD }}
retention-days: 1
- name: "Teardown"
run: sandpaper::reset_site()
shell: Rscript {0}