datacarpentry · carpentries-bot · Oct 22, 2024
diff --git a/.github/workflows/README.md b/.github/workflows/README.md
@@ -2,7 +2,7 @@
 
 This directory contains workflows to be used for Lessons using the {sandpaper}
 lesson infrastructure. Two of these workflows require R (`sandpaper-main.yaml`
-and `pr-recieve.yaml`) and the rest are bots to handle pull request management.
+and `pr-receive.yaml`) and the rest are bots to handle pull request management.
 
 These workflows will likely change as {sandpaper} evolves, so it is important to
 keep them up-to-date. To do this in your lesson you can do the following in your
@@ -94,7 +94,7 @@ branch called `update/workflows` and a pull request is created. Maintainers are
 encouraged to review the changes and accept the pull request if the outputs
 are okay.
 
-This update is run ~~weekly or~~ on demand.
+This update is run weekly or on demand.
 
 ### 03 Maintain: Update Package Cache (update-cache.yaml)
 
@@ -140,7 +140,7 @@ Once the checks are finished, a comment is issued to the pull request, which
 will allow maintainers to determine if it is safe to run the 
 "Receive Pull Request" workflow from new contributors.
 
-### Recieve Pull Request (pr-recieve.yaml)
+### Receive Pull Request (pr-receive.yaml)
 
 **Note of caution:** This workflow runs arbitrary code by anyone who creates a
 pull request. GitHub has safeguarded the token used in this workflow to have no
@@ -171,7 +171,7 @@ The artifacts produced are used by the next workflow.
 
 ### Comment on Pull Request (pr-comment.yaml)
 
-This workflow is triggered if the `pr-recieve.yaml` workflow is successful.
+This workflow is triggered if the `pr-receive.yaml` workflow is successful.
 The steps in this workflow are:
 
 1. Test if the workflow is valid and comment the validity of the workflow to the

diff --git a/.github/workflows/pr-close-signal.yaml b/.github/workflows/pr-close-signal.yaml
@@ -8,16 +8,15 @@ on:
 jobs:
   send-close-signal:
     name: "Send closing signal"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ github.event.action == 'closed' }}
     steps:
       - name: "Create PRtifact"
         run: |
           mkdir -p ./pr
           printf ${{ github.event.number }} > ./pr/NUM
       - name: Upload Diff
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pr
           path: ./pr
-
diff --git a/.github/workflows/pr-comment.yaml b/.github/workflows/pr-comment.yaml
@@ -20,7 +20,7 @@ jobs:
   #  - no .github files were committed
   test-pr:
     name: "Test if pull request is valid"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'
@@ -74,15 +74,15 @@ jobs:
   create-branch:
     name: "Create Git Branch"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
     permissions:
       contents: write
     steps:
       - name: 'Checkout md outputs'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: md-outputs
           path: built
@@ -120,7 +120,7 @@ jobs:
   comment-pr:
     name: "Comment on Pull Request"
     needs: [test-pr, create-branch]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
@@ -150,7 +150,7 @@ jobs:
   comment-changed-workflow:
     name: "Comment if workflow files have changed"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ always() && needs.test-pr.outputs.is_valid == 'false' }}
     env:
       NR: ${{ github.event.workflow_run.pull_requests[0].number }}
@@ -182,4 +182,3 @@ jobs:
         with:
           pr: ${{ env.NR }}
           body: ${{ env.body }}
-
diff --git a/.github/workflows/pr-post-remove-branch.yaml b/.github/workflows/pr-post-remove-branch.yaml
@@ -9,7 +9,7 @@ on:
 jobs:
   delete:
     name: "Delete branch from Pull Request"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'

diff --git a/.github/workflows/pr-preflight.yaml b/.github/workflows/pr-preflight.yaml
@@ -11,7 +11,7 @@ jobs:
   test-pr:
     name: "Test if pull request is valid"
     if: ${{ github.event.action != 'closed' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
     permissions:

diff --git a/.github/workflows/pr-receive.yaml b/.github/workflows/pr-receive.yaml
@@ -13,7 +13,7 @@ jobs:
   test-pr:
     name: "Record PR number"
     if: ${{ github.event.action != 'closed' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
     steps:
@@ -25,7 +25,7 @@ jobs:
       - name: "Upload PR number"
         id: upload
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pr
           path: ${{ github.workspace }}/NR
@@ -48,7 +48,7 @@ jobs:
   build-md-source:
     name: "Build markdown source files if valid"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -58,10 +58,10 @@ jobs:
       MD: ${{ github.workspace }}/site/built
     steps:
       - name: "Check Out Main Branch"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "Check Out Staging Branch"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: md-outputs
           path: ${{ env.MD }}
@@ -107,20 +107,21 @@ jobs:
         shell: Rscript {0}
 
       - name: "Upload PR"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pr
           path: ${{ env.PR }}
+          overwrite: true
 
       - name: "Upload Diff"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: diff
           path: ${{ env.CHIVE }}
           retention-days: 1
 
       - name: "Upload Build"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: built
           path: ${{ env.MD }}

diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml
@@ -21,7 +21,10 @@ on:
 jobs:
   full-build:
     name: "Build Full Site"
-    runs-on: ubuntu-latest
+
+    # 2024-10-01: ubuntu-latest is now 24.04 and R is not installed by default in the runner image
+    # pin to 22.04 for now
+    runs-on: ubuntu-22.04
     permissions:
       checks: write
       contents: write
@@ -32,7 +35,7 @@ jobs:
     steps:
 
       - name: "Checkout Lesson"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2

diff --git a/.github/workflows/sandpaper-version.txt b/.github/workflows/sandpaper-version.txt
@@ -1 +1 @@
-0.13.0
+0.16.9
diff --git a/.github/workflows/update-cache.yaml b/.github/workflows/update-cache.yaml
@@ -14,7 +14,7 @@ on:
 jobs:
   preflight:
     name: "Preflight Check"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       ok: ${{ steps.check.outputs.ok }}
     steps:
@@ -36,14 +36,14 @@ jobs:
 
   check_renv:
     name: "Check if We Need {renv}"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: preflight
     if: ${{ needs.preflight.outputs.ok == 'true'}}
     outputs:
       needed: ${{ steps.renv.outputs.exists }}
     steps:
       - name: "Checkout Lesson"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - id: renv
         run: |
           if [[ -d renv ]]; then
@@ -52,7 +52,7 @@ jobs:
 
   check_token:
     name: "Check SANDPAPER_WORKFLOW token"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: check_renv
     if: ${{ needs.check_renv.outputs.needed == 'true' }}
     outputs:
@@ -69,14 +69,14 @@ jobs:
     name: "Update Package Cache"
     needs: check_token
     if: ${{ needs.check_token.outputs.repo== 'true' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
 
       - name: "Checkout Lesson"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2

diff --git a/.github/workflows/update-workflows.yaml b/.github/workflows/update-workflows.yaml
@@ -18,7 +18,7 @@ on:
 jobs:
   check_token:
     name: "Check SANDPAPER_WORKFLOW token"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       workflow: ${{ steps.validate.outputs.wf }}
       repo: ${{ steps.validate.outputs.repo }}
@@ -31,12 +31,12 @@ jobs:
 
   update_workflow:
     name: "Update Workflow"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: check_token
     if: ${{ needs.check_token.outputs.workflow == 'true' }}
     steps:
       - name: "Checkout Repository"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Update Workflows
         id: update