Merge pull request #1 from carpentries/update-workflows-version-0.11.15

Update Workflows to Version 0.11.15

.github/workflows/README.md

@@ -46,8 +46,11 @@ This workflow has two caches; one cache is for the lesson infrastructure and
 the other is for the the lesson dependencies if the lesson contains rendered
 content. These caches are invalidated by new versions of the infrastructure and
 the `renv.lock` file, respectively. If there is a problem with the cache, 
-manual invaliation is necessary and can be done by setting the `CACHE_VERSION`
-secret to the current date.
+manual invaliation is necessary. You will need maintain access to the repository
+and you can either go to the actions tab and [click on the caches button to find
+and invalidate the failing cache](https://github.blog/changelog/2022-10-20-manage-caches-in-your-actions-workflows-from-web-interface/) 
+or by setting the `CACHE_VERSION` secret to the current date (which will
+invalidate all of the caches).
 
 ## Updates
 
@@ -86,24 +89,25 @@ will do the following:
 1. check the recorded version of sandpaper against the current version on github
 2. update the files if there is a difference in versions
 
-After the files are updated, a pull request is created if there are any changes.
-Maintainers are encouraged to review the changes and accept the pull request.
+After the files are updated, if there are any changes, they are pushed to a
+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.
 
-TODO: 
-  - perform check if a pull request exists before creating pull request
-
 ### 03 Maintain: Update Pacakge Cache (update-cache.yaml)
 
 For lessons that have generated content, we use {renv} to ensure that the output
 is stable. This is controlled by a single lockfile which documents the packages
-needed for the lesson and the version numbers.
+needed for the lesson and the version numbers. This workflow is skipped in 
+lessons that do not have generated content.
 
 Because the lessons need to remain current with the package ecosystem, it's a
 good idea to make sure these packages can be updated periodically. The 
-update cache workflow will do this by checking for updates, applying them and
-creating a pull request with _only the lockfile changed_. 
+update cache workflow will do this by checking for updates, applying them in a
+branch called `updates/packages` and creating a pull request with _only the
+lockfile changed_. 
 
 From here, the markdown documents will be rebuilt and you can inspect what has
 changed based on how the packages have updated. 
@@ -143,6 +147,11 @@ pull request. GitHub has safeguarded the token used in this workflow to have no
 priviledges in the repository, but we have taken precautions to protect against
 spoofing.
 
+This workflow is triggered with every push to a pull request. If this workflow
+is already running and a new push is sent to the pull request, the workflow
+running from the previous push will be cancelled and a new workflow run will be
+started.
+
 The first step of this workflow is to check if it is valid (e.g. that no
 workflow files have been modified). If there are workflow files that have been
 modified, a comment is made that indicates that the workflow is not run. If 
@@ -156,7 +165,7 @@ request. This builds the content and uploads three artifacts:
 3. The rendered files (build)
 
 Because this workflow builds generated content, it follows the same general 
-process as the sandpaper-main workflow with the same caching mechanisms.
+process as the `sandpaper-main` workflow with the same caching mechanisms.
 
 The artifacts produced are used by the next workflow.
 
@@ -172,7 +181,7 @@ The steps in this workflow are:
 3. If it is valid: update the pull request comment with the summary of changes
 
 Importantly: if the pull request is invalid, the branch is not created so any
-malicious code is not published. 
+malicious code is not published.
 
 From here, the maintainer can request changes from the author and eventually 
 either merge or reject the PR. When this happens, if the PR was valid, the 

.github/workflows/pr-close-signal.yaml

@@ -16,8 +16,8 @@ jobs:
           mkdir -p ./pr
           printf ${{ github.event.number }} > ./pr/NUM
       - name: Upload Diff
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
-          name: pr 
+          name: pr
           path: ./pr
 

.github/workflows/pr-comment.yaml

@@ -8,6 +8,11 @@ on:
     types:
       - completed
 
+concurrency:
+  group: pr-${{ github.event.workflow_run.pull_requests[0].number }}
+  cancel-in-progress: true
+
+
 jobs:
   # Pull requests are valid if:
   #  - they match the sha of the workflow run head commit
@@ -16,8 +21,8 @@ jobs:
   test-pr:
     name: "Test if pull request is valid"
     runs-on: ubuntu-latest
-    if: > 
-      github.event.workflow_run.event == 'pull_request' && 
+    if: >
+      github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
@@ -37,7 +42,7 @@ jobs:
         id: get-pr
         run: |
           unzip pr.zip
-          echo "::set-output name=NUM::$(<./NR)"
+          echo "NUM=$(<./NR)" >> $GITHUB_OUTPUT
 
       - name: "Fail if PR number was not present"
         id: bad-pr
@@ -48,14 +53,17 @@ jobs:
       - name: "Get Invalid Hashes File"
         id: hash
         run: |
-          echo "::set-output name=json::"$(curl -sL https://files.carpentries.org/invalid-hashes.json)
+          echo "json<<EOF
+          $(curl -sL https://files.carpentries.org/invalid-hashes.json)
+          EOF" >> $GITHUB_OUTPUT
       - name: "Check PR"
         id: check-pr
         if: ${{ steps.dl.outputs.success == 'true' }}
         uses: carpentries/actions/check-valid-pr@main
         with:
           pr: ${{ steps.get-pr.outputs.NUM }}
           sha: ${{ github.event.workflow_run.head_sha }}
+          headroom: 3 # if it's within the last three commits, we can keep going, because it's likely rapid-fire
           invalid: ${{ fromJSON(steps.hash.outputs.json)[github.repository] }}
           fail_on_error: true
 
@@ -70,9 +78,11 @@ jobs:
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
+    permissions:
+      contents: write
     steps:
       - name: 'Checkout md outputs'
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3
         with:
           ref: md-outputs
           path: built
@@ -96,11 +106,11 @@ jobs:
           git config --local user.name "GitHub Actions"
           CURR_HEAD=$(git rev-parse HEAD)
           git checkout --orphan md-outputs-PR-${NR}
-          git add -A 
+          git add -A
           git commit -m "source commit: ${CURR_HEAD}"
-          ls -A | grep -v '^.git' | xargs rm -r
+          ls -A | grep -v '^.git$' | xargs -I _ rm -r '_'
           cd ..
-          unzip -d built built.zip
+          unzip -o -d built built.zip
           cd built
           git add -A
           git commit --allow-empty -m "differences for PR #${NR}"
@@ -114,14 +124,16 @@ jobs:
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
+    permissions:
+      pull-requests: write
     steps:
       - name: 'Download comment artifact'
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
           name: 'diff'
-          
+
       - if: ${{ steps.dl.outputs.success == 'true' }}
         run: unzip ${{ github.workspace }}/diff.zip
 
@@ -130,7 +142,7 @@ jobs:
         if: ${{ steps.dl.outputs.success == 'true' }}
         uses: carpentries/actions/comment-diff@main
         with:
-          pr: ${{ env.NR }} 
+          pr: ${{ env.NR }}
           path: ${{ github.workspace }}/diff.md
 
   # Comment if the PR is open and matches the SHA, but the workflow files have
@@ -143,6 +155,8 @@ jobs:
     env:
       NR: ${{ github.event.workflow_run.pull_requests[0].number }}
       body: ${{ needs.test-pr.outputs.msg }}
+    permissions:
+      pull-requests: write
     steps:
       - name: 'Check for spoofing'
         id: dl

.github/workflows/pr-post-remove-branch.yaml

@@ -13,6 +13,8 @@ jobs:
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'
+    permissions:
+      contents: write
     steps:
       - name: 'Download artifact'
         uses: carpentries/actions/download-workflow-artifact@main
@@ -23,7 +25,7 @@ jobs:
         id: get-pr
         run: |
           unzip pr.zip
-          echo "::set-output name=NUM::$(<./NUM)"
+          echo "NUM=$(<./NUM)" >> $GITHUB_OUTPUT
       - name: 'Remove branch'
         uses: carpentries/actions/remove-branch@main
         with:

.github/workflows/pr-preflight.yaml

@@ -14,11 +14,15 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
+    permissions:
+      pull-requests: write
     steps:
       - name: "Get Invalid Hashes File"
         id: hash
         run: |
-          echo "::set-output name=json::"$(curl -sL https://files.carpentries.org/invalid-hashes.json)
+          echo "json<<EOF
+          $(curl -sL https://files.carpentries.org/invalid-hashes.json)
+          EOF" >> $GITHUB_OUTPUT
       - name: "Check PR"
         id: check-pr
         uses: carpentries/actions/check-valid-pr@main

.github/workflows/pr-receive.yaml

@@ -5,6 +5,10 @@ on:
     types:
       [opened, synchronize, reopened]
 
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test-pr:
     name: "Record PR number"
@@ -21,17 +25,19 @@ jobs:
       - name: "Upload PR number"
         id: upload
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: pr
           path: ${{ github.workspace }}/NR
       - name: "Get Invalid Hashes File"
         id: hash
         run: |
-          echo "::set-output name=json::"$(curl -sL https://files.carpentries.org/invalid-hashes.json)
+          echo "json<<EOF
+          $(curl -sL https://files.carpentries.org/invalid-hashes.json)
+          EOF" >> $GITHUB_OUTPUT
       - name: "echo output"
         run: |
-          echo ${{ steps.hash.outputs.json }}
+          echo "${{ steps.hash.outputs.json }}"
       - name: "Check PR"
         id: check-pr
         uses: carpentries/actions/check-valid-pr@main
@@ -52,10 +58,10 @@ jobs:
       MD: ${{ github.workspace }}/site/built
     steps:
       - name: "Check Out Main Branch"
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: "Check Out Staging Branch"
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: md-outputs
           path: ${{ env.MD }}
@@ -68,8 +74,6 @@ jobs:
 
       - name: "Set up Pandoc"
         uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: "2.11.4"
 
       - name: "Setup Lesson Engine"
         uses: carpentries/actions/setup-sandpaper@main
@@ -103,20 +107,20 @@ jobs:
         shell: Rscript {0}
 
       - name: "Upload PR"
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: pr
           path: ${{ env.PR }}
 
       - name: "Upload Diff"
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: diff
           path: ${{ env.CHIVE }}
           retention-days: 1
-      
+
       - name: "Upload Build"
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: built
           path: ${{ env.MD }}

.github/workflows/sandpaper-main.yaml

@@ -32,7 +32,7 @@ jobs:
     steps:
 
       - name: "Checkout Lesson"
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: "Set up R"
         uses: r-lib/actions/setup-r@v2
@@ -42,8 +42,6 @@ jobs:
 
       - name: "Set up Pandoc"
         uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: "2.11.4"
 
       - name: "Setup Lesson Engine"
         uses: carpentries/actions/setup-sandpaper@main