Merge c78a384 into 4b1e727

jhudsl · Jan 26, 2024 · 7c7e80b · 7c7e80b
2 parents 4b1e727 + c78a384
commit 7c7e80b
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Showing 10 changed files with 73 additions and 114 deletions.
diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
@@ -18,7 +18,7 @@ jobs:
 
       # Check out current repository
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Login as jhudsl-robot
         run: |

diff --git a/.github/workflows/docker-test.yml b/.github/workflows/docker-test.yml
@@ -33,10 +33,10 @@ jobs:
 
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Verify Dockerfiles changed?
-        uses: tj-actions/verify-changed-files@v8.8
+        uses: tj-actions/verify-changed-files@v17
         id: verify-changed-files
         with:
           files: |

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -14,9 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -31,23 +32,24 @@ jobs:
       # Make the branch fresh
       - name: Make the branch fresh
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
         shell: bash
 
+
     outputs:
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
 
 ########################## Make the error reports ##############################
   spell-check:
@@ -59,6 +61,7 @@ jobs:
       check_type: spelling
       error_min: 3
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   url-check:
     name: Check URLs
@@ -69,6 +72,7 @@ jobs:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   quiz-check:
     name: Check quiz formatting
@@ -79,6 +83,7 @@ jobs:
       check_type: quiz_format
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
 ############################# Style the code ###################################
   style-code:
@@ -91,7 +96,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -117,47 +122,27 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       # Set up git checkout
       - name: Set up git checkout
         run: |
-          git config --system --add safe.directory "$GITHUB_WORKSPACE"
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all
           git checkout $branch_name
           git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
         shell: bash
-
-      # Make sure the link for AnVIL feedback is prepopulated for the specific course
-      - name: Set up feedback link
-        id: feedback
-        run: bash scripts/AnVIL_Feedback_Script.sh
-
+
       # Run bookdown rendering
       - name: Run bookdown render
         id: bookdown
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-
-      # Render a student guide if specified. This is a bit clunky because
-      # Bookdown does not work well if the files aren't named as such in the
-      # root directory
-      - name: Run student guide render
-        if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
-        id: student_guide
-        run: |
-          mkdir tmp1
-          mv _bookdown.yml _output.yml tmp1
-          mv student-guide/_bookdown.yml student-guide/_output.yml .
-          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-          mv _bookdown.yml _output.yml student-guide
-          mv tmp1/_bookdown.yml tmp1/_output.yml .
-          rm -r tmp1
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
@@ -199,13 +184,13 @@ jobs:
       - name: Build components of the comment
         id: build-components
         run: |
-          course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
+          course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
           tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
-          student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
+          docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
           echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
           echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
-          echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
+          echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
@@ -220,7 +205,7 @@ jobs:
             Re-rendered previews from the latest commit:
             - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
             - See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
-            - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.student_docx_link }})
+            - Download the [preview of .docx file](${{ steps.build-components.outputs.docx_link }})
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace