Merge pull request #512 from jhudsl/pdfs-ugh

Working on fixing some pdf rendering stuff

.github/workflows/pull_request.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -71,7 +71,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -165,7 +165,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -188,7 +188,7 @@ jobs:
 
     steps:
     - name: checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Configure git
       run: |
@@ -281,7 +281,7 @@ jobs:
 
       # # Checks-out your repository with the token so your job can access it
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # get the full repo
           fetch-depth: 0
@@ -302,7 +302,7 @@ jobs:
 
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v37
+        uses: tj-actions/changed-files@v41
       # NOTE: `since_last_remote_commit: true` is implied by default and falls back to the previous local commit.
 
       - name: List all changed files
@@ -316,7 +316,7 @@ jobs:
         run: Rscript -e "rmarkdown::clean_site(preview = FALSE)"
 
        # Now we want to render all the html files from the Rmd files
-      - name: Run render html for the main site
+      - name: Run render html for the main website
         id: site
         run: Rscript -e "rmarkdown::render_site()"
 
@@ -325,7 +325,7 @@ jobs:
         run: Rscript "scripts/render_module_details_for_syllabus.R"
 
        # Render all module files
-      - name: Render html of modules
+      - name: Render html of modules where .Rmd has changed
         run: |
           Rscript --vanilla "scripts/render_modules.R" --files "${{ steps.changed-files.outputs.all_changed_files }}"
           
@@ -339,13 +339,14 @@ jobs:
         run: |
           Rscript --vanilla "scripts/render_resources.R" --files "${{ steps.changed-files.outputs.all_changed_files }}"
         
-       # Generate list of files that need pdfs
-      - name: Get list of html to pdfs
+        # Generate list of files that need pdfs
+      - name: Generate list of lectures that need pdfs generated
         run: |
           Rscript --vanilla "scripts/render_html_list.R"
+          echo the following need pdfs:
           echo "$(cat files.txt)"
         
-      - name: Read html and pdf files
+      - name: Store list of lectures that need pdfs generated // Delete intermediate files
         id: getfiles
         run: |
           echo "files=$(cat files.txt)" >> $GITHUB_OUTPUT 
@@ -441,7 +442,7 @@ jobs:
           git config --global --add safe.directory /__w/$repo_name/$repo_name
           
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
@@ -472,7 +473,7 @@ jobs:
           branch_name='preview-${{ github.event.pull_request.number }}'
           git diff origin/main -- '*.pdf' >/dev/null && changes=true || changes=false
           echo "changes=$changes" >> $GITHUB_OUTPUT 
-          git add . --force
+          git add *.pdf --force
           git commit -m 'Render preview' || echo "No changes to commit"
           git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push --force || echo "No changes to commit"

.github/workflows/render-site.yml

@@ -11,9 +11,6 @@ on:
   workflow_dispatch:
   push:
     branches: [ main, staging ]
-    paths:
-      - '**.Rmd'
-      - '**.md'
 
 jobs:
 
@@ -33,7 +30,7 @@ jobs:
     
       # # Checks-out your repository with the token so your job can access it
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # get the full repo
           fetch-depth: 0
@@ -42,7 +39,7 @@ jobs:
 
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v37
+        uses: tj-actions/changed-files@v41
       # NOTE: `since_last_remote_commit: true` is implied by default and falls back to the previous local commit.
 
       - name: List all changed files
@@ -80,12 +77,13 @@ jobs:
           Rscript --vanilla "scripts/render_resources.R" --files "${{ steps.changed-files.outputs.all_changed_files }}"
         
        # Generate list of files that need pdfs
-      - name: Get list of html to pdfs
+      - name: Generate list of lectures that need pdfs generated
         run: |
           Rscript --vanilla "scripts/render_html_list.R"
+          echo the following need pdfs:
           echo "$(cat files.txt)"
         
-      - name: Read html and pdf files
+      - name: Store list of lectures that need pdfs generated // Delete intermediate files
         id: getfiles
         run: |
           echo "files=$(cat files.txt)" >> $GITHUB_OUTPUT 
@@ -135,7 +133,7 @@ jobs:
           git config --global --add safe.directory /__w/$repo_name/$repo_name
     
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
@@ -152,7 +150,7 @@ jobs:
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "jhudsl-robot"
-          git add . --force
+          git add *.pdf --force
           git commit -m 'Render pdfs' || echo "No changes to commit"
           git pull --rebase --set-upstream origin main --allow-unrelated-histories --strategy-option=ours
           git push --force || echo "No changes to commit"

modules/Manipulating_Data_in_R/Manipulating_Data_in_R.Rmd

@@ -609,3 +609,12 @@ wide2
 https://sebkrantz.github.io/collapse/
 
 Might be helpful if your data is very large. However, `dplyr` and `tidyr` functions are great for most applications.
+
+
+
+
+
+
+
+
+

scripts/render_html_list.R

@@ -4,7 +4,7 @@
 
 # Read in all files needed
 
-files <- readr::read_csv("lecture_files.csv")
+files <- readr::read_csv("lecture_files.csv", show_col_types = FALSE)
 
 if(nrow(files) > 0) {
   files$files <- sapply(files$files, gsub, pattern = ".Rmd", replacement = "")