Merge branch 'main' into kweav-nameChunks

trying to fix url checker with most recent sync changes

Author: carriewright11

.github/workflows/check-url.yml

@@ -78,6 +78,16 @@ jobs:
       run: |
         echo ${{ steps.check-report.outputs.error_url }}
         echo ${{ steps.check-report.outputs.error_num }}
+        
+      # Commit file
+    - name: Commit tocless bookdown files
+      if: ${{ steps.check-report.outputs.error_num >= 1 }}
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        git add --force check_reports/url_checks.tsv
+        git commit -m 'Add spell check file' || echo "No changes to commit"
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
 
     - name: Find issues
       id: find-issue

.github/workflows/pull_request.yml

@@ -17,7 +17,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -49,6 +48,8 @@ jobs:
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
+      toggle_md_linter: "${{ env.MARKDOWN_LINTER }}"
+      toggle_readability: "${{ env.READABILITY_REPORT }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
 
@@ -61,8 +62,9 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      gh_pat: secrets.GH_PAT
       branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs
@@ -72,8 +74,9 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: secrets.GH_PAT
       branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   quiz-check:
     name: Check quiz formatting
@@ -83,8 +86,9 @@ jobs:
     with:
       check_type: quiz_format
       error_min: 0
-      gh_pat: secrets.GH_PAT
       branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
 ############################# Style the code ###################################
   style-code:
@@ -111,6 +115,26 @@ jobs:
           git commit -m 'Style *mds' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
 
+############################# Readability Report ###################################
+
+  readability-report:
+    name: Readability report
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    if: ${{needs.yaml-check.outputs.toggle_readability == 'yes'}}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Readability report
+        uses: Rebilly/lexi@v2
+        with:
+          github-token: ${{ secrets.GH_PAT }}
+          glob: '**/*.md'
+
 ############################# Render Preview ###################################
 
   render-preview:

.github/workflows/render-all.yml

@@ -8,7 +8,8 @@ on:
   push:
     branches: [ main, staging ]
     paths:
-      - '**md$'
+      - '*.qmd'
+      - '*.Rmd'
       - assets/*
       - quizzes/*
 
@@ -101,7 +102,7 @@ jobs:
           git add --force docs/*
           git commit -m 'Render course' || echo "No changes to commit"
           git status docs/*
-          git push -u origin main  || echo "No changes to push"
+          git push --force -u origin main  || echo "No changes to push"
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
@@ -149,7 +150,7 @@ jobs:
           git add --force docs/no_toc*
           git commit -m 'Render toc-less' || echo "No changes to commit"
           git status docs/no_toc*
-          git push -u origin main  || echo "No changes to push"
+          git push --force -u origin main  || echo "No changes to push"
 
   render-leanpub:
     name: Finish Leanpub prep
@@ -188,6 +189,7 @@ jobs:
             --git_pat ${{ secrets.GH_PAT }} \
             --repo $GITHUB_REPOSITORY \
             --output_dir resources/chapt_screen_images)
+          rm make_screenshots.R
 
       # We want a fresh run of the renders each time
       - name: Delete manuscript/
@@ -276,4 +278,4 @@ jobs:
           git add --force docs/*
           git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
           git status
-          git push -u origin main  || echo "No changes to push"
+          git push --force -u origin main  || echo "No changes to push"

config_automation.yml

@@ -1,3 +1,4 @@
+
 ##### Checks run at pull request #####
 # Check quiz formatting
 check-quizzes: no
@@ -9,6 +10,10 @@ render-preview: yes
 spell-check: yes
 # Style any R code
 style-code: yes
+# Would you like your markdown files to be checked for formatting
+markdown-linter: yes
+# Would you like a readability report on your markdowns?
+readability-report: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
 # Should URLs be tested periodically?
@@ -18,8 +23,12 @@ url-check-periodically: yes
 # Rendering each platform's content
 render-website: rmd
 render-leanpub: yes
-render-coursera: yes
+render-coursera: no
+
+## Automate the creation of Book.txt file? yes/no
+## This is only relevant if render-leanpub is yes, otherwise it will be ignored
+make-book-txt: yes
 
 # What docker image should be used for rendering?
-# The default is jhudsl/course_template:main
-rendering-docker-image: 'jhudsl/course_template:main'
+# The default is jhudsl/base_ottr:main
+rendering-docker-image: 'jhudsl/base_ottr:main'

style-sets/itcr/index.Rmd

@@ -20,4 +20,4 @@ knitr::write_bib(c(
 
 # About this Course {-}
 
-This course is part of a series of courses for the [Informatics Technology for Cancer Research (ITCR)](https://itcr.cancer.gov/) called the Informatics Technology for Cancer Research Education Resource. This material was created by the ITCR Training Network (ITN)  which is a collaborative effort of researchers around the United States to support cancer informatics and data science training through resources, technology, and events. This initiative is funded by the following grant:  [National Cancer Institute (NCI)](https://www.cancer.gov/)  UE5 CA254170. Our courses feature tools developed by ITCR Investigators and make it easier for principal investigators, scientists, and analysts to integrate cancer informatics into their workflows. Please see our website at [www.itcrtraining.org](www.itcrtraining.org) for more information.
+This course is part of a series of courses for the [Informatics Technology for Cancer Research (ITCR)](https://www.cancer.gov/about-nci/organization/cssi/research/itcr). This material was created by the ITCR Training Network (ITN) which is a collaborative effort of researchers around the United States to support cancer informatics and data science training through resources, technology, and events. This initiative is funded by the following grant:  [National Cancer Institute (NCI)](https://www.cancer.gov/)  UE5 CA254170. Our courses feature tools developed by ITCR Investigators and make it easier for principal investigators, scientists, and analysts to integrate cancer informatics into their workflows. Please see our website at [www.itcrtraining.org](www.itcrtraining.org) for more information.