Add readability report and secrets: bug fix (#794)

* Try this out

* ${secrets.GH_PAT}

* Update README

* ${{ secrets. }}

* Fix secrets

* adding readability reports

* Markdown

* indent

* Will this work?

* Try it out

* Fix image:

* Try not fetch-depth: 0

* Try not actually on the docker image

* Try this way

* Try once more

* markdownlint-cli2

* Update linter

* continue-on-error: true

* Try this out

* echo it

* Delete for now

.github/workflows/pull_request.yml

@@ -48,6 +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 }}"
 
@@ -60,8 +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
@@ -71,8 +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
@@ -82,8 +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:
@@ -110,6 +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:

README.md

@@ -25,8 +25,13 @@ _This template and guide helps you_:
 - [Advanced Reproducibility in Cancer Informatics](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/)
 
 ## To Get Started
+
 - Go to the [ottrproject.org](https://www.ottrproject.org/).
 - Check out the [rendered version of the template](https://jhudatascience.org/OTTR_Template/).
 - Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform.
 - Please take a look at the [code of conduct](./code_of_conduct.md).
 - If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated.
+
+## Contributing
+
+If you'd like to contribute, we love that! Please go to the [CONTRIBUTING.md doc](https://github.com/jhudsl/OTTR_Template/blob/main/CONTRIBUTING.md).

_output.yml

@@ -16,3 +16,4 @@ bookdown::gitbook:
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
 bookdown::word_document2:
   toc: true
+  always_allow_html: true

config_automation.yml

@@ -10,6 +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?