Merge branch 'main' into cansavvy/buggs

.github/automatic-issues/git-secrets.md

@@ -0,0 +1,14 @@
+
+**Note these steps are only pertinent if you are setting up this website outside of the jhudsl organization**
+
+For more information on these settings see instructions in the [getting started on ottrproject.org](https://www.ottrproject.org/getting_started.html#6_Set_up_your_GitHub_personal_access_token).
+
+It's important that these are set up and named exactly what they are below in order for Github actions to work correctly.
+
+To set up these repository secrets, on your repository's main Github page, go to `Settings` and scroll down to see `Secrets` on the left side menu bar.
+
+- [ ] Set `GH_PAT`
+`Name`:  `GH_PAT`
+`value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token).
+Underneath `Select scopes`, check both `repo` and `workflow`.
+Then copy the PAT and save as the value.

.github/automatic-issues/set-repo-settings.md

@@ -0,0 +1,23 @@
+
+For more information on these settings see instructions in [Starting a new OTTR website](https://www.ottrproject.org/getting_started.html#starting-a-new-ottr-course).
+
+- [ ] This website repository is set to `public`.
+
+- [ ] [Github secret `GH_PAT` has been set](https://www.ottrproject.org/getting_started.html#6_Set_up_your_GitHub_personal_access_token)
+  `Name`:  `GH_PAT`
+  `value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token).
+  Underneath `Select scopes`, check both `repo` and `workflow`.
+  Then copy the PAT and save as the value.
+
+- [ ] GitHub pages is turned on
+  - [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`.  
+  - [ ] Check `Enforce HTTPS`.
+
+- [ ] [Set branch protections settings](https://www.ottrproject.org/getting_started.html#8_Set_up_branch_rules)
+  - [ ] `main` branch has been set up:
+    - [ ] `Require pull request reviews before merging` box is checked.
+    - [ ] `Require status checks to pass before merging` box is checked.
+      - [ ] Underneath that `Require branches to be up to date before merging` box is checked.
+  - [ ] Click `Save` at the bottom of the page!
+
+- [ ] [Customize GitHub actions](https://www.ottrproject.org/customize-robots.html) for what you will need in this website.

.github/automatic-issues/templates-to-edit.md

@@ -0,0 +1,32 @@
+
+[Follow the instructions here in ottrproject.org](https://www.ottrproject.org/editing_website.html) for details on how to start editing your OTTR website.
+
+The following files need to be edited to get this new website started!
+
+### Files that need edited upon creating a new website.
+
+- [ ] `README.md` - Fill in the README with the title of the website, a brief description of the website, and any other details that would be useful for anyone who encounters your website.
+- [ ] `index.Rmd` - Update the `title` field. Since this Rmd file serves as the website's landing page, include any information you believe will be beneficial for visitors upon their arrival.
+
+
+### Files that need to be edited upon adding each new page.
+
+- [ ] `_site.yml` - Include the title of your newly created page in the `text` field, and insert the corresponding html file name into the `href` field.
+
+### Picking a style
+
+See more [about customizing style on this page in the guide](https://www.ottrproject.org/customize-style.html).
+By default this website template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.
+
+#### Using a style set
+
+[Read more about the style sets here](https://www.ottrproject.org/customize-style.html#Using_a_style_set).
+
+- [ ] On a new branch, copy the `style-sets/<set-name>/index.Rmd` and `style-sets/<set-name>/_output.yml` to the top of the repository to overwrite the default `index.Rmd` and `_output.yml`.
+- [ ] Copy over all the files in the `style-sets/<set-name>/copy-to-assets` to the `assets` folder in the top of the repository.
+- [ ] [Create a pull request](https://www.ottrproject.org/writing_content.html#Open_a_pull_request) with these changes, and double check the rendered preview to make sure that the style is what you are looking for.
+
+### Files that need to be edited upon adding new packages that the book's code uses:
+
+- `docker/Dockerfile` needs to have the new package added so it will be installed. See [instructions](https://www.ottrproject.org/customize-docker.html).
+- The code chunk in `index.Rmd` should be edited to add the new package.

.github/automatic-issues/update-enrollment.md

@@ -0,0 +1,7 @@
+
+The original template: https://github.com/jhudsl/OTTR_Template_Website is always a work in progress.
+We are working on adding more features and smoothing out bugs as we go.
+
+If you want to receive updates from the original template to your website template, you will need to enroll this repository to the template updates by adding it to the `sync.yml` file.
+
+- [ ] [Follow these instructions](https://www.ottrproject.org/getting_started.html#9_Enroll_your_repository_for_OTTR_updates) to enroll your website repository to receive these updates.

.github/sync.yml

@@ -21,7 +21,7 @@ group:
         dest: config_automation.yml
   # Repositories to receive changes
     repos: |
-      jhudsl/ottr-website
+      jhudsl/ottrproject.org
       jhudsl/Baltimore_Community_Course
       maculatus/test-ottr-website
       dr-sayyadhury/OTTR_Template_Website_repo
@@ -30,8 +30,12 @@ group:
       buriedsand/glbio-personal-website
       PurplFeesh/test-ottr-site
       jcha40/ottr_test_site
-      jhudsl/ITCR_Tables
-      fhdsl/ITN_search
+      jhudsl/ITN_computing_resources
+      fhdsl/ITN_course_search
+      cansavvy/cansavvy_website
+      fhdsl/metricminer-dashboard
+      fhdsl/Intermediate_R
+      fhdsl/AnVIL_Poll_2024
 ###ADD NEW REPO HERE following the format above#
 
 ### These are custom groups for syncing -- not all files needs to be synced # will update later

.github/workflows/docker-test.yml

@@ -36,7 +36,7 @@ jobs:
         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: |

.github/workflows/file-automatic-issues.yml

@@ -0,0 +1,43 @@
+# Code adapted from https://github.com/JetBrains/intellij-platform-plugin-template/blob/deb171483598ee8a5d7621154db880e87b4db4ef/.github/workflows/template-cleanup.yml
+# by Candace Savonen for this repository.
+
+name: Starting a website
+
+on:
+  push:
+    branches: [ main, staging ]
+  workflow_dispatch:
+
+jobs:
+  # Run cleaning process only if workflow is triggered by not being in the Bookdown template anymore
+  template-cleanup:
+    name: Template Cleanup
+    runs-on: ubuntu-latest
+    if: github.event.repository.name != 'OTTR_Template_Website'
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+
+        # Issue for what repository settings need to be set
+      - name: New Course - Set Repository Settings
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: New Course - Set Repository Settings
+          content-filepath: .github/automatic-issues/set-repo-settings.md
+          labels: automated training issue
+
+      # Issue for what needs to be edited
+      - name: New Course - Templates to Edit
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: New Course - Templates to Edit
+          content-filepath: .github/automatic-issues/templates-to-edit.md
+          labels: automated training issue
+
+      # Issue for how to enroll repo for updates
+      - name: New Course - Template Update Enrollment
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: New Course - Template Update Enrollment
+          content-filepath: .github/automatic-issues/update-enrollment.md
+          labels: automated training issue

.github/workflows/render-site.yml

@@ -70,11 +70,14 @@ jobs:
           exit 1
 
 # Commit the rendered site files - html files and site_libs files
+# The git reset step will remove any other files created in this workflow, such as API keys
       - name: Commit rendered site files
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
           git add --force docs/*
           git commit -m 'Render site' || echo "No changes to commit"
-          git push --force origin main || echo "No changes to push"
+          git reset --hard HEAD
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          git push origin main || echo "No changes to push"

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+.DS_Store

config_automation.yml

@@ -12,13 +12,19 @@ spell-check: yes
 style-code: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
+# Should URLs be tested periodically?
+url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
 render-bookdown: yes
 render-leanpub: yes
 render-coursera: no
 
+## Automate the creation of Book.txt file? TRUE/FALSE?
+## This is only relevant if render-leanpub is yes, otherwise it will be ignored
+make-book-txt: TRUE
+
 # What docker image should be used for rendering?
 # The default is jhudsl/base_ottr:main
 rendering-docker-image: 'jhudsl/base_ottr:main'

docs/check_reports/spell_check_results.tsv

@@ -0,0 +1,2 @@
+word	file	lines
+ottrproject	README.md	3

docs/check_reports/url_checks.tsv

@@ -0,0 +1,2 @@
+urls	urls_status	file
+https://www.ottrproject.org/writing_content.html	failed	/github/workspace/editing.Rmd

docs/editing.html

@@ -290,7 +290,7 @@ <h1 class="title toc-ignore">Editing</h1>
 
 <p>Now that your website is alive and hosted, how do you start customizing it to have your content?</p>
 <p>If you already know how to file pull requests, feel free to start making edits as you see fit using some of the structure points we’ve noted below.</p>
-<p>If you are not familiar with pull requests, <a href="https://www.ottrproject.org/writing_content.html">read this guide to get started</a>.</p>
+<p>If you are not familiar with pull requests, <a href="https://www.ottrproject.org/editing_website.html">read this guide to get started</a>.</p>
 <div id="title" class="section level2">
 <h2>Title</h2>
 <p>To change the title of the website, modify the <code>name</code> line of the <code>_site.yml</code> file.</p>

resources/dictionary.txt

@@ -9,12 +9,16 @@ GH
 Github
 GitHub
 HTTPS
+ITN
+ITCR
 lightblue
 lightgreen
 OTTR
 Rmd
+repo
 subdir
 th
+tibble
 www
 automations
 Bootstap