malachig · cansavvy · May 2, 2023 · May 11, 2023 · May 13, 2023 · May 22, 2023
diff --git a/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md b/.github/ISSUE_TEMPLATE/new-course-add-to-sync.md
@@ -0,0 +1,14 @@
+---
+name: Add your new course to syncs/OTTR updates
+about: Provide information about your new course (which uses the OTTR template) so that we can enroll it in OTTR updates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+## What is the name of your new repository?
+<!-- The name of the repo. Ex the name of this repo is OTTR_Template -->
+
+## What username or organization is your new repository associated with?
+<!-- The name of the username or organization where the new repository is located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
diff --git a/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md b/.github/ISSUE_TEMPLATE/update-course-info-for-sync.md
@@ -0,0 +1,26 @@
+---
+name: Update your course's info for syncs/OTTR updates
+about: Provide information about your moved/renamed course (which uses the OTTR template) so that it can continue to be enrolled in OTTR updates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+<!-- Remove headings if they are not applicable to the changes/updates you made for your repo-->
+
+## If the name of your repository was changed ...
+
+### What was the old name?
+<!-- The old/original name of the repo. Ex the name of this repo is OTTR_Template -->
+
+### What is the new name?
+<!-- The new/modified name of the repo. Ex the name of this repo is OTTR_Template -->
+
+## If the repository was moved ...
+
+### What was the original username or organization your repository was associated with?
+<!-- The old/original name of the username or organization where the new repository was located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
+
+### What is the new username or organization your repository was associated with?
+<!-- The new/modified name of the username or organization where the new repository is located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
@@ -0,0 +1,8 @@
+---
+title: Broken URLs found in the course!
+labels: url-error
+---
+URL's in this course were just checked and some broken URLs were found.
+
+**Number of errors:** {{ env.ERROR_NUM }}  
+**File where errors are:** [url checks file here]({{ env.FILE_URL }})
diff --git a/.github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md b/.github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md
@@ -0,0 +1,9 @@
+---
+name: Add new repository to sync
+about: Enroll your repository for OTTR updates
+title: OTTR Updates Enrollment
+labels: ''
+assignees: cansavvy
+---
+
+Added __ repository to sync.yml in order to enroll in OTTR updates.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md → ...TEMPLATE/pull_request_template_general.md b/.github/PULL_REQUEST_TEMPLATE.md → ...TEMPLATE/pull_request_template_general.md
@@ -1,3 +1,12 @@
+---
+name: New Content or Feature
+about: New Content or Feature Update
+title: General Update
+labels: ''
+assignees:
+---
+
+
 <!--This PR Template was modified from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/.github/PULL_REQUEST_TEMPLATE.md-->
 
 ### Purpose/implementation Section
@@ -30,9 +39,9 @@
 
 - [ ] Any newly necessary packages that are needed have been added to the [Dockerfile and image](https://www.ottrproject.org/customize-docker.html).
 
-- [ ] Images are in the [correct format for rendering](https://www.ottrproject.org/writing_content.html#set-up-images).
+- [ ] Images are in the [correct format for rendering](https://www.ottrproject.org/writing_content_courses.html#set-up-images).
 
-- [ ] Every new image has [alt text and is in a Google Slide](https://www.ottrproject.org/writing_content.html#Accessibility).
+- [ ] Every new image has [alt text and is in a Google Slide](https://www.ottrproject.org/writing_content_courses.html#Accessibility).
 
 - [ ] Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this.
 

diff --git a/.github/automatic-issues/add-feedback-method.md b/.github/automatic-issues/add-feedback-method.md
@@ -1,4 +1,8 @@
 
 To help users report issues or areas of improvement for your course, you should provide a clear method of feedback for your users to route their concerns through.
 
-[Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html).
+- [ ] [Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html).
+
+It's also a good idea to collect passive feedback via Google Analytics.
+
+- [ ] [Read our guide to Google Analytics here](https://www.ottrproject.org/more_features.html#google-analytics).
diff --git a/.github/automatic-issues/images-checklist.md b/.github/automatic-issues/images-checklist.md
@@ -1,7 +1,7 @@
 
 Use this checklist to make sure your slides and images are set up correctly!
 
-See [Setting Up Images and Graphics](https://www.ottrproject.org/writing_content.html#set-up-images) for more info!
+See [Setting Up Images and Graphics](https://www.ottrproject.org/writing_content_courses.html#Set_up_images) for more info!
 
 - [ ] Create your course's main Google Slides.
 

diff --git a/.github/automatic-issues/set-repo-settings.md b/.github/automatic-issues/set-repo-settings.md
@@ -2,14 +2,12 @@
 For more information on these settings see instructions in [Starting a new OTTR course](https://www.ottrproject.org/getting_started.html#starting-a-new-ottr-course).
 
 - [ ] This course repository is set to `public`.
-- [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://www.ottrproject.org/getting_started.html#5_Add_jhudsl-robot_as_a_collaborator).
-
 - [ ] [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`.

diff --git a/.github/automatic-issues/templates-to-edit.md b/.github/automatic-issues/templates-to-edit.md
@@ -1,5 +1,5 @@
 
-[Follow the instructions here in ottrproject.org](https://www.ottrproject.org/writing_content.html) for details on how to start editing your OTTR course
+[Follow the instructions here in ottrproject.org](https://www.ottrproject.org/writing_content_courses.html) for details on how to start editing your OTTR course
 
 The following files need to be edited to get this new course started!
 
@@ -12,7 +12,7 @@ The following files need to be edited to get this new course started!
 
 ### Files that need to be edited upon adding each new chapter (including upon creating a new course):
 
-- [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://www.ottrproject.org/examples.html#publishing-with-bookdown).
+- [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://www.ottrproject.org/course_publishing.html#publishing-with-bookdown).
 - [ ] `book.bib` - any citations need to be added. See [instructions](https://www.ottrproject.org/more_features.html#citing-sources).
 
 ### Picking a style
@@ -26,7 +26,7 @@ By default this course template will use the jhudsl data science lab style. Howe
 
 - [ ] 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.
+- [ ] [Create a pull request](https://www.ottrproject.org/writing_content_courses.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:
 

diff --git a/.github/automatic-issues/update-enrollment.md b/.github/automatic-issues/update-enrollment.md
@@ -5,5 +5,7 @@ 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 course 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 course repository to receive these updates.
+  - [ ] Alternatively, [open an issue in the OTTR_Template repo](https://github.com/jhudsl/OTTR_Template/issues/new?assignees=cansavvy&labels=&projects=&template=new-course-add-to-sync.md&title=), providing us with the necessary information to add the course for you.
 
-- [ ] [Ensure that you have followed these instructions](https://www.ottrproject.org/getting_started.html#5_Add_jhudsl-robot_as_a_collaborator) to add the `jhudsl-robot` as a collaborator to your repository.
+In order for these syncs to happen we need credentials to do so. Our `jhudsl-robot` is what you need to give access to. 
+- [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://www.ottrproject.org/getting_started.html#5_Add_jhudsl-robot_as_a_collaborator).
diff --git a/.github/course_README_template.md b/.github/course_README_template.md
@@ -0,0 +1,24 @@
+# {Course Name}
+
+This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).
+
+You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.}
+
+If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/).
+
+## About this course
+
+This course introduces {info on what this course introduces}
+
+## Learning Objectives
+
+This course will teach learners to:  
+
+- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here}
+- {More learning objectives}
+
+## Encountering problems?
+
+If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}.
+
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />All materials in this course are licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> unless noted otherwise.
diff --git a/.github/sync.yml b/.github/sync.yml
@@ -20,41 +20,66 @@ group:
         dest: .github/ISSUE_TEMPLATE/course-problem-report.md
       - source: .github/ISSUE_TEMPLATE/course-content-add.md
         dest: .github/ISSUE_TEMPLATE/course-content-add.md
+      - source: .github/ISSUE_TEMPLATE/url-error.md
+        dest: .github/ISSUE_TEMPLATE/url-error.md
       - source: style-sets
         dest: style-sets
       - source: assets/box_images/
         dest: assets/box_images/
+      - source: resources/exclude_files.txt
+        dest: resources/exclude_files.txt
+      - source: config_automation.yml
+        dest: config_automation.yml
   # Repositories to receive changes
     repos: |
       jhudsl/Documentation_and_Usability
       jhudsl/Informatics_Research_Leadership
       jhudsl/Data_Management_for_Cancer_Research
-      jhudsl/Ethical_Data_Handling_for_Cancer_Research
       jhudsl/Computing_for_Cancer_Informatics
       jhudsl/Adv_Reproducibility_in_Cancer_Informatics
       jhudsl/Reproducibility_in_Cancer_Informatics
       jhudsl/Dissemination_and_Engagement
-      jhudsl/Cancer_Clinical_Informatics
+      fhdsl/Cancer_Clinical_Informatics
       jhudsl/Machine_Learning_for_Cancer_Informatics
       jhudsl/Cancer_Informatics_Data_Visualization
       jhudsl/Cancer_Genome_Informatics
-      jhudsl/Cancer-Imaging-Informatics
+      fhdsl/Cancer_Imaging_Informatics
       datatrail-jhu/DataTrail_Template
       abyzovlab/CNVpytor-course
-      opencasestudies/OCS_Guide
       tmm211/dsp-terra-mooc-test2
       fhdsl/Choosing_Genomics_Tools
       fhdsl/NIH_Data_Sharing
       fhdsl/FH_Cluster_Guide
       fhdsl/Using_Leanpub
-      fhdsl/Overleaf_Tutorial
+      fhdsl/Ethical_Data_Handling_for_Cancer_Research
+      fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles
       fhdsl/Design_of_Data_Analysis
       fhdsl/Tools_for_Reproducible_Workflows_in_R
       fhdsl/Introduction_to_reproducible_research
       mccoy-lab/hgv_modules
-
+      griffithlab/pVACtools_Intro_Course
+      griffithlab/CIVIC_SVI_Course
+      PracticalGenomics/cogaps-on-sciserver
+      fhdsl/AI_for_Efficient_Programming
+      fhdsl/AI_for_Decision_Makers
+      griffithlab/Immuno_Workflow_Course
+      fhdsl/Intro_to_R
+      fhdsl/Intro_to_Command_Line
+      fhdsl/Intro_to_Git_GitHub
+      fhdsl/WDL_Workflows_Guide
+      fhdsl/Intermediate-Git-GitHub
+      fhdsl/GitHub_Automation_for_Scientists
+      williamtmillsiv/introduction_to_bioinformatics
+      fhdsl/OTTR_Quarto
+      fhdsl/bench_to_bytes
+      fhdsl/Intermediate_R
+      fhdsl/DataViz_Practice
+      fhdsl/DataViz_Considerations
+      fhdsl/Intro_to_Python
+      fhdsl/Containers_for_Scientists
+      acmadeo/GARDE_try2
 ###ADD NEW REPO HERE following the format above#
-
+       
 ### These are custom groups for syncing -- not all files needs to be synced
   - files:
     - source: config_automation.yml
@@ -77,6 +102,8 @@ group:
       dest: scripts/make_screenshots.R
     - source: scripts/switch_sync_repo.R
       dest: scripts/switch_sync_repo.R
+    - source: config_automation.yml
+      dest: config_automation.yml
     repos: |
       jhudsl/OTTR_Quizzes
 
@@ -105,5 +132,49 @@ group:
       deleteOrphaned: true
     - source: style-sets/fhdasl/
       dest: style-sets/fhdasl/
+    - source: config_automation.yml
+      dest: config_automation.yml
     repos: |
       jhudsl/AnVIL_Template
+
+  - files:
+    - source: config_automation.yml
+      dest: config_automation.yml
+    - source: .github/workflows/
+      dest: .github/workflows/
+      deleteOrphaned: true
+    - source: .github/switch_sync_repo.R
+      dest: .github/switch_sync_repo.R
+    - source: .github/automatic-issues/
+      dest: .github/automatic-issues/
+    - source: assets/box_images/
+      dest: assets/box_images/
+    - source: assets/style.css
+      dest: assets/style.css
+    - source: assets/toc_close.css
+      dest: assets/toc_close.css
+    - source: scripts/
+      dest: scripts/
+    - source: config_automation.yml
+      dest: config_automation.yml
+      deleteOrphaned: true
+    repos: |
+      C-MOOR/C-MOOR_Template
+
+  - files:
+    - source: config_automation.yml
+      dest: config_automation.yml
+    - source: .github/workflows/
+      dest: .github/workflows/
+      deleteOrphaned: true
+    - source: .github/switch_sync_repo.R
+      dest: .github/switch_sync_repo.R
+    - source: assets/box_images/
+      dest: assets/box_images/
+    - source: scripts/
+      dest: scripts/
+      deleteOrphaned: true
+    - source: config_automation.yml
+      dest: config_automation.yml
+    repos: |
+      opencasestudies/OCS_Guide