Merge branch 'main' into cansavvy/quarto-compatability

.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. -->

.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. -->

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

@@ -5,3 +5,4 @@ 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.

.github/sync.yml

@@ -58,17 +58,21 @@ group:
       griffithlab/pVACtools_Intro_Course
       griffithlab/CIVIC_SVI_Course
       PracticalGenomics/cogaps-on-sciserver
-      fhdsl/AI_for_software
+      fhdsl/AI_for_Efficient_Programming
       fhdsl/AI_for_Decision_Makers
       griffithlab/Immuno_Workflow_Course
-      fhdsl/S1_Intro_to_R
-      fhdsl/S1_Intro_to_Command_Line
-      fhdsl/S1_Intro_to_Git_GitHub
+      fhdsl/Intro_to_R
+      fhdsl/Intro_to_Command_Line
+      fhdsl/Intro_to_Git_GitHub
       fhdsl/WDL_Workflows_Guide
-      fhdsl/S2-Collaborative-Git-GitHub
+      fhdsl/Intermediate-Git-GitHub
       fhdsl/GitHub_Automation_for_Scientists
       williamtmillsiv/introduction_to_bioinformatics
-      fhdsl/ottr
+      fhdsl/OTTR_Quarto
+      fhdsl/bench_to_bytes
+      fhdsl/Intermediate_R
+      fhdsl/DataViz_Practice
+      fhdsl/DataViz_Considerations
 ###ADD NEW REPO HERE following the format above#
 
 ### These are custom groups for syncing -- not all files needs to be synced

.github/workflows/render-all.yml

@@ -200,7 +200,7 @@ jobs:
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
         run: |
           echo needs.yaml-check.outputs.toggle_make_book_txt == 'yes'
           echo needs.yaml-check.outputs.toggle_make_book_txt
@@ -211,7 +211,7 @@ jobs:
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \

.github/workflows/starting-course.yml

@@ -40,6 +40,8 @@ jobs:
             .github/workflows/starting-course.yml \
             .github/ISSUE_TEMPLATE/course-template-problem-report.md \
             .github/ISSUE_TEMPLATE/course-template-feature-request.md \
+            .github/ISSUE_TEMPLATE/new-course-add-to-sync.md \
+            .github/ISSUE_TEMPLATE/update-course-info-for-sync.md \
             .github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md \
             resources/code_output \
             resources/screenshots \

CONTRIBUTING.md

@@ -25,6 +25,10 @@ The [OTTR_Template_Website repository](https://github.com/jhudsl/OTTR_Template_W
 
 The [ottr-reports repository](https://github.com/jhudsl/ottr-reports) houses the functionality for reporting the results of the GitHub Action checks on spelling, URLs, and quiz formatting.
 
+#### ottr-docker
+
+The [ottr_docker repository](https://github.com/jhudsl/ottr_docker) holds the Dockerfiles for docker images available for use with OTTR.
+
 #### ottrpal
 
 The [ottrpal repository](https://github.com/jhudsl/ottrpal) provides the functionality to convert an OTTR course to files ready for use in Leanpub and Coursera
@@ -71,6 +75,7 @@ Open an issue describing the bug or feature request for the relevant repository
 | OTTR_Quizzes          | [Open an issue here](https://github.com/jhudsl/OTTR_Quizzes/issues/new/choose)         |
 | OTTR_Template_Website | [Open an issue here](https://github.com/jhudsl/OTTR_Template_Website/issues/new/choose)|
 | ottr-reports          | [Open an issue here](https://github.com/jhudsl/ottr-reports/issues/new/choose)         |
+| ottr-docker           | [Open an issue here](https://github.com/jhudsl/ottr_docker/issues/new/choose)          |
 | ottrpal               | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose)              |
 | cow                   | [Open an issue here](https://github.com/jhudsl/cow/issues/new/choose)                  |
 | ottrproject.org       | [Open an issue here](https://github.com/jhudsl/ottrpal/issues/new/choose)              |

docs/01-intro.md

@@ -17,77 +17,83 @@ The course covers...
 
 
 
-```r
+``` r
 devtools::session_info()
 ```
 
 ```
 ## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value                       
-##  version  R version 4.0.2 (2020-06-22)
-##  os       Ubuntu 20.04.5 LTS          
-##  system   x86_64, linux-gnu           
-##  ui       X11                         
-##  language (EN)                        
-##  collate  en_US.UTF-8                 
-##  ctype    en_US.UTF-8                 
-##  tz       Etc/UTC                     
-##  date     2024-04-12                  
+##  setting  value
+##  version  R version 4.3.2 (2023-10-31)
+##  os       Ubuntu 22.04.4 LTS
+##  system   x86_64, linux-gnu
+##  ui       X11
+##  language (EN)
+##  collate  en_US.UTF-8
+##  ctype    en_US.UTF-8
+##  tz       Etc/UTC
+##  date     2024-06-26
+##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
-##  package     * version date       lib source                            
-##  askpass       1.1     2019-01-13 [1] RSPM (R 4.0.3)                    
-##  assertthat    0.2.1   2019-03-21 [1] RSPM (R 4.0.5)                    
-##  bookdown      0.24    2024-03-13 [1] Github (rstudio/bookdown@88bc4ea) 
-##  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.0.2)                    
-##  callr         3.5.0   2020-10-08 [1] RSPM (R 4.0.2)                    
-##  cli           3.6.2   2023-12-11 [1] CRAN (R 4.0.2)                    
-##  crayon        1.3.4   2017-09-16 [1] RSPM (R 4.0.0)                    
-##  desc          1.2.0   2018-05-01 [1] RSPM (R 4.0.3)                    
-##  devtools      2.3.2   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  digest        0.6.25  2020-02-23 [1] RSPM (R 4.0.0)                    
-##  ellipsis      0.3.1   2020-05-15 [1] RSPM (R 4.0.3)                    
-##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.0.2)                    
-##  fansi         0.4.1   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.0.2)                    
-##  fs            1.5.0   2020-07-31 [1] RSPM (R 4.0.3)                    
-##  glue          1.4.2   2020-08-27 [1] RSPM (R 4.0.5)                    
-##  hms           0.5.3   2020-01-08 [1] RSPM (R 4.0.0)                    
-##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.0.2)                    
-##  httr          1.4.2   2020-07-20 [1] RSPM (R 4.0.3)                    
-##  jsonlite      1.7.1   2020-09-07 [1] RSPM (R 4.0.2)                    
-##  knitr         1.33    2024-03-13 [1] Github (yihui/knitr@a1052d1)      
-##  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.0.2)                    
-##  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.0.2)                    
-##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.0.2)                    
-##  openssl       1.4.3   2020-09-18 [1] RSPM (R 4.0.3)                    
-##  ottrpal       1.2.1   2024-03-13 [1] Github (jhudsl/ottrpal@48e8c44)   
-##  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.0.2)                    
-##  pkgbuild      1.1.0   2020-07-13 [1] RSPM (R 4.0.2)                    
-##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.0.3)                    
-##  pkgload       1.1.0   2020-05-29 [1] RSPM (R 4.0.3)                    
-##  prettyunits   1.1.1   2020-01-24 [1] RSPM (R 4.0.3)                    
-##  processx      3.4.4   2020-09-03 [1] RSPM (R 4.0.2)                    
-##  ps            1.4.0   2020-10-07 [1] RSPM (R 4.0.2)                    
-##  R6            2.4.1   2019-11-12 [1] RSPM (R 4.0.0)                    
-##  readr         1.4.0   2020-10-05 [1] RSPM (R 4.0.2)                    
-##  remotes       2.2.0   2020-07-21 [1] RSPM (R 4.0.3)                    
-##  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.0.2)                    
-##  rmarkdown     2.10    2024-03-13 [1] Github (rstudio/rmarkdown@02d3c25)
-##  rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.0.2)                    
-##  sessioninfo   1.1.1   2018-11-05 [1] RSPM (R 4.0.3)                    
-##  stringi       1.5.3   2020-09-09 [1] RSPM (R 4.0.3)                    
-##  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.0.3)                    
-##  testthat      3.0.1   2024-03-13 [1] Github (R-lib/testthat@e99155a)   
-##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.0.2)                    
-##  usethis       1.6.3   2020-09-17 [1] RSPM (R 4.0.2)                    
-##  utf8          1.1.4   2018-05-24 [1] RSPM (R 4.0.3)                    
-##  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.0.2)                    
-##  withr         2.3.0   2020-09-22 [1] RSPM (R 4.0.2)                    
-##  xfun          0.26    2024-03-13 [1] Github (yihui/xfun@74c2a66)       
-##  xml2          1.3.2   2020-04-23 [1] RSPM (R 4.0.3)                    
-##  yaml          2.2.1   2020-02-01 [1] RSPM (R 4.0.3)                    
+##  package     * version date (UTC) lib source
+##  askpass       1.2.0   2023-09-03 [1] RSPM (R 4.3.0)
+##  bookdown      0.39.1  2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
+##  cachem        1.0.8   2023-05-01 [1] RSPM (R 4.3.0)
+##  cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
+##  devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
+##  digest        0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
+##  ellipsis      0.3.2   2021-04-29 [1] RSPM (R 4.3.0)
+##  evaluate      0.23    2023-11-01 [1] RSPM (R 4.3.0)
+##  fansi         1.0.6   2023-12-08 [1] RSPM (R 4.3.0)
+##  fastmap       1.1.1   2023-02-24 [1] RSPM (R 4.3.0)
+##  fs            1.6.3   2023-07-20 [1] RSPM (R 4.3.0)
+##  glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
+##  hms           1.1.3   2023-03-21 [1] RSPM (R 4.3.0)
+##  htmltools     0.5.7   2023-11-03 [1] RSPM (R 4.3.0)
+##  htmlwidgets   1.6.4   2023-12-06 [1] RSPM (R 4.3.0)
+##  httpuv        1.6.14  2024-01-26 [1] RSPM (R 4.3.0)
+##  httr          1.4.7   2023-08-15 [1] RSPM (R 4.3.0)
+##  jsonlite      1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
+##  knitr         1.47.3  2024-06-11 [1] Github (yihui/knitr@e1edd34)
+##  later         1.3.2   2023-12-06 [1] RSPM (R 4.3.0)
+##  lifecycle     1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
+##  magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
+##  memoise       2.0.1   2021-11-26 [1] RSPM (R 4.3.0)
+##  mime          0.12    2021-09-28 [1] RSPM (R 4.3.0)
+##  miniUI        0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
+##  openssl       2.1.1   2023-09-25 [1] RSPM (R 4.3.0)
+##  ottrpal       1.2.1   2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
+##  pillar        1.9.0   2023-03-22 [1] RSPM (R 4.3.0)
+##  pkgbuild      1.4.3   2023-12-10 [1] RSPM (R 4.3.0)
+##  pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.3.0)
+##  pkgload       1.3.4   2024-01-16 [1] RSPM (R 4.3.0)
+##  profvis       0.3.8   2023-05-02 [1] RSPM (R 4.3.0)
+##  promises      1.2.1   2023-08-10 [1] RSPM (R 4.3.0)
+##  purrr         1.0.2   2023-08-10 [1] RSPM (R 4.3.0)
+##  R6            2.5.1   2021-08-19 [1] RSPM (R 4.3.0)
+##  Rcpp          1.0.12  2024-01-09 [1] RSPM (R 4.3.0)
+##  readr         2.1.5   2024-01-10 [1] RSPM (R 4.3.0)
+##  remotes       2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
+##  rlang         1.1.4   2024-06-04 [1] CRAN (R 4.3.2)
+##  rmarkdown     2.27.1  2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
+##  sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
+##  shiny         1.8.0   2023-11-17 [1] RSPM (R 4.3.0)
+##  stringi       1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
+##  stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
+##  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.2)
+##  tzdb          0.4.0   2023-05-12 [1] RSPM (R 4.3.0)
+##  urlchecker    1.0.1   2021-11-30 [1] RSPM (R 4.3.0)
+##  usethis       2.2.3   2024-02-19 [1] RSPM (R 4.3.0)
+##  utf8          1.2.4   2023-10-22 [1] RSPM (R 4.3.0)
+##  vctrs         0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
+##  xfun          0.44.4  2024-06-11 [1] Github (yihui/xfun@9da62cc)
+##  xml2          1.3.6   2023-12-04 [1] RSPM (R 4.3.0)
+##  xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
+##  yaml          2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
 ## 
-## [1] /usr/local/lib/R/site-library
-## [2] /usr/local/lib/R/library
+##  [1] /usr/local/lib/R/site-library
+##  [2] /usr/local/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────
 ```