Initial commit

.github/workflows/style-and-sp-check.yml

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+
+# This code was originally written by Josh Shapiro and Candace Savonen
+# for the Childhood Cancer Data Lab, an initiative of Alexs Lemonade Stand Foundation.
+# https://github.com/AlexsLemonade/refinebio-examples/blob/33cdeff66d57f9fe8ee4fcb5156aea4ac2dce07f/.github/workflows/style-and-sp-check.yml#L1
+
+# Adapted for this jhudsl repository by Candace Savonen Apr 2021
+
+name: Style and spell check R markdowns
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the main branch
+on:
+  pull_request:
+    branches: [ main ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "style and check"
+  style-n-check:
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/tidyverse:4.0.2
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - uses: actions/checkout@v2
+        # What branch to commit to: the one from the pull request
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Install packages
+        run: Rscript -e "install.packages(c('styler', 'spelling'))"
+
+      - name: Run spell check
+        id: spell_check_run
+        run: |
+          results=$(Rscript "scripts/spell-check.R")
+          echo "::set-output name=sp_chk_results::$results"
+          cat spell_check_results.tsv
+      - name: Archive spelling errors
+        uses: actions/upload-artifact@v2
+        with:
+          name: spell-check-results
+          path: spell_check_results.tsv
+
+      # If there are too many spelling errors, this will stop the workflow
+      - name: Check spell check results - fail if too many errors
+        if: ${{ steps.spell_check_run.outputs.sp_chk_results > 3 }}
+        run: exit 1
+
+      - name: Run styler
+        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+
+      - name: Commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add \*.Rmd
+          git commit -m 'Style Rmds' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.github/workflows/url-checker.yml

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+# Adapted from https://github.com/marketplace/actions/url-checker by Candace Savonen
+
+# This github actions tests URLs in the Rmd files, README, and CONTRIBUTING.md
+name: Check URLs
+
+# This will be run upon PRs to main
+on:
+  pull_request:
+    branches: [ main ]
+
+# Here's the main action of checking URLs
+jobs:
+  check_urls:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        # What branch to commit to: the one from the pull request
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Get Rmd file names
+        id: get_rmds
+        run: |
+          rmd_files=$(find . -type f -name '*.Rmd' -exec basename {} \;)
+          rmd_files=$(echo "$rmd_files" | xargs | sed -e 's/ /,/g')
+          file_list="CONTRIBUTING.md,README.md,${rmd_files[@]}"
+          echo "::set-output name=all_files::$file_list"
+          echo $file_list
+
+      - name: Check URLs
+        uses: paramt/url-checker@master
+        with:
+          files: "${{ steps.get_rmds.outputs.all_files }}"
+          blacklist: "${{ steps.get_rmds.outputs.all_files }},01-intro.md,about.md"

.gitignore

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+
+# ignore nonsense files
+.DS_Store
+.Rhistory
+.local
+.rstudio
+.bash_history
+
+spell_check_results.tsv
+
+

01-intro.Rmd

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+---
+title: "Course Title"
+output: html_document
+---
+
+# Introduction 
+
+## Motivation
+This course will cover 
+
+**Target Audience:**  
+The course is intended for 
+
+**Curriculum:**  
+The curriculum will cover

02-chapter_of_course.Rmd

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+---
+title: "Chapter title"
+output: html_document
+---
+
+## Learning Objectives
+
+This chapter will cover:  
+
+- {You can use https://www.bu.edu/cme/forms/RSS_forms/tips_for_writing_objectives.pdf to define some learning objectives here}
+- {Another learning objective}
+
+## Libraries
+
+For this chapter, we'll need the following packages attached. 
+
+```{r}
+library(here)
+library(ggplot2)
+library(magrittr)
+```
+
+# Topic of Section
+
+Text Text
+
+## Subtopic
+
+Text Text 
+
+### Code examples
+
+```{r}
+output_dir <- "code_output"
+if (!dir.exists(output_dir)) {
+  dir.create(output_dir)
+}
+```
+
+```{r}
+iris %>%
+  ggplot(aes(Sepal.Length, Sepal.Width, color = Species)) +
+  geom_point() +
+  theme_bw()
+```
+
+```{r}
+ggsave(file.path(output_dir, "test_ggplot2.png"))
+```
+
+### Image examples
+
+![](resources/images/itcr_training_network.png)
+
+![](resources/images/tools.png)
+
+### Video example
+
+![Introducing Markua](https://www.youtube.com/watch?t=105&v=VOCYL-FNbr0)
+
+### Citation examples
+
+We can put citations at the end of a sentence like this [@bookdown2016]. 
+
+In text, we can put citations like this @bookdown2016. 
+
+## Print out session info
+
+```{r}
+devtools::session_info()
+```
+

About.Rmd

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+---
+title: "about"
+output: html_document
+---
+
+# About the Authors {-}
+
+
+**Author Name** is a Blank in the Blank at the Blank.
+