adding updates from padma & Allissa

CONTRIBUTING.Qmd

@@ -8,7 +8,7 @@ The [Contributor Covenant Code of Conduct can be found here](https://github.com/
 
 To make a new cheatsheet, you can create a Rmd or md in the top of the repository. GitHub Actions will automatically render the cheatsheet as a PNG which will be saved to the `docs` folder.
 
-There are two style options: `css/ITN_style.css` and `css/OTTR_style.css`.
+There are two style options: `css/ITN_style.css` and `css/OTTR_style.css`.  
 
 Specify this in the yaml header: 
 
@@ -83,4 +83,4 @@ To get icons you can use the following:
 ## Adding cheatsheets to main page
 
 - Add information about the cheatsheet (and links) to the `gallery.yml` file
-- Check render of index.Qmd
+- Check render of index.Qmd

chunks/create_ottr_header.md

@@ -6,3 +6,6 @@
  <div class = "png_button"><a href="{PATH_TO_PNG}">Download cheatsheet</a></div>
 
  <div class = "time">**Last updated: `r format(Sys.time(), '%B %d, %Y')`** </div>
+
+<!-- Open all links in new tab-->  
+<base target="_blank" rel="noopener noreferrer"/> 

chunks/enable_actions.md

@@ -2,11 +2,13 @@
 
 <input type="checkbox">  In your OTTR repository, go to **Settings** in the top navigation tabs `r config::get("settings")`
 
-<input type="checkbox">  Go to **Actions** (General) in the side navigation `r config::get("actions")`
+<input type="checkbox">  Go to **Actions** in the menu on the left side `r config::get("actions")`
 
-<input type="checkbox">   Under **Workflow permissions**
+<input type="checkbox">  Select **General** just below **Actions**
 
-1. <input type="checkbox"> Select **Read and write permissions**
+<input type="checkbox">   Scroll down to **Workflow permissions**
+
+1. <input type="checkbox"> Ensure **Read and write permissions** is selected
 
 2. <input type="checkbox">  Check **Allow GitHub Actions to create and approve pull requests**
 

chunks/secrets.md

@@ -2,6 +2,8 @@
 
 <input type="checkbox"> In your OTTR repository, go to **Settings** in the top navigation tabs `r config::get("settings")`
 
+Note that this is different from your profile settings where you made your token. 
+
 <input type="checkbox"> Go to **Secrets and variables** in the side navigation `r config::get("secrets")`
 
 <input type="checkbox"> Click on **Actions**
@@ -16,4 +18,10 @@
 
 <br>
 
-[Click here to see GitHub documentation on setting repository secrets.](https://docs.github.com/en/codespaces/managing-codespaces-for-your-organization/managing-development-environment-secrets-for-your-repository-or-organization#adding-secrets-for-a-repository)
+
+<a
+  href="https://docs.github.com/en/codespaces/managing-codespaces-for-your-organization/managing-development-environment-secrets-for-your-repository-or-organization#adding-secrets-for-a-repository"
+  target="_blank"
+  rel="noopener noreferrer">
+  Click here to see GitHub documentation on setting repository secrets.
+</a>

chunks/starter_template.md

@@ -1,16 +1,18 @@
+
+
 ## Log into GitHub or make a GitHub profile if you are new to GitHub
 
-<input type="checkbox"> Go to https://github.com/
+<input type="checkbox"> Go to [github.com](https://github.com)
 
 <input type="checkbox"> Sign up for GitHub if you haven't already - it's free!
 
 <input type="checkbox"> Make sure you are logged into GitHub - check at https://github.com/ - you should see your profile in the upper right corner
 
-## Create a repository from the [{TEMPLATE_NAME}]({TEMPLATE_URL}) template
+## Create a repository from the {TEMPLATE_NAME} template
 
-<input type="checkbox"> Go to {TEMPLATE_URL}
+<input type="checkbox"> Go to [{TEMPLATE_NAME}]({TEMPLATE_URL})
 
-<input type="checkbox"> In the upper right, _click on_: <div class = "github_button"> <a href="https://github.com/new?template_name={TEMPLATE_NAME}"> Use this template</a></div>
+<input type="checkbox"> In the upper right, _click on_: <div class = "github_button">Use this template</div>
 
 Make sure you don't click on the green "Code" button instead!
 

chunks/token.md

@@ -2,27 +2,30 @@
 
 <input type="checkbox"> Click on your **profile photo** in the upper right `r config::get("profile")`
 
-<input type="checkbox"> Go to **Settings** `r config::get("settings")`
+<input type="checkbox"> Scroll down to **Settings** `r config::get("settings")`
 
-<input type="checkbox"> Go to **Developer Settings** in the lower left side navigation `r config::get("settings")`
+<input type="checkbox"> Scroll down in the menu on the left side to **Developer Settings** in the lower left side navigation `r config::get("settings")`
 
-<input type="checkbox"> Click on **Personal access tokens** `r config::get("token")`
+<input type="checkbox"> Scroll down in the left side menu on the left side to **Personal access tokens** `r config::get("token")`
 
 <input type="checkbox"> Select **Tokens (classic)** 
 
-<input type="checkbox"> Click gray "Generate new token" button
+<input type="checkbox"> Click very light gray button that says  <div class = "github_gray_button"> Generate new token ▾ </div> (upper right)
 
 <input type="checkbox"> Select **Generate new token (classic)** 
 
-<input type="checkbox"> Confirm your access
+<input type="checkbox"> Confirm your access if you have two factor authentication set up (you will be asked to submit a code or something similar)
 
-<input type="checkbox"> Name your token GH_PAT
+<input type="checkbox"> Name your token GH_PAT in the "Note" section
 
-<input type="checkbox"> Underneath **Select Scopes**, *check both* **repo** and **workflow** (all check boxes in those sections)
+Note that your token will expire based on the date that you set in the Expiration section. You will have to complete this process again when your token expires. GitHub will let you know as you will get an error about credentials. It is a good idea to use the default settings.
 
-<input type="checkbox"> Click: <div class = "github_button"><a href="https://github.com/settings/tokens/new"> Generate token</a></div>
+<input type="checkbox"> Underneath **Select Scopes** (where the check boxes are), check **repo** (so everything under it is checked) and **workflow** 
+
+<input type="checkbox"> Click: <div class = "github_button"> Generate token</div>
+
+<input type="checkbox"> Copy the **personal access token** `r config::get("copy")` and save somewhere safe and private. **Please note that you cannot retrieve this personal access token again later from GitHub.**  If you lose it, you just need to complete this process again. 
 
-<input type="checkbox"> Copy the **personal access token** `r config::get("copy")` and save somewhere safe and private
 
 <br>
 

css/OTTR_style.css

@@ -29,11 +29,26 @@ input[type="checkbox"] {
     font-size: 16px;
     margin: 4px 2px;
     transition-duration: 0.4s;
-    cursor: pointer;
 }
 
 /*------------- png boxes button style---------------- */
 
+
+.github_gray_button {
+    border-radius: 8px;
+    border: 1px solid #black;
+    background: #E8E8E8;
+    color: black !important;
+    box-shadow: 0 12px 16px 0 rgba(0,0,0,0.24), 0 17px 50px 0 rgba(0,0,0,0.19);
+    padding: 8px 16px;
+    text-align: center;
+    text-decoration: none;
+    display: inline-block;
+    font-size: 16px;
+    margin: 4px 2px;
+    transition-duration: 0.4s;
+}
+
 .png_button {
     position: absolute; /*----placement of button--*/
     top: 20px; /*----placement of button--*/
@@ -52,6 +67,8 @@ input[type="checkbox"] {
     cursor: pointer;
 }
 
+
+
 /*------------- timestamp style---------------- */
 .time {
   margin-top:60px;

ottr_course.Rmd

@@ -48,6 +48,6 @@ ottrpal::borrow_chapter(
 ottrpal::borrow_chapter(
   doc_path = "chunks/create_ottr_footer.md",
   tag_replacement = list(
-    "{AUTHORS}" = "Kate Isaac wrote the content and created the original styling, Carrie Wright did the css styling and Carrie Wright and Candace Savonen did the publishing engineering for the cheatsheet."
+    "{AUTHORS}" = "Kate Isaac wrote the content and created the original styling, Carrie Wright did the css styling and Carrie Wright and Candace Savonen did the publishing engineering for the cheatsheet. Padmashri Saravanan and Allissa Dillman from [BioDataSage](https://www.biodatasage.com/) worked with Carrie Wright to review and improve the cheatsheet."
     ))
 ```

ottr_quarto_website.Rmd

@@ -48,6 +48,6 @@ ottrpal::borrow_chapter(
 ottrpal::borrow_chapter(
   doc_path = "chunks/create_ottr_footer.md",
   tag_replacement = list(
-    "{AUTHORS}" = "Kate Isaac wrote the content and created the original styling, Carrie Wright did the css styling and Carrie Wright and Candace Savonen did the publishing engineering for the cheatsheet."
+    "{AUTHORS}" = "Kate Isaac wrote the content and created the original styling, Carrie Wright did the css styling and Carrie Wright and Candace Savonen did the publishing engineering for the cheatsheet. Padmashri Saravanan and Allissa Dillman from [BioDataSage](https://www.biodatasage.com/) worked with Carrie Wright to review and improve the cheatsheet."
     ))
 ```