Updating callouts in part i

Author: Susan Vanderplas

part-tools/04-scripts-notebooks.qmd

@@ -86,8 +86,8 @@ There are lots of other things you *can* do, but those are the two big ones.
 Let's try launching R and python from a system terminal, and then see that we can get the same windows within RStudio. 
 Keeping all of the windows you need for programming in one place is one of the most important features of an **integrated development environment (IDE)** like RStudio. 
 
-::: callout-tip
-### Your Turn - Interactive Command Prompts in R and Python
+::: diy
+### Try it out! Interactive Command Prompts in R and Python
 
 ::: panel-tabset
 
@@ -159,10 +159,8 @@ In many languages, scripts are intended to run on their own, from start to finis
 We often call this **executing** a script, and this is typically done from a terminal prompt. 
 
 
-::: callout-tip
-
-
-#### Your Turn - Scripts and Terminals
+::: diy
+#### Try it out! Scripts and Terminals
 
 Let's take a minute and see how someone might **call** or **run** a script from the terminal. 
 
@@ -249,8 +247,8 @@ This is because in R, to include a file of commands within another script, you r
 
 The difference between sourcing, running, and executing a script is fairly nuanced and the vocabulary is often used interchangeably, which doesn't help you as you're learning!
 
-::: callout-tip
-#### Your Turn - Sourcing a Script
+::: diy
+#### Try it out! Sourcing a Script
 
 If you haven't already, download [scripts.zip](../files/scripts.zip) and unzip the file.
 
@@ -363,7 +361,7 @@ We will use quarto markdown documents for most of the components of this class b
 
 While literate documents aren't ideal for jobs where a computer is doing things unobserved (such as pulling data from a web page every hour), they are extremely useful in situations where it is desireable to have both code and an explanation of what the code is doing and what the results of that code are in the same document.
 
-::: callout-tip
+::: diy
 
 #### Your Turn - Words in quarto
 
@@ -385,7 +383,7 @@ Congratulations, you've just compiled your first Quarto document!
 :::
 
 
-::: callout-tip
+::: diy
 #### Your turn -  Quarto Markdown
 
 In RStudio, create a new quarto markdown document: File \> New File \> Quarto Document. Give your document a title and an author, and select HTML as the output.
@@ -451,7 +449,7 @@ Where quarto comes primarily out of the R community and those who are agnostic w
 Quarto supports using the jupyter engine for chunk compilation, but jupyter notebooks have some (rather technical) features that make them less desirable for an introductory computing class [@xieFirstNotebookWar2018].
 As a result, this book makes an opinionated decision to prefer quarto over jupyter. 
 
-::: callout-learnmore
+::: learnmore
 #### Learn More about Notebooks
 
 There are some excellent opinions surrounding the use of notebooks in data analysis:

part-tools/05-git-and-github.qmd

@@ -13,7 +13,8 @@ There is an entire textbook on how to use git and GitHub with R, Happy Git and G
 ## What is Version Control ?
 
 ::: {.callout-note}
-Most of this section is either heavily inspired by Happy Git and Github for the UseR [@bryanHappyGitGitHub2021] or directly links to that book. There's no sense trying to repeat something that's pretty close to perfect. 
+Most of this section is either heavily inspired by Happy Git and Github for the UseR [@bryanHappyGitGitHub2021] or directly links to that book. 
+There's no sense trying to repeat something that's pretty close to perfect. 
 :::
 
 Git is a **version control system** - a structured way for tracking changes to files over the course of a project that may also make it easy to have multiple people working on the same files at the same time. 
@@ -100,10 +101,7 @@ Make sure you've completed the steps in  @sec-setting-up-github before you proce
 **Repositories** are single-project containers. You may have code, documentation, data, TODO lists, and more associated with a project. If you combine a git repository with an RStudio project, you get a very powerful combination that will make your life much easier, allowing you to focus on writing code instead of figuring out where all of your files are for each different project you start.
 
 To create a repository, you can start with your local computer first, or you can start with the online repository first. 
-
-::: {.callout-important}
-Both methods are relatively simple, but the options you choose depend on which method you're using, so be careful not to get them confused. 
-:::
+Both methods are relatively simple, but the options you choose depend on which method you're using, so be careful to pick one approach (and remember which one you picked!) for each new project. 
 
 ::: panel-tabset
 
@@ -231,7 +229,10 @@ These files are used by your operating system or by RStudio, and pushing them ma
 Tracking changes to  these files also doesn't really do much good.
 This is why I recommend that you run `usethis::git_vaccinate()`, which tells git to ignore these files for every repository on a machine.
 
-I **highly** recommend that you make a point to only add and commit files which you consciously want to track. 
+
+**While you are learning, you should only add and commit files which you created manually and consciously want to track.**
+You do not need to commit both a quarto `.qmd` file and the `.html` file it generates -- keeping only the quarto file is enough. 
+You *do* need to make sure to commit any pictures or files referenced in the files you create, though (as long as they're relatively small in size and not confidential), because otherwise, your project won't be self-contained. 
 
 ### Staging your changes
 
@@ -268,7 +269,7 @@ Work to commit  every time you've accomplished a small task. This will do two th
 When you're working alone, you generally won't need to worry about having to update your local copy of the repository (unless you're using multiple machines). 
 However, statistics  is collaborative, and one of the most powerful parts of git is that you can use it to keep track of changes when multiple people are working on the same document. 
 
-::: .watch-out
+::: callout-caution
 If you are working collaboratively and you and your collaborator are working on the same file, git will be able to resolve the change you make SO LONG AS YOU'RE NOT EDITING THE SAME LINE. 
 Git works based on lines of text - it detects when there is a change in any line of a text document.
 

part-tools/06-documents.qmd

@@ -258,7 +258,7 @@ I'm not convinced LaTeX succeeds at freeing you from layout concerns, but it's c
 The philosophy of LaTeX is that presentation shouldn't get in the way of content: you should be able to change the presentation formatting systematically, without having to mess with the content.
 This (theoretically) allows you to switch templates easily, make document-wide changes in a single command, and more.
 
-::: callout-tip
+::: diy
 
 ### Try it out
 
@@ -303,7 +303,7 @@ You can, for instance, start your document with `\documentclass[12pt]{article}`
 One of the most useful features in LaTeX is math mode, which you can enter by enclosing text in `$ ... $` (for inline statements), `$$ ... $$` or `\[ ... \]` (for statements on their own line), or using other environments like `\begin{array} ... \end{array}` that come in math-specific packages.
 Once in math mode, you can use [math symbol commands](https://www.caam.rice.edu/~heinken/latex/symbols.pdf) to get characters like $\theta, \pi, \sum, \int, \infty$, and more.
 
-::: callout-tip
+::: diy
 ### Try it out
 
 With any document creation software, the easiest way to learn how to do it is to find a sample document, tinker with it, see if you can make things the way you want them to be, and then google the errors when you inevitably screw something up.
@@ -394,7 +394,7 @@ Standard trade-offs (formatting details vs. document complexity) apply.
 Check out the [UNL-themed Beamer quarto template](https://github.com/unl-statistics/Templates/tree/main/slides-beamer-markdown)
 :::
 
-::: callout-tip
+::: diy
 #### Try it out
 
 Download and compile [beamer-demo.Rnw](../files/beamer-demo.Rnw).
@@ -477,7 +477,7 @@ UNL themed HTML presentations:
 -   [quarto reveal.js](https://github.com/unl-statistics/Templates/tree/main/slides-revealjs-quarto) ([zip of all required files](https://github.com/unl-statistics/Templates/raw/main/slides-revealjs-quarto.zip))
 :::
 
-::: callout-tip
+::: diy
 ### Try it out
 
 Take a few minutes and try each of them out to see what feels right to you.
@@ -500,7 +500,7 @@ As with beamer, you can easily integrate knitr code chunks into a document, so t
 
 Basic code for a poster in beamer (along with the necessary style files) that I've minimally customized to meet UNL branding requirements can be found [here](https://github.com/unl-statistics/Templates/raw/main/poster-beamer.zip).
 
-::: callout-tip
+::: diy
 #### Try it out
 
 Download the beamer template and do the following:
@@ -538,7 +538,7 @@ The `pagedown` package also has a couple of poster templates, including [poster-
 
 There are also templates for letters, business cards, and more in pagedown, if you're feeling ambitious.
 
-::: callout-tip
+::: diy
 #### Try it out
 
 Download the pagedown template and do the following: