Merge pull request #123 from AlexsLemonade/sjspielman/113-posit-and-o…

…ther-links

Update some links in setup instructions

docs/setup_instructions/github_gitkraken_setup_instructions.md

@@ -2,26 +2,19 @@
 title: Setting up `git` and GitKraken
 ---
 
-<!-- START doctoc generated TOC please keep comment here to allow auto update -->
-<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
-### Table of Contents
-
-- [Setting up your computer](#setting-up-your-computer)
-- [Creating a GitHub account](#creating-a-github-account)
-- [Enabling Two-Factor Authentication (2FA) on GitHub](#enabling-two-factor-authentication-2fa-on-github)
-- [Setting up GitKraken](#setting-up-gitkraken)
-
-<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+**Table of contents**
 
+* TOC goes here
+{:toc}
 
 ## Setting up your computer
 
-Before setting up `git` and GitKraken, you'll need to follow these steps to install certain softwares on your computer: [Setup for macOS users](./installation_instructions_mac.html) or [Setup for Windows/PC users](./installation_instructions_windows.html). 
+Before setting up `git` and GitKraken, you'll need to follow these steps to install certain softwares on your computer: [Setup for macOS users](./mac_installation_instructions.html) or [Setup for Windows/PC users](./windows_installation_instructions.html).
 
 
 ## Creating a GitHub account
 
-Navigate in the browser to https://github.com, and click "Sign Up" in the top-right corner.
+Navigate in the browser to <https://github.com>, and click "Sign Up" in the top-right corner.
 
 <img src="screenshots/github/github_landing.png" alt="GitHub Sign In or Sign Up Page" width="500">
 
@@ -35,7 +28,7 @@ After you have filled the required information, GitHub will send the email you p
 
 <img src="screenshots/github/github_launchcode.png" alt="GitHub Launch Code Prompt" width="500">
 
-Next, GitHub will prompt you to fill out certain **Optional** personalization settings. 
+Next, GitHub will prompt you to fill out certain **Optional** personalization settings.
 You can skip this if you prefer (yellow arrow below), or you can follow the prompts accordingly.
 
 <img src="screenshots/github/github_personalization.png" alt="GitHub Personalization Page" width="500">
@@ -59,7 +52,7 @@ From the top-right corner Account dropdown icon (looks like weirdly arranged squ
 
 
 From the left-hand menu, select "Password and Authentication."
-Note, you can also take this moment to fill in your GitHub Public Profile, including your public-facing name, picture, email, bio, any anything else you like. 
+Note, you can also take this moment to fill in your GitHub Public Profile, including your public-facing name, picture, email, bio, any anything else you like.
 
 <img src="screenshots/github/github_settings_leftpane.png" alt="GitHub Settings Left Pane" width="500">
 
@@ -70,7 +63,7 @@ Click the large green button to "Enable two-factor authentication":
 You will then see several options for what _type_ of 2FA you can set up.
 _For the best security, we **strongly** recommend that you click "Set up using an app."_
 _The only reason not to choose this option is if you do not have a smartphone._
-This action requires that you install a separate app on your smart phone to generate authentication codes if you don't already have one.  
+This action requires that you install a separate app on your smart phone to generate authentication codes if you don't already have one.
 There are many authenticator app options, including the ones listed by GitHub (1Password, Authy, etc.) or others like Google Authenticator.
 Take a moment to either download a preferred 2FA app on your smartphone, or open a 2FA app if you already have one on your smartphone.
 
@@ -82,7 +75,7 @@ Click "Continue" to proceed with setup.
 
 
 **2FA with an Authenticator App**
- 
+
 After clicking "Continue,", you will see a QR code to scan _into your smartphone app_ (or click "enter this text code" if you prefer not to use the QR code with camera).
 
 <img src="screenshots/github/2fa_qr.png" alt="GitHub 2FA Setup for Authenticator App" width="500">
@@ -144,7 +137,7 @@ If you are _not_ already signed into GitHub in your browser, you will then be pr
 
 <img src="screenshots/github/gitkraken_git_signin.png" alt="GitKraken GitHub signin website" width="500">
 
-Next, you will have to grant GitKraken permission to link with your GitHub account. 
+Next, you will have to grant GitKraken permission to link with your GitHub account.
 Click "Authorize Axosoft:"
 
 <img src="screenshots/github/gitkraken_authorize_axosoft.png" alt="GitKraken Axosoft Authorization " width="500">
@@ -155,8 +148,8 @@ Finally, you will be redirected to a website confirming that you successfully li
 
 <img src="screenshots/github/gitkraken_success.png" alt="GitKraken GitHub Successful connection" width="500">
 
-When you return to GitKraken, you may be prompted to activate a free trial of GitKraken and to agree to the license. 
-We will only be using the free features of GitKraken during the workshop, so don't worry about when the trial will expire. 
+When you return to GitKraken, you may be prompted to activate a free trial of GitKraken and to agree to the license.
+We will only be using the free features of GitKraken during the workshop, so don't worry about when the trial will expire.
 (The paid version adds a number of advanced features, the most useful of which is probably the ability to interact with private repositories on GitHub.)
 
 <img src="screenshots/github/gitkraken_eula.png" alt="GitKraken End User License Agreement" width="400" >
@@ -168,7 +161,7 @@ After agreeing to the GitKraken license, you will be prompted to set up your pro
 Choose your favorite avatar, and add information as follows:
 
 - `Profile Name`: We recommend leaving this at its default, "Default Profile"
-- `Author Name`: Enter the preferred name you wish to be publicly associated with the actions you'll perform on GitHub. 
+- `Author Name`: Enter the preferred name you wish to be publicly associated with the actions you'll perform on GitHub.
 - `Author Email`: Enter the preferred email you wish to be publicly associated with the actions you'll perform on GitHub. This email does not have to be the same as the one you used to sign up for GitHub.
 
 <img src="screenshots/github/gitkraken_profile.png" alt="GitKraken Profile" width="500">
@@ -179,7 +172,7 @@ Click create profile, and on the following screen select to open a "Repo Tab:"
 
 <img src="screenshots/github/gitkraken_repo_terminal.png" alt="GitKraken Choose Repo or Terminal Tab" width="500">
 
- 
+
 Finally, you'll arrive on the GitKraken application's home view, and you're all set!
 
 <img src="screenshots/github/gitkraken_home.png" alt="GitKraken home view" width="500">

docs/setup_instructions/mac_installation_instructions.md

@@ -2,21 +2,10 @@
 title: macOS Installation Instructions
 ---
 
-<!-- START doctoc generated TOC please keep comment here to allow auto update -->
-<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of contents**
 
-### Table of Contents
-
-- [Apple Command Line Tools](#apple-command-line-tools)
-- [R and RStudio](#r-and-rstudio)
-  - [Installing R](#installing-r)
-  - [Installing the RStudio IDE](#installing-the-rstudio-ide)
-  - [Installing necessary R packages](#installing-necessary-r-packages)
-- [GitKraken](#gitkraken)
-- [A suitable text editor](#a-suitable-text-editor)
-  - [Installing Visual Studio Code](#installing-visual-studio-code)
-
-<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+* TOC goes here
+{:toc}
 
 
 
@@ -85,15 +74,13 @@ If you already have R and RStudio installed, you can skip this section!
 
 ### Installing R
 
-First, navigate to the CRAN website in the browser: https://cran.r-project.org/.
+First, navigate to the CRAN website in the browser: <https://cran.r-project.org/>.
 Click the link `Download R for macOS`:
 
 <img src="screenshots/mac/cran_1.png" alt="CRAN Landing Page" width="500">
 
 
-On the next page, click the link to install the **Intel 64-bit** of R, `R-4.2.0.pkg` (blue box in the image below).
-This Intel version will still work on M1 computers.
-We do **NOT** recommend installing the Apple silicon arm64 build (crossed out in the image below) because it tends to conflict with some Bioconductor packages which you may want to use in your own research.
+On the next page, click the link to install either `R-4.3.1-arm64.pkg` for M1/M2 Macs, or `R-4.3.1-x86_64.pkg` for Intel Macs.
 
 
 <img src="screenshots/mac/cran_2.png" alt="Website with link to download R" width="500">
@@ -103,27 +90,23 @@ We do **NOT** recommend installing the Apple silicon arm64 build (crossed out in
 Open the downloaded R installer, and follow instructions to install R onto your computer.
 Make sure to agree to the license in the setup menu and give your computer's password when prompted!
 
-<img src="screenshots/mac/r_installer.png" alt="R 4.2.0 Installer" width="500">
-
 
+#### An alternative installation approach
 
+Instead of manually downloading R, we in the Data Lab have enjoyed using the command-line software [`rig`](https://github.com/r-lib/rig) to manage different versions of R.
+If you are comfortable with command-line software, you are welcome to install `rig` and use it to install your preferred R version.
 
 ### Installing the RStudio IDE
 
 
-First, navigate to the RStudio website's Download page in the browser: https://www.rstudio.com/products/rstudio/download/#download.
+First, navigate to the RStudio website's Download page in the browser: <https://posit.co/download/rstudio-desktop/#download>.
 Click the large link to Download RStudio for Mac:
 
 <img src="screenshots/mac/rstudio.png" alt="RStudio Download Page" width="500">
 
 Open the downloaded RStudio installer, and follow instructions to install it onto your computer.
-Note that if you're using an Apple Silicon (M1) chip, you may be prompted to install something called `Rosetta 2` in order to use RStudio.
-`Rosetta 2` is a software made by Apple to support the Intel to M1 transition, and it is currently needed to run RStudio on M1 chips.
-If prompted to install `Rosetta 2`, agree to the prompt and follow instructions accordingly.
-
 Once the installation process is completed, you can now safely delete (eject) the disk image file.
 
-
 ### Installing necessary R packages
 
 For this workshop, you will need to have the following R packages installed:
@@ -168,7 +151,7 @@ The following image shows, for example, what these messages look like for a succ
 ## GitKraken
 
 We will use the GUI (graphical user interface) called `GitKraken` to work with `git` in this workshop.
-This GUI can be installed from https://www.gitkraken.com/, where you can click "Download GitKraken Client Free" (_do not pay!!_):
+This GUI can be installed from <https://www.gitkraken.com>, where you can click "Download GitKraken Client Free" (_do not pay!!_):
 
 <img src="screenshots/mac/gitkraken_mac_1.png" alt="GitKraken Landing Page" width="500">
 
@@ -192,7 +175,7 @@ For more information on setting up a GitHub account and the initial GitKraken se
 
 We will use a text editor to write code as part of this workshop, (and more generally, having a good text editor is something you want anyways!).
 We recommend [Visual Studio Code ("VS Code")](https://code.visualstudio.com/), but if you already have a text editor you prefer, please feel free to stick with that!
-Some alternatives you may have encountered are [Sublime Text](https://www.sublimetext.com/), [BBEdit](https://www.barebones.com/products/bbedit/), and [Atom](https://atom.io/).
+Some alternatives you may have encountered are [Sublime Text](https://www.sublimetext.com/) and [BBEdit](https://www.barebones.com/products/bbedit/).
 
 
 
@@ -202,7 +185,7 @@ Some alternatives you may have encountered are [Sublime Text](https://www.sublim
 
 ### Installing Visual Studio Code
 
-If you choose to  install VS Code, navigate to https://code.visualstudio.com/download in the browser.
+If you choose to  install VS Code, navigate to <https://code.visualstudio.com/download> in the browser.
 
 <img src="screenshots/mac/vscode_download.png" alt="Visual Studio Code Download Page" width="500">
 

docs/setup_instructions/windows_installation_instructions.md

@@ -2,27 +2,10 @@
 title: Windows Installation Instructions
 ---
 
-<!-- START doctoc generated TOC please keep comment here to allow auto update -->
-<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of contents**
 
-### Table of Contents
-
-- [Windows Subsystem for Linux (WSL)](#windows-subsystem-for-linux-wsl)
-  - [Optional: Enabling copy and paste in Ubuntu](#optional-enabling-copy-and-paste-in-ubuntu)
-- [R and RStudio](#r-and-rstudio)
-  - [Windows Installation of R, RStudio, and R Packages](#windows-installation-of-r-rstudio-and-r-packages)
-    - [R for Windows](#r-for-windows)
-    - [Optional: Install Rtools](#optional-install-rtools)
-    - [RStudio for Windows](#rstudio-for-windows)
-    - [R packages for Windows](#r-packages-for-windows)
-  - [WSL (Ubuntu Linux) Installation of R and R Packages](#wsl-ubuntu-linux-installation-of-r-and-r-packages)
-    - [R for WSL](#r-for-wsl)
-    - [R packages for WSL](#r-packages-for-wsl)
-- [GitKraken](#gitkraken)
-- [A suitable text editor](#a-suitable-text-editor)
-  - [Installing Visual Studio Code](#installing-visual-studio-code)
-
-<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+* TOC goes here
+{:toc}
 
 
 > Please be aware this setup process may take 1-2 hours to complete!
@@ -130,7 +113,7 @@ Otherwise, we may have to install them twice... [once for Windows](#r-packages-f
 
 #### R for Windows
 
-First, navigate to the CRAN website in the browser: https://cran.r-project.org/.
+First, navigate to the CRAN website in the browser: <https://cran.r-project.org/>.
 Click the link `Download R for Windows`:
 
 <img src="screenshots/windows/cran.png" alt="CRAN Landing Page" width="500">
@@ -157,7 +140,7 @@ Open the downloaded `.exe` file and follow the prompts to allow changes and inst
 
 #### RStudio for Windows
 
-First, navigate to the RStudio website's Download page in the browser: https://www.rstudio.com/products/rstudio/download/#download.
+First, navigate to the RStudio website's Download page in the browser: <https://posit.co/download/rstudio-desktop/#download>.
 Click the button to download RStudio for Windows.
 
 <img src="screenshots/windows/rstudio_download.png" alt="RStudio download page" width=500>
@@ -278,7 +261,7 @@ We will use the GUI (graphical user interface) called `GitKraken` to work with `
 
 
 
-GitKraken can be installed from https://www.gitkraken.com/, where you can click "Download GitKraken Client Free" (_do not pay!!_):
+GitKraken can be installed from <https://www.gitkraken.com>, where you can click "Download GitKraken Client Free" (_do not pay!!_):
 
 <img src="screenshots/windows/gitkraken_download.png" alt="GitKraken landing page" width="500">
 
@@ -296,11 +279,10 @@ For more information on setting up a GitHub account and the initial GitKraken se
 
 We will use a text editor to write code as part of this workshop, (and more generally, having a good text editor is something you want anyways!).
 We recommend [Visual Studio Code ("VS Code")](https://code.visualstudio.com/), but if you already have a text editor you prefer, please feel free to stick with that!
-Some alternatives you may have encountered are [Sublime Text](https://www.sublimetext.com/), [Notepad++](https://notepad-plus-plus.org), and [Atom](https://atom.io/).
-
+Some alternatives you may have encountered are [Sublime Text](https://www.sublimetext.com/) and [Notepad++](https://notepad-plus-plus.org).
 ### Installing Visual Studio Code
 
-To install VS Code, navigate to https://code.visualstudio.com/download in the browser.
+To install VS Code, navigate to <https://code.visualstudio.com/download> in the browser.
 Click the button labeled "Download for Windows".
 
 <img src="screenshots/windows/vscode_download.png" alt="VSCode landing page">