Clone the repo

.github/components/dictionary.txt

@@ -6,6 +6,7 @@ conda
 config
 DM
 doxxing
+dropdown
 formatters
 GitHub
 GitKraken

docs/contributing.md

@@ -19,6 +19,7 @@ To serve the documentation during local development, run `mkdocs serve` from the
 - [Docs organization](#docs-organization)
 - [Adding new documentation](#adding-new-documentation)
 - [Linking to other pages](#linking-to-other-pages)
+- [Phrasing](#phrasing)
 
 
 ## Docs organization
@@ -85,3 +86,10 @@ For example:
 ```
 This sentence should link to the [pull request documentation](STUB_LINK).
 ```
+
+
+## Phrasing
+
+For consistency, please use the following:
+
+- Refer to `github.com` as `GitHub`

docs/technical-setup/clone-the-repo.md

@@ -0,0 +1,52 @@
+# Clone the repository
+
+After [forking the `OpenScPCA` repository](./fork-the-repo.md), you will need to _clone_ your forked repository to your computer.
+Cloning provides you with a local copy of the repository to work with.
+You will need to clone the repository to every computer (or remote server) you want to use to contribute to the project.
+
+!!! note
+    You should clone your forked repository from `<username>/OpenScPCA-analysis`, _not_ `AlexsLemonade/OpenScPCA-analysis`.
+
+
+## Clone your forked repository
+
+Please follow the [instructions in this GitKraken video](https://help.gitkraken.com/gitkraken-client/open-clone-init/#cloning-an-existing-project) to clone your repository.
+
+This video presents two approaches to cloning: `Clone with URL`, and Clone based on your integrated `GitHub` account.
+Either approach is fine to take!
+
+While watching these instructions, please bear in mind the following:
+
+- Do not change the "Full path" field when cloning.
+You should retain the folder name `OpenScPCA-analysis`.
+- You can feel free to ignore all references to `LFS` ("large file storage") in this video.
+This does not apply to `OpenScPCA-analysis`.
+
+## Add the project repository as a remote repository
+
+The next step is to link the upstream repository (`AlexsLemonade/OpenScPCA-analysis`) as a remote.
+A _remote_ is a repository on `GitHub` that you are connected to.
+Each remote repository is given a name to make referring to them easier.
+For example, your forked repository on `GitHub` is called `origin` because it is where your local repository was cloned from.
+
+We will add another remote repository named `upstream` that refers to the original `AlexsLemonade/OpenScPCA-analysis` repository on `GitHub`.
+This will be called `upstream` because it was the source that your fork came from.
+
+Adding the `AlexsLemonade` _upstream remote_ will allow you to interact with it from your computer which can help you keep your fork in sync with the `OpenScPCA` project.
+But, you will still be working in your fork when writing analysis code.
+
+Follow these steps to add the upstream remote:
+
+1. From your repository in GitKraken, hover over the `1/1` text on the left-hand side `Remote` menu.
+This text will then turn into a plus-sign icon.
+Click that icon.
+![Click button to add the remote.](../img/add-upstream-remote-1.png){width="600"} <!-- No new line above, to keep tabbed in -->
+
+1. The following screen will prompt you to add a remote.
+Select `AlexsLemonade/OpenScPCA-analysis` from the dropdown menu, and click the button `Add remote`.
+![Add the upstream remote.](../img/add-upstream-remote-2.png){width="400"} <!-- No new line above, to keep tabbed in -->
+
+1. You should then see a second remote called `AlexsLemonade` on the left-hand side `Remote` panel.
+The specific listed items under this remote that you see will look different from the screenshot below; this is expected.
+As long as you see that `AlexsLemonade` is listed in the menu, you have successfully added the upstream remote.
+![View the added remote.](../img/add-upstream-remote-3.png){width="325"} <!-- No new line above, to keep tabbed in. Width needs to be >=325 for proper spacing, it seems. -->

docs/technical-setup/fork-the-repo.md

@@ -2,8 +2,9 @@
 
 You will need to create a [_fork_](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo#about-forks) of the [`OpenScPCA-analysis`](https://github.com/AlexsLemonade/OpenScPCA-analysis/) repository.
 
-A fork is a copy of an _upstream_ repository (here, `AlexsLemonade/OpenScPCA-analysis` is the _upstream_) that you will own and will be in your GitHub account.
+A fork is a copy of an _upstream_ repository (here, `AlexsLemonade/OpenScPCA-analysis` is the _upstream_) that you will own and will be in your `GitHub` account.
 As a contributor, you will perform analyses in your fork.
+Just like the upstream `AlexsLemonade/OpenScPCA-analysis` repository, your fork will also be a public repository.
 
 One benefit of using a fork is that changes you make will not affect the upstream project in `AlexsLemonade/OpenScPCA-analysis`.
 This means you can safely work on your analyses without worrying about messing anything up in the upstream repository.
@@ -19,10 +20,10 @@ Follow these steps to create your fork:
 
 1. At the top right corner, click the "Fork" button:
 (The numbers you see in this screenshot may differ from the numbers on the website - that's ok!)
-![Button on GitHub.com to fork a repository.](../img/fork-button.png){width="400"} <!-- No new line above, to keep tabbed in -->
+![Button on `GitHub` to fork a repository.](../img/fork-button.png){width="400"} <!-- No new line above, to keep tabbed in -->
 
 
-1. On the next screen, GitHub will prompt you for some settings about your fork.
+1. On the next screen, `GitHub` will prompt you for some settings about your fork.
 Make sure that these conditions are met, and then click the "Create fork" button on the bottom right.
     - Although the screenshot below shows an "Owner" username of `sjspielman`, you should see your username in this field.
     - Keep the default Repository name as `OpenScPCA-analysis`.
@@ -32,4 +33,4 @@ Make sure that these conditions are met, and then click the "Create fork" button
 
 
 1. That's it! 🎉
-In a few moments, GitHub will redirect to your newly forked repository at `https://github.com/YOUR_USERNAME/OpenScPCA-analysis`, and you're ready to proceed to the next step of [cloning your repository](./clone-the-repo.md).
+In a few moments, `GitHub` will redirect to your newly forked repository at `https://github.com/YOUR_USERNAME/OpenScPCA-analysis`, and you're ready to proceed to the next step of [cloning your repository](./clone-the-repo.md).

docs/technical-setup/install-a-github-client.md

@@ -1,6 +1,6 @@
 # Install a GitHub client
 
-You will need a platform on your computer to run Git commands and interact with [GitHub.com](https://github.com).
+You will need a platform on your computer to run Git commands and interact with [GitHub.com](https://github.com) (`GitHub`).
 
 There are many platforms you can choose, but we recommend using either [**GitKraken**](https://www.gitkraken.com/) or the [Git **command line interface**](https://git-scm.com/book/en/v2/Getting-Started-The-Command-Line).
 
@@ -19,8 +19,8 @@ GitKraken is free to use with public repositories like `OpenScPCA-analysis`; you
 
 1. Install GitKraken [using this link](https://www.gitkraken.com/download).
 
-2. Set up GitKraken on your machine by [directly signing in with your GitHub account](https://help.gitkraken.com/gitkraken-client/github-gitkraken-client/#sign-in-with-github).
-This will automatically provide you with the credentials you need to interact with GitHub without further setup.
+2. Set up GitKraken on your machine by [directly signing in with your `GitHub` account](https://help.gitkraken.com/gitkraken-client/github-gitkraken-client/#sign-in-with-github).
+This will automatically provide you with the credentials you need to interact with `GitHub` without further setup.
 
 
 ## Why use the Git command line interface?
@@ -38,7 +38,7 @@ The instructions for this depend on your operating system, as described below.
 
 After installing Git, you will also need take these steps:
 
-- [Set up an SSH key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh) to interact with GitHub
+- [Set up an SSH key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh) to interact with `GitHub`
 - [Set up your Git config file](https://git-scm.com/book/en/v2/Getting-Started-First-Time-Git-Setup)
 
 ### Install Git on macOS

mkdocs.yml

@@ -22,7 +22,7 @@ plugins:
 
 markdown_extensions:
   - admonition  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition
-  - attr_list # https://github.com/squidfunk/mkdocs-material/blob/master/docs/setup/extensions/python-markdown.md#attribute-lists
+  - attr_list   # https://github.com/squidfunk/mkdocs-material/blob/master/docs/setup/extensions/python-markdown.md#attribute-lists
 
 # Here is the basic structure of our navigation setup.
 #nav:
@@ -41,6 +41,7 @@ nav:
     - technical-setup/index.md
     - technical-setup/install-a-github-client.md
     - technical-setup/fork-the-repo.md
+    - technical-setup/clone-the-repo.md
   - Tools for communication:   # Slack, issues, discussions
     - communications-tools/index.md
   - Contributing to analyses:  # Setting up an analysis, all the git stuff