first attempt at an example git/github workflow lecture -- may need s…

…ome pruning, perhaps no audio -- just for reference?

01_DataScientistToolbox/02_07_02_gitWorkflow/index.Rmd

@@ -1,5 +1,5 @@
 ---
-title       : Git Workflow Example
+title       : Example Git/GitHub Workflow
 subtitle    : 
 author      : Jeffrey Leek, Assistant Professor of Biostatistics 
 job         : Johns Hopkins Bloomberg School of Public Health
@@ -26,100 +26,171 @@ mode        : selfcontained # {standalone, draft}
 
 ## Create a new repo on GitHub
 
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/01createNewRepo.png" height='500'/>
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/01createNewRepo.png" height='400'/>
+
+* Leave the box next to "Initialize this repository with a README" __unchecked__, since we will add one later
 
 ---
 
 ## Copy repo URL to clipboard
 
+* After clicking "create repository", you will get a screen with some basic instructions for getting started
+* They are a good starting point, but we won't follow them exactly here
+* Copy the URL displayed below to your clipboard (yours will be slightly different since it depends on your username and repo name)
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/02copyURL.png" height='160'/>
 
 ---
 
 ## Create a new local directory
 
+* Open Git Bash or Terminal (Windows or Mac, respectively) and create a new directory on your computer
+* "Step inside" of this new directory with the `cd` command
+* `mkdir` stands for "make directory", `cd` stands for "change directory", and `ls` stands for "list"
+* Since we get no output after typing `ls`, we can see that the directory we created is still empty
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/03makeDirectory.png" height='250'/>
 
 ---
 
 ## Create a new file in directory
 
+* Open your favorite text editor and create a new text file
+* Make sure to save it in the directory you just created
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/04createFile1.png" height='100'/>
 <br>
-<br>
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/05saveFile.png" height='250'/>
 
 ---
 
 ## Create a new repo locally
 
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/06newFileStatus.png" height='350'/>
+* We already created a __GitHub__ repository, but we still need to create a __Git__ repository locally on your computer
+* We can see that our new file is now in our chosen directory with `ls`
+* `git init` initializes a Git repo in our current directory
+* `git status` is a helpful command that we'll make frequent use of
+  * Does exactly what is sounds like -- gives us a "status report" for our local repo
 
----
-
-## Add link to remote repo
-
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/09gitRemoteAdd.png" height='150'/>
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/06newFileStatus.png" height='250'/>
 
 ---
 
 ## Stage file for commit
 
+* Notice that our newly created file falls under "untracked files" when we look at `git status`
+* Use `git add` to tell Git that we want it to start "paying attention" to this file
+  * Could have used `git add test_file.txt` for the same result, but `git add .` is often easier if you are okay tracking all currently untracked files
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/07gitAdd.png" height='350'/>
 
 ---
 
 ## Commit changes
 
+* Using `git commit` with a `-m` after it tells Git that whatever follows in double quotes is the message that we want to attach to this round of changes
+* Another call to `git status` confirms that there is nothing new to commit (since our first commit)
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/08_01gitCommit.png" height='250'/>
 
 ---
 
 ## Check log
 
+* `git log` shows us a history of all commits
+* So far, there's only one
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/08_02gitLog.png" height='250'/>
 
 ---
 
+## Add link to remote repo
+
+* We now have a remote repo on GitHub's servers and a local repo on our computer, but they still don't know about each other
+* To establish a link between the two, we paste the URL copied earlier from GitHub as follows
+
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/09gitRemoteAdd.png" height='150'/>
+
+* `git remote -v` shows us that our GitHub repo is now set up as a "remote" repository for our local repo, which allows the two repos to communicate
+
+---
+
 ## Push changes to GitHub
 
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/10gitPush.png" height='300'/>
+* We want our GitHub repo to reflect the changes we've made locally (i.e. to contain our new text file)
+* `git push -u origin master` tells Git to push our changes to the "master" (or main) branch of the "origin" (or primary) remote
+* You only need to include the `-u origin master` once, as Git will remember this configuration for future `push`es
+  * `git push` then becomes sufficient, assuming you don't want to do anything fancy
+
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/10gitPush.png" height='240'/>
 
 ---
 
 ## Check status
 
+* Check status again for piece of mind
+* Notice that it confirms _Your branch is up-to-date with 'origin/master'_
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/11gitStatus.png" height='250'/>
 
 ---
 
 ## Check GitHub
 
+* We want to make sure that our changes made it to GitHub safely and indeed they did
+* Our text file shows up in the file list
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/12checkGitHub.png" height='300'/>
 
 ---
 
+## Add README file from GitHub
+
+* How can we can "pull" changes from a remote repository to our local repository?
+* To illustrate, we'll add and edit a README file directly from the GitHub website 
+* A more common scenario would be that a collaborator makes changes to a shared repository and you want to incorporate those changes into your local repo
+* Click on the "Add a README" button on your GitHub repo page, under the list of files
+
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/13_01addReadme.png" height='75'/>
+
+---
+
 ## Edit README file from GitHub
 
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/13editReadme.png" height='300'/>
+* Put anything you want in the README, then press "Commit New File" to commit the file to your GitHub repo
+
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/13_02editReadme.png" height='225'/>
 <br>
 <br>
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/14commitNewFile.png" height='100'/>
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/14commitNewFile.png" height='75'/>
 
 ---
 
 ## Fetch changes from GitHub
 
+* Now that README.md exists on GitHub, we want to "pull" it down to our local repo
+* There is a `git pull` command that allows you to do this, but it's recommended that you instead use a combination of `git fetch` and `git merge`
+* `git fetch origin` tells Git to fetch all changes from the "origin" (primary) remote repo, which we set up earlier with `git remote add origin ...`
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/15gitFetch.png" height='300'/>
 
 ---
 
 ## Merge changes into local repo
 
-<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/16gitMerge.png" height='350'/>
+* Git is now aware of all changes that have been made to the remote (i.e. GitHub) repo
+* Still need to incorporate these changes into our local repo
+* `git branch -a` shows us that we now have two "branches" stored on our computer: `master` and `remotes/origin/master`
+* `master` represents the files on our local repo and `remotes/origin/master` represents the files we pulled from our remote repo
+* Use `git merge origin/master` to incorporate the changes from our remote repo
+
+<img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/16gitMerge.png" height='250'/>
 
 ---
 
 ## Check status
 
+* A quick call to `ls` confirms that the README.md file is now in our local directory
+* `git status` tells us that we have no new changes and are up-to-date with our remote repo
+
 <img class=center src="../../assets/img/01_DataScientistToolbox/gitWorkflow/17gitStatus.png" height='300'/>