From b15f66c47f6d41705f2439d0f2267e96610fa6fa Mon Sep 17 00:00:00 2001
From: Timothy Middelkoop <tmiddelkoop@internet2.edu>
Date: Tue, 4 Jun 2024 06:48:43 -0500
Subject: [PATCH] Expand and refine Git materials

---
 Notes.md  | 31 +++++++++++++++++++++++++------
 ReadMe.md |  9 +++++----
 2 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/Notes.md b/Notes.md
index 7579945..f32f0f8 100644
--- a/Notes.md
+++ b/Notes.md
@@ -13,7 +13,7 @@
     * Username: Enter username (your_name), which is the same as the first part of your your_name@skc.edu email address.
     * Click on "Complete Account" (you may need to click on "Leave")
   * Set a password:
-    * Click your avitar (colorful box in the top right) for a dropdown box
+    * Click your avatar (colorful box in the top right) for a dropdown box
     * Click "Settings" in the dropdown box
     * Click on "Account" tab on the left
       * **DO NOT USE YOUR SKC PASSWORD HERE!**
@@ -22,7 +22,7 @@
   * Create new repo:
     * Click the"+" in the upper right and select "+ New Repository"
     * Repository Name: skc-your_name
-    * Make repository private (Visiblity): check the checkbox
+    * Make repository private (Visibility): check the checkbox
     * Initialize Repository: check the checkbox
     * Click "Create Repository"
   * Navigate to your repo:
@@ -49,7 +49,7 @@
     * Under "Workspace" 
       * Set "Restore .RData into workspace at startup" to "No"
       * Set "Save workspace to .RData on exit" to "No"
-      * Set "Always save histroy" to "No"
+      * Set "Always save history" to "No"
       * Click "Ok"
   * Setup Git
     * This needs to be done only once when you create a "new project".
@@ -111,7 +111,7 @@ git config --local --list
       * Enter the username and password for the Git repo (not your account)
       * Make sure there is not an error
     * Verify push
-      * Click "Push" again and make sure it says "Everyting up-to-date"
+      * Click "Push" again and make sure it says "Everything up-to-date"
       * Close git window
     * Verify commit:
       * Click "Commit" under the *Git menu*
@@ -122,14 +122,14 @@ git config --local --list
   * Move Terminal and Console pane to the right
     * "View" -> Panes -> Console on Right
 
-## Quit Envrionment
+## Quit Environment
 
   * Git Commit: (see above)
   * Shutdown RStudio: "File" -> "Quit Session"
   * Shutdown Jupyter: "File" -> "Hub Control Panel" -> "Stop My Server"
   * Close all Jupyter and RStudio windows
 
-## Start Envrionment after Setup
+## Start Environment after Setup
 
   * Navigate to https://ci.skc.edu/ and click "Login to OSG Jupyter Notebook"
   * Start Jupyter: Select "Data Science with RStudio" and click "Start"
@@ -194,6 +194,25 @@ git fetch
 git status
 ```
 
+### Git Workflow
+
+  * Fetch any changes from the remote repository (Gitea): `git fetch`
+  * Check the status of your repository: `git status`
+  * If there are changes from the remote repository:
+    * See what changed: `git log origin` and `git diff origin` (more detail)
+    * Merge the changes: `git merge`
+  * Do work and edit your files
+  * Find a logical spot to stop and commit (save)
+  * See what changed:
+    * `git status`
+    * `git diff`
+  * Stage files (index): `git add file.txt`
+  * Double check that nothing has been added to the remote repository: `git fetch`
+  * Check the status: `git status`
+  * Commit changes: `git commit` (write a good commit title and message!)
+  * Push the changes to the remote repository: `git push`
+  * Rest
+
 ### R Configuration
 
 R packages must be installed every time the environment is started, to do this a `setup.R` script or a R Markdown document must be run with the following:
diff --git a/ReadMe.md b/ReadMe.md
index cf3add5..2ee694d 100644
--- a/ReadMe.md
+++ b/ReadMe.md
@@ -1,6 +1,6 @@
 # SKC CI Workshop June 2024
 
-*"If it's not Reproducible, it's Magic"*
+*"Getting started with Cyberinfrastructure"*
 
 ## Lessons
 
@@ -18,8 +18,8 @@ Lessons (Day 2):
 
   * Welcome and overview
   * Sharing & collaborating with code (Github introduction)
-    * Introduction: https://happygitwithr.com/big-picture.html
     * https://swcarpentry.github.io/git-novice/01-basics.html
+      * Motivation: https://happygitwithr.com/big-picture.html (extra background)
     * https://swcarpentry.github.io/git-novice/04-changes.html
     * https://swcarpentry.github.io/git-novice/05-history.html
     * https://swcarpentry.github.io/git-novice/06-ignore.html
@@ -34,17 +34,18 @@ Lessons (Day 2):
   * Login to the environment (SKC-CARE): https://ci.skc.edu/
   * Instructor Notes: [Notes.md](Notes.md)
   * Git and R (recommended for students and as a teaching resource): https://happygitwithr.com/
+    * Introduction: https://dx.doi.org/10.7287%2Fpeerj.preprints.3159v2
   * R Markdown: https://bookdown.org/yihui/rmarkdown/markdown-syntax.html
   * Git book: https://git-scm.com/book/en
-  * Git branching: 
+  * Git branching:
     * https://happygitwithr.com/git-branches (and remotes https://happygitwithr.com/git-remotes)
     * https://nvie.com/posts/a-successful-git-branching-model/
     * https://git-scm.com/book/en/v2/Git-Branching-Branches-in-a-Nutshell
   * R Tutorial: https://www.cyclismo.org/tutorial/R/
   * R project introduction http://cran.r-project.org/doc/manuals/R-intro.html
   * R Language: https://www.r-project.org/
-  * Test Driven Development (TDD) http://www.agiledata.org/essays/tdd.html
 
 ### Advanced Materials
 
   * Git internals: "Git for Ages 4 And Up" - https://youtu.be/1ffBJ4sVUb4
+  * Test Driven Development (TDD) http://www.agiledata.org/essays/tdd.html