update some git

Author: zingale

content/_toc.yml

@@ -75,6 +75,13 @@ parts:
     - file: 09-packages/python-packages
     - file: 09-packages/python-tools
 
+  - caption: Git and Github
+    chapters:
+    - file: git/version-control
+    - file: git/git
+    - file: git/github
+    - file: git/pull-requests
+
   - caption: Unit tests
     chapters:
     - file: 10-testing/testing
@@ -88,9 +95,3 @@ parts:
     - file: 12-extensions/extensions-overview
     - file: 12-extensions/extensions-example
 
-  - caption: Git and Github
-    chapters:
-    - file: git/version-control
-    - file: git/git
-    - file: git/github
-    - file: git/pull-requests

content/git/git.md

@@ -29,7 +29,7 @@ git config --global core.editor "nano -w"
 
 Replace `name` with your name and `email` with your email.  This sets `nano`
 as our default editor, but you can choose something else that you are comfortable
-with (see https://swcarpentry.github.io/git-novice/02-setup/index.html#line-endings).
+with (see https://swcarpentry.github.io/git-novice/02-setup.html).
 
 This information will be stored in a file called ``.gitconfig`` in your home directory.
 
@@ -99,7 +99,7 @@ project.
 
    ```
    commit 2001a0e996110926a576dcb5fc13fc8022864d0b (HEAD -> main)
-   Author: Michael Zingale <michael.zingake@stonybrook.edu>
+   Author: Michael Zingale <michael.zingale@stonybrook.edu>
    Date:   Sun Jan 30 13:11:24 2022 -0500
 
        my first change
@@ -165,8 +165,7 @@ project.
            modified:   README
    ```
 
-   ```{note}
-   **What is add really doing?**
+   ```{admonition} What is `add` really doing?
 
    Git has a concept call the *staging area*.  When we ``add`` a
    file, git puts the changes into the staging area.  We can add

content/git/version-control.md

@@ -1,5 +1,23 @@
 # Version Control
 
+````{note}
+To follow along, you will need to install `git` on your computer.
+You can follow the instructions from the [Software Carpentry lessons](https://carpentries.github.io/workshop-template/install_instructions/#git).  In particular, for:
+
+* Windows: use [git for Windows](https://gitforwindows.org/)
+
+* Mac: in a teminal, do:
+
+  ```
+  git --version
+  ```
+  
+  If it is not already installed, it will prompt you for installation.
+
+* Linux: it is probably already installed, but otherwise, use your
+  package manager.
+````
+
 ## Why use version control?
 
 When we develop code, we are going to be making lots of changes over
@@ -13,7 +31,7 @@ time.  And you will find yourself in the following situations:
 * *Your research group is all working on the same code* and you need to sync up with
   everyone's changes and make sure that no one breaks the code.
 
-This is what version control does for us.
+This is what [version control](https://en.wikipedia.org/wiki/Version_control) does for us.
 
 
 ```{note}