Merge pull request #140 from janash/2024-updates

updates including major documentation lesson updates

_episodes/02-git.md

@@ -27,18 +27,18 @@ point.
 You will need to make sure that you have `git` installed and configured,
 as described in the set-up instructions.
 
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip)
-
-Alternatively, download the repository using the command line:
-
 ````{tab-set-code} 
 
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout git-start
+git switch -c main
 ```
 ````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
 :::
 
 ## What is version control?

_episodes/03-github.md

@@ -21,17 +21,21 @@ To follow along with this lesson, you can complete the previous lessons,
 or you can download a pre-made workshop repository that is at the starting 
 point.
 
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/github-start.zip)
-
-Alternatively, download the repository using the command line:
+You will need to make sure that you have `git` installed and configured,
+as described in the set-up instructions.
 
 ````{tab-set-code} 
+
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout github-start
+git switch -c main
 ```
 ````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
 :::
 
 ## Securely accessing GitHub

_episodes/04-function-style.md

@@ -18,22 +18,25 @@ Objectives:
 :::{admonition} Follow Along with This Lesson
 :class: tip
 
-To follow along with this lesson, you should first complete
-the 'Using Branches Exercise' in Episode 2 or you can download a pre-made workshop repository that is at the starting 
+To follow along with this lesson, you can complete the previous lessons,
+or you can download a pre-made workshop repository that is at the starting 
 point.
 
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/python-coding-style-start.zip)
-
-Alternatively, download the repository using the command line:
+You will need to make sure that you have `git` installed and configured,
+as described in the set-up instructions.
 
 ````{tab-set-code} 
+
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout python-coding-style-start
-
+git switch -c main
 ```
 ````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
 :::
 
 ## Editing a function in our package

_episodes/05-package-structure.md

@@ -17,24 +17,29 @@ Objectives:
 * Understand how the `__init__.py` file affects your Python package.
 
 ```
+
 :::{admonition} Follow Along with This Lesson
 :class: tip
 
 To follow along with this lesson, you can complete the previous lessons,
 or you can download a pre-made workshop repository that is at the starting 
 point.
 
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/deciding-package-structure-start.zip)
-
-Alternatively, download the repository using the command line:
+You will need to make sure that you have `git` installed and configured,
+as described in the set-up instructions.
 
 ````{tab-set-code} 
+
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout deciding-package-structure-start
+git switch -c main
 ```
 ````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
 :::
 
 As new features are implemented in codes, it is natural for new functions and objects to be added.

_episodes/06-type-hinting.md

@@ -1,5 +1,6 @@
 # Type Hinting in Python
 
+
 ````{admonition} Overview
 :class: overview
 
@@ -14,23 +15,29 @@ Objectives:
 - Learn the syntax to utilize type hinting in Python.
 
 ````
+
 :::{admonition} Follow Along with This Lesson
 :class: tip
 
 To follow along with this lesson, you can complete the previous lessons,
 or you can download a pre-made workshop repository that is at the starting 
 point.
 
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/python-type-hinting-start.zip)
-
-Alternatively, download the repository using the command line:
+You will need to make sure that you have `git` installed and configured,
+as described in the set-up instructions.
 
 ````{tab-set-code} 
+
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout python-type-hinting-start
+git switch -c main
 ```
+````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
 :::
 
 Python does not inherently require or enforce the *types* of variables in code.

_episodes/08-testing.md

@@ -18,17 +18,21 @@ To follow along with this lesson, you can complete the previous lessons,
 or you can download a pre-made workshop repository that is at the starting 
 point.
 
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/python-testing-start.zip)
-
-Alternatively, download the repository using the command line:
+You will need to make sure that you have `git` installed and configured,
+as described in the set-up instructions.
 
 ````{tab-set-code} 
+
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout python-testing-start
+git switch -c main
 ```
 ````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
 :::
 
 Until now, we have been writing functions and checking their behavior using an interactive Python interpreter and manually inspecting the output.

_episodes/09-CI.md

@@ -14,28 +14,29 @@ Objectives:
 - Familiarize learners with YAML configuration files.
 ````
 
-:::{admonition}  Follow Along with This Lesson
+:::{admonition} Follow Along with This Lesson
 :class: tip
 
-To follow along with this lesson, either you meet the following prerequisites:
-- All Python code and tests described so far in the workshop.
-- Configured Git and GitHub account (described in [Set Up](setup.md))
-- Pushed up-to-date version - with tests - of the `molecool` project to GitHub.
-
-
+To follow along with this lesson, you can complete the previous lessons,
 or you can download a pre-made workshop repository that is at the starting 
 point.
-- [Download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/CI-Github-actions-start.zip)
 
-Alternatively, download the repository using the command line:
+You will need to make sure that you have `git` installed and configured,
+as described in the set-up instructions.
 
 ````{tab-set-code} 
+
 ```{code-block} shell
 git clone https://github.com/MolSSI-Education/molecool.git
 cd molecool
 git checkout CI-Github-actions-start
+git switch -c main
 ```
 ````
+You can also [download the pre-made workshop repository as a zip file](https://github.com/MolSSI-Education/molecool/archive/refs/tags/git-start.zip).
+If downloading as a zip file, you will need to initialize `git` in the repository and make an initial commit in order to use git.
+
+:::
 
 **Note** - For this lesson, you must be able to push to GitHub.
 If you are using the pre-made repository, you will need to create an *empty* repository on GitHub, then