Merge pull request #133 from janash/standalone-lessons

add standalone lessons for command line, git, and github

_episodes/00-command-line-basics.md

@@ -0,0 +1,259 @@
+# Introduction to the Command Line
+
+````{admonition} Overview
+:class: overview
+
+Questions:
+- What is the command line?
+- How can I navigate files and directories on the command line?
+
+Objectives:
+- Learn basic shell commands for navigating and creating directories.
+````
+
+## Opening the Terminal
+
+In this workshop, we will be navigating files and using git (a software for version control) using the command line. 
+The Linux command line is a text interface to your computer. 
+When you use the command line, you use something called a shell.
+You can access the command line, or shell, using a *terminal*. 
+If you are using WSL, the only type of interface you have to your Linux operating system is a command line, or terminal.
+
+In scientific computing, you will need to use the Linux command line on high performance computing (HPC) servers.
+Knowing the command line will also allow you to perform repetitive tasks quickly through shell scripting.
+For this course, we will focus on basic navigation, file creation, and using git from the command line.
+
+Most modern operating systems have graphical user interfaces, or GUIs (often pronounced "gooey"), that are used to interact with the computer.
+However, you can also interact with the computer using text only.
+
+[Open your terminal](https://towardsdatascience.com/a-quick-guide-to-using-command-line-terminal-96815b97b955). 
+On Mac, you should be able to find a terminal application.
+If you are using WSL, open your Linux distribution.
+You can use this interface to issue commands to your computer using text.
+
+## Viewing Directory Contents
+
+The first command we will discuss is the command `pwd`. 
+`pwd` stands for "**p**rint **w**orking **d**irectory." 
+This command gives the name of the folder you are currently in.
+In Linux, "directory" means the same thing as "folder".
+
+````{tab-set-code} 
+
+```{code-block} shell
+pwd
+```
+````
+
+
+````{tab-set-code} 
+
+```{code-block} output
+/YOUR/PATH
+```
+````
+
+
+When you open a terminal initially, you will be in your home directory. 
+The path displayed as your output will be whatever your home directory is if you type `pwd` immediately after opening your terrminal.
+
+The `ls` command shows you the contents of the directory you are in. 
+`ls` stands for "list", and the command shows you the contents of the directory you are in.
+
+````{tab-set-code} 
+
+```{code-block} shell
+ls
+```
+````
+
+
+If you want to see contents of another directory, you can follow `ls` with the path to that directory. 
+In the command below, you should substitute a directory you can see from the previous `ls` command.
+
+````{tab-set-code} 
+
+```{code-block} shell
+ls DIRECTORY_NAME
+```
+````
+
+```{admonition} Clearing the screen
+:class: note
+
+If you'd like to make room on your screen, you can use the `clear` command too get a fresh terminal.
+Pressing `ctrl+L` on your keyboard will also clear the screen.
+```
+
+## Creating and navigating directories
+We will make a directory to keep our work in for the course.
+For the sake of uniformity, these directions will tell you how to create a folder in your home directory.
+If you have another preference for where you would like to store your files and you are able to navigate files, you can use that location.
+
+The command to **m**a**k**e a **dir**ectory is `mkdir`.
+
+````{tab-set-code} 
+
+```{code-block} shell
+mkdir command_line_lesson
+```
+````
+
+``````{admonition} Check Your Understanding
+:class: exercise
+
+What command that you have learned so far could you use to see that your newly created folder is in your current location?
+
+````{admonition} Solution
+:class: solution dropdown
+
+You could use the `ls` command to confirm that there is now a folder called `command_line_lesson` in your home directory.
+
+``````
+
+
+This has created an empty folder, or directory, named `chem_280` in your home directory.
+To navigate to be inside of that directory, we need to **c**hange the **d**irectory we are in using the `cd` command.
+
+```{admonition} Spaces in file and directory names
+:class: note
+
+In general, you will notice that most file and directory names created on systems where the command line is used do not contain spaces.
+
+On the command line, many applications and scripts may not work with file names or directories containing spaces. 
+It is best to use underscores `_` or dashes `-` to separate words in file names.
+
+```
+
+
+````{tab-set-code} 
+
+```{code-block} shell
+cd command_line_lesson
+```
+````
+
+
+We will create a file that has a description of what is in this folder. 
+
+You can verify what folder you are in using the `pwd` command.
+
+````{tab-set-code} 
+
+```{code-block} shell
+pwd
+```
+````
+
+
+Open a text file in your text editor of choice. 
+If you installed [VSCode](https://code.visualstudio.com/download)  you will be able to open a file called `README.md` using VSCode with the following command. **Note** If you are on MacOS it will be necessary to [add VSCode to your path manually](https://code.visualstudio.com/docs/setup/mac).
+
+````{tab-set-code} 
+
+```{code-block} shell
+code README.md
+```
+````
+
+
+The Visual Studio Code text editor will open with a file called `README.md`. 
+Type some information in the file and save it.
+
+````{tab-set-code} 
+
+```{code-block} README.md
+# MolSSI Best Practices - Command Line
+This folder contains files and directories associated with the MolSSI Best Practices Workshop.
+```
+````
+
+
+This file uses something called [Markdown](https://www.markdownguide.org/), which a mark-up, or text formatting language.
+This is often used for README files, and we will use `Markdown` throughout the bootcamp. 
+The hashtag (`#`) followed by the space results indicates a title.
+Save this file and exit.
+
+Now, when you type `ls`, you will see that you have a file called `README.md` in your directory.
+
+To navigate out of this folder, you can use `..` as the file location. 
+
+````{tab-set-code} 
+
+```{code-block} shell
+cd ..
+```
+````
+
+
+This will move you back to your home directory. 
+
+```{admonition} Changing to the home directory from anywhere
+:class: note
+
+If you use the `cd` command followed by no path, you will always be returned to your home directory.
+```
+
+Other commands which will be useful to you are `mv` which is used for moving files from one place to another, and `cp` for copying files from one place to another. For example, you can create a copy of your README.md file:
+
+````{tab-set-code} 
+
+```{code-block} shell
+cp command_line_lesson/README.md .
+```
+````
+
+
+This command will create a copy of the README.md file in your current directory. 
+The dot (`.`) is a short-cut for your current directory. 
+In this case, the created file will have the same name as the one you copied it from.
+You could also give the file another name:
+
+````{tab-set-code} 
+
+```{code-block} shell
+cp command_line_lesson/README.md README_copy.md
+```
+````
+
+
+The `mv` command behaves the same way except that the original file is removed.
+
+You can remove a file using the `rm` command.
+Let's get rid of those copies we just made:
+
+````{tab-set-code} 
+
+```{code-block} shell
+rm README.md
+rm README_copy.md
+```
+````
+
+``````{admonition} Challenge
+:class: exercise
+
+Navigate to your `command_line_lesson` directory and list the directory contents.
+
+`````{admonition} Solution
+:class: dropdown solution
+
+The commands you should execute are
+
+````{tab-set-code} 
+```{code-block} shell
+cd command_line_lesson
+ls
+```
+````
+`````
+``````
+
+
+````{admonition} Key Points
+:class: key
+
+- The terminal or "command line" is a text interface to your computer.
+- You can use text commands in the command line to navigate directories and change files.
+- We will use a text mark-up notation called "markdown". This will be in text files and doesn't directly have to do with the terminal.
+````

_episodes/00-git-and-github.rst

@@ -10,6 +10,10 @@ GitHub is a web-based hosting service for git repositories, and it provides a nu
 
 This section covers the basics of version control using git and sharing and collaborating on code using GitHub.
 
+If you would like to do the `git` and GitHub lessons outside of the context of the CookieCutter, 
+see our :doc:`standalone lesson on git<00-git-standalone>` and :doc:`standalone lesson on GitHub<00-github-standalone>`.
+
+
 .. csv-table:: 
   :file: csv_tables/git_and_github.csv
   :header-rows: 1