README.md

# Homework 1: Using GitHub

This assignment is due by 11:59PM ET 2/2.

## Overview

This assignment will familiarize you with using Git to submit your assignments.

## Fork

1. Sign in to [this website](https://github.uconn.edu/) with your NetID to create your UConn Enterprise GitHub account.
2. Click the ![](img/fork.png) button at the top right of the page to  copy this repository to your account. After clicking fork, the page will refresh and display your copy of the repository. By default, your new repository will be located at https://github.uconn.edu/NetID/hw1. The repository name in the upper left will indicate that it is a fork: ![](img/forked.png).

## Clone 

### Using the command line

*If you use Windows, try the GitHub Desktop directions below*

1. From your fork, click the green **Clone or download** button and copy the displayed URL
2. At your command line prompt (e.g. /Applications/Utilities/Terminal) type `git clone ` followed by the URL you just copied and press return.
3. You now have a local repository to work with. Type `pwd` to see where the repository is located on your computer or `open hw1` to open a Finder window.

If you get the error message `git: command not found`, you may need to [install git](https://git-scm.com).

### Using GitHub Desktop

As an alternative to the command line, you can also use a graphical interface. We'll use the free [GitHub Desktop](https://desktop.github.com)

1. Download and install GitHub Desktop
2. Open GitHub Desktop and sign in to GitHub Enterprise with the address [https://github.uconn.edu](https://github.uconn.edu)
	![](img/signin.png)
3. After setup, select the option to Clone a repository and select the GitHub Enterprise Server tab. Select your `NetID/hw1` repository, choose a directory to save the repository on your computer, and click Clone.


## Install required software

Please download and install the following *required* software:

- [x] A code editor (e.g. [Visual Studio Code](https://code.visualstudio.com) or [Sublime](https://www.sublimetext.com)
- [x] [Connectome Workbench](https://www.humanconnectome.org/software/connectome-workbench) for viewing MRI data
- [x] [Globus Connect Personal](https://wiki.hpc.uconn.edu/index.php/Globus_Connect) for transferring files to the compute cluster. You may need to be on the campus netwokr to access this site.
- [x] [Python 3.7 Anaconda distribution](https://www.anaconda.com/distribution/)
- [x] For Windows users, you need an SSH client such as [PuTTY](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html).


## Create accounts

- [x] Neuroimaging analysis takes lots of computing time. You’ll want to run some of your analysis on the UConn Storrs HPC cluster, for which you’ll need to [request an account](http://hpc.uconn.edu/storrs/account-application). You can find your advisor’s NetID at [http://phonebook.uconn.edu](http://phonebook.uconn.edu).
- [x] Once you get your account, make sure you can SSH to the cluster as described [here](https://wiki.hpc.uconn.edu/index.php/HPC_Getting_Started)

## Learn Bash
- [x] Work through these modules at the free tutorial site [learnshell.org](https://www.learnshell.org):
	- Hello world
	- Variables
	- Passing Arguments to the Script
	- Arrays
	- Basic String Operations
	- Loops

## Learn Git
- [x] Follow along with the examples in the [Beginner's Guide to Git](https://www.freecodecamp.org/news/the-beginners-guide-to-git-github/) (for command line users)


## Edit this file

Open this file (`README.md`) in your favorite code editor. Do not use a word processor to edit files for this course! Word processors can introduce special characters that will break scripts.

### Check off the steps you completed

This file (`README.md`) is written in [Markdown](https://www.markdownguide.org). GitHub will automatically show any file named `README.md` as a webpage when viewed on Github.com using [Github-flavored Markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet).

When you see this online, you should see that the steps you need to complete have empty checkboxes like this:

- [ ]

In Markdown, a checkbox is a special list element written as:

```markdown
- [ ] Todo Item 1
- [ ] Todo Item 2

```

To tick the checkbox, write an `x` between the brackets, like this:

```markdown
- [x] Todo Item 1
- [x] Todo Item 2

```

which appears like so:

- [x] Todo Item 1
- [x] Todo Item 2

Tick the boxes for all the steps you have completed.

### Describe any installation issues

Sometimes installation instructions can be a bit vague. Use Markdown to add a bulleted list here of any problems you encountered and how you solved them here:


### Rank order your presentation preference

Rearrange the lines below to reflect your preference for the pipeline presentation, from most to least favored:

- ciftify
- fmriprep
- Human Connectome Project


## Submit the assignment

### Using the command line

1. `cd` to the `hw1` directory you created when you cloned your fork.
1. Using git, `commit` your changes to this file (remember to `git add` your files first). 
1. Using git, `push` your code to your forked repository.
1. On GitHub, [create a pull request](https://help.github.com/articles/creating-a-pull-request/) to submit your work.

### using GitHub Desktop

1. The lefthand pane will show any new or modified files in your workspace. `README.md` should have a yellow icon, indicating it has uncommited changes.
2. Click **Commit to master** to commit changes to your local repository
	![](img/commit.png)

3. Click **Push origin** to send your changes to your remote repository
	![](img/push.png)
	
4. On GitHub, [create a pull request](https://help.github.com/articles/creating-a-pull-request/) to submit your work.