University of Texas at Arlington

Sep 7 and 14, 2019

9:00 am - 5:00 pm

Instructors: Ayda Mirsalehi, Farah Shamma, Feroz Ahmed, Kristopher Row, Balan Ramesh, Anna Williford

Helpers: Ebrahim Bharmal, Isaac Williams, M. Adnan Qureshi, Hammad Khan, Peace Ossom-Williamson, Muhammad Khan, Fatema Begum Ruma

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is for everyone interested in learning computational tools. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: UTA campus, Main Library, 6th floor.. Get directions with OpenStreetMap or Google Maps.

When: Sep 7 and 14, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Contact: Please email balan.ramesh@uta.edu for more information.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1 Sep 07

09:00 Pre-workshop survey, Introduction
09:30 Unix Shell Part 1
11:00 Morning break
11:15 Unix Shell Part 2
12:45 Lunch Break
01:15 Introduction to R Part 1
02:45 Afternoon break
03:00 Introduction to R Part 2
04:30 Wrap-Up
05:00 END

Day 2 Sep 14

09:00 Recap
09:30 Version Control with Git
11:00 Morning break
11:15 Writing R Scripts
12:45 Lunch break
01:15 Data Visualization with R
02:45 Afternoon break
03:00 Reproducible Research Workflows with R
04:30 Post-workshop Survey
05:00 END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select "Use the nano editor by default" and click on "Next".
    3. Keep "Git from the command line and also from 3rd-party software" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Select "Use the native Windows Secure Channel library", and click "Next".
    6. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    7. Select "Use Windows' default console window" and click on "Next".
    8. Leave all three items selected, and click on "Next".
    9. Do not select the experimental option. Click "Install".
    10. Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

You can use your favorite text editor. If you do not have one, we recommend Sublime Text 3. After installation is complete, follow steps below to use Sublime Text from Git-Bash window:
1) Open Git-Bash from the start menu.
2) Type: cd Enter to make sure you are in your home directory.
3) Type: notepad .bash_profile Enter. This will create .bash_profile file in Notepad.
Add the following text to the file:
export PATH=$PATH:"/c/Program Files/Sublime Text 3/"
4) Save the file and exit Notepad.
5) In the Git-Bash window type: source ~/.bash_profile Enter The changes you made to .bashrc are now in effect. You should now be able to launch Sublime Text by typing: subl Enter. If you run into trouble please ask your instructor for help.

You can use your favorite text editor. If you do not have one, we recommend Sublime Text.
To open Sublime Text from the terminal/bash.
1) Go to the Utilities in Finder and open terminal.
2) Type: open ~/.bash_profile in the terminal. This will open a text file.
3) Add the following text to the file:
alias subl="open -a /Applications/Sublime\ Text.app"

4) Save the file and exit TextEdit.

5) Type: source ~/.bash_profile in the terminal.
You should now be able to launch Sublime Text by typing: subl Return. If you run into trouble please ask your instructor to help you with this.

You can use your favorite text editor. If you do not have one, we recommend Sublime Text.
Please follow this link for installation instructions depending on your linux distribution. If you run into trouble please ask your instructor to help you with this.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.