University of Texas at Arlington

Feb 23-24, 2019

9:00 am - 5:00 pm

Instructors: Balan Ramesh, Nitin Kanwar, Farah Shamma, Joe Cloud, Ayda Mirsalehi, Anna Williford

Helpers: Ebrahim Bharmal, Nicky Hales, Arnav Bajwa, Robert Ruggiero

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 aimed at graduate students and other researchers. 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: Feb 23-24, 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). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please email awillifo@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 Feb 23

09:00 Pre-workshop survey
09:10 Unix Shell Part 1
10:45 Coffee
11:00 Unix Shell Part 2
12:30 Lunch break
1:30 Introduction to Python Part 1
3:00 Coffee
3:15 Introduction to Python Part 2
5:00 END

Day 2 Feb 24

09:00 Version control with Git and Github
10:45 Coffee
11:00 Python Programming
12:30 Lunch break
1:30 Data visualization with Python
3:00 Coffee
3:15 Reproducible Research Workflows with Python
4:50 Post-workshop Survey
5:00 END

We will use Etherpad 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.

The Bash Shell

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

Windows

  1. Download the Git for Windows installer.
  2. Run the installer with default options except:
    When choosing the default editor, select:
    Use the Nano editor by default
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter )
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

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

macOS

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.

Linux

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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

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.

Windows

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

macOS

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.

Linux

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. Every operating system has its own default text editor with different functionality: notepad for Windows, TextEdit for mac and vim for Linux. To standardize our lessons across all platforms, we recommend installing Sublime Text, a popular text editor that works on every platform.

Windows

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.

macOS

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.

Linux

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.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Click on Windows icon at the top panel.
  3. Download the Python 3 installer for Windows.
  4. Install Python 3 using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
    5. After installation is complete, check that you can launch Jupyter Notebook from start menu.
    Start → Anaconda3 → Jupyter Notebook
    In order to run python 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 open .bash_profile file in Notepad. Add the following text to the file:
    export PATH=$PATH:"$HOME/Anaconda3/" alias python='winpty python.exe'
    4) Save the file and exit Notepad.
    5) In the Git-Bash window type: source ~/.bash_profileEnter. The changes you made to .bash_profile are now in effect.
    You should now be able to launch pyhton by typing: pythonEnter. To exit python shell, type: quit() You should NOT see command not found .
    If you do, please come 10-15 minutes before the workshop starts - we will be there to help you.

macOS

Video Tutorial
  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type 
    bash Anaconda3-
    and then press Tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with: 
    cd Downloads
    Then, try again.
  5. Press Return. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.