Materials Physics Center - University of the Basque Country
Software Carpentry Workshop

Elbira Zipitria Center, room 0.01, UPV/EHU Ibaeta Campus, San Sebastian - Donostia

27-28 June 2018, 9:00 am - 6:00 pm
29 June 2018, 9:00 am - 13:00 pm

Instructors: Inigo Aldazabal Mensa, Andrés Diaz-Gil, David de Sancho, Anita C. Schürch

Helpers: Jose Aguasvivas, Daniel Alcalá, Daniel J. Arismendi, Abel Carreras, Doug Davidson, Dana Scarinci, Xiang Xu

Contents

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, post-doctoral researchers, and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Applicants from the organizing and collaborating entities will have priority, but the course is open to all scientific community.

There is no cost to attend and coffee breaks are included.

Where: Elbira Zipitria Center, room 0.01, UPV/EHU Ibaeta Campus, San Sebastian - Donostia. Get directions with OpenStreetMap or Google Maps.

When: 27-29 June 2018. Add to your Google Calendar.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

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 inigo.aldazabalm@ehu.eus for more information.

Registration

Registration is closed as of June the 25th. All available seats for the workshop have been filled.

Sponsors

This workshop is possible thanks to the contributions of

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

09:00 Software setup and account signup
09:30 Welcome Address (IAM)
09:45 Introduction to the Unix shell (AS)
11:00 Coffee break
11:30 Introduction to the Unix shell (continued) (AS)
13:00 Lunch Break
14:30 Version control with Git (IAM)
16:00 Coffee Break
16:30 Version control with Git (continued) (IAM)
18:00 Wrap Up (IAM)

Day 2

09:00 Doors opening, setup, personal doubts, ...
09:25 Review of day 1 (IAM)
09:30 Introduction to Python (AS)
11:00 Coffee break
11:30 Introduction to Python (continued) (AS)
13:00 Lunch break
14:30 Python data analysis with pandas (DS)
16:00 Coffee break
16:30 Python data analysis with pandas (continued) (DS)
18:00 Wrap Up (IAM)

Day 3 (optional extra day)

09:00 Doors opening, setup, personal doubts, ...
09:25 Review of day 2 (IAM)
09:30 HPC in a morning(ADG)
11:00 Coffee break
11:30 HPC in a morning (continued) (ADG)
13:10 Wrap up (IAM)

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

Syllabus

See the lessons links below for the reference material we will be using along the workshop.

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Lesson
  • Reference...

Programming in Python

  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Lesson
  • Reference
  • Using libraries
  • DataFrames with pandas
  • Data visualization with pandas
  • Lesson
  • Files
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Lesson
  • Reference...

HPC in a morning

  • What is a super computer
  • How to connect to a super computer
  • Transfering data to and from it
  • Launching programs in the remote cluster
  • Capturing the ouput of these programs
  • Working with the scheduler
  • Working with the shared file system
  • Lesson

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.

Beware of the Warning! sign! It shows changes from the installer default options. Should you forget to change these options, the programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.

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 and follow the steps bellow:
    1. Click on "Next".
    2. Keep default options and click on "Next".
    3. Warning! Select "Use the Nano editor by default" from the dropdown list and click on "Next".
    4. Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
    5. Keep "Use the OpenSSL library" selected and click on "Next".
    6. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    7. Warning! Select "Use Windows' default console window" and click on "Next".
    8. Keep default options and click on "Next".
    9. Click on "Install".
    10. Click on "Finish".
  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. 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. 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, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop. It should be installed on your computer as part of your Bash install (described above).

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

macOS

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

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.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

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

Video Tutorial
  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3.6 installer for Windows.
  3. Run the installer and follow the steps below:
    1. Click on "I Agree" to agree the License Terms.
    2. Keep "Just Me (recommended)" selected and click on "Next".
    3. Keep default destination folder and click on "Next".
    4. Warning! Select both "Add Anaconda to my PATH environment variable" and "Register Anaconda as my default Python 3.6" and click on "Next".
    5. Click on "Install".
  4. Reboot Windows.

macOS

Video Tutorial
  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3.6 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 3.6 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 enter. You will follow the text-only prompts. To move through the text, press the space key. 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.