McMaster Software Carpentry Workshop

July 27 & 28, 2017

McMaster University, Hamilton Hall room 104

Instructors: Ben Bolker, Jake Cowper Szamosi

Helpers: Laura Rossi, Shahrokh Shekarriz

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 the Unix shell, version control, data management in R, 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-docs, staff, and PIs who want to improve their informatics skills. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: McMaster University, Hamilton Hall room 104.
Get directions with OpenStreetMap or Google Maps. Campus map available here.

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 read and abide by Software Carpentry's Code of Conduct.

We expect all participants to come with needed software installed. If you have trouble, or would like help with, installing any of the software, please attend our software installation party, July 25 at 4 p.m. in LSB 216.

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

Materials will be provided in advance of the workshop; please notify the organizers in advance if you need large-print handouts.

Contact: Please email Jake at szamosjc@mcmaster.ca for more information.


Enrollment

Enrollment in this workshop must be done in advance and costs $20. You can sign up on Eventbrite. We encourage PIs to cover the cost of the workshop for their trainees out of grants wherever possible. If payment by credit card/p-card is not possible, please email us to arrange to pay with a grant number.

Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Thursday, July 27

09:00 Automating tasks with the Unix shell (Jake): data file
10:30 Coffee
10:45 More automating tasks with the Unix shell (Ben)
12:00 Lunch break
13:00 Programming with R (Jake): intro, data structures part 1: data file
14:30 Coffee
14:45 More Programming with R (Ben): exploring data frames, subsetting data frames
16:00 Wrap-up

Friday, July 28

09:00 Version control with Git (Jake)
10:30 Coffee
10:45 More version control with Git (Ben)
12:00 Lunch break
13:00 Back to Programming with R (Jake): control flow, functions explained
14:30 Coffee
14:45 End with Programming with R (Ben) data manipulation with dplyr, writing good software
16:00 Wrap-up

(Tentative) Syllabus

The Unix Shell

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

Programming in R

  • Introduction R and R Studio
  • Data structures
  • Subsetting data
  • Flow control
  • Functions
  • Data manipulation with dplyr (time permitting)
  • Reference...

Version Control with Git

  • What is version control and why does it matter?
  • Manual version control tracking
  • Creating a repository
  • Working on the web: clone, pull, push, ...
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference 1...
  • Reference 2...

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.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow. If there is a step not mentioned here, please leave the default settings:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" 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. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. 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.

Mac OS X

The default shell in all versions of Mac OS X 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).

Mac OS X

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 yum install git.

Text Editor

For the purposes of this workshop, we'll be using the lightweight nano text editor wherever possible. If you use Windows and can't instal nano, please use Notepad++.

Windows

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, try downloading the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection and may not work on all versions of Windows.

Notepad++ or Sublime Text are reasonable options for Windows users who cannot install nano.

Mac OS X

nano (which should be pre-installed with your Git installation; type nano in the shell), Text Wrangler or Sublime Text.

Linux

nano (which should be pre-installed), Gedit, Kate or Sublime Text.

Vim alert: 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 Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it ("beep mode"), try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

R

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

If you have previously installed R and/or RStudio, please make sure if at all possible that you have the most up-to-date versions. If your current R version is 3.2.5 or older, you will need to re-install packages and will get the latest versions of all packages by default; please be careful if you depend on a particular release of a package. Feel free to contact the organizers if you have any concerns.

Windows

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.

Mac OS X

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

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 yum install R). Also, please install the RStudio IDE.

Once you've installed R and RStudio, launch RStudio, go to the console and install the dplyr and tidyr packages by typing

      install.packages("dplyr")
      install.packages("tidyr")
	  install.packages("ggplot2")
(while you are connected to the Internet). If this is giving you prolems on Windows, try restarting R by right clicking and choosing "run R as administrator."