ARCHER Software Carpentry @ The University of Leicester: Feb 26-27, 2018

ARCHER Software Carpentry @ The University of Leicester

Feb 26-27, 2018

10:00 - 17:00

Instructors: Manos Farsarakis, Juan Herrera

Helpers: Sam Cox, Duncan Law-Green, TJ Ragan, John Roberts

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 workshop is hosted by EPCC, Edinburgh Parallel Computing Centre, and organised in collaboration by ARCHER, the Software Sustainability Institute, and UoE Research Data Service.

ARCHER, the UK's national supercomputing service, offers training in software development and high-performance computing to scientists and researchers across the UK. As part of our training service we are running a two-day Data Carpentry workshop.

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 need to have previous experience working with the Unix Shell. For a brief introduction to bash, you can refer to the SWC material available online You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: IT Room 2, David Wilson Library, University Rd, Leicester, LE1 9QD. Get directions with OpenStreetMap or Google Maps.

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.

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

The room is wheelchair / scooter accessible.
Accessible restrooms are available.
You can get information on room accessibility from this page.

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 and we will attempt to provide them.

Contact: Please email support@archer.ac.uk for more information.

Registration

To register, or to get more information, please, visit the ARCHER training page.

Schedule

Day 1

10:00	Welcome and set-up
10:30	Automating tasks with Make
11:30	Coffee break
12:00	Automating tasks with Make
13:00	Lunch break
14:00	Version control with Git
15:30	Coffee break
16:00	Version control with Git
17:00	Close

Day 2

10:00	Python
11:30	Coffee break
12:00	Python
13:00	Lunch break
14:00	Data Management with SQL
15:30	Coffee break
16:00	Data Management with SQL
16:30	Wrap-up and feedback
17:00	Close

Sharing is caring: Etherpad.
We will use this etherpad for sharing thoughts, exercises, URLs and bits of code.

Workshop Feedback: http://www.archer.ac.uk/training/feedback/.
Feedback helps us improve and also helps us continue to get funding to run more workshops like this. Thank you!

Syllabus

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
Reference...

Automating tasks with Make

Make is not just for compiling code
Basic Tasks
Automatic Variables and Wildcards
Patterns
Variables
Reference...

Building programs with Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals: for, if, else, ...
Defensive programming
Using Python from the command line
Reference...

Data Management with SQL

Introduction to SQL
Basic Queries
Aggregation
Joins and aliases
Reference...

Setup

To participate in a Software Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your workshop.

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

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
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".
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

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, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

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.

Mac OS X

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., 3.4 is fine).

We will teach Python using the IPython 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

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Windows.
Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for OS X.
Install Python 3 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Linux.
(Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
Open a terminal window.
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.
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).
Close the terminal window.

Make

Originally invented to manage compilation of programs written in languages like C, Make can be used to automatically update any set of files that depend on another set of files. This makes it a good solution for many data analysis and data management problems. While there are many build tools now in existence (e.g. ANT and CMake) they share the same fundamental concepts as Make.

Windows

Make will have been installed by the SWC installer.

Mac OS X

For OS X, version 10.9 (Mavericks) or above, download the Command Line Tools by doing:

xcode-select  --install

For more information, see the OSX Daily blog.

If you have an older OS X version and you do not already have access to make from within your shell, you will need to install XCode (which is free, but over a gigabyte to download).

Go to the Apple app store
Search for XCode
Click Free
Click Install App

Once XCode has installed:

Click Applications
Click XCode
Select XCode→Preferences...
Click Downloads
Select Command Line Tools
Click Install

You will now be able to run make within your shell.

Linux

Make is a standard tool on Linux systems and should already be available.

SQLite

For this workshop we're going to use the Firefox SQLite Plugin. It works through the web browser Firefox.

Windows

If you don't already have Firefox installed install Firefox
Start Firefox
Go to the plugin homepage.
Click the "Add Now" button.
Click "Install Now" on the dialog that appears after the download completes.
Restart Firefox when prompted.
Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

Mac OS X

If you don't already have Firefox installed install Firefox
Start Firefox
Go to the plugin homepage.
Click the "Add Now" button.
Click "Install Now" on the dialog that appears after the download completes.
Restart Firefox when prompted.
Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

Linux

If you don't already have Firefox installed install Firefox
Start Firefox
Go to the plugin homepage.
Click the "Add Now" button.
Click "Install Now" on the dialog that appears after the download completes.
Restart Firefox when prompted.
Select "SQLite Manager" from the "Tools" menu and it will open within Firefox

Recognising prompts and how to exit

Useful links

Software Carpentry online lessons:

Git:

GitHub interactive Git tutorials
Git pretty - a flowchart about how to recover from mistakes.

Changing History, or How to Git pretty

Python:

matplotlib examples gallery - includes source code.
SciPy Cookbook - examples of how to do useful stuff using numpy, scipy, matplotlib, interfacing, etc.
Scientific Python lecture notes

Training:

ARCHER Training - free HPC training all over the UK.
Code Academy - free online programming courses

Papers:

Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745.

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285.

Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424.

Ram K (2013) "git can facilitate greater reproducibility and increased transparency in science", Source Code for Biology and Medicine 2013, 8:7 doi:10.1186/1751-0473-8-7.

Glass, R. (2002) Facts and Fallacies of Software Engineering, Addison-Wesley, 2002. (PDF).