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 organised by EPCC in collaboration with ARCHER, and the Software Sustainability Institute. 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 Software 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.
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.
You need to have previous experience working with the Bash shell.
For a brief introduction to bash, you can refer to the Bash shell lesson available online.
Where:
the Debye Lecture Theatre, GN/120, York Plasma Institute.
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).
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.
Accessibility: We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
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.
The workshop starts at 10:00 on Monday 10th of June, but we will be there a short while before, so if you have any issues with the setup, please pop along from 09:45 onwards.
Monday, 10th June
10:00
Automation and Make
11:30
Morning break
11:45
Automation and Make
13:00
Lunch break
14:00
Version Control with Git
15:30
Afternoon break
15:45
Version Control with Git
17:00
END
Tuesday, 11th June
10:00
Building Programs with Python
11:30
Morning break
11:45
Building Programs with Python
13:00
Lunch break
14:00
Managing Data with SQL
15:30
Afternoon break
15:45
Managing Data with SQL
17:00
END
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
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.
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.
Select "Use the nano editor by default" and click on "Next".
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.
Click on "Next".
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
Select "Use Windows' default console window" and click on "Next".
Click on "Install".
Click on "Finish".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing [Enter]
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.
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.
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.
Make is a standard tool on Linux systems and should already be available.
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.
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.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
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.
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.
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).
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.)
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 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).
Close the terminal window.
SQLite
SQL is a specialized programming language used with databases. We
use a simple database manager called
SQLite in our lessons.
Copy the following curl https://hpcarcher.github.io/2019-06-10-york/getsql.sh | bash
Paste it into the window that git bash opened. If you're unsure, ask an instructor for help
You should see something like 3.27.2 2019-02-25 16:06:06 ...
If you want to do this manually, download sqlite3, make a bin directory in the user's home directory, unzip sqlite3, move it into the bin directory, and then add the bin directory to the path.
SQLite comes pre-installed on macOS.
SQLite comes pre-installed on Linux.
In case of problems: register for an account at Python Anywhere