Software Carpentry at STFC

Science and Technology Facilities Council

4-5 Oct, 11-12 Oct, 1-2 Nov, 8-9 Nov, 2022

09:00 - 13:00

Instructors: Eli Chadwick, Patrick Austin, James Acris, Kyle Pidgeon, Ivan Finch, Mathew Sims

Helpers: STFC Volunteers

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 workshops are aimed primarily at STFC graduates, apprentices and industrial placement students, but they are open to all STFC staff (this does not include those who are STFC-funded but employed at another institution). You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This is a hybrid workshop which can be attended online or in person. If attending online, the instructors will provide you with the information you will need to connect to this meeting. The in-person component will take place at Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0QX. Get directions with OpenStreetMap or Google Maps.

When: 4-5 Oct, 11-12 Oct, 1-2 Nov, 8-9 Nov, 2022. 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). If you are attending in person but cannot bring a suitable laptop, inform the organizers in advance and a computer will be provided.

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, 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.

Contact: Please email Carpentries@stfc.ac.uk for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to STFC staff (this does not include those who are STFC-funded but employed at another institution).


Registration

Please complete this registration form using your STFC email address to register for the workshop.


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.


Collaborative Notes

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


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Unix & Git - 4th Oct

09:00 Welcome & Icebreaker
09:30 Introducing the Shell
Navigating Files and Directories
10:30 Morning Break
Working With Files and Directories
Pipes and Filters
Loops
Shell Scripts
Finding Things
12:50 Wrap-Up
13:00 END

Unix & Git - 5th Oct

09:00 Welcome
09:10 Automated Version Control
09:15 Setting Up Git
09:25 Creating a Repository
09:35 Tracking Changes
10:00 Exploring History
10:20 Ignoring Things
10:25 Morning Break
10:45 Remotes in GitHub
11:30 Collaborating
Conflicts
Open Science
Licensing
Citation
Hosting
12:50 Wrap-Up
13:00 END

Intro to Python Day 1 - 11th Oct

09:00 Welcome & Icebreaker
09:15 Python Fundamentals
09:40 Analyzing Patient Data
10:30 Morning Break
10:50 Visualizing Tabular Data
11:30 Storing Multiple Values in Lists
12:00 Repeating Actions with Loops
12:25 Analyzing Data from Multiple Files
12:50 Wrap-Up
13:00 END

Intro to Python Day 2 - 12th Oct

09:00 Welcome
09:10 Making Choices
09:45 Creating Functions
11:00 Morning Break
11:20 Errors and Exceptions
11:35 Defensive Programming
11:55 Debugging
12:20 Command-Line Programs
12:50 Wrap-Up
13:00 END

Intermediate Software Development Day 1 - 1st Nov

09:00 Welcome & Icebreaker
09:30 Setting Up Environment For Collaborative Code Development
Introduction to a Software Project
Virtual Environments For Software Development
10:30 Morning Break
Integrated Software Development Environments
Collaborative Software Development Using Git and GitHub
Python Coding Conventions
12:50 Wrap-Up
13:00 END

Intermediate Software Development Day 2 - 2nd Nov

09:00 Welcome
09:10 Ensuring Correctness of Software at Scale
Automatically Testing Software
Scaling Up Unit Testing
10:30 Morning Break
Continuous Integration for Automated Testing
Diagnosing Issues and Improving Robustness
12:50 Wrap-Up
13:00 END

Intermediate Software Development Day 3 - 8th Nov

09:00 Welcome
09:10 Software Architecture and Design
Programming Paradigms
Object Oriented Programming
Functional Programming
10:30 Morning Break
Software Design
Persistence
12:50 Wrap-Up
13:00 END

Intermediate Software Development Day 4 - 9th Nov

09:00 Welcome
09:10 Improving and Managing Software Over its Lifetime
Preparing Software for Reuse
10:30 Morning Break
Assessing Software for Suitability and Improvement
Software Improvement Through Feedback
12:50 Wrap-Up
13:00 END

Setup

To participate in a Software Carpentry workshop, you will need access to software as 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.

Install the videoconferencing client

If you are attending in person, you do not need a video conferencing client. You can skip to installing The Bash Shell.

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

This workshop requires Zoom version 5.7.3 or later. You can check and update your Zoom version by clicking 'Check for Updates' or 'Help > About Zoom' in the Zoom menu.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The Bash Shell

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

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. 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.
    2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. Click on "Finish" or "Next".
  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.

Video Tutorial

The default shell in some versions of macOS is Bash, and Bash is available in all versions, 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.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

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 macOS, 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.

Video Tutorial

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.

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.

Video Tutorial

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

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. Note that the Anaconda install process can take 20 minutes or more, so make sure to do it in advance of the workshop.

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 (Jupyter Notebook will be installed by Anaconda). 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).

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable. Note that the install can take 20 minutes or more.

Video Tutorial

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 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 and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter (or Return depending on your keyboard). 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 (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.