Carpentries@Manchester: Software Carpentry Workshop (Python)

University of Manchester

Online

13 - 16 July 2021

9:30 - 12:30 , BST (UTC+1)

Instructors: Nilani Ganeshwaran

Helpers: Kamilla Kopec-Harding

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".

This Software Carpentry workshop is organised jointly by colleagues from Methods@Manchester, the University of Manchester Library, the University of Manchester Research IT, and Manchester branch of the Software Sustainability Institute.

We are committed to providing a positive and accessible learning environment for all. Please notify the hosts in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Audience

The workshop is aimed at the University of Manchester’s postgraduate students and research and other staff who develop software or deal with or analyse data as part of their work. You don’t need to have any previous knowledge of the tools that will be presented at the workshop - this is an introductory-level course.

When & Where

The workshop will be run online over 4 half-days, from 13 - 16 July 2021, 9:30 - 12:30. We will meet using the online videoconference software Zoom. You will need to download and install Zoom client to connect with your instructors. The Zoom link to use for this event will be announced via email to registered participants.

Registration

Registration is free via EventBrite. You will need a special code to register - please get in touch with Aleksandra Nenadic using your Manchester email address.

Requirements

Participants must have a laptop/PC with a Mac, Linux, or Windows operating system (rather than a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct

All participants (including instructors, helpers and observers) are required to abide by The Carpentries Code of Conduct.

Contact

Please email a.nenadic@manchester.ac.uk for more information.


Collaborative Notes

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


Surveys

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

Pre-workshop survey

Post-workshop survey


Schedule

Day 1, 13 July 2021, 9:30 - 12:30 BST (UTC+1)

Automating Tasks with shell

Day 2, 14 July 2021, 9:30 - 12:30 BST (UTC+1)

Building Programs with Python - Part 1

Day 3, 15 July 2021, 9:30 - 12:30 BST (UTC+1)

Building Programs with Python - Part 2

Day 4, 16 July 2021, 9:30 - 12:30 BST (UTC+1)

Version Control with Git

Setup

Installation instructions

To participate in this workshop, you will need to install all of the software described below before coming to the workshop. We will run a pre-workshop installation session to help everyone set up and make sure they have the required software installed.

The Bash Shell

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

Video Tutorial
  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 select "Use the nano editor by default" and click on "Next".
    3. 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.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    8. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    9. Click on "Install".
    10. 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.

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".

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.

Video Tutorial

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.

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.

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

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 (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).

Video Tutorial
  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.
  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.

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.