Instructors:
Fred Feng, Pariksheet Nanda, Peter Cerda, Gandhimathi Padmanaban
Helpers:
Pat Schloss, Cynthia Sopko, Irene Morse, Gregory Johnson
Registration
Registration Link You will need to sign in to your Google account to view the registration Google Forms.
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.
This is a pilot workshop, testing out a lesson that is still under development. The lesson authors would appreciate any feedback you can give them about the lesson content and suggestions for how it could be further improved.
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.
Where:
You'll find out once you send your installation materials.
Get directions with
OpenStreetMap
or
Google Maps.
Requirements:
Participants must bring a laptop with a
Mac, Windows, or Linux operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.
They should have a few specific software packages installed (listed below).
Accessibility:
We are committed to making this workshop
accessible to everybody. For workshops at a physical location, 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.
Roles:
To learn more about the roles at the workshop (who will be doing what),
refer to our Workshop FAQ.
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.
The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include regular breaks. Please contact the workshop organisers if you would like more information about the planned schedule.
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.
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.
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".
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.
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.)
Select "Use bundled OpenSSH".
Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
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.
Video Tutorial
The default shell in newer versions of macOS is Z shell, also known as zsh, and
it comes pre-installed with your MacOS.
You access shell from the Terminal, which can be launched with a Spotlight Search by typing "terminal" or in /Applications/Utilities.
See the Git installation video tutorial
for an example on how to launch the Terminal.
You may want to keep Terminal in your dock for this workshop.
If you use an earlier version of MacOS with a different shell, see
this Apple Support article and follow the instructions on how to make zsh the 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.
Before signing up, you may want to review this short list of GitHub username advice.
Please also 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 general-purpose programming language.
Installing Python and its scientific packages individually can be a bit difficult, so we recommend
Anaconda,
a Python distribution bundled with common scientific packages and other popular tools.
We will teach Python using JupyterLab,
a programming environment that runs in a web browser. For this to work you will need a reasonably
up-to-date web browser. The latest versions of the Chrome, Safari and Firefox browsers are all
supported.
Note you do not need to install JupyterLab separately as it comes pre-installed with Anaconda.
Note if you have already installed Anaconda previously, you don't need to install it again for this workshop.
However, you do need to make sure your Python libraries meet the version requirements for this workshop by running the provided check_setup.ipynb file.
If a library does not meet a version requirement,
you can run pip install library_name --upgrade in your command window (i.e., Anaconda Prompt for windows and Terminal for MacOS/Linux) to upgrade the library.
Download the Anaconda 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 and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
Type bash Anaconda3- and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
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).
Once Anaconda is installed, type jupyter lab in your Terminal and press Return. This will launch JupyterLab in your browser.
Launch JupyterLab
Once Anaconda is installed, launch the Terminal window, type in jupyter lab, and press Return. This will launch JupyterLab in your browser.
Note to keep the JupyterLab running, do not close the Terminal window (you can minimize it), as it works as JupterLab's "local host server".