The Carpentries project comprises the Software Carpentry, Data Carpentry, and
Library Carpentry communities of Instructors, Trainers, Maintainers,
helpers, and supporters who share a mission to teach foundational computational and data science
skills to researchers.
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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.
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:
912 18th Street South, Birmingham, Alabama.
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).
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.
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.
Bash is a commonly-used shell that gives you the power to do
tasks more quickly.
Please also download the data available
here to
ensure everything is working before the workshop. If the text link is not working,
copy and paste the below url into your browser:
https://swcarpentry.github.io/shell-novice/#download-files
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 Mac OS X Ventura and newer versions is Zsh, but
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, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
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 Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
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.
R
R is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R, we use
RStudio.
Install R by downloading and running
this .exe file
from CRAN.
Also, please install the
RStudio IDE.
Note that if you have separate user and admin accounts, you should run the
installers as administrator (right-click on .exe file and select "Run as
administrator" instead of double-clicking). Otherwise problems may occur later,
for example when installing R packages.
Instructions for R installation on various Linux platforms (debian,
fedora, redhat, and ubuntu) can be found at
<https://cran.r-project.org/bin/linux/>. These will instruct you to
use your package manager (e.g. for Fedora run
sudo dnf install R and for Debian/Ubuntu, add a ppa
repository and then run sudo apt-get install r-base).
Also, please install the
RStudio IDE.
R Packages
R has a variety of existing
and pre-built packages that ease the burden of analysis. We will be
using a few of these packages to complete the lesson taught at this
workshop.
Please only complete this step AFTER
successfully installing R and Rstudio above
In the central panel (known as the 'Source Code Panel') type the below commands:
# Install the tidyverse package:
install.packages("tidyverse")
# Install the ggplot2 package
install.packages("ggplot2")
# install the dplyr package
install.packages('dplyr')
Run each command by highlighting each line one at a time
and clicking the 'Run' button that is located near
the top-right of the 'Source Code Panel'
(NOTE: The exact location may differ dependent on the OS
you are using, but the button should still be visible
around the 'Source Code Panel'). Repeat this for each line
that was typed in the above step
Once installation has completed for all packages, type
the below commands to make sure packages installed correctly:
library("dplyr")
library("ggplot2")
Run these commands similar to the steps described above,
highlight each line and click the 'Run' button
individually for each line.
If everything worked correctly, you will not see any
output from the 'Console' panel located in your RStudio
window other than seeing the command copied on each line