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 anyone in the NYU community interested in learning computational skills.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where: This training will take place online.
When you register for the event on LibCal, you the Zoom link and password will be emailed to you.
When:
April 28-29, 2022.
Requirements:
Participants must have access to a computer 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 dedicated to providing a positive and accessible learning environment for all. Please
notify the instructors 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.
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.
Surveys
Please be sure to complete these surveys before and after the workshop.
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.
If you haven't used Zoom before, go to the
official website
to download and install the Zoom client for your computer.
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:
Two monitors: If you have two monitors,
plan to have the tool you are learning up on one monitor and
the video conferencing software on the other.
Two devices: If you don't have two monitors,
do you have another device (tablet, smartphone) with a medium to large
sized screen? If so, try using the smaller device as your video
conference connection and your larger device (laptop or desktop)
to follow along with the tool you will be learning about.
Divide your screen: If you only have one device
and one screen, practice having two windows
(the video conference program and one of the tools you will be using
at the workshop) open together.
How can you best fit both on your screen?
Will it work better for you to toggle between them
using a keyboard shortcut?
Try it out in advance to decide what will work best for you.
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.
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 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.
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.
SQLite
SQL is a specialized programming language used with databases. We
use a database manager called
SQLite in our lessons.
Copy the following curl -fsSL https://nyu-dataservices.github.io/2022-04-28-nyu-online/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.
If you installed Anaconda, it also has a copy of SQLite
without support to readline.
Instructors will provide a workaround for it if needed.
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).
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)
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.
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.)
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).