Instructors:
Dilip Banerjee, Chandler Becker, Jon Guyer, Trevor Keller, Bill Krekelberg, Justin Senseney, Josh Taillon, Zach Trautt, Daniel Wheeler
Helpers:
TBD
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.
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:
Online (as indicated by group leader)
When:
April 2020
How:
Although specific implementations will vary by cohort and instructor, groups
will generally meet virtually via a web conferencing tool, and the instructor
will present with a shared screen to a group of no more than 10 learners.
Learners will follow along, running commands on their own systems and can
interact with the instructor and helpers throughout the process.
We appreciate your patience and understanding as moving these sessions to an
online-only format is a first-time learning experience for us and you alike,
and hiccups in the process are certain to arise. We will try our hardest to
ensure a good learning experience regardless of the circumstances, but
feel free to let us know if you have any suggestions for improvements.
Requirements:
Participants must have a computer with a Mac, Linux, or Windows operating
system (not a tablet, iPad, etc.) that they have administrative privileges on.
They should have a few specific software packages installed (listed
below). If this is not possible, we can also provide a
remote virtual desktop that can be used for the session (contact your
instructor for details), but we prefer that you install the software on your
NIST machine as a learning exercise.
Due to limited screen "real estate", you may find it easier if you have
multiple monitors: one for the instructor's display and webinar, and another
on which to evaluate commands and practice in realtime. If this is not
possible, another solution is to use a second device (such as a tablet or
another perhaps personal laptop) to login to the web conference and view the
instructor, while you follow along interactively on your "main" computer.
Accessibility: We are committed to making this workshop
accessible to everybody. As the workshop will be conducted entirely online,
you will be able to participate from the comfort of your teleworking location,
but please let your instructor know in advance if we can make any
accommodations to help make learning easier for 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.
The schedule is planned for about 6 hours total of instruction for this topic. The detailed
schedule will be determined by each instructor and the learners in their cohort,
and communicated separately. We will be following the curriculum of the
Introduction to Programming with Python carpentry
course, adapted for online teaching.
Syllabus
This lesson assumes some familiarity with Bash Shell.
To participate in a
Software Carpentry
workshop,
you will need access to the software 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 select "Use the nano editor by default" and click on "Next".
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.)
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 "Enable file system caching" and "Enable Git Credential Manager" are selected
and click on "Next".
Click on "Install".
Click on "Finish".
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.
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 enter/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.
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/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.
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 terminal-based editor and the default that instructors use in the workshop.
It is installed along with Git.
Other free graphical editors that you can use are
Visual Studio Code,
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 terminal-based 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.
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.
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 to approve the default location
for the files.
Type yes and press Enter
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).