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layout venue address country language latitude longitude humandate humantime startdate enddate instructor helper email collaborative_notes eventbrite
workshop
University of Arizona
online
us
en
32.231901
110.9495000
June 8, 2021
8:00 am - 12:00 pm
2021-06-07
2021-06-11
Uwe Hilgert et al.
KEYS Crew
KEYS Staff
Jonathan King
Isabella Viney

FOUNDATIONAL COMPUTATIONAL SKILLS

General Information

{% comment %} INTRODUCTION

Edit the general explanatory paragraph below if you want to change the pitch. {% endcomment %} {% if site.carpentry == "swc" %} {% include swc/intro.html %} {% elsif site.carpentry == "dc" %} {% include dc/intro.html %} {% elsif site.carpentry == "lc" %} {% include lc/intro.html %} {% endif %}

{% comment %} AUDIENCE

Explain who your audience is. (In particular, tell readers if the workshop is only open to people from a particular institution. {% endcomment %} {% if site.carpentry == "swc" %} {% include swc/who.html %} {% elsif site.carpentry == "dc" %} {% include dc/who.html %} {% elsif site.carpentry == "lc" %} {% include lc/who.html %} {% endif %}

{% comment %} LOCATION

This block displays the address and links to maps showing directions if the latitude and longitude of the workshop have been set. You can use https://itouchmap.com/latlong.html to find the lat/long of an address. {% endcomment %} {% assign begin_address = page.address | slice: 0, 4 | downcase %} {% if page.address == "online" %} {% assign online = "true_private" %} {% elsif begin_address contains "http" %} {% assign online = "true_public" %} {% else %} {% assign online = "false" %} {% endif %} {% if page.latitude and page.longitude and online == "false" %}

Where: {{page.address}}. Get directions with OpenStreetMap or Google Maps.

{% elsif online == "true_public" %}

Where: online at {{page.address}}. If you need a password or other information to access the training, the instructor will pass it on to you before the workshop.

{% elsif online == "true_private" %}

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

{% endif %}

{% comment %} DATE

This block displays the date and links to Google Calendar. {% endcomment %} {% if page.humandate %}

When: {{page.humandate}}. {% include workshop_calendar.html %}

{% endif %}

{% comment %} SPECIAL REQUIREMENTS

Modify the block below if there are any special requirements. {% endcomment %}

Requirements: {% if online == "false" %} Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. {% else %} 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. {% endif %} They should have a few specific software packages installed (listed below).

{% comment %} ACCESSIBILITY

Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}

Accessibility: {% if online == "false" %} We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

Material will be provided in advance of the workshop. 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. {% else %} We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of KEYS Training Week if you require any accommodations or if there is anything we can do to make the workshops more accessible to you.

{% endif %}

{% comment %} CONTACT EMAIL ADDRESS

Display the contact email address set in the configuration file. {% endcomment %}

Contact: Please email {% if page.email %} {% for email in page.email %} {% if forloop.last and page.email.size > 1 %} or {% else %} {% unless forloop.first %} , {% endunless %} {% endif %} {{email}} {% endfor %} {% else %} to-be-announced {% endif %} for more information.

{% comment %} Collaborative Notes

If you want to use an Etherpad, go to

https://pad.carpentries.org/YYYY-MM-DD-site

where 'YYYY-MM-DD-site' is the identifier for your workshop, e.g., '2015-06-10-esu'.

Note we also have a CodiMD (the open-source version of HackMD) available at https://codimd.carpentries.org {% endcomment %} {% if page.collaborative_notes %}

Collaborative Notes

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

{% endif %}

Workshop Preparation

This Google Doc at https://docs.google.com/document/d/1b3c4Um68zARppshBoxQ5uotrOjG0_Vn50VuVo-Wk1z8/edit?usp=sharing holds additional IMPORTANT information on the workshop and how to prepare for it.

{% comment %} SURVEYS - DO NOT EDIT SURVEY LINKS {% endcomment %}

{% comment %} SCHEDULE

Show the workshop's schedule.

Small changes to the schedule can be made by modifying the schedule.html found in the _includes folder for your workshop type (swc, lc, or dc). Edit the items and times in the table to match your plans. You may also want to change 'Day 1' and 'Day 2' to be actual dates or days of the week.

For larger changes, a blank template for a 4-day workshop (useful for online teaching for instance) can be found in _includes/custom-schedule.html. Add the times, and what you will be teaching to this file. You may also want to add rows to the table if you wish to break down the schedule further. To use this custom schedule here, replace the block of code below the Schedule <h2> header below with {% include custom-schedule.html %}. {% endcomment %}

Syllabus

The Command Shell

The command shell (a.k.a. UNIX Shell, Bash Shell, Shell) is a power tool that allows computer users to do complex things with just a few keystrokes. Contrary to graphical user interfaces (GUI) it allows users to direct the computer from a more foundational level, using written commands. Even what happens when you click on items in GUIs is directed by written commands. Working in the 'Shell' helps users combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Shell proficiency is fundamental to using a wide range of other powerful tools and computing resources, including “high-performance computing” supercomputers.

Using the Bash Shell the workshop will introduce these concepts and procedures:

  • Files and Directories
  • History and Tab Completion
  • Pipes and Redirection
  • Looping Over Files
  • Creating and Running Shell Scripts
Additional Resources:

Version Control with Git

Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Every large software development project relies on it, and most programmers use it for their small jobs as well. And it isn’t just for software: books, papers, small data sets, and anything that changes over time or might need to be shared can and should be stored in a version control system.

Using git (on your local computer) and GitHub (in the cloud), the workshop will introduce these version control concepts and procedures:

  • Creating and initializing a Repository: init
  • Recording Changes to Files: add, commit, ...
  • Viewing Changes: status, ...
  • Working on the Web: clone, pull, push, ...
Additional Resources:

Setup

To participate in the workshop, you will need to have the software listed below on your computer; please install it following the instructions provided for your computer's operating system (Windows, Mac, Unix). If you already have some of it, please uninstall it and then install the versions below - this is the only way to ensure that you will be using the same software as your instructors and fellow KEYS interns. This includes installing UA VPN, regardless of whether you already have another type of vpn software or not.

In addition, you will need an up-to-date web browser. We recommend Firefox and/or Safari. Chrome may work, too; if you only have Chrome, install Firefox and/or Safari as well. MS Edge or Internet Explorer will not suffice.

You can find a list of common issues that may occur during installation at Configuration Problems and Solutions wiki page.

We will try to address any remaining issues in the Zoom Practice meetings – so, if you experience unsurmountable hurdles, take good notes about what you did and what went wrong. (Screenshots would be helpful for trouble-shooting!) You can also send an email to [email protected] with any computational issues you may encounter and we'll try to get you help as quickly as possible.

{% comment %} These are the installation instructions for the tools used during the workshop. {% endcomment %}

{% if site.carpentry == "swc" %} {% include swc/setup.html %} {% elsif site.carpentry == "dc" %} {% include dc/setup.html %} {% elsif site.carpentry == "lc" %} {% include lc/setup.html %} {% elsif site.carpentry == "pilot" %} Please check the "Setup" page of [the lesson site]({{ site.lesson_site }}) for instructions to follow to obtain the software and data you will need to follow the lesson. {% endif %}

Very Private Network (VPN)

The UA Virtual Private Network (VPN) provides a secure connection from your home computer, laptop, or mobile device to the UA's network. It is also a valuable security tool when you are on an unsecured wireless network (e.g., coffee shops, airports).

Install UA VPN on your computer

  • Go to the University of Arizona’s Information Technology (UITS) site at https://it.arizona.edu/.
  • Click on the ‘UA Virtual Private Network (VPN)’ Tile.
  • Click on the ‘Support, How-To’s & Info’ tab.
  • In the ‘Installation’ section select the ‘UA VPN Download and Installation Instructions’ for your Operating System.
  • Follow the instructions to install VPN on your computer.
  • In the ‘Prerequisite and Training Links’ section, open ‘Connecting the UA VPN Basics for Mac and PC’ and watch the video applicable to your operating system. Then, follow the instructions to connect your machine to the UA VPN.
Again, we will try to address any issues in the Zoom Practice meetings – so, if you experience unsurmountable hurdles, take good notes about what you did and what went wrong. (Screenshots would be helpful for trouble-shooting!) You can also send an email to [email protected] with any comutational issues you may encounter and we'll try to get you help as quickly as possible.

{% comment %} For online workshops, the section below provides:

  • installation instructions for the Zoom client
  • recommendations for setting up Learners' workspace so they can follow along the instructions and the videoconferencing

If you do not use Zoom for your online workshop, edit the file _includes/install_instructions/videoconferencing.html to include the relevant installation instrucctions. {% endcomment %}

{% if online != "false" %} {% include install_instructions/videoconferencing.html %} {% endif %}