| layout | carpentry | venue | address | country | language | latlng | humandate | humantime | startdate | enddate | instructor | helper | collaborative_notes | eventbrite | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
workshop |
lc |
University of California |
full_address |
USA |
FIXME |
FIXME |
FIXME |
FIXME |
FIXME |
FIXME |
|
|
|
{% comment %} See instructions in the comments below for how to edit specific sections of this workshop template. {% endcomment %}
{% comment %} HEADER
Edit the values in the block above to be appropriate for your workshop. If the value is not 'true', 'false', 'null', or a number, please use double quotation marks around the value, unless specified otherwise. And run 'make workshop-check' before committing to make sure that changes are good. {% endcomment %}
{% comment %} For a workshop please delete the following block {% endcomment %}
{% if page.carpentry != site.carpentry %}
carpentry: {{page.carpentry}} in index.md and
carpentry: {{site.carpentry}} in _config.yml. Make sure you edit both files. After editing _config.yml, you need to run make serve again to
see the changes take effect locally.
{% comment %} EVENTBRITE
This block includes the Eventbrite registration widget if 'eventbrite' has been set in the header. You can delete it if you are not using Eventbrite, or leave it in, since it will not be displayed if the 'eventbrite' field in the header is not set. {% endcomment %} {% if page.eventbrite %}
<iframe src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt" frameborder="0" width="100%" height="280px" scrolling="auto"> </iframe> {% endif %}{% comment %} INTRODUCTION
Edit the general explanatory paragraph below if you want to change the pitch. {% endcomment %} {% if page.carpentry == "swc" %} {% include sc/intro.html %} {% elsif page.carpentry == "dc" %} {% include dc/intro.html %} {% elsif page.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 page.carpentry == "swc" %} {% include sc/who.html %} {% elsif page.carpentry == "dc" %} {% include dc/who.html %} {% elsif page.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 %} {% if page.latlng %}
Where: {{page.address}}. Get directions with OpenStreetMap or Google Maps.
{% 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: 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).
{% comment%} CODE OF CONDUCT {% endcomment %}
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.
{% comment %} ACCESSIBILITY
Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}
Accessibility: 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.
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.
{% 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 %} SURVEYS - DO NOT EDIT SURVEY LINKS {% endcomment %}
Please be sure to complete these surveys before and after the workshop.
{% if site.carpentry == "swc" %} {% elsif site.carpentry == "dc" %} {% elsif site.carpentry == "lc" %} {% endif %}{% comment %} SCHEDULE
Show the workshop's schedule. 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. {% endcomment %}
{% if page.carpentry == "swc" %} {% include sc/schedule.html %} {% elsif page.carpentry == "dc" %} {% include dc/schedule.html %} {% elsif page.carpentry == "lc" %} {% include lc/schedule.html %} {% endif %}
{% comment %} Collaborative Notes
If you want to use an Etherpad, go to
http://pad.carpentries.org/YYYY-MM-DD-site
where 'YYYY-MM-DD-site' is the identifier for your workshop, e.g., '2015-06-10-esu'. {% endcomment %} {% if page.collaborative_notes %}
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
{% endif %}{% comment %} SYLLABUS
Show what topics will be covered.
- If your workshop is R rather than Python, remove the comment around that section and put a comment around the Python section.
- Some workshops will delete SQL.
- Please make sure the list of topics is synchronized with what you intend to teach.
- You may need to move the div's with class="col-md-6" around inside the div's with class="row" to balance the multi-column layout.
This is one of the places where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %}
{% if page.carpentry == "swc" %} {% include sc/syllabus.html %} {% elsif page.carpentry == "dc" %} {% include dc/syllabus.html %} {% elsif page.carpentry == "lc" %} {% include lc/syllabus.html %} {% endif %}
{% comment %} SETUP
Delete irrelevant sections from the setup instructions. Each section is inside a 'div' without any classes to make the beginning and end easier to find.
This is the other place where people frequently make mistakes, so please preview your site before committing, and make sure to run 'tools/check' as well. {% endcomment %}
To participate in a {% if page.carpentry == "swc" %} Software Carpentry {% elsif page.carpentry == "dc" %} Data Carpentry {% elsif page.carpentry == "lc" %} Library Carpentry {% endif %} workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="shell-windows">
<a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
<ol>
<li>Download the Git for Windows <a href="https://git-for-windows.github.io/">installer</a>.</li>
<li>Run the installer and follow the steps below:
<ol>
{% comment %} Git 2.22.0 Setup {% endcomment %}
<li>
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.
</li>
<li>
<strong>
Select "Use the nano editor by default" and click on "Next".
</strong>
</li>
{% comment %} Adjusting your PATH environment {% endcomment %}
<li>
Keep "Git from the command line and also from 3rd-party software" selected and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.
</li>
{% comment %} Choosing the SSH executable {% endcomment %}
<li>Click on "Next".</li>
{% comment %} Choosing HTTPS transport backend {% endcomment %}
<li>Select "Use the native Windows Secure Channel library", and click "Next".</li>
{% comment %} This should mean that people stuck behind corporate firewalls that do MITM attacks
with their own root CA are still able to access remote git repos. {% endcomment %}
{% comment %} Configuring the line ending conversions {% endcomment %}
<li>
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
</li>
{% comment %} Configuring the terminal emulator to use with Git Bash {% endcomment %}
<li>
<strong>
Select "Use Windows' default console window" and click on "Next".
</strong>
</li>
{% comment %} Configuring extra options {% endcomment %}
<li>Leave all three items selected, and click on "Next".</li>
{% comment %} Configuring experimental options {% endcomment %}
<li>Do not select the experimental option. Click "Install".</li>
{% comment %} Installing {% endcomment %}
{% comment %} Completing the Git Setup Wizard {% endcomment %}
<li>Click on "Finish".</li>
</ol>
</li>
<li>
If your "HOME" environment variable is not set (or you don't know what this is):
<ol>
<li>Open command prompt (Open Start Menu then type <code>cmd</code> and press [Enter])</li>
<li>
Type the following line into the command prompt window exactly as shown:
<p><code>setx HOME "%USERPROFILE%"</code></p>
</li>
<li>Press [Enter], you should see <code>SUCCESS: Specified value was saved.</code></li>
<li>Quit command prompt by typing <code>exit</code> then pressing [Enter]</li>
</ol>
</li>
</ol>
<p>This will provide you with both Git and Bash in the Git Bash program.</p>
</article>
<article role="tabpanel" class="tab-pane active" id="shell-macos">
<p>
The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
<code>/Applications/Utilities</code>).
See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="shell-linux">
<p>
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing <code>bash</code>. There is no need to
install anything.
</p>
</article>
</div>
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.
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="git-windows">
<p>
Git should be installed on your computer as part of your Bash
install (described above).
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="git-macos">
<a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">Video Tutorial</a>
<p>
<strong>For OS X 10.9 and higher</strong>, install Git for Mac
by downloading and running the most recent "mavericks" installer from
<a href="http://sourceforge.net/projects/git-osx-installer/files/">this list</a>.
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 <code>/Applications</code> folder,
as Git is a command line program.
<strong>For older versions of OS X (10.5-10.8)</strong> use the
most recent available installer labelled "snow-leopard"
<a href="http://sourceforge.net/projects/git-osx-installer/files/">available here</a>.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="git-linux">
<p>
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
<code>sudo apt-get install git</code> and for Fedora run
<code>sudo dnf install git</code>.
</p>
</article>
</div>
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.
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="editor-windows">
<p>
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
</p>
<p>
Others editors that you can use are
<a href="https://notepad-plus-plus.org/">Notepad++</a> or
<a href="https://www.sublimetext.com/">Sublime Text</a>.
<strong>Be aware that you must
add its installation directory to your system path.</strong>
Please ask your instructor to help you do this.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="editor-macos">
<p>
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
for an example on how to open nano.
It should be pre-installed.
</p>
<p>
Others editors that you can use are
<a href="https://www.barebones.com/products/bbedit/">BBEdit</a> or
<a href="https://www.sublimetext.com/">Sublime Text</a>.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="editor-linux">
<p>
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
</p>
<p>
Others editors that you can use are
<a href="https://wiki.gnome.org/Apps/Gedit">Gedit</a>,
<a href="https://kate-editor.org/">Kate</a> or
<a href="https://www.sublimetext.com/">Sublime Text</a>.
</p>
</article>
</div>
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. 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).
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="python-windows">
<a href="https://www.youtube.com/watch?v=xxQ0mzZ8UvA">Video Tutorial</a>
<ol>
<li>Open <a href="https://www.anaconda.com/download/#windows">https://www.anaconda.com/download/#windows</a> with your web browser.</li>
<li>Download the Python 3 installer for Windows.</li>
<li>Install Python 3 using all of the defaults for installation <em>except</em> make sure to check <strong>Add Anaconda to my PATH environment variable</strong>.</li>
</ol>
</article>
<article role="tabpanel" class="tab-pane active" id="python-macos">
<a href="https://www.youtube.com/watch?v=TcSAln46u9U">Video Tutorial</a>
<ol>
<li>Open <a href="https://www.anaconda.com/download/#macos">https://www.anaconda.com/download/#macos</a> with your web browser.</li>
<li>Download the Python 3 installer for OS X.</li>
<li>Install Python 3 using all of the defaults for installation.</li>
</ol>
</article>
<article role="tabpanel" class="tab-pane active" id="python-linux">
<ol>
<li>Open <a href="https://www.anaconda.com/download/#linux">https://www.anaconda.com/download/#linux</a> with your web browser.</li>
<li>Download the Python 3 installer for Linux.<br>
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
</li>
<li>
Open a terminal window.
</li>
<li>
Type <pre>bash Anaconda3-</pre> and then press
<kbd>Tab</kbd>. The name of the file you just downloaded should
appear. If it does not, navigate to the folder where you
downloaded the file, for example with:
<pre>cd Downloads</pre>
Then, try again.
</li>
<li>
Press <kbd>Return</kbd>. You will follow the text-only prompts. To move through
the text, press <kbd>Spacebar</kbd>. Type <code>yes</code> and
press enter to approve the license. Press enter to approve the
default location for the files. Type <code>yes</code> and
press enter to prepend Anaconda to your <code>PATH</code>
(this makes the Anaconda distribution the default Python).
</li>
<li>
Close the terminal window.
</li>
</ol>
</article>
</div>
Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.
{% endcomment %}R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="rstats-windows">
<a href="https://www.youtube.com/watch?v=q0PjTAylwoU">Video Tutorial</a>
<p>
Install R by downloading and running
<a href="https://cran.r-project.org/bin/windows/base/release.htm">this .exe file</a>
from <a href="https://cran.r-project.org/index.html">CRAN</a>.
Also, please install the
<a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio IDE</a>.
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.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="rstats-macos">
<a href="https://www.youtube.com/watch?v=5-ly3kyxwEg">Video Tutorial</a>
<p>
Install R by downloading and running
<a href="https://cran.r-project.org/bin/macosx/R-latest.pkg">this .pkg file</a>
from <a href="https://cran.r-project.org/index.html">CRAN</a>.
Also, please install the
<a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio IDE</a>.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="rstats-linux">
<p>
You can download the binary files for your distribution
from <a href="https://cran.r-project.org/index.html">CRAN</a>. Or
you can use your package manager (e.g. for Debian/Ubuntu
run <code>sudo apt-get install r-base</code> and for Fedora run
<code>sudo dnf install R</code>). Also, please install the
<a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio IDE</a>.
</p>
</article>
</div>
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
Visit SqliteBrowser and download and install it. Version 3.11.0 or greater.
Visit SqliteBrowser and download and install it. Version 3.11.0 or greater.
Visit SqliteBrowser and download and install it. Version 3.11.0 or greater.
</div>
{%else%}
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="sql-windows">
<p>
<ul>
<li>Run git-bash from the start menu</li>
<li>Copy the following <code>curl {{site.url}}{{site.baseurl}}/getsql.sh | bash</code></li>
<li>Paste it into the window that git bash opened. If you're unsure, ask an instructor for help</li>
<li>You should see something like <code>3.27.2 2019-02-25 16:06:06 ...</code></li>
</ul>
<p>If you want to do this manually, download <a href="https://www.sqlite.org/2019/sqlite-tools-win32-x86-3270200.zip">sqlite3</a>, 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.</p>
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="sql-macos">
<p>
SQLite comes pre-installed on macOS.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="sql-linux">
<p>
SQLite comes pre-installed on Linux.
</p>
</article>
<article role="tabpanel" class="tab-pane active" id="sql-web">
<p>
<ul>
<li>In case of problems: register for an account at <a href="http://pythonanywhere.com/">Python Anywhere</a></li>
<li>Download <a href="http://swcarpentry.github.io/sql-novice-survey/files/survey.db">survey.db</a></li>
<li>Click on files and upload survey.db</li>
<li>Click on dashboard and Choose new console <code>$ bash</code></li>
</ul>
</p>
</article>
</div>
{%endif%}
If you installed Anaconda, it also has a copy of SQLite
without support to readline.
Instructors will provide a workaround for it if needed.
For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.
<div class="tab-content">
<article role="tabpanel" class="tab-pane active" id="openrefine-windows">
<p>
Check that you have either the Firefox or the Chrome browser installed and set as your default browser.
<strong>OpenRefine runs in your default browser.</strong>
It will not run correctly in Internet Explorer.
</p>
<p>Download software from <a href="http://openrefine.org/">http://openrefine.org/</a></p>
<p>Create a new directory called OpenRefine.</p>
<p>Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...". </p>
<p>Go to your newly created OpenRefine directory.</p>
<p>Launch OpenRefine by clicking <code>openrefine.exe</code> (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).</p>
<p>If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at <a href="http://127.0.0.1:3333/">http://127.0.0.1:3333/</a> or <a href="http://localhost:3333">http://localhost:3333</a> to use the program.</p>
</article>
<article role="tabpanel" class="tab-pane active" id="openrefine-macos">
<p>Check that you have either the Firefox or the Chrome browser installed and set as your default browser. <strong>OpenRefine runs in your default browser.</strong> It may not run correctly in Safari.</p>
<p>Download software from <a href="http://openrefine.org/">http://openrefine.org/</a>.</p>
<p>Create a new directory called OpenRefine.</p>
<p>Unzip the downloaded file into the OpenRefine directory by double-clicking it.</p>
<p>Go to your newly created OpenRefine directory.</p>
<p>Launch OpenRefine by dragging the icon into the Applications folder.</p>
<p>Use <code>Ctrl-click/Open ... </code> to launch it.</p>
<p>If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at <a href="http://127.0.0.1:3333/">http://127.0.0.1:3333/</a> or <a href="http://localhost:3333">http://localhost:3333</a> to use the program.</p>
</article>
<article role="tabpanel" class="tab-pane active" id="openrefine-linux">
<p>Check that you have either the Firefox or the Chrome browser installed and set as your default browser. <strong>OpenRefine runs in your default browser.</strong></p>
<p>Download software from <a href="http://openrefine.org/">http://openrefine.org/</a>.</p>
<p>Make a directory called OpenRefine.</p>
<p>Unzip the downloaded file into the OpenRefine directory.</p>
<p>Go to your newly created OpenRefine directory.</p>
<p>Launch OpenRefine by entering <code>./refine</code> into the terminal within the OpenRefine directory.</p>
<p>If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at <a href="http://127.0.0.1:3333/">http://127.0.0.1:3333/</a> or <a href="http://localhost:3333">http://localhost:3333</a> to use the program.</p>
</article>
</div>
{% comment %}
Some instructors prefer to have learners use a virtual machine (VM) rather than install software on their own computers. If your instructors have chosen to do this, please:
- Install VirtualBox.
- Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your workshop.
-
Load the VM into VirtualBox by selecting "Import Appliance" and
loading the
.ovafile.