| layout | carpentry | venue | address | country | language | latlng | humandate | humantime | startdate | enddate | instructor | helper | collaborative_notes | eventbrite | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
workshop |
swc |
AMT/SD Git LaTeX Tutorial |
Alison House: Faculty Room 2.02 |
UK |
English |
55.946154, -3.186409 |
May 6th 2019 |
12:00 - 14:00 |
May 6th 2019 |
May 6th 2019 |
|
This hands-on workshop will cover the principles of using Git for version control and LaTeX for typesetting. We encourage you to help one another and to apply what they you learned to your own research problems. This tutorial is based on the principles of Software Carpentry, which aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills.
For more information on Software Carpentries, please see this paper "Best Practices for Scientific Computing".
{% 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 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 %} 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 %}
- Creating a Repository
- Recording Changes to Files:
add,commit, ... - Viewing Changes:
status,diff, ... - Ignoring Files
- Working on the Web:
clone,pull,push, ... - Resolving Conflicts
- Open Licenses
- Where to Host Work, and Why
- Reference...
- Building a LaTeX Project
- Formatting equations and images
- Citations with BibTeX
- Using Packages
- Reference...
{% 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 %}
OS: First off, let us know which operating system you are using in this poll. This will make it a lot easier to debug problems in advance
To participate in 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.
<p>
Bash is a commonly-used shell that gives you the power to do simple
tasks more quickly.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="shell-windows"><i class="fab fa-windows"></i> Windows</h4>
<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 2.18.0 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 "Use Git from the command line and..." 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 %} 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 experimental performance tweaks {% endcomment %}
<li>Click on "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>
</div>
<div class="col-md-4">
<h4 id="shell-macosx"><i class="fab fa-apple"></i> macOS</h4>
<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>
</div>
<div class="col-md-4">
<h4 id="shell-linux"><i class="fab fa-linux"></i> Linux</h4>
<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>
</div>
</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.
<p>
As a solo developer who wishes to version control, you will likely not need more than the <a href="https://desktop.github.com">GitHub Desktop App</a>. We will be using this app to begin with, so follow the instructions for installing the app
</p>
<div class="row">
<div class="col-md-4">
<h4 id="git-windows"><i class="fab fa-windows"></i> Windows</h4>
<p>
Git should be installed on your computer as part of your Bash
install (described above).
</p>
</div>
<div class="col-md-4">
<h4 id="git-macosx"><i class="fab fa-apple"></i> macOS</h4>
<p>
Please open the Terminal app, type <code>git --version</code> and press
<kbd>Enter</kbd>/<kbd>Return</kbd>. If it's not installed already,
follow the instructions to <code>Install</code> the "command line
developer tools". <strong>Don't click</strong> "Get Xcode", because that will
take too long and is not necessary for our Git lesson.
After installing these tools, there won't be anything in your <code>/Applications</code>
folder, as they and Git are command line programs.
<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>.
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 in the pop-up dialog. You can watch
<a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">a video tutorial about this case</a>.
</p>
</div>
<div class="col-md-4">
<h4 id="git-linux"><i class="fab fa-linux"></i>Linux</h4>
<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>
</div>
</div>
<p>
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 <kbd>Esc</kbd> key, followed by <kbd>:</kbd>+<kbd>Q</kbd>+<kbd>!</kbd>
(colon, lower-case 'q', exclamation mark), then hitting <kbd>Return</kbd> to
return to the shell.
</p>
<h4><i class="fas fa-atom"></i> Atom</h4>
<p>
For this session we recommend installing <a href="https://atom.io">Atom</a> as it is a versatile text editor with syntax highlighting available for most programming languages.
</p>
<div class="row">
<div class="col-md-4">
<h4 id="editor-windows"><i class="fab fa-windows"></i> Windows</h4>
<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>
</div>
<div class="col-md-4">
<h4 id="editor-macosx"><i class="fab fa-apple"></i> macOS</h4>
<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>
</div>
<div class="col-md-4">
<h4 id="editor-linux"><i class="fab fa-linux"></i> Linux</h4>
<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>
</div>
</div>
LaTeX is a high-quality typesetting system designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents.
<h4><i class="fas fa-globe"></i> Online</h4>
<p>
<a href="https://www.overleaf.com/">Overleaf</a> is a great tool for getting started with LaTeX quickly. Sadly, git integration comes at a premium, but the basic LaTeX functionality is free.
</p>
<br>
</p>
<div class="row">
<div class="col-md-4">
<h4 id="editor-windows"><i class="fab fa-windows"></i> Windows</h4>
<p>Check out the <a href="http://miktex.org/">MiKTeX</a> distribution
and it's associated editor, TeXWorks.
</p>
</div>
<div class="col-md-4">
<h4 id="editor-macosx"><i class="fab fa-apple"></i> macOS</h4>
<p>The <a href="http://www.tug.org/mactex/">MacTeX</a>
distribution contains everything you need, including a complete
TeX system with LaTeX itself and editors to write documents.
</p>
</div>
<div class="col-md-4">
<h4 id="editor-linux"><i class="fab fa-linux"></i> Linux</h4>
<p>Check your Linux distributions software source for a TeX
distribution including LaTeX. You can also
install the current <a href="https://www.tug.org/texlive">TeX Live distribution</a>
directly---in fact this may be advisable as many Linux distributions only contain
older versions of TeX Live, see
<a href="https://repology.org/metapackage/texlive/versions">Linux TeX Live package status</a>
for details.</p>
</div>
</div>
<h4><i class="fas fa-atom"></i> Atom</h4>
<p>
After you have installed one of the above LaTeX distributions, I would highly recommend using Atom. There are a couple of packages that need to be installed, but the benefits out-weigh the inconvenience. You will need to download the following packages:
</p>
<ul>
<li><a href="https://atom.io/packages/latex">Latex</a> compile tool by thomasjo</li>
<li><a href="https://atom.io/packages/latex-autocomplete">latex-autocomplete</a> by evpok</li>
<li><a href="https://atom.io/packages/language-latex">Language-LaTeX</a> by area</li>
</ul>
<p>
NB: Windows users may want to download <a href="https://www.tug.org/texlive/acquire-netinstall.html">TexLive</a> if they are having trouble with getting atom to work with LaTeX.
</p>
<h3>BibTeX</h3>
<p>On of the powerful aspects of LaTeX is bibliography management using BibTeX. Bibliography files (\*.bib) are most easily edited and modified using a management system. These graphical user interfaces all feature a database form, where information is entered for each reference item, and the resulting text file can be used directly by BibTeX.</p>
<p>For this session we will be using <a href="http://www.jabref.org">JabRef</a>.</p>