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_sources/pages/git_and_github.md

@@ -20,7 +20,7 @@ To [install git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
 
 While you can install [Git for Windows](https://gitforwindows.org/), because
 the other software packages used in this course are Mac- or Linux-only, you
-will be forced to use WSL to complete this course on Windows. Still, we'll
+will be forced to use git via {term}`WSL` to complete this course. Still, we'll
 provide a [download link](https://git-scm.com/download/win) for git on Windows.
 
 :::
@@ -64,9 +64,9 @@ sudo dnf install git-all
 
 ::::
 
-GitHub is the most well known hosting service, and it provides free accounts
-(and free private repositories) to all users. This bootcamp, for example, is
-hosted on GitHub, along with many of the most popular open-source Python
-projects (including numpy, scipy, and matplotlib). If you want to version
-control your code, we recommend creating an account on GitHub and keeping your
-source code there.
+[GitHub](https://github.com/) is the most well known hosting service, and it 
+provides free accounts (and free private repositories) to all users. This 
+bootcamp, for example, is hosted on GitHub, along with many of the most popular 
+open-source Python projects (including numpy, scipy, and matplotlib). If you 
+want to version control your code, we recommend creating an account on GitHub 
+and keeping your source code there.

_sources/pages/glossary.md

@@ -64,6 +64,9 @@ silicon-on-insulator
 SOI
     See {term}`silicon-on-insulator`.
 
+vscode
+    Visual Studio Code, also commonly referred to as VS Code, is a source-code editor developed by Microsoft for Windows, Linux and macOS. Features include support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git ([Wikipedia](https://en.wikipedia.org/wiki/Visual_Studio_Code)).
+
 WSL
     Windows Subsystem for Linux. WSL lets developers install and run a Linux distribution on Windows and use Linux applications, utilities, and Bash command-line tools directly on Windows, unmodified, without the overhead of a traditional virtual machine or dual-boot setup.
 

_sources/pages/klayout.md

@@ -7,3 +7,16 @@
 </div>
 
 [KLayout](https://www.klayout.de/) is a free and open-source software for layout design and verification. It's most basic use case is as a layout viewer (it can read and display GDS files, the most common format for laying out photonic chips), but it is a powerful tool for designing photonic devices and integrated circuits as well. It has features for {term}`DRC`, viewing chip cross-sections, tracing nets (to help you detect shorts), and more, while also being scriptable in several languages including Ruby and Python. KLayout is available for Windows, Mac, and Linux. You can download KLayout [here](https://www.klayout.de/build.html).
+
+## klive
+
+klive is a small extension to KLayout that allows automatic loading for GDS 
+files when some external program sends a json request with the gds path to a 
+klive server, running in the background. This essentially allows for 
+"hot-reloading" of your layouts within KLayout each time you rerun your code.
+
+Once KLayout is installed, you can install klive from within KLayout's package
+manager, by going to `Tools > Manage Packages > Install New Packages`. Then, 
+search for `klive` and double click it to select it, then click "Apply".
+
+![klive installation screenshot](../klive_installation.png)

_sources/pages/setup.md

@@ -1,27 +1,42 @@
 # Setting up the tools
 
-Since we use a lot of python tools in this course, there are some things which you'd need to install. In short:
-
-1. You'd need to either have a Linux machine, a Mac, or a Windows machine with the Windows Subsystem for Linux (WSL) installed.
-2. You'd need a Code Editor. The recommended code editor is VSCode, which you can set up [here](/pages/vscode.md).
-3. You'd need Miniconda. Some of the tools are available through pip, while some are only available through Conda. Miniconda is a nice way to manage all these tools in a single place.
-4. You'd need KLayout. This is a layout viewer, which we'll use to view the layouts we create.
+Since we primarily use Python tools in this course, there are some things 
+you'll need to install. In short, you'll need:
+
+1. A Linux machine, a Mac, or a Windows machine with the 
+    [Windows Subsystem for Linux (WSL)](https://learn.microsoft.com/en-us/windows/wsl/about) 
+    installed.
+2. A code editor. The recommended code editor is 
+    [Visual Studio Code](https://code.visualstudio.com/), (installation 
+    instructions [here](/pages/vscode.md)).
+3. Miniconda. Most of the tools are installable through the 
+    [Python Package Index (PyPI)](https://pypi.org/), i.e. "pip" installable, 
+    while some precompiled packages are only available through Conda 
+    repositories. Miniconda, which also provides a Python installation and 
+    virtual environments by default, is a nice way to manage all these tools 
+    in a single place.
+4. KLayout, a layout/GDS file viewer, which we'll use to view the circuits we 
+    create.
 
 ## Install WSL
-If you are using Windows, you'd have to install WSL. To install:
 
-1. Open Command Prompt as Administrator
-2. Type `wsl --install` and press Enter
-3. Restart your computer
-4. Click on the Start menu and type "Ubuntu" and press Enter
-5. Set up your username and password
+If you are using Windows, you'll need to install {term}`WSL``. This can be 
+easily installed through the Windows store (recommended), or via the command 
+line:
+
+1. Open Command Prompt as Administrator.
+2. Run the command ``wsl --install``.
+3. Restart your computer.
+4. From the Start menu, run Ubuntu.
+5. On the first run, set up a new user account on the Linux machinen (username 
+    and password, which can be different from your Windows machine).
 
 ## Install VSCode
 You now need to install VSCode. Refer to the chapter on VSCode [here](/pages/vscode.md), which explains what VSCode is and how to install it.
 
 Open VSCode. You can setup a theme and other things. If you are using WSL, make sure to [open VSCode in your WSL environment](https://code.visualstudio.com/docs/remote/wsl#_open-a-remote-folder-or-workspace). You can check this by checking the green box in the bottom left-hand corner. If VSCode is connected to WSL it will say "WSL" in this box. If it doesn't then click the green box. A menu will pop up. Click the option "Connect to WSL" and VSCode will now be connected to WSL.
 
-## Setup Script
+<!-- ## Setup Script
 To install Miniconda and KLayouts we have created a setup script you can download [here](../scripts/setup.sh). If you want to install these manual, skip this step by going to the [next page](/pages/git_and_github).
 
 If you are using Linux, and assuming the script was downloaded to your Downloads folder, run the following command:
@@ -49,4 +64,4 @@ conda activate photonics
 ```
 If everything installed correctly you are ready to move onto the [next chapter](/pages/what_is_a_photonic_device).
 
-The following pages in this section would explain how to use the tools. They also include instructions on how to install the tools individually, if you don't want to use Miniconda.  
+The following pages in this section would explain how to use the tools. They also include instructions on how to install the tools individually, if you don't want to use Miniconda.   -->

_sources/pages/vscode.md

@@ -3,7 +3,7 @@
 While you can write computer code using any text editor, some text editors have
 special features that make writing code easier.  In this course, we will be
 using [Visual Studio Code](https://code.visualstudio.com) (also known as
-vscode), a popular open-source text editor by Microsoft that is desiged
+{term}`vscode`), a popular open-source text editor by Microsoft that is desiged
 specifically for writing code. It boasts a healthy set of extensions that 
 can provide integrated development environment (IDE)-like capabilities in a 
 much lighter program.

genindex.html

@@ -265,6 +265,7 @@ <h1 id="index">Index</h1>
  | <a href="#P"><strong>P</strong></a>
  | <a href="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
+ | <a href="#V"><strong>V</strong></a>
  | <a href="#W"><strong>W</strong></a>
 </div>
 <h2 id="C">C</h2>
@@ -369,6 +370,13 @@ <h2 id="S">S</h2>
 </li>
 </ul></td>
 </tr></table>
+<h2 id="V">V</h2>
+<table class="indextable genindextable" style="width: 100%"><tr>
+<td style="width: 33%; vertical-align: top;"><ul>
+<li><a href="pages/glossary.html#term-vscode"><strong>vscode</strong></a>
+</li>
+</ul></td>
+</tr></table>
 <h2 id="W">W</h2>
 <table class="indextable genindextable" style="width: 100%"><tr>
 <td style="width: 33%; vertical-align: top;"><ul>

pages/git_and_github.html

@@ -302,7 +302,7 @@ <h1>Git (and GitHub)<a class="headerlink" href="#git-and-github" title="Permalin
 Windows</label><div class="sd-tab-content docutils">
 <p>While you can install <a class="reference external" href="https://gitforwindows.org/">Git for Windows</a>, because
 the other software packages used in this course are Mac- or Linux-only, you
-will be forced to use WSL to complete this course on Windows. Still, we’ll
+will be forced to use git via <a class="reference internal" href="glossary.html#term-WSL"><span class="xref std std-term">WSL</span></a> to complete this course. Still, we’ll
 provide a <a class="reference external" href="https://git-scm.com/download/win">download link</a> for git on Windows.</p>
 </div>
 <input id="sd-tab-item-1" name="sd-tab-set-0" type="radio"/>
@@ -332,12 +332,12 @@ <h1>Git (and GitHub)<a class="headerlink" href="#git-and-github" title="Permalin
 </div>
 </div>
 </div>
-<p>GitHub is the most well known hosting service, and it provides free accounts
-(and free private repositories) to all users. This bootcamp, for example, is
-hosted on GitHub, along with many of the most popular open-source Python
-projects (including numpy, scipy, and matplotlib). If you want to version
-control your code, we recommend creating an account on GitHub and keeping your
-source code there.</p>
+<p><a class="reference external" href="https://github.com/">GitHub</a> is the most well known hosting service, and it
+provides free accounts (and free private repositories) to all users. This
+bootcamp, for example, is hosted on GitHub, along with many of the most popular
+open-source Python projects (including numpy, scipy, and matplotlib). If you
+want to version control your code, we recommend creating an account on GitHub
+and keeping your source code there.</p>
 </section>
 <script type="text/x-thebe-config">
     {

pages/glossary.html

@@ -328,6 +328,8 @@ <h1>Glossary<a class="headerlink" href="#glossary" title="Permalink to this head
 </dd>
 <dt id="term-SOI">SOI<a class="headerlink" href="#term-SOI" title="Permalink to this term">#</a></dt><dd><p>See <a class="reference internal" href="#term-silicon-on-insulator"><span class="xref std std-term">silicon-on-insulator</span></a>.</p>
 </dd>
+<dt id="term-vscode">vscode<a class="headerlink" href="#term-vscode" title="Permalink to this term">#</a></dt><dd><p>Visual Studio Code, also commonly referred to as VS Code, is a source-code editor developed by Microsoft for Windows, Linux and macOS. Features include support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git (<a class="reference external" href="https://en.wikipedia.org/wiki/Visual_Studio_Code">Wikipedia</a>).</p>
+</dd>
 <dt id="term-WSL">WSL<a class="headerlink" href="#term-WSL" title="Permalink to this term">#</a></dt><dd><p>Windows Subsystem for Linux. WSL lets developers install and run a Linux distribution on Windows and use Linux applications, utilities, and Bash command-line tools directly on Windows, unmodified, without the overhead of a traditional virtual machine or dual-boot setup.</p>
 </dd>
 </dl>

pages/klayout.html

@@ -270,6 +270,9 @@
   </button>
 `);
 </script>
+<label class="sidebar-toggle secondary-toggle btn btn-sm" data-bs-placement="bottom" data-bs-toggle="tooltip" for="__secondary" title="Toggle secondary sidebar">
+<span class="fa-solid fa-list"></span>
+</label>
 </div></div>
 </div>
 </div>
@@ -279,6 +282,14 @@ <h1>KLayout</h1>
 <!-- Table of contents -->
 <div id="print-main-content">
 <div id="jb-print-toc">
+<div>
+<h2> Contents </h2>
+</div>
+<nav aria-label="Page">
+<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#klive">klive</a></li>
+</ul>
+</nav>
 </div>
 </div>
 </div>
@@ -291,6 +302,17 @@ <h1>KLayout<a class="headerlink" href="#klayout" title="Permalink to this headin
 <p>(<a class="reference external" href="https://www.klayout.de/">source</a>)</p>
 </div>
 <p><a class="reference external" href="https://www.klayout.de/">KLayout</a> is a free and open-source software for layout design and verification. It’s most basic use case is as a layout viewer (it can read and display GDS files, the most common format for laying out photonic chips), but it is a powerful tool for designing photonic devices and integrated circuits as well. It has features for <a class="reference internal" href="glossary.html#term-DRC"><span class="xref std std-term">DRC</span></a>, viewing chip cross-sections, tracing nets (to help you detect shorts), and more, while also being scriptable in several languages including Ruby and Python. KLayout is available for Windows, Mac, and Linux. You can download KLayout <a class="reference external" href="https://www.klayout.de/build.html">here</a>.</p>
+<section id="klive">
+<h2>klive<a class="headerlink" href="#klive" title="Permalink to this heading">#</a></h2>
+<p>klive is a small extension to KLayout that allows automatic loading for GDS
+files when some external program sends a json request with the gds path to a
+klive server, running in the background. This essentially allows for
+“hot-reloading” of your layouts within KLayout each time you rerun your code.</p>
+<p>Once KLayout is installed, you can install klive from within KLayout’s package
+manager, by going to <code class="docutils literal notranslate"><span class="pre">Tools</span> <span class="pre">&gt;</span> <span class="pre">Manage</span> <span class="pre">Packages</span> <span class="pre">&gt;</span> <span class="pre">Install</span> <span class="pre">New</span> <span class="pre">Packages</span></code>. Then,
+search for <code class="docutils literal notranslate"><span class="pre">klive</span></code> and double click it to select it, then click “Apply”.</p>
+<p><img alt="klive installation screenshot" src="klive_installation.png"/></p>
+</section>
 </section>
 <script type="text/x-thebe-config">
     {
@@ -331,7 +353,17 @@ <h1>KLayout<a class="headerlink" href="#klayout" title="Permalink to this headin
 </div>
 </footer>
 </div>
-<div class="bd-sidebar-secondary bd-toc"></div>
+<div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+<div class="sidebar-secondary-item">
+<div class="page-toc tocsection onthispage">
+<i class="fa-solid fa-list"></i> Contents
+  </div>
+<nav class="bd-toc-nav page-toc">
+<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#klive">klive</a></li>
+</ul>
+</nav></div>
+</div></div>
 </div>
 <footer class="bd-footer-content">
 <div class="bd-footer-content__inner container">