From 0633516de6306f34d0cf1d3bae5562b720054b25 Mon Sep 17 00:00:00 2001
From: k204229 <lucio-eceiza@dkrz.de>
Date: Mon, 1 Jul 2024 15:58:33 +0200
Subject: [PATCH] update freva workshop slides, day2

---
 .../day 2/index.slides.html                   | 1598 +----------------
 1 file changed, 36 insertions(+), 1562 deletions(-)

diff --git a/talks/Freva_Workshop_2024/day 2/index.slides.html b/talks/Freva_Workshop_2024/day 2/index.slides.html
index d0e1c36..2bacef8 100644
--- a/talks/Freva_Workshop_2024/day 2/index.slides.html	
+++ b/talks/Freva_Workshop_2024/day 2/index.slides.html	
@@ -6,7 +6,7 @@
 <meta content="yes" name="apple-mobile-web-app-capable"/>
 <meta content="black-translucent" name="apple-mobile-web-app-status-bar-style"/>
 <title>Day 2 - Introduction to Freva Plugins slides</title><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script><script type="module">
-  import mermaid from 'https://cdnjs.cloudflare.com/ajax/libs/mermaid/10.6.0/mermaid.esm.min.mjs';
+  import mermaid from 'https://cdnjs.cloudflare.com/ajax/libs/mermaid/10.7.0/mermaid.esm.min.mjs';
   mermaid.initialize({ startOnLoad: true });
 </script>
 <!-- General and theme style sheets -->
@@ -7441,7 +7441,7 @@
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
 <h1 id="Freva:-Plugin-Development">Freva: Plugin Development<a class="anchor-link" href="#Freva:-Plugin-Development">¶</a></h1><img align="center" alt="freva dev" src="media/plugin_intro/freva-plugindev.png" width="500"/>
-<p><strong>Martin Bergemann, Bijan Fallah, Andrej Fast, Mostafa Hadizadeh, 
+<p><strong>Martin Bergemann, Bijan Fallah, Andrej Fast, Mostafa Hadizadeh,
 Christopher Kadow, Etor E. Lucio-Eceiza,  Felix Örtel, Manuel Reis, and many others…</strong></p>
 <p>Deutsches Klimarechenzentrum @ CLINT in Data Analysis Dpt. (+ Data Management Dpt.*)</p>
 </div>
@@ -7536,1538 +7536,6 @@ <h2 id="Structure-of-a-Plugin:-The-tool">Structure of a Plugin: The tool<a class
 </div>
 *caveat: we encourage <i>free</i> software
 
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Structure-of-a-Plugin:-Installer">Structure of a Plugin: Installer<a class="anchor-link" href="#Structure-of-a-Plugin:-Installer">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<p>Installs the plugin environment:</p>
-<ul>
-<li>Usually: Makefile (<i>instructions</i>) + .yaml file (<i>libraries</i>)</li>
-<li>It can also be more elaborated: e.g. binary compilation, installation of subroutines...</li>
-</ul>
-</div>
-<div style="text-align: right; width: 50%;">
-<img align="center" alt="parts" src="media/plugin_intro/make-yaml.jpg" width="500"/>
-</div>
-</div>
-<p><strong>NOTE:</strong> It replaces the dependencies on the HPC (e.g. <code>modules</code>) and makes it more transferable to other e.g. institutions</p>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="Git-and-Gitlab">Git and Gitlab<a class="anchor-link" href="#Git-and-Gitlab">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2>What is git? <img align="center" alt="freva dev" src="media/gitlab/git-logo.jpg" width="70"/></h2>
-<p>Is a free and open source <em>Distributed</em> <strong>Version Control System</strong>:</p>
-<ul>
-<li><strong>Version Control System</strong>: a system that tracks and provides control over changes to source code, documentation and configuration files.</li>
-<li><em>Distributed</em>: a form of version control in which the complete codebase, including its full history, is mirrored on every developer's computer</li>
-</ul>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2>What is gitlab? <img align="center" alt="freva dev" src="media/gitlab/gitlab-logo.jpg" width="70"/></h2>
-<div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<li>GitLab is a web-based tool: provides version control, issue tracking, CI/CD etc.</li>
-<li>DKRZ hosts its own framework at <a href="https://gitlab.dkrz.de">https://gitlab.dkrz.de</a> </li>
-</div>
-<div style="text-align: right; width: 50%;">
-<img align="center" alt="freva dev" src="media/gitlab/gitlab-flow.jpg" width="500"/>
-</div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Gitlab-and-Freva:">Gitlab and Freva:<a class="anchor-link" href="#Gitlab-and-Freva:">¶</a></h2><ul>
-<li>One central local repository for the plugged plugins</li>
-<li>Other local repositories for different developers</li>
-<li>One remote repository for the plugin at gitlab</li>
-</ul>
-<img align="center" alt="freva dev" src="media/gitlab/freva-gitlab-flow.jpg" width="900"/>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Gitlab-and-Freva:-location-of-the-plugins">Gitlab and Freva: location of the plugins<a class="anchor-link" href="#Gitlab-and-Freva:-location-of-the-plugins">¶</a></h2><ul>
-<li>Under <a href="https://gitlab.dkrz.de/freva/plugins4freva">https://gitlab.dkrz.de/freva/plugins4freva</a> project:</li>
-</ul>
-<img align="center" alt="freva dev" src="media/gitlab/freva-gitlab.jpg" width="900"/>
-- Other projects have also their own, e.g.: 
-    - climxtreme: https://gitlab.dkrz.de/bm1159/plugins4freva
-    - regiklim-nukleus: https://gitlab.dkrz.de/ch1187/plugins4freva
-- some plugins can be found in different projects (see [forks](https://docs.gitlab.com/ee/user/project/repository/forking_workflow.html)).
-
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Gitlab-and-Freva:-cloning-a-repository">Gitlab and Freva: cloning a repository<a class="anchor-link" href="#Gitlab-and-Freva:-cloning-a-repository">¶</a></h2><p>To download a repository there are 2 ways: via <code>https</code> and via <code>ssh</code>:</p>
-<img align="center" alt="freva dev" src="media/gitlab/clone-repo.jpg" width="550"/>
-- `https`: straightforward, requires to enter (dkrz) username and password (usually). 
-- `ssh`: convenient, requires to provide a ssh key previously.
-<p>In both cases:</p>
-<pre><code>$ ssh &lt;username&gt;@levante.dkrz.de
-&gt; cd /path/to/my/work/
-&gt; git clone https://gitlab.dkrz.de/freva/plugins4freva/plugin_workshop/example_plugin.git
-</code></pre>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Gitlab-and-Freva:-setting-your-SSH-key">Gitlab and Freva: setting your SSH key<a class="anchor-link" href="#Gitlab-and-Freva:-setting-your-SSH-key">¶</a></h2><ol>
-<li>generate a ssh a private and public (<code>.pub</code>) key locally (e.g. laptop or levante):</li>
-</ol>
-<pre><code>$ ssh-keygen -t ed25519
-$ cd ~/.ssh/
-$ ls
-id_ed25519  id_ed25519.pub
-</code></pre>
-<ol start="2">
-<li>copy the <strong>public</strong> key:</li>
-</ol>
-<pre><code>$ cat id_ed25519.pub
-ssh-ed25519 AAAAC3NzaC1lFDI1YTE5AAAAICUqpXx8AyrNH7HQgPSq9LuB7sTEmXP4ODqOnaHVPPQ6 username@levante
-</code></pre>
-<ol start="3">
-<li>add the public key in gitlab (<code>user&gt;preferences&gt;ssh keys</code>): <img align="center" alt="freva dev" src="media/gitlab/ssh-keyadd.jpg" width="500"/></li>
-</ol>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Gitlab-and-Freva:-creating-a-new-project">Gitlab and Freva: creating a new project<a class="anchor-link" href="#Gitlab-and-Freva:-creating-a-new-project">¶</a></h2><ul>
-<li>If we already had an existing Git repository:</li>
-</ul>
-<div class="highlight"><pre><span></span>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>NEW_PLUGIN<span class="w"> </span><span class="c1"># for example</span>
-$<span class="w"> </span>git<span class="w"> </span>remote<span class="w"> </span>rename<span class="w"> </span>origin<span class="w"> </span>old-origin
-$<span class="w"> </span>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>origin<span class="w"> </span>git@gitlab.dkrz.de:freva/plugins4freva/new_plugin.git
-$<span class="w"> </span>git<span class="w"> </span>push<span class="w"> </span>-u<span class="w"> </span>origin<span class="w"> </span>--all
-$<span class="w"> </span>git<span class="w"> </span>push<span class="w"> </span>-u<span class="w"> </span>origin<span class="w"> </span>--tags
-</pre></div>
-<ul>
-<li>If we did not already have an existing Git repository:</li>
-</ul>
-<div class="highlight"><pre><span></span>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>NEW_PLUGIN<span class="w"> </span><span class="c1"># for example</span>
-$<span class="w"> </span>git<span class="w"> </span>init
-$<span class="w"> </span>git<span class="w"> </span>remote<span class="w"> </span>add<span class="w"> </span>origin<span class="w"> </span>git@gitlab.dkrz.de:freva/plugins4freva/new_plugin.git
-<span class="c1"># create your new files and folders</span>
-$<span class="w"> </span>git<span class="w"> </span>add<span class="w"> </span>.
-$<span class="w"> </span>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">"Initial commit of my new project"</span>
-$<span class="w"> </span>git<span class="w"> </span>push<span class="w"> </span>-u<span class="w"> </span>origin<span class="w"> </span>master
-</pre></div>
-<p>Now you could (hypothetically) go to <a href="https://gitlab.dkrz.de/freva/plugins4freva/new_plugin">https://gitlab.dkrz.de/freva/plugins4freva/new_plugin</a></p>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="License-of-Plugins">License of Plugins<a class="anchor-link" href="#License-of-Plugins">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="What-kind-of-License-should-I-follow?">What kind of License should I follow?<a class="anchor-link" href="#What-kind-of-License-should-I-follow?">¶</a></h2><p><a href="https://github.com/FREVA-CLINT/freva/blob/main/LICENSE.md">The Freva code</a> follows a <a href="https://opensource.org/license/bsd-3-clause">BSD3 license</a>, a permissive open-source license with minimal restrictions:</p>
-<ul>
-<li>It allows for wide usage, including in proprietary software.</li>
-<li>it imposes very few restrictions on how the software can be redistributed.</li>
-</ul>
-<p>In principle, any derived product from Freva (i.e. plugins), should follow this license. <em>Unless</em> stated otherwise by the developer.</p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="What-kind-of-License-should-I-follow?">What kind of License should I follow?<a class="anchor-link" href="#What-kind-of-License-should-I-follow?">¶</a></h2><ul>
-<li>We encourage open-source software to foster collaboration within and outside your projects.</li>
-<li>That said, common courtesy should be expected, e.g.:<ul>
-<li>reference to the first manuscript where the developer used the plugin (the plugin documentation is useful for this!).</li>
-<li>contacting him/her in case there is no such manuscript.</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="Connecting-your-IDE-/-Code-Editor-to-a-remote-session-using-SSH">Connecting your IDE / Code Editor to a remote session using SSH<a class="anchor-link" href="#Connecting-your-IDE-/-Code-Editor-to-a-remote-session-using-SSH">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2>1. VS-Code <img align="center" alt="freva dev" src="media/vscode/vscode_logo.svg" width="50"/></h2>
-<p>Open a new window in VS Code. There are several ways to connect to a remote session, as indicated in the picture below:</p>
-<p><img alt="Image depicting multiple ways to start a remote session in VS Code" src="media/vscode/01_connect_to_remote.png"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/vscode/vscode_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>Clicking either of the buttons opens a prompt at the top of the window, giving you several options to start a remote session:</p>
-<p><img alt='Image depicting the prompt that opens when clicking one of the "Connect to..." buttons in the new VS Code window' src="media/vscode/02_remote_connection_options.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/vscode/vscode_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>Click "Connect Current Window to Host..." ("Connect to Host..." opens a new window for the connection).</p>
-<p>You can type in the address of the remote host that you want to connect to or, in case the host is specified in your ssh config file (.ssh/config or ssh_config), select them from the list of hosts. To connect to levante, enter [k-number@]levante.dkrz.de  :</p>
-<p><img alt="Image depicting the prompt to enter a remote SSH host, with k202195@levante.dkrz.de manually entered" src="media/vscode/03_remote_host_entered.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/vscode/vscode_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>The first time connecting to a host, you will be prompted to specify the OS of the remote host (i.e. Linux / Windows / macOS).</p>
-<p>Depending on the authentication set up for the remote host, you might be prompted to type in a password. Once the connection has been established, your can open a folder on the remote host, like you would do on your local machine (by pressing <kbd>Ctrl</kbd> + <kbd>K</kbd>, <kbd>Ctrl</kbd> + <kbd>O</kbd> or by pressing "Open Folder"):</p>
-<p><img alt="Image depicting how to open a folder once connected to the remote host, similar to opening a local folder" src="media/vscode/04_opening_remote_folder.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/vscode/vscode_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>You may be prompted again to type in the password at this point. The window should refresh and give you access to the remote folder that you selected in the previous step, similar to what can be seen in the following image:</p>
-<img align="center" alt="freva dev" src="media/vscode/05_remote_folder_success.jpg" width="300"/>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/vscode/vscode_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>From here you can use the editor to work with remote files basically as you would with files on your local machine. Any terminals opened in this window will also connect to the remote host.</p>
-<p>For detailed documentation on remote development using VS Code, including development on dev containers or WSL, click <a href="https://code.visualstudio.com/docs/remote/remote-overview">here</a>.</p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2>2. PyCharm <img align="center" alt="freva dev" src="media/pycharm/pycharm_logo.svg" width="50"/></h2>
-<blockquote>
-<p>😱
-Remote Development is currently in beta and only supported for the Professional Version of PyCharm!</p>
-</blockquote>
-<p>Open your Plugins (<kbd>Ctrl</kbd>+<kbd>Alt</kbd>+<kbd>S</kbd>) and confirm that "Remote Development Gateway" is installed and that it is enabled:</p>
-<p><img alt='Image depicting a list of installed PyCharm plugins, with the "Remote Development Gateway" being installed and enabled.' src="media/pycharm/01_remote_development_gateway.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/pycharm/pycharm_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>To open a remote session in PyCharm, go to the welcome screen and click on the "Remote Development" Tab in the left side bar. This should give you a number of options, including the option to connect to a remote session using SSH:</p>
-<p><img alt='Image depiciting the welcome screen of PyCharm Professional, with the "Remote Development" Tab highlighted using red arrows.' src="media/pycharm/02_remote_development_tab.png"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/pycharm/pycharm_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>To establish a new SSH Connection, click "New Connection" below the SSH Connection option. This should open the following dialogue:</p>
-<p><img alt="Image depicting the dialogue that opens when creating a new SSH connection on PyCharm. Includes fields for the username, the host name or address, and the port that should be used connected to." src="media/pycharm/03_ssh_connection_dialogue.jpg"/></p>
-<blockquote>
-<p>⚠
-Note that PyCharm currently only supports connecting to remote hosts running Linux.</p>
-</blockquote>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/pycharm/pycharm_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>Again, depending on the type of authentication set up by the remote host, you may be prompted to enter a password to establish the remote connection.</p>
-<p>In the next step (pending the successful connection to the remote host), you will be asked to set the IDE version (i.e. the version of the IDE that will be installed on the remote host) and the project directory (i.e. the directory on the remote host that contains the project files that you will be working with):</p>
-<p><img alt="Image depicting the PyCharm window that prompts you to set the IDE Version to be installed on the remote host, as well as the project directory that you will be working in" src="media/pycharm/04_choose_ide_and_project.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/pycharm/pycharm_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>Click "Download IDE and Connect". The installation of the selected IDE on the remote host might take a while. Once the installation is complete, a window containing the remote IDE should open.</p>
-<p><img alt="Image depicting the remote IDE window, after successfully installing it to the remote host" src="media/pycharm/05_remote_IDE_successfully_opened.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/pycharm/pycharm_logo.svg" width="30"/>
-<br/>
-<br/>
-<br/>
-<p>The remote IDE gives you the ability to work with project files, much like you would with local project files. Any terminal sessions started in this IDE will also be connected to the remote host.</p>
-<p>For detailed documentation on remote development using PyCharm, click <a href="https://www.jetbrains.com/help/pycharm/remote-development-starting-page.html">here</a>.</p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2>3. R Studio <img align="center" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="120"/></h2>
-<p>There is currently only one method of using R Studio on a remote host that is officially supported by R, namely by connecting to an instance of R Studio Server running on the remote host. The previously available alternative, by creating a remote connection in <a href="https://docs.posit.co/ide/desktop-pro/2022.02.1+461.pro1/remote-desktop.html">R Studio Desktop Pro</a>, has been removed since version <a href="https://docs.posit.co/ide/desktop-pro/remote_desktop/remote_desktop.html">2023.06.2</a>.</p>
-<p>However, R Studio Server is not available on Levante, so creating a remote development environment instance this way is not possible. However, it is possible to remotely develop and execute R-code by using the <a href="https://code.visualstudio.com/docs/languages/r">VS Code R Extension</a>.</p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>First, connect to Levante as outlined in the VS Code <img alt="No description has been provided for this image" src="media/vscode/vscode_logo.svg" style="vertical-align:middle; display:inline-block; height:1em; width:auto "/> section of this guide. Once the connection is established, you will want to install the R (<code>REditorSupport.r</code>) and R Debugger (<code>RDebugger.r-debugger</code>) Extensions, as shown below:
-<img alt="Image depicting R VS Code Plugins" src="media/rstudio/01_rstudio_vscode_extensions.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>Make sure that you have installed the extensions to the remote host, and not your local machine, by going to Extensions (<kbd>Ctrl</kbd>+<kbd>Shift</kbd>+<kbd>X</kbd>):</p>
-<p><img alt="Image showing that R VS Code Plugins where installed on Levante" src="media/rstudio/02_rstudio_extensions_on_remote.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>In a terminal that is connected to levante via ssh (e.g. in the VS Code window connected to levante), type in the following command:</p>
-<div class="highlight"><pre><span></span>$<span class="w"> </span>module<span class="w"> </span>load<span class="w"> </span>r
-</pre></div>
-<p>The result should be something along the lines of:</p>
-<div class="highlight"><pre><span></span><span class="o">[</span>k202195@levante3<span class="w"> </span>~<span class="o">]</span>$<span class="w"> </span>module<span class="w"> </span>load<span class="w"> </span>r
-Autoloading<span class="w"> </span>openjdk/17.0.0_35-gcc-11.2.0
-
-Loading<span class="w"> </span>r/4.1.2-gcc-11.2.0
-<span class="w">  </span>Loading<span class="w"> </span>requirement:<span class="w"> </span>openjdk/17.0.0_35-gcc-11.2.0
-<span class="o">[</span>k202195@levante3<span class="w"> </span>~<span class="o">]</span>$
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>We'll need to find out, where R is located on the remote host. We do this by using the command:</p>
-<div class="highlight"><pre><span></span>$<span class="w"> </span>which<span class="w"> </span>R
-</pre></div>
-<p>The output should be something like:</p>
-<div class="highlight"><pre><span></span><span class="o">[</span>k202195@levante3<span class="w"> </span>~<span class="o">]</span>$<span class="w"> </span>which<span class="w"> </span>R
-/sw/spack-levante/r-4.1.2-eprwea/bin/R
-<span class="o">[</span>k202195@levante3<span class="w"> </span>~<span class="o">]</span>$
-</pre></div>
-<p>Copy this path to your clipboard.</p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>Install the <a href="https://github.com/nx10/httpgd">httpgd</a> package to embed live R graphics into the VS Code environment. You can do this by running the following commands in a terminal on the remote host:</p>
-<div class="highlight"><pre><span></span><span class="c1"># Start and R command line session</span>
-$<span class="w"> </span>R
-</pre></div>
-<p>The following command is executed in the R command line session</p>
-<div class="highlight"><pre><span></span><span class="nf">install.packages</span><span class="p">(</span><span class="s">"httpgd"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>Open the settings (<kbd>Ctrl</kbd> + <kbd>,</kbd>) and type <code>r.rterm.linux</code> in the search bar as shown in the image below. Make sure that you paste the previously copied path into the field, as depicted:</p>
-<p><img alt="Image depicting how to set the path for the R Terminal in VS Code" src="media/rstudio/03_rterm_linux_settings.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>Once that is done, open any R file on the remote host. Once an R terminal is ready, you could either select the code or put the cursor at the beginning or ending of the code you want to run, press (<kbd>Ctrl</kbd>+<kbd>Enter</kbd>), and then code will be sent to the active R terminal.</p>
-<p>If you want to run an entire R file, open the file in the editor, and press <kbd>Ctrl</kbd>+<kbd>Shift</kbd>+<kbd>S</kbd> and the file will be sourced in the active R terminal:</p>
-<p><img alt="Image depicting some R code being run remotely on Levante and the resulting interactive plots" src="media/rstudio/04_opening_and_running_r_file_in_vscode.jpg"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<img align="right" alt="freva dev" src="media/rstudio/RStudio_logo.svg" width="70"/>
-<br/>
-<br/>
-<br/>
-<p>For more information on working with R in VS Code, click <a href="https://code.visualstudio.com/docs/languages/r">here</a>.</p>
-</div>
-</div>
-</div>
-</div>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="What-is-a-Freva-Wrapper?">What is a Freva Wrapper?<a class="anchor-link" href="#What-is-a-Freva-Wrapper?">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2> Freva Wrapper Main Classes <img alt="No description has been provided for this image" src="media/plugin_general/python-logo.png" style="vertical-align:middle; display:inline-block; height:1em; width:auto "/> </h2>
-<div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<ul style="font-size: 29px; line-height: 1.5;">
-<li>PluginAbstract Class Functions</li>
-<br>
-<li>parameters.py Classes</li>
-<br>
-<li>_ConfigWrapper Class</li>
-</br></br></ul>
-</div>
-<div style="text-align: right; width: 50%;">
-<img alt="What is wrapper" src="media/plugin_general/wrapper.gif" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Special-Variables:">Special Variables:<a class="anchor-link" href="#Special-Variables:">¶</a></h2><table>
-<thead>
-<tr>
-<th>Variables</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td>USER_BASE_DIR</td>
-<td>Absolute path to the central directory for this user.</td>
-</tr>
-<tr>
-<td>USER_OUTPUT_DIR</td>
-<td>Absolute path to where the plugin outputs for this user are stored.</td>
-</tr>
-<tr>
-<td>USER_PLOTS_DIR</td>
-<td>Absolute path to where the plugin plots for this user are stored.</td>
-</tr>
-<tr>
-<td>USER_CACHE_DIR</td>
-<td>Absolute path to the cached data (temp data) for this user.</td>
-</tr>
-<tr>
-<td>USER_UID</td>
-<td>The users’ User Identifier.</td>
-</tr>
-<tr>
-<td>SYSTEM_DATE</td>
-<td>Current date in the form YYYYMMDD (e.g. 20120130).</td>
-</tr>
-<tr>
-<td>SYSTEM_DATETIME</td>
-<td>Current date in the form YYYYMMDD_HHmmSS (e.g. 20120130_101123).</td>
-</tr>
-<tr>
-<td>SYSTEM_TIMESTAMP</td>
-<td>Milliseconds since epoch (i.e. e.g. 1358929581838).</td>
-</tr>
-<tr>
-<td>SYSTEM_RANDOM_UUID</td>
-<td>A random Universal Unique Identifier (e.g. 912cca21-6364-4f46-9b03-4263410c9899).</td>
-</tr>
-</tbody>
-</table>
-<p>Example:</p>
-<div class="highlight"><pre><span></span><span class="nv">output_file</span><span class="o">=</span><span class="s1">'$USER_OUTPUT_DIR/myfile_${SYSTEM_DATETIME}blah.nc'</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-class_basedir">Function: class_basedir<a class="anchor-link" href="#Function:-class_basedir">¶</a></h2><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">PluginAbstract</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABC</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">"""Base class that is used as a template for all Freva plugins.</span>
-<span class="sd">    Any api wrapper class defining Freva plugins must inherit from this class."""</span>
-
-    <span class="nd">@deprecated_method</span><span class="p">(</span><span class="s2">"PluginAbstract"</span><span class="p">,</span> <span class="s2">"class_basedir"</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">getClassBaseDir</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
-<span class="w">        </span><span class="sd">"""Deprecated method for class_basedir."""</span>
-
-    <span class="k">def</span> <span class="nf">class_basedir</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">"""Get absolute path to the module defining the plugin class."""</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-call">Function: call<a class="anchor-link" href="#Function:-call">¶</a></h2><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">PluginAbstract</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABC</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">"""Base class that is used as a template for all Freva plugins.</span>
-<span class="sd">    Any api wrapper class defining Freva plugins must inherit from this class."""</span>
-
-    <span class="k">def</span> <span class="nf">call</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span>
-        <span class="n">cmd_string</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]],</span>
-        <span class="n">check</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
-        <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">sub</span><span class="o">.</span><span class="n">Popen</span><span class="p">[</span><span class="n">Any</span><span class="p">]:</span>
-<span class="w">        </span><span class="sd">"""Run command with arguments and return a CompletedProcess instance."""</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-call-and-class_basedir---Example">Function: call and class_basedir - Example<a class="anchor-link" href="#Function:-call-and-class_basedir---Example">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api</span> <span class="kn">import</span> <span class="n">plugin</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">run_tool</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">call</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">class_basedir</span><span class="si">}</span><span class="s2">/main_code.sh </span><span class="si">{</span><span class="n">config_dict</span><span class="si">}</span><span class="s2">"</span>
-        <span class="p">)</span>
-        <span class="c1"># or</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">call</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="si">}</span><span class="s2">/main_code.sh </span><span class="si">{</span><span class="n">config_dict</span><span class="si">}</span><span class="s2">"</span>
-        <span class="p">)</span>
-        <span class="c1"># or</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">call</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="n">USER_BASE_DIR</span><span class="p">)</span><span class="si">}</span><span class="s2">/main_code.sh </span><span class="si">{</span><span class="n">config_dict</span><span class="si">}</span><span class="s2">"</span>
-        <span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-add_output_to_databrowser">Function: add_output_to_databrowser<a class="anchor-link" href="#Function:-add_output_to_databrowser">¶</a></h2><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">PluginAbstract</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABC</span><span class="p">):</span>
-    <span class="nd">@deprecated_method</span><span class="p">(</span><span class="s2">"PluginAbstract"</span><span class="p">,</span> <span class="s2">"add_output_to_databrowser"</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">linkmydata</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>  <span class="c1"># pragma: no cover</span>
-
-    <span class="k">def</span> <span class="nf">add_output_to_databrowser</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span>
-        <span class="n">plugin_output</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">PathLike</span><span class="p">,</span>
-        <span class="n">project</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="c1"># user-&lt;user-id&gt;</span>
-        <span class="n">product</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="c1"># project.product</span>
-        <span class="o">*</span><span class="p">,</span>
-        <span class="n">model</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"freva"</span><span class="p">,</span>
-        <span class="n">institute</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">ensemble</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"r1i1p1"</span><span class="p">,</span>
-        <span class="n">time_frequency</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">variable</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">experiment</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">index_data</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span><span class="p">:</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-add_output_to_databrowser---Example">Function: add_output_to_databrowser - Example<a class="anchor-link" href="#Function:-add_output_to_databrowser---Example">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api</span> <span class="kn">import</span> <span class="n">plugin</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">run_tool</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">add_output_to_databrowser</span><span class="p">(</span>
-            <span class="n">plugin_output</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"outputdir"</span><span class="p">],</span>
-            <span class="n">project</span><span class="o">=</span><span class="n">config_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"project"</span><span class="p">,</span> <span class="s2">"default_project"</span><span class="p">),</span>
-            <span class="n">product</span><span class="o">=</span><span class="n">config_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"product"</span><span class="p">,</span> <span class="s2">"default_product"</span><span class="p">),</span>
-            <span class="n">model</span><span class="o">=</span><span class="n">config_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"model"</span><span class="p">,</span> <span class="s2">"default_model"</span><span class="p">),</span>
-            <span class="n">institute</span><span class="o">=</span><span class="n">config_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"institute"</span><span class="p">,</span> <span class="s2">"default_institute"</span><span class="p">),</span>
-            <span class="n">time_frequency</span><span class="o">=</span><span class="s2">"mon"</span><span class="p">,</span>
-        <span class="p">)</span>
-</pre></div>
-<h3 id="How-to-find-it-in-Freva:">How to find it in Freva:<a class="anchor-link" href="#How-to-find-it-in-Freva:">¶</a></h3><div class="highlight"><pre><span></span>freva<span class="w"> </span>databrowser<span class="w"> </span><span class="nv">product</span><span class="o">=</span>project.product<span class="w"> </span><span class="nv">project</span><span class="o">=</span>user-&lt;user-id&gt;
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-prepare_output">Function: prepare_output<a class="anchor-link" href="#Function:-prepare_output">¶</a></h2><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">PluginAbstract</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABC</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">"""Base class that is used as a template for all Freva plugins.</span>
-<span class="sd">    Any api wrapper class defining Freva plugins must inherit from this class."""</span>
-
-    <span class="nd">@deprecated_method</span><span class="p">(</span><span class="s2">"PluginAbstract"</span><span class="p">,</span> <span class="s2">"prepare_output"</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">prepareOutput</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]]:</span>
-<span class="w">        </span><span class="sd">"""Deprecated method for :class:`prepare_output`. """</span>
-
-    <span class="k">def</span> <span class="nf">prepare_output</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span> <span class="n">output_files</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]]]</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]]:</span>
-<span class="w">        </span><span class="sd">"""Prepare output for files supposedly created."""</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="PluginAbstract-Class">PluginAbstract Class<a class="anchor-link" href="#PluginAbstract-Class">¶</a></h1><h2 id="Function:-prepare_output---Example">Function: prepare_output - Example<a class="anchor-link" href="#Function:-prepare_output---Example">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api</span> <span class="kn">import</span> <span class="n">plugin</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">run_tool</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">prepare_output</span><span class="p">(</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"outputdir"</span><span class="p">])</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="ParameterType-Class">ParameterType Class<a class="anchor-link" href="#ParameterType-Class">¶</a></h1><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">ParameterType</span><span class="p">(</span><span class="n">initOrder</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">"""Base class for all parameter types.</span>
-<span class="sd">    All available parameter types inherit from this class. The class creates</span>
-<span class="sd">    a parameter object holding the following user defined information.</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span>
-        <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-        <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-        <span class="n">mandatory</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-        <span class="n">max_items</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
-        <span class="n">item_separator</span><span class="o">=</span><span class="s2">","</span><span class="p">,</span>
-        <span class="n">regex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-        <span class="n">version</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
-        <span class="n">help</span><span class="o">=</span><span class="s2">"No help available."</span><span class="p">,</span>
-        <span class="n">print_format</span><span class="o">=</span><span class="s2">"</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
-        <span class="n">impact</span><span class="o">=</span><span class="n">Parameter</span><span class="o">.</span><span class="n">Impact</span><span class="o">.</span><span class="n">affects_values</span><span class="p">,</span>
-    <span class="p">):</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="ParameterDictionary-Class">ParameterDictionary Class<a class="anchor-link" href="#ParameterDictionary-Class">¶</a></h1><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">ParameterDictionary</span><span class="p">(</span><span class="nb">dict</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">"""Directory holding all plugin parameters for a ``Freva`` plugin.</span>
-<span class="sd">    This class behaves like a built-in ``dict`` with additional features.</span>
-<span class="sd">    The most prominent feature is that the order of added items is preserved,</span>
-<span class="sd">    as opposed to a normal build-in ``dict``.</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">parameters</span><span class="p">:</span> <span class="n">ParameterType</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="_ConfigWrapper-class">_ConfigWrapper class<a class="anchor-link" href="#_ConfigWrapper-class">¶</a></h1><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">_ConfigWrapper</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">"""Convenience class that helps to dynamically set the location of the</span>
-<span class="sd">    evaluation system config file."""</span>
-    <span class="n">_env</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"EVALUATION_SYSTEM_CONFIG_FILE"</span>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span>
-        <span class="n">default_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
-    <span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">default_file</span> <span class="o">=</span> <span class="n">default_file</span>
-    <span class="k">def</span> <span class="nf">__fspath__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_env</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_file</span><span class="p">)</span>
-    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__fspath__</span><span class="p">()</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2> Freva Wrapper Structure </h2>
-<div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<ul style="font-size: 29px; line-height: 1.5;">
-<li>Plugin Details</li>
-<br>
-<li>Plugin Parameters</li>
-<br>
-<li>Plugin Methods</li>
-</br></br></ul>
-</div>
-<div style="text-align: right; width: 50%;">
-<img alt="wrapper's structure" src="media/plugin_general/structure.gif" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Freva-Wrapper-Structure:-1.-Details">Freva Wrapper Structure: 1. Details<a class="anchor-link" href="#Freva-Wrapper-Structure:-1.-Details">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api</span> <span class="kn">import</span> <span class="n">plugin</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="n">__version__</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
-<span class="w">    </span><span class="sd">"""</span>
-<span class="sd">    def __version__(self) -&gt; tuple[int, int, int]:</span>
-<span class="sd">        # 3-value tuple representing the plugin version.</span>
-<span class="sd">    """</span>
-    <span class="n">__short_description__</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"template plugin"</span>
-    <span class="n">__category__</span> <span class="o">=</span> <span class="s2">"something"</span>
-<span class="w">    </span><span class="sd">"""</span>
-<span class="sd">    def __category__(self) -&gt; str:</span>
-<span class="sd">        # Optional category this plugin belongs to.</span>
-<span class="sd">        return ""</span>
-<span class="sd">    """</span>
-    <span class="n">__tags__</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"something"</span><span class="p">,</span> <span class="s2">"somethingelse"</span><span class="p">]</span>
-<span class="w">    </span><span class="sd">"""</span>
-<span class="sd">    def __tags__(self) -&gt; list[str]:</span>
-<span class="sd">        # Optional tags, that are the plugin can be described with.</span>
-<span class="sd">        return [""]</span>
-<span class="sd">    """</span>
-    <span class="n">tool_developer</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"someonename someonefamily"</span>
-    <span class="n">__long_description__</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"template plugin long"</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Freva-Wrapper-Structure:-2.-Parameters">Freva Wrapper Structure: 2. Parameters<a class="anchor-link" href="#Freva-Wrapper-Structure:-2.-Parameters">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api.parameters</span> <span class="kn">import</span> <span class="n">ParameterDictionary</span><span class="p">,</span> <span class="n">String</span><span class="p">,</span> <span class="n">Bool</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="n">__parameters__</span> <span class="o">=</span> <span class="n">ParameterDictionary</span><span class="p">(</span>
-        <span class="n">String</span><span class="p">(</span><span class="n">ParameterType</span><span class="p">),</span>
-<span class="w">        </span><span class="sd">"""</span>
-<span class="sd">        Example:</span>
-<span class="sd">            String(</span>
-<span class="sd">                name="string",</span>
-<span class="sd">                default="None",</span>
-<span class="sd">                help=(</span>
-<span class="sd">                    "some helps"</span>
-<span class="sd">                ),</span>
-<span class="sd">            )</span>
-<span class="sd">        """</span>
-        <span class="n">Bool</span><span class="p">(</span><span class="n">ParameterType</span><span class="p">),</span>
-<span class="w">        </span><span class="sd">"""</span>
-<span class="sd">        Example:</span>
-<span class="sd">            Bool(</span>
-<span class="sd">                name="checkbox",</span>
-<span class="sd">                default=True,</span>
-<span class="sd">            )</span>
-<span class="sd">        """</span>
-    <span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Freva-Wrapper-Structure:-2.-Parameters">Freva Wrapper Structure: 2. Parameters<a class="anchor-link" href="#Freva-Wrapper-Structure:-2.-Parameters">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api.parameters</span> <span class="kn">import</span> <span class="n">ParameterDictionary</span><span class="p">,</span> <span class="n">SolrField</span><span class="p">,</span> <span class="n">InputDirectory</span><span class="p">,</span> <span class="n">String</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="n">__parameters__</span> <span class="o">=</span> <span class="n">ParameterDictionary</span><span class="p">(</span>     
-        <span class="n">InputDirectory</span><span class="p">(</span><span class="n">String</span><span class="p">),</span>
-<span class="w">        </span><span class="sd">"""</span>
-<span class="sd">        Example:</span>
-<span class="sd">            InputDirectory(</span>
-<span class="sd">                name="inputdirectory",</span>
-<span class="sd">            ),</span>
-<span class="sd">        """</span>
-        <span class="n">SolrField</span><span class="p">(</span><span class="n">String</span><span class="p">),</span>
-<span class="w">        </span><span class="sd">"""</span>
-<span class="sd">        class SolrField(String):</span>
-<span class="sd">            # A parameter using solr for finding valid values.</span>
-<span class="sd">            def __init__(</span>
-<span class="sd">                self,</span>
-<span class="sd">                *args,</span>
-<span class="sd">                facet: str,</span>
-<span class="sd">                group: int = 1,</span>
-<span class="sd">                multiple: bool = False,</span>
-<span class="sd">                predefined_facets: Optional[list[str]] = None,</span>
-<span class="sd">                editable: bool = True,</span>
-<span class="sd">                **kwargs,</span>
-<span class="sd">            ): </span>
-<span class="sd">        """</span>
-    <span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Freva-Wrapper-Structure:-2.-Parameters">Freva Wrapper Structure: 2. Parameters<a class="anchor-link" href="#Freva-Wrapper-Structure:-2.-Parameters">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api.parameters</span> <span class="kn">import</span> <span class="n">ParameterDictionary</span><span class="p">,</span> <span class="n">String</span><span class="p">,</span> <span class="n">CacheDirectory</span><span class="p">,</span> <span class="n">SelectField</span><span class="p">,</span> <span class="n">Directory</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="n">__parameters__</span> <span class="o">=</span> <span class="n">ParameterDictionary</span><span class="p">(</span>
-        <span class="n">Directory</span><span class="p">(</span><span class="n">String</span><span class="p">),</span>
-        <span class="n">CacheDirectory</span><span class="p">(</span><span class="n">Directory</span><span class="p">),</span>
-        <span class="n">SelectField</span><span class="p">(</span><span class="n">String</span><span class="p">),</span>
-<span class="w">        </span><span class="sd">"""</span>
-<span class="sd">        class SelectField(String):</span>
-<span class="sd">            # Select field to select parameter from predefined values.</span>
-<span class="sd">            def __init__(self, options: dict[str, str], *args, **kwargs):</span>
-<span class="sd">        Example:</span>
-<span class="sd">        SelectField(</span>
-<span class="sd">            options={"first": "1st", "second": "2nd"},</span>
-<span class="sd">        ),</span>
-<span class="sd">        """</span>
-        <span class="n">Integer</span><span class="p">(</span><span class="n">ParameterType</span><span class="p">),</span>
-<span class="w">        </span><span class="sd">"""</span>
-<span class="sd">        Example:</span>
-<span class="sd">            Integer(</span>
-<span class="sd">                name="integer",</span>
-<span class="sd">                default=1,</span>
-<span class="sd">            )</span>
-<span class="sd">        """</span>
-    <span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Freva-Wrapper-Structure:-3.-Methods">Freva Wrapper Structure: 3. Methods<a class="anchor-link" href="#Freva-Wrapper-Structure:-3.-Methods">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api</span> <span class="kn">import</span> <span class="n">plugin</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">run_tool</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">call</span><span class="p">(</span><span class="sa">f</span><span class="s2">"python template_plugin.py arg1 arg2 </span><span class="si">{</span><span class="n">config_dict</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">call</span><span class="p">(</span><span class="sa">f</span><span class="s2">"template_runner.sh </span><span class="si">{</span><span class="n">config_dict</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">add_output_to_databrowser</span><span class="p">(</span>
-            <span class="n">output_dir</span><span class="p">,</span>
-            <span class="n">project</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"project"</span><span class="p">],</span> <span class="c1"># user-&lt;user-id&gt;</span>
-            <span class="n">product</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"product"</span><span class="p">],</span> <span class="c1"># f"{config_dict["project"]}.{config_dict["project"]}"</span>
-            <span class="n">institute</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"institute"</span><span class="p">],</span>
-            <span class="n">model</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"model"</span><span class="p">],</span>
-            <span class="n">experiment</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"experiment"</span><span class="p">],</span>
-            <span class="n">time_frequency</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"time_frequency"</span><span class="p">],</span>
-            <span class="n">variable</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"variable"</span><span class="p">],</span>
-            <span class="n">ensemble</span><span class="o">=</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"ensemble"</span><span class="p">],</span>
-        <span class="p">)</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">prepare_output</span><span class="p">(</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"outputdir"</span><span class="p">])</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Recommended:-Keep-track-of-errors">Recommended: Keep track of errors<a class="anchor-link" href="#Recommended:-Keep-track-of-errors">¶</a></h2><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">evaluation_system.api</span> <span class="kn">import</span> <span class="n">plugin</span>
-<span class="kn">import</span> <span class="nn">json</span>
-<span class="k">class</span> <span class="nc">TemplatePlugin</span><span class="p">(</span><span class="n">plugin</span><span class="o">.</span><span class="n">PluginAbstract</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">run_tool</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-        <span class="n">json_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">config_dict</span><span class="p">[</span><span class="s2">"cache"</span><span class="p">])</span> <span class="o">/</span> <span class="s2">"out.json"</span>
-        <span class="k">with</span> <span class="n">json_file</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">json_f</span><span class="p">:</span>
-            <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">config_dict</span><span class="p">,</span> <span class="n">json_f</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
-        <span class="k">with</span> <span class="n">errorfile</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">error_f</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">call</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">class_basedir</span><span class="si">}</span><span class="s2">/main_runner.sh </span><span class="si">{</span><span class="n">json_file</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
-                <span class="n">stderr</span><span class="o">=</span><span class="n">error_f</span><span class="p">,</span>
-            <span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Additional:-How-to-deal-with-JSON-files-in-the-main-script-of-plugin">Additional: How to deal with JSON files in the main script of plugin<a class="anchor-link" href="#Additional:-How-to-deal-with-JSON-files-in-the-main-script-of-plugin">¶</a></h3><h4 id="Python:">Python:<a class="anchor-link" href="#Python:">¶</a></h4><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">json</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
-    <span class="n">config_dict</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-</pre></div>
-<h4 id="Bash">Bash<a class="anchor-link" href="#Bash">¶</a></h4><div class="highlight"><pre><span></span>_jq<span class="o">(){</span>
-<span class="w">    </span>jq<span class="w"> </span>-r<span class="w"> </span><span class="si">${</span><span class="nv">1</span><span class="si">}</span><span class="w"> </span><span class="si">${</span><span class="nv">2</span><span class="si">}</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>sed<span class="w"> </span><span class="s2">"s/null/None/g;s/true/True/g;s/false/False/g"</span>
-
-<span class="o">}</span>
-<span class="nb">export</span><span class="w"> </span><span class="nv">CACHE</span><span class="o">=</span><span class="s2">"</span><span class="k">$(</span>_jq<span class="w"> </span>.cache<span class="w"> </span><span class="nv">$1</span><span class="k">)</span><span class="s2">"</span>
-<span class="nb">export</span><span class="w"> </span><span class="nv">OUTPUTDIR</span><span class="o">=</span><span class="s2">"</span><span class="k">$(</span>_jq<span class="w"> </span>.outputdir<span class="w"> </span><span class="nv">$1</span><span class="k">)</span><span class="s2">"</span>
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
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-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Wrapper-Illustration">Wrapper Illustration<a class="anchor-link" href="#Wrapper-Illustration">¶</a></h3><p><img alt="First Wrapper" src="media/wrapper/First_wrapper.png"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
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-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Wrapper-Illustration">Wrapper Illustration<a class="anchor-link" href="#Wrapper-Illustration">¶</a></h3><p><img alt="Second Wrapper" src="media/wrapper/Second_wrapper.png"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
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-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Wrapper-Illustration">Wrapper Illustration<a class="anchor-link" href="#Wrapper-Illustration">¶</a></h3><p><img alt="Third Wrapper" src="media/wrapper/Third_wrapper.png"/></p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h3 id="Wrapper-Illustration">Wrapper Illustration<a class="anchor-link" href="#Wrapper-Illustration">¶</a></h3><p><img alt="Fourth Wrapper" src="media/wrapper/Fourth_wrapper.png"/></p>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="How-To-Install-All-Needed-Libraries-Of-A-Plugin">How To Install All Needed Libraries Of A Plugin<a class="anchor-link" href="#How-To-Install-All-Needed-Libraries-Of-A-Plugin">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Why-the-need?">Why the need?<a class="anchor-link" href="#Why-the-need?">¶</a></h2><ul>
-<li>Formerly, we relied on HPC modules to run plugins' software.</li>
-<li>Less than ideal when migrating to newer HPC/other institutions!</li>
-<li>Now, all necessary software installed in a <code>conda/mamba</code> environment at <strong>each</strong> repo folder.</li>
-</ul>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2> Steps to Install Necessary Packages <img alt="No description has been provided for this image" src="media/plugin_general/yaml.png" style="vertical-align:middle; display:inline-block; height:1em; width:auto "/> <img alt="No description has been provided for this image" src="media/plugin_general/gnu-make.jpg" style="vertical-align:middle; display:inline-block; height:1em; width:auto "/></h2>
-<div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<ul style="font-size: 29px; line-height: 1.5;">
-<li>Define an Env YAML file</li>
-<br>
-<li>Install env via Conda</li>
-<br>
-<li>Activate Environment</li>
-<br>
-<li>Alternative: Makefile</li>
-</br></br></br></ul>
-</div>
-<div style="text-align: right; width: 50%;">
-<img alt="install env" src="media/plugin_general/env.gif" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Define-an-Env-YAML-file">Define an Env YAML file<a class="anchor-link" href="#Define-an-Env-YAML-file">¶</a></h2><p>e.g. <code>plugin-env.yml</code>:</p>
-<div class="highlight"><pre><span></span><span class="nt">channels</span><span class="p">:</span>
-<span class="w">    </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">conda-forge</span>
-<span class="nt">dependencies</span><span class="p">:</span>
-<span class="w">    </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">r-base</span>
-<span class="w">    </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pip</span>
-</pre></div>
-<h2 id="Install-env-via-Conda">Install env via Conda<a class="anchor-link" href="#Install-env-via-Conda">¶</a></h2><ul>
-<li>The environment <strong>must</strong> be located at the same level as the wrapper file!</li>
-<li>The environment <strong>must</strong> be located named <code>plugin_env/</code> so Freva recognizes it!</li>
-</ul>
-<div class="highlight"><pre><span></span>mamba<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>--prefix<span class="w"> </span>./plugin_env<span class="w"> </span>-f<span class="w"> </span>plugin-env.yml
-</pre></div>
-<h2 id="Activate-Environment">Activate Environment<a class="anchor-link" href="#Activate-Environment">¶</a></h2><div class="highlight"><pre><span></span>conda<span class="w"> </span>activate<span class="w"> </span>plugin_env/bin/activate
-</pre></div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="More-flexible-approach-via-Makefile">More flexible approach via Makefile<a class="anchor-link" href="#More-flexible-approach-via-Makefile">¶</a></h2><p>We can define a <code>Makefile</code> as below and then after definition of <code>environment.yml</code>, install all the dependencies listed above via <code>make</code> commands. But first and foremost, we need to ensure, we have <code>make</code> installed on our machine.</p>
-<div class="highlight"><pre><span></span><span class="nf">env</span><span class="o">:</span>
-<span class="c">    @# Installs a conda environment with R and the IDF package</span>
-<span class="w">    </span>@if<span class="w"> </span><span class="o">[</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">"./plugin_env"</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    	</span>rm<span class="w"> </span>-rf<span class="w"> </span>./plugin_env<span class="p">;</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    </span><span class="k">fi</span>
-<span class="w">    </span>conda<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>--prefix<span class="w"> </span>./plugin_env<span class="w"> </span>-f<span class="w"> </span>environment.yml<span class="w"> </span>--force
-<span class="w">    </span>Rscript<span class="w"> </span>-e<span class="w"> </span><span class="s1">'install.packages("IDF", repos="https://CRAN.R-project.org/")'</span>
-<span class="nf">cartopy</span><span class="o">:</span>
-<span class="c">    @# Download various cartopy shape-files</span>
-<span class="w">    </span>@if<span class="w"> </span><span class="o">[</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">"./cartopy"</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    	</span>rm<span class="w"> </span>-rf<span class="w"> </span>./cartopy<span class="p">;</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    </span><span class="k">fi</span>
-<span class="w">    </span>./plugin_env/bin/python3<span class="w"> </span>assets/cartopy_download.py<span class="w"> </span>physical<span class="w"> </span>cultural
-<span class="nf">.PHONY</span><span class="o">:</span><span class="w"> </span><span class="n">env</span> <span class="n">cartopy</span>
-</pre></div>
-<ul>
-<li>Using <code>mamba</code> instead of using <code>conda</code> can make the way of installation faster.</li>
-</ul>
-<p>You can take a look at a plugin template <a href="https://gitlab.dkrz.de/freva/plugins4freva/plugintemplate">here</a>.</p>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="How-To-Plug-a-Tool-into-Freva">How To Plug a Tool into Freva<a class="anchor-link" href="#How-To-Plug-a-Tool-into-Freva">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2> Plug a Tool into Freva <img alt="No description has been provided for this image" src="media/plugin_general/freva.png" style="vertical-align:middle; display:inline-block; height:1em; width:auto "/> </h2>
-<div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<ul style="font-size: 29px; line-height: 1.5;">
-<li>Plug into Freva via CLI</li>
-<br>
-<li>Plug into Freva via Freva-Web</li>
-<br>
-</br></br></ul>
-</div>
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/plugin_general.png" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Plug-a-tool-into-Freva">Plug a tool into Freva<a class="anchor-link" href="#Plug-a-tool-into-Freva">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/module_load_code.png" width="400">
-</img></div>
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/module_load.png" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Plug-a-tool-into-Freva">Plug a tool into Freva<a class="anchor-link" href="#Plug-a-tool-into-Freva">¶</a></h2><p>In this step we need to clone a plugin in the user directory of freva-dev and replace <code>&lt;username&gt;</code> with your <code>k-number</code> or <code>b-number</code> username:</p>
-<div class="highlight"><pre><span></span>ssh<span class="w"> </span>&lt;username&gt;@levante.dkrz.de
-<span class="c1">#After login to Levante</span>
-<span class="nb">cd</span><span class="w"> </span>work/ch1187/clint/freva-dev/share/work/&lt;username&gt;/freva-dev/
-git<span class="w"> </span>clone<span class="w"> </span>https://gitlab.dkrz.de/freva/plugins4freva/plugin_workshop/example_plugin.git
-</pre></div>
-<p>In this step you need to install the dependencies. Have a look at the previous section (How To Install All Needed Libraries Of A Plugin)</p>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Plug-a-tool-into-Freva">Plug a tool into Freva<a class="anchor-link" href="#Plug-a-tool-into-Freva">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/plug_in_code.png" width="400">
-</img></div>
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/plug_in_web.png" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Plug-a-tool-into-Freva">Plug a tool into Freva<a class="anchor-link" href="#Plug-a-tool-into-Freva">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/plugin_list_code.png" width="400">
-</img></div>
-<div style="text-align: right; width: 50%;">
-<img alt="plug in plugin" src="media/plugin_general/plugin_list_web.png" width="400">
-</img></div>
-</div>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="Freva:-Plugin-Development">Freva: Plugin Development<a class="anchor-link" href="#Freva:-Plugin-Development">¶</a></h1><img align="center" alt="freva dev" src="media/plugin_intro/freva-plugindev.png" width="500"/>
-<p><strong>Martin Bergemann, Bijan Fallah, Andrej Fast, Mostafa Hadizadeh, 
-Christopher Kadow, Etor E. Lucio-Eceiza,  Felix Örtel, Manuel Reis, and many others…</strong></p>
-<p>Deutsches Klimarechenzentrum @ CLINT in Data Analysis Dpt. (+ Data Management Dpt.*)</p>
-</div>
-</div>
-</div>
-</div></section></section><section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h1 id="Overview-of-a-Freva-plugin">Overview of a Freva plugin<a class="anchor-link" href="#Overview-of-a-Freva-plugin">¶</a></h1>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Why-should-I-build-a-Freva-plugin?">Why should I build a Freva plugin?<a class="anchor-link" href="#Why-should-I-build-a-Freva-plugin?">¶</a></h2><p>It allows you to be part of "The Freva Cycle"</p>
-<img align="center" alt="parts" src="media/plugin_intro/plugin-livecycle.png" width="900"/>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Structure-of-a-Plugin">Structure of a Plugin<a class="anchor-link" href="#Structure-of-a-Plugin">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 60%;">
-<p>There are 3 main building blocks in a plugin:</p>
-<ul>
-<li><b>Wrapper:</b> connects the tool to Freva</li>
-<li><b>Tool:</b> scientific code</li>
-<li><b>Installer:</b> they install the necessary libraries </li>
-</ul>
-</div>
-<div style="text-align: right; width: 40%;">
-<img align="center" alt="parts" src="media/plugin_intro/plugin-parts.png" width="300"/>
-</div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Structure-of-a-Plugin:-The-Wrapper">Structure of a Plugin: The Wrapper<a class="anchor-link" href="#Structure-of-a-Plugin:-The-Wrapper">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 40%;">
-<p>The connection to Freva:</p>
-<ul>
-<li>Written in python 3</li>
-<li>Needs to follow a series of standards</li>
-</ul>
-</div>
-<div style="text-align: right; width: 60%;">
-<img align="center" alt="parts" src="media/plugin_intro/wrapper.jpg" width="500"/>
-</div>
-</div>
-</div>
-</div>
-</div>
-</div></section><section>
-<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
-<div class="jp-Cell-inputWrapper" tabindex="0">
-<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
-</div>
-<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
-</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Structure-of-a-Plugin:-The-tool">Structure of a Plugin: The tool<a class="anchor-link" href="#Structure-of-a-Plugin:-The-tool">¶</a></h2><div style="display: flex; justify-content: space-between; align-items: center;">
-<div style="text-align: left; width: 50%;">
-<p>The scientific code:</p>
-<ul>
-<li>Written in any* language (python, R, C, FORTRAN, a mix...)</li>
-<li>A single script or multiple scripts and/or folders (subroutines, libraries, etc.).</li>
-</ul>
-</div>
-<div style="text-align: right; width: 50%;">
-<img align="center" alt="parts" src="media/plugin_intro/code.jpg" width="500"/>
-</div>
-</div>
-*caveat: we encourage <i>free</i> software
 
 </div>
 </div>
@@ -9152,9 +7620,9 @@ <h2>What is gitlab? <img align="center" alt="freva dev" src="media/gitlab/gitlab
 <h2 id="Gitlab-and-Freva:">Gitlab and Freva:<a class="anchor-link" href="#Gitlab-and-Freva:">¶</a></h2><ul>
 <li>One central local repository for the plugged plugins</li>
 <li>Other local repositories for different developers</li>
-<li>One remote repository for the plugin at gitlab</li>
+<li>One remote repository for the plugin at gitlab
+<img align="center" alt="freva dev" src="media/gitlab/freva-gitlab-flow.jpg" width="900"/></li>
 </ul>
-<img align="center" alt="freva dev" src="media/gitlab/freva-gitlab-flow.jpg" width="900"/>
 </div>
 </div>
 </div>
@@ -9166,14 +7634,15 @@ <h2 id="Gitlab-and-Freva:">Gitlab and Freva:<a class="anchor-link" href="#Gitlab
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
 <h2 id="Gitlab-and-Freva:-location-of-the-plugins">Gitlab and Freva: location of the plugins<a class="anchor-link" href="#Gitlab-and-Freva:-location-of-the-plugins">¶</a></h2><ul>
-<li>Under <a href="https://gitlab.dkrz.de/freva/plugins4freva">https://gitlab.dkrz.de/freva/plugins4freva</a> project:</li>
+<li>Under <a href="https://gitlab.dkrz.de/freva/plugins4freva">https://gitlab.dkrz.de/freva/plugins4freva</a> project:
+<img align="center" alt="freva dev" src="media/gitlab/freva-gitlab.jpg" width="900"/></li>
+<li>Other projects have also their own, e.g.:<ul>
+<li>climxtreme: <a href="https://gitlab.dkrz.de/bm1159/plugins4freva">https://gitlab.dkrz.de/bm1159/plugins4freva</a></li>
+<li>regiklim-nukleus: <a href="https://gitlab.dkrz.de/ch1187/plugins4freva">https://gitlab.dkrz.de/ch1187/plugins4freva</a></li>
+</ul>
+</li>
+<li>some plugins can be found in different projects (see <a href="https://docs.gitlab.com/ee/user/project/repository/forking_workflow.html">forks</a>).</li>
 </ul>
-<img align="center" alt="freva dev" src="media/gitlab/freva-gitlab.jpg" width="900"/>
-- Other projects have also their own, e.g.: 
-    - climxtreme: https://gitlab.dkrz.de/bm1159/plugins4freva
-    - regiklim-nukleus: https://gitlab.dkrz.de/ch1187/plugins4freva
-- some plugins can be found in different projects (see [forks](https://docs.gitlab.com/ee/user/project/repository/forking_workflow.html)).
-
 </div>
 </div>
 </div>
@@ -9184,10 +7653,12 @@ <h2 id="Gitlab-and-Freva:-location-of-the-plugins">Gitlab and Freva: location of
 </div>
 <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
-<h2 id="Gitlab-and-Freva:-cloning-a-repository">Gitlab and Freva: cloning a repository<a class="anchor-link" href="#Gitlab-and-Freva:-cloning-a-repository">¶</a></h2><p>To download a repository there are 2 ways: via <code>https</code> and via <code>ssh</code>:</p>
-<img align="center" alt="freva dev" src="media/gitlab/clone-repo.jpg" width="550"/>
-- `https`: straightforward, requires to enter (dkrz) username and password (usually). 
-- `ssh`: convenient, requires to provide a ssh key previously.
+<h2 id="Gitlab-and-Freva:-cloning-a-repository">Gitlab and Freva: cloning a repository<a class="anchor-link" href="#Gitlab-and-Freva:-cloning-a-repository">¶</a></h2><p>To download a repository there are 2 ways: via <code>https</code> and via <code>ssh</code>:
+<img align="center" alt="freva dev" src="media/gitlab/clone-repo.jpg" width="550"/></p>
+<ul>
+<li><code>https</code>: straightforward, requires to enter (dkrz) username and password (usually).</li>
+<li><code>ssh</code>: convenient, requires to provide a ssh key previously.</li>
+</ul>
 <p>In both cases:</p>
 <pre><code>$ ssh &lt;username&gt;@levante.dkrz.de
 &gt; cd /path/to/my/work/
@@ -9335,7 +7806,7 @@ <h2>1. VS-Code <img align="center" alt="freva dev" src="media/vscode/vscode_logo
 <br/>
 <br/>
 <p>Clicking either of the buttons opens a prompt at the top of the window, giving you several options to start a remote session:</p>
-<p><img alt='Image depicting the prompt that opens when clicking one of the "Connect to..." buttons in the new VS Code window' src="media/vscode/02_remote_connection_options.jpg"/></p>
+<p><img alt="Image depicting the prompt that opens when clicking one of the &amp;quot;Connect to...&amp;quot; buttons in the new VS Code window" src="media/vscode/02_remote_connection_options.jpg"/></p>
 </div>
 </div>
 </div>
@@ -9418,7 +7889,7 @@ <h2>2. PyCharm <img align="center" alt="freva dev" src="media/pycharm/pycharm_lo
 Remote Development is currently in beta and only supported for the Professional Version of PyCharm!</p>
 </blockquote>
 <p>Open your Plugins (<kbd>Ctrl</kbd>+<kbd>Alt</kbd>+<kbd>S</kbd>) and confirm that "Remote Development Gateway" is installed and that it is enabled:</p>
-<p><img alt='Image depicting a list of installed PyCharm plugins, with the "Remote Development Gateway" being installed and enabled.' src="media/pycharm/01_remote_development_gateway.jpg"/></p>
+<p><img alt="Image depicting a list of installed PyCharm plugins, with the &amp;quot;Remote Development Gateway&amp;quot; being installed and enabled." src="media/pycharm/01_remote_development_gateway.jpg"/></p>
 </div>
 </div>
 </div>
@@ -9434,7 +7905,7 @@ <h2>2. PyCharm <img align="center" alt="freva dev" src="media/pycharm/pycharm_lo
 <br/>
 <br/>
 <p>To open a remote session in PyCharm, go to the welcome screen and click on the "Remote Development" Tab in the left side bar. This should give you a number of options, including the option to connect to a remote session using SSH:</p>
-<p><img alt='Image depiciting the welcome screen of PyCharm Professional, with the "Remote Development" Tab highlighted using red arrows.' src="media/pycharm/02_remote_development_tab.png"/></p>
+<p><img alt="Image depiciting the welcome screen of PyCharm Professional, with the &amp;quot;Remote Development&amp;quot; Tab highlighted using red arrows." src="media/pycharm/02_remote_development_tab.png"/></p>
 </div>
 </div>
 </div>
@@ -10372,18 +8843,18 @@ <h2 id="Activate-Environment">Activate Environment<a class="anchor-link" href="#
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
 <h2 id="More-flexible-approach-via-Makefile">More flexible approach via Makefile<a class="anchor-link" href="#More-flexible-approach-via-Makefile">¶</a></h2><p>We can define a <code>Makefile</code> as below and then after definition of <code>environment.yml</code>, install all the dependencies listed above via <code>make</code> commands. But first and foremost, we need to ensure, we have <code>make</code> installed on our machine.</p>
 <div class="highlight"><pre><span></span><span class="nf">env</span><span class="o">:</span>
-<span class="c">    @# Installs a conda environment with R and the IDF package</span>
-<span class="w">    </span>@if<span class="w"> </span><span class="o">[</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">"./plugin_env"</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    	</span>rm<span class="w"> </span>-rf<span class="w"> </span>./plugin_env<span class="p">;</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    </span><span class="k">fi</span>
-<span class="w">    </span>conda<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>--prefix<span class="w"> </span>./plugin_env<span class="w"> </span>-f<span class="w"> </span>environment.yml<span class="w"> </span>--force
-<span class="w">    </span>Rscript<span class="w"> </span>-e<span class="w"> </span><span class="s1">'install.packages("IDF", repos="https://CRAN.R-project.org/")'</span>
+<span class="c">	@# Installs a conda environment with R and the IDF package</span>
+<span class="w">	</span>@if<span class="w"> </span><span class="o">[</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">"./plugin_env"</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="se">\</span>
+<span class="w">		</span>rm<span class="w"> </span>-rf<span class="w"> </span>./plugin_env<span class="p">;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">	</span><span class="k">fi</span>
+<span class="w">	</span>conda<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>--prefix<span class="w"> </span>./plugin_env<span class="w"> </span>-f<span class="w"> </span>environment.yml<span class="w"> </span>--force
+<span class="w">	</span>Rscript<span class="w"> </span>-e<span class="w"> </span><span class="s1">'install.packages("IDF", repos="https://CRAN.R-project.org/")'</span>
 <span class="nf">cartopy</span><span class="o">:</span>
-<span class="c">    @# Download various cartopy shape-files</span>
-<span class="w">    </span>@if<span class="w"> </span><span class="o">[</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">"./cartopy"</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    	</span>rm<span class="w"> </span>-rf<span class="w"> </span>./cartopy<span class="p">;</span><span class="w"> </span><span class="se">\</span>
-<span class="w">    </span><span class="k">fi</span>
-<span class="w">    </span>./plugin_env/bin/python3<span class="w"> </span>assets/cartopy_download.py<span class="w"> </span>physical<span class="w"> </span>cultural
+<span class="c">	@# Download various cartopy shape-files</span>
+<span class="w">	</span>@if<span class="w"> </span><span class="o">[</span><span class="w"> </span>-d<span class="w"> </span><span class="s2">"./cartopy"</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span><span class="w"> </span><span class="se">\</span>
+<span class="w">		</span>rm<span class="w"> </span>-rf<span class="w"> </span>./cartopy<span class="p">;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">	</span><span class="k">fi</span>
+<span class="w">	</span>./plugin_env/bin/python3<span class="w"> </span>assets/cartopy_download.py<span class="w"> </span>physical<span class="w"> </span>cultural
 <span class="nf">.PHONY</span><span class="o">:</span><span class="w"> </span><span class="n">env</span> <span class="n">cartopy</span>
 </pre></div>
 <ul>
@@ -10561,7 +9032,10 @@ <h2 id="Plug-a-tool-into-Freva">Plug a tool into Freva<a class="anchor-link" hre
             history: true,
             transition: "slide",
             slideNumber: "",
-            plugins: [RevealNotes]
+            plugins: [RevealNotes],
+            width: 960,
+			      height: 700,
+
         });
 
         var update = function(event){