adds giscus

mkdocs.yml

@@ -13,11 +13,29 @@ theme:
   name: material
   logo: assets/images/SIB_logo.svg
   favicon: assets/images/SIB_logo.svg
+  custom_dir: overrides
   icon:
     repo: fontawesome/brands/github
+  features:
+    - announce.dismiss
+
 extra:
   version:
     provider: mike
+  consent:
+    title: Cookie consent
+    description: >- 
+      We use cookies to recognize your repeated visits and preferences, as well
+      as to measure the effectiveness of our documentation and whether users
+      find what they're searching for. With your consent, you're helping us to
+      make our documentation better.
+  analytics:
+    provider: google
+    property: G-1HJVS56CBX
+
+copyright: >
+  Copyright © 2021-2022 SIB Swiss institute of Bioinformatics –
+  <a href="#__consent">Change cookie settings</a>
 
 # Repository
 repo_name: sib-swiss/containers-introduction-training

overrides/main.html

@@ -1,11 +1,109 @@
-
 {% extends "base.html" %}
 
+{% block announce %}
+  <b>Issues, questions or feedback? &#128591; &#128640; </b> Use the "Questions and Answers" section at the bottom &#128071; of every page
+{% endblock %}
+
+{% block site_meta %}
+<script type="application/ld+json">
+  {
+    "@context": "https://schema.org/",
+    "@type": "LearningResource",
+    "@id": "https://sib-swiss.github.io/containers-introduction-training",
+    "http://purl.org/dc/terms/conformsTo": {
+        "@type": "CreativeWork",
+        "@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE"
+    },
+    "description": "Course on containers for reproducible research",
+    "keywords": "container, docker, singularity, reproducible",
+    "name": " Docker and Singularity for reproducible research: getting started with containers ",
+
+    "abstract": "Reproducible analysis in bioinformatics goes beyond good documentation and sharing code. Often, analyses depend on an entire environment with many different programs, libraries and settings. For the sake of reproducibility, but also for productivity, you might want to store, reuse, and share your environments using container software such as Docker and Singularity. Containerization is a lightweight and scalable way of working with such isolated environments. For example, with Docker you can develop, store and manage environments based on Linux operating systems which can run in mostly any computer. Often, bioinformatic calculations also require large memory and CPU resources, therefore you might want to use a shared computer environment (e.g. a HPC cluster). However, to run Docker you need to have privileged rights (i.e. as root), which is not the case for Singularity, a program that enables you to run environments from a wide range of resources (including Docker) in a safe manner without the need for privileged access. Combining Singularity and Docker thus makes you extremely flexible in how, when and where you use your computer environments and those of others. To introduce you to working with containers in the context of bioinformatics research, we will take a practical approach with several hands-on exercises to go through the basics of using, developing and sharing containers.",
+    "audience": "Biologists, bioinformaticians and computational biologists",
+    "author": [
+        {
+            "@type": "Person",
+            "name": "Geert van Geest",
+            "email": "[email protected]"
+        },
+        {
+            "@type": "Person",
+            "name": "Patricia Palagi"
+        },
+        {
+            "@type": "Organization",
+            "name": "SIB Swiss Institute of Bioinformatics"
+        }
+    ],
+    "identifier": "https://doi.org/10.5281/zenodo.6787081",
+    "license": "https://creativecommons.org/licenses/by/4.0/",
+    "teaches": [
+        "Understand the basic concepts and terminology associated with virtualization with containers",
+        "Be able to customize, store and share a containerized environment with Docker",
+        "Understand the essential differences between Docker and Singularity",
+        "Be able to use Singularity to run containers on a shared computer environment (e.g. a HPC cluster)"
+    ]
+}
+</script>
+{% endblock %}
+
+{% block content %}
+  {{ super() }}
+
+  <!-- Giscus -->
+  <h2>Questions & Answers</h2>
+
+    <script src="https://giscus.app/client.js"
+            data-repo="sib-swiss/containers-introduction-training"
+            data-repo-id="MDEwOlJlcG9zaXRvcnkzMzE4OTA0MzA="
+            data-category="Q&A"
+            data-category-id="DIC_kwDOE8g-_s4CSEuU"
+            data-mapping="pathname"
+            data-strict="0"
+            data-reactions-enabled="1"
+            data-emit-metadata="0"
+            data-input-position="top"
+            data-theme="preferred_color_scheme"
+            data-lang="en"
+            crossorigin="anonymous"
+            async>
+    </script>
+  <!-- Synchronize Giscus theme with palette -->
+  <script>
+    var giscus = document.querySelector("script[src*=giscus]")
+
+    /* Set palette on initial load */
+    var palette = __md_get("__palette")
+    if (palette && typeof palette.color === "object") {
+      var theme = palette.color.scheme === "slate" ? "dark" : "light"
+      giscus.setAttribute("data-theme", theme) 
+
+
+    }
+
+    /* Register event handlers after documented loaded */
+    document.addEventListener("DOMContentLoaded", function() {
+      var ref = document.querySelector("[data-md-component=palette]")
+      ref.addEventListener("change", function() {
+        var palette = __md_get("__palette")
+        if (palette && typeof palette.color === "object") {
+          var theme = palette.color.scheme === "slate" ? "dark" : "light"
+
+          /* Instruct Giscus to change theme */
+          var frame = document.querySelector(".giscus-frame")
+          frame.contentWindow.postMessage(
+            { giscus: { setConfig: { theme } } },
+            "https://giscus.app"
+          )
+        }
+      })
+    })
+  </script>
+{% endblock %}
+
 {% block outdated %}
   You're not viewing the latest version.
   <a href="{{ '../' ~ base_url }}"> 
-
-
     <strong>Click here to go to latest.</strong>
   </a>
 {% endblock %}