Additional user guide updates (#283)

* Improve blog feature

Includes author name and description.

* update header and footer

* Small updates to header and footer

gen3/docs/blog/authors.yml

@@ -1,10 +1,9 @@
 authors:
   qureshi:
     name: Jawad Qureshi
-    description: Lead Platform Engineer
+    description: Lead Platform Engineer, CTDS
     avatar: https://github.com/jawadqur.png
   elise:
     name: Elise Castle
-    description: Platform Engineer - Gen3
-    url: https://github.com/EliseCastle23
+    description: Platform Engineer, CTDS
     avatar: https://github.com/EliseCastle23.png

gen3/docs/blog/posts/gen3-laptop.md

@@ -6,6 +6,7 @@ date: 2023-09-13
 slug: Gen3 on laptop
 categories:
   - Operator
+  - CTDS
 tags:
   - Kubernetes
   - Minikube

gen3/docs/blog/posts/gen3-observability.md

@@ -1,8 +1,12 @@
 ---
-draft: false
-slug: Observability
+title: "Observability"
+slug: observability
 authors:
  - elise
+date: 2024-10-15
+categories:
+  - Operator
+  - CTDS
 tags:
   - Observability
   - Helm Chart
@@ -14,17 +18,14 @@ tags:
   - Real User Monitoring (RUM)
   - Metrics
   - Log Aggregation
+  - Kubernetes
   - Dashboards
   - Kubernetes Monitoring
   - Time-Series Database
   - Alerting
   - Frontend Monitoring
   - Grafana Dashboards
   - Open Source Monitoring
-date: 2024-10-15
-categories:
-  - Operator
-
 ---
 
 # Deploying a Comprehensive Observability Stack with Helm
@@ -44,9 +45,7 @@ A log aggregation system designed to index and query logs with minimal resource
 
 In this setup, Loki and Mimir are configured with internal ingress resources, enabling Alloy to send metrics and logs securely via VPC peering connections. Both Loki and Mimir write the ingested data to Amazon S3 for scalable and durable storage. This data can be queried and visualized through Grafana, which is hosted behind an internet-facing ingress. Access to Grafana can be restricted using CIDR ranges defined through the ALB ingress annotation: alb.ingress.kubernetes.io/inbound-cidrs: "cidrs". Additionally, the chart supports SAML authentication for Grafana, configured through the grafana.ini field, ensuring secure user access.
 
-<p align="center">
- <img src="Grafana.png" alt="Grafana Architecture" />
-</p>
+![Grafana architecutre](Grafana.png)
 
 
 ### Fips compliant images

gen3/docs/blog/posts/k8s-for-dev.md

@@ -5,6 +5,7 @@ authors:
 date: 2023-08-13
 categories:
   - Operator
+  - CTDS
 slug: k8s for development
 tags:
   - Kubernetes

gen3/docs/blog/posts/k8s-productivity-tools.md

@@ -6,6 +6,7 @@ date: 2023-10-13
 slug: k8s tools
 categories:
   - Operator
+  - CTDS
 tags:
   - Kubernetes
   - Minikube

gen3/mkdocs.yml

@@ -104,12 +104,14 @@ nav:
 
 theme:
   favicon: img/Gen3-3.ico
-  logo: img/Gen3_Logo-01_blue_no_commons.png
+  logo: img/gen3_new_logo_white.svg
   name: material
   features:
     - navigation.footer
-
+  custom_dir: overrides
   palette:
+    - primary: black
+
 
    # Palette toggle for light mode
     - media: "(prefers-color-scheme: light)"
@@ -128,8 +130,6 @@ theme:
     - navigation.indexes
     - navigation.tracking
     - navigation.path
-extra_css:
-  - stylesheets/extra.css
 use_directory_urls: true
 markdown_extensions:
   - admonition
@@ -145,8 +145,23 @@ plugins:
   - tags
   - blog:
       enabled: true
+      authors: true
       authors_file: blog/authors.yml
       blog_dir: blog
       blog_toc: true
   - mkdocs-video:
       is_video: True
+extra:
+  social:
+    - icon: fontawesome/brands/linkedin
+      link: https://www.linkedin.com/company/center-for-translational-data-science/
+    - icon: fontawesome/brands/x-twitter
+      link: https://x.com/UChicagoCTDS
+    - icon: fontawesome/brands/x-twitter
+      link: https://x.com/gen3data
+    - icon: fontawesome/brands/slack
+      link: https://docs.google.com/forms/d/e/1FAIpQLSczyhhOXeCK9FdVtpQpelOHYnRj1EAq1rwwnm9q6cPAe5a7ug/viewform
+    - icon: fontawesome/brands/youtube
+      link: https://www.youtube.com/channel/UCMCwQy4EDd1BaskzZgIOsNQ/featured
+    - icon: fontawesome/brands/github
+      link: https://github.com/uc-cdis

gen3/overrides/partials/footer.html

@@ -0,0 +1,106 @@
+<!--
+  Copyright (c) 2016-2024 Martin Donath <[email protected]>
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to
+  deal in the Software without restriction, including without limitation the
+  rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+  sell copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in
+  all copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+  IN THE SOFTWARE.
+-->
+
+<!-- Footer -->
+<footer class="md-footer">
+
+  <!-- Link to previous and/or next page -->
+  {% if "navigation.footer" in features %}
+    {% if page.previous_page or page.next_page %}
+      {% if page.meta and page.meta.hide %}
+        {% set hidden = "hidden" if "footer" in page.meta.hide %}
+      {% endif %}
+      <nav
+        class="md-footer__inner md-grid"
+        aria-label="{{ lang.t('footer') }}"
+        {{ hidden }}
+      >
+
+        <!-- Link to previous page -->
+        {% if page.previous_page %}
+          {% set direction = lang.t("footer.previous") %}
+          <a
+            href="{{ page.previous_page.url | url }}"
+            class="md-footer__link md-footer__link--prev"
+            aria-label="{{ direction }}: {{ page.previous_page.title | e }}"
+          >
+            <div class="md-footer__button md-icon">
+              {% set icon = config.theme.icon.previous or "material/arrow-left" %}
+              {% include ".icons/" ~ icon ~ ".svg" %}
+            </div>
+            <div class="md-footer__title">
+              <span class="md-footer__direction">
+                {{ direction }}
+              </span>
+              <div class="md-ellipsis">
+                {{ page.previous_page.title }}
+              </div>
+            </div>
+          </a>
+        {% endif %}
+
+        <!-- Link to next page -->
+        {% if page.next_page %}
+          {% set direction = lang.t("footer.next") %}
+          <a
+            href="{{ page.next_page.url | url }}"
+            class="md-footer__link md-footer__link--next"
+            aria-label="{{ direction }}: {{ page.next_page.title | e }}"
+          >
+            <div class="md-footer__title">
+              <span class="md-footer__direction">
+                {{ direction }}
+              </span>
+              <div class="md-ellipsis">
+                {{ page.next_page.title }}
+              </div>
+            </div>
+            <div class="md-footer__button md-icon">
+              {% set icon = config.theme.icon.next or "material/arrow-right" %}
+              {% include ".icons/" ~ icon ~ ".svg" %}
+            </div>
+          </a>
+        {% endif %}
+      </nav>
+    {% endif %}
+  {% endif %}
+
+  <!-- Further information -->
+  <div class="md-footer-meta md-typeset">
+    <div class="md-footer-meta__inner md-grid">
+      {% include "partials/copyright.html" %}
+
+      <!-- Custom link to Center for Translational Data Science -->
+      <div class="md-footer__link" style="vertical-align: middle; padding-bottom: 10px;">
+        <a href="https://ctds.uchicago.edu/" target="_blank" rel="noopener noreferrer">
+          Center for Translational Data Science
+        </a>
+      </div>
+      <!-- End of custom link -->
+
+      <!-- Social links -->
+      {% if config.extra.social %}
+        {% include "partials/social.html" %}
+      {% endif %}
+    </div>
+  </div>
+</footer>

gen3/overrides/partials/header.html

@@ -0,0 +1,78 @@
+{#-
+  This file was automatically generated - do not edit
+-#}
+{% set class = "md-header" %}
+{% if "navigation.tabs.sticky" in features %}
+  {% set class = class ~ " md-header--shadow md-header--lifted" %}
+{% elif "navigation.tabs" not in features %}
+  {% set class = class ~ " md-header--shadow" %}
+{% endif %}
+<header class="{{ class }}" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="{{ lang.t('header') }}">
+    <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}" class="md-header__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
+      {% include "partials/logo.html" %}
+    </a>
+    <label class="md-header__button md-icon" for="__drawer">
+      {% set icon = config.theme.icon.menu or "material/menu" %}
+      {% include ".icons/" ~ icon ~ ".svg" %}
+    </label>
+    <div class="md-header__title" data-md-component="header-title">
+      <div class="md-header__ellipsis">
+        <div class="md-header__topic">
+          <span class="md-ellipsis">
+            {{ config.site_name }}
+          </span>
+        </div>
+        <div class="md-header__topic" data-md-component="header-topic">
+          <span class="md-ellipsis">
+            {% if page.meta and page.meta.title %}
+              {{ page.meta.title }}
+            {% else %}
+              {{ page.title }}
+            {% endif %}
+          </span>
+        </div>
+      </div>
+    </div>
+    {% if config.theme.palette %}
+      {% if not config.theme.palette is mapping %}
+        {% include "partials/palette.html" %}
+      {% endif %}
+    {% endif %}
+    {% if not config.theme.palette is mapping %}
+      {% include "partials/javascripts/palette.html" %}
+    {% endif %}
+    {% if config.extra.alternate %}
+      {% include "partials/alternate.html" %}
+    {% endif %}
+
+    <!-- Custom link to Gen3.org (with an external link icon) -->
+    <div style="margin-right: 10px; display: flex; align-items: center;">
+      <h1 href="https://gen3.org/" class="md-header__button" aria-label="Gen3.org" target="_blank" rel="noopener noreferrer" style="display: flex; align-items: center;">
+        Gen3.org
+        <!-- Insert your preferred external link icon here -->
+        <svg xmlns="http://www.w3.org/2000/svg" width="1em" height="1em" style="margin-left: 5px;" viewBox="0 0 16 16"><g fill="currentColor" fill-rule="evenodd"><path d="M8.636 3.5a.5.5 0 0 0-.5-.5H1.5A1.5 1.5 0 0 0 0 4.5v10A1.5 1.5 0 0 0 1.5 16h10a1.5 1.5 0 0 0 1.5-1.5V7.864a.5.5 0 0 0-1 0V14.5a.5.5 0 0 1-.5.5h-10a.5.5 0 0 1-.5-.5v-10a.5.5 0 0 1 .5-.5h6.636a.5.5 0 0 0 .5-.5"/><path d="M16 .5a.5.5 0 0 0-.5-.5h-5a.5.5 0 0 0 0 1h3.793L6.146 9.146a.5.5 0 1 0 .708.708L15 1.707V5.5a.5.5 0 0 0 1 0z"/></g></svg>
+      </h1>
+    </div>
+    <!-- End of custom link to Gen3.org with an external link icon -->
+
+
+    {% if "material/search" in config.plugins %}
+      <label class="md-header__button md-icon" for="__search">
+        {% set icon = config.theme.icon.search or "material/magnify" %}
+        {% include ".icons/" ~ icon ~ ".svg" %}
+      </label>
+      {% include "partials/search.html" %}
+    {% endif %}
+    {% if config.repo_url %}
+      <div class="md-header__source">
+        {% include "partials/source.html" %}
+      </div>
+    {% endif %}
+  </nav>
+  {% if "navigation.tabs.sticky" in features %}
+    {% if "navigation.tabs" in features %}
+      {% include "partials/tabs.html" %}
+    {% endif %}
+  {% endif %}
+</header>