Using NOMAD docs layout now, fixes #24

docs/index.md

@@ -2,7 +2,8 @@
 hide: toc
 ---
 
-# pynxtools-em documentation
+# Documentation for pynxtools-em
+
 pynxtools-em is a free and open-source data software for creating standardized semantic serializations of electron microscopy data and metadata for research data management using NeXus, implemented with the goal to make scientific research data FAIR (findable, accessible, interoperable and reusable).
 
 pynxtools-em, which is a plugin for pynxtools, provides a tool for reading data from various proprietary and open data formats from technology partners and the wider electron microscopy community and standardizing it such that it is compliant with the NeXus application definition NXem.
@@ -64,4 +65,8 @@ for the respective file formats of technology partners of the electron microscop
 </div>
 
 <h2>Project and community</h2>
+<!-- - [NOMAD code guidelines](https://nomad-lab.eu/prod/v1/staging/docs/reference/code_guidelines.html) -->
+
+Any questions or suggestions? [Get in touch!](https://www.fair-di.eu/fairmat/about-fairmat/team-fairmat)
+
 [The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 460197019 (FAIRmat)](https://gepris.dfg.de/gepris/projekt/460197019?language=en).

docs/theme/partials/header.html

@@ -0,0 +1,86 @@
+{#-
+  This file was automatically generated - do not edit
+-#}
+{% set class = "md-header" %}
+{% if "navigation.tabs.sticky" in features %}
+  {% set class = class ~ " md-header--lifted" %}
+{% endif %}
+<header class="{{ class }}" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="{{ lang.t('header.title') }}">
+    <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">
+      {% include ".icons/material/menu" ~ ".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 and page.meta and page.meta.title %}
+              {{ page.meta.title }}
+            {% else %}
+              {{ page.title }}
+            {% endif %}
+          </span>
+        </div>
+      </div>
+    </div>
+    {% if not config.theme.palette is mapping %}
+      <form class="md-header__option" data-md-component="palette">
+        {% for option in config.theme.palette %}
+          {% set primary = option.primary | replace(" ", "-") | lower %}
+          {% set accent  = option.accent  | replace(" ", "-") | lower %}
+          <input class="md-option" data-md-color-media="{{ option.media }}" data-md-color-scheme="{{ option.scheme }}" data-md-color-primary="{{ primary }}" data-md-color-accent="{{ accent }}" {% if option.toggle %} aria-label="{{ option.toggle.name }}" {% else %} aria-hidden="true" {% endif %} type="radio" name="__palette" id="__palette_{{ loop.index }}">
+          {% if option.toggle %}
+            <label class="md-header__button md-icon" title="{{ option.toggle.name }}" for="__palette_{{ loop.index0 or loop.length }}" hidden>
+              {% include ".icons/" ~ option.toggle.icon ~ ".svg" %}
+            </label>
+          {% endif %}
+        {% endfor %}
+      </form>
+    {% endif %}
+    {% if config.extra.alternate %}
+      <div class="md-header__option">
+        <div class="md-select">
+          {% set icon = config.theme.icon.alternate or "material/translate" %}
+          <button class="md-header__button md-icon" aria-label="{{ lang.t('select.language.title') }}">
+            {% include ".icons/" ~ icon ~ ".svg" %}
+          </button>
+          <div class="md-select__inner">
+            <ul class="md-select__list">
+              {% for alt in config.extra.alternate %}
+                <li class="md-select__item">
+                  <a href="{{ alt.link | url }}" hreflang="{{ alt.lang }}" class="md-select__link">
+                    {{ alt.name }}
+                  </a>
+                </li>
+                {% endfor %}
+            </ul>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+    {% if "search" in config["plugins"] %}
+      <label class="md-header__button md-icon" for="__search">
+        {% include ".icons/material/magnify.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>

mkdocs.yaml

@@ -1,7 +1,10 @@
 site_name: pynxtools-em
 site_description: |
   The documentation for the pynxtools-em plugin
-site_author: The FAIRmat authors
+site_author: The NOMAD authors
+repo_url: https://github.com/FAIRmat-NFDI/pynxtools-em
+edit_uri: ""
+
 nav:
   - Home: index.md
   - Tutorials:
@@ -21,11 +24,26 @@ nav:
     - reference/vemd.md
     - reference/apex.md
     - reference/nion.md
+plugins:
+  - search
+  - macros:
+      module_name: pynxtools_em/mkdocs
+
 theme:
   name: material
+  palette:
+    primary: '#2A4CDF'
+    accent: '#008A67'
+  font:
+    text: 'Titillium Web'
+  logo: assets/nomad-logo.png
+  favicon: assets/favicon.png
   features:
+    - navigation.instant
     - content.code.copy
     - content.code.annotate
+  custom_dir: docs/theme
+
 markdown_extensions:
   - attr_list
   - md_in_html
@@ -40,16 +58,24 @@ markdown_extensions:
   - pymdownx.arithmatex:
       generic: true
   - pymdownx.emoji
+  - mkdocs-click
   - pymdownx.extra
   - pymdownx.superfences:
       custom_fences:
         - name: mermaid
           class: mermaid
           format: !!python/name:pymdownx.superfences.fence_code_format
+
+extra:
+  generator: false
+  homepage: https://nomad-lab.eu
+
 use_directory_urls: false
-plugins:
-    - search
-    - macros:
-        module_name: docs/macros
+
 extra_css:
-  - stylesheets/extra.css
+  - stylesheets/extra.css
+
+extra_javascript:
+  - javascript.js
+  - https://polyfill.io/v3/polyfill.min.js?features=es6
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js