elixir-toolkit-theme 1.6.1 → 1.7.2
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- checksums.yaml +4 -4
- data/README.md +82 -24
- data/_includes/affiliation-tiles-selection.html +2 -2
- data/_includes/head.html +3 -3
- data/_includes/sidebar.html +12 -14
- data/_layouts/page.html +9 -0
- data/assets/css/main.scss +5 -1
- data/assets/img/site.webmanifest +5 -1
- data/assets/js/main.js +1 -1
- metadata +2 -2
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 07ed353aa7d90f0c32deb99b0fc5960a9dd710b0faacf207f9f7a898d8d1ef12
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data.tar.gz: 343072727244f36fc174b9d13b4b0c11cb6ab8c7da628e2b76d415afba363fd1
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e583ed108e3a0820a3a4808d5880b43804837c38488e0247225829afd762353a96042f1413f17a7d3c437ec0c414cce83392127bcd2f8e4a2ba21d6ea94a6ffa
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data.tar.gz: ebf24972f2dba358d7a67793034941223279660f2212d26d8ff067ab93acf75c728a0836abf486c8e13daf1658d0bb04eda959f4c441a3cb8d351b1e5dd32bbb
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data/README.md
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[](https://badge.fury.io/rb/elixir-toolkit-theme)
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[](https://badge.fury.io/rb/elixir-toolkit-theme) [](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/actions/workflows/jekyll.yml)
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<p align="center">
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<img src="assets/img/main_logo.svg" width="100" float="center"/>
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<h1 align="center">ELIXIR toolkit theme </h1>
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</p>
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The ELIXIR toolkit theme is a Jekyll theme designed to support easy deployment of documentation websites but also more complex ones that require a central tool table and linking towards ELXIR resources.
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Its key features:
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- Easy deployment using GitHub pages
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- Advanced content search
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- Create your own look with the many theme variables
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- Change style using custom classes
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- Support for a central tools table
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- Page tagging and listing of those tagged pages
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- Linking to ELIXIR resources including Bio.tools, FAIRSHARING, FAIR Cookbook, TeSS and DSW
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- Easy side navigation, top navigation and footer management
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- Mobile friendly
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- Create website sections with each section having its own sidebar
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- Out of the box search engine optimizations including schema.org attributes and many other matadata attributes
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- Support for Google Analytics and Plausible
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- [DataTables](https://datatables.net/examples/styling/bootstrap5.html)
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- [AnchorJS](https://www.bryanbraun.com/anchorjs/)
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- [lunr.js](https://lunrjs.com/)
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- [jQuery](https://jquery.com/)
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- [jekyll-table-of-contents](https://github.com/ghiculescu/jekyll-table-of-contents)
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- [jQuery Navgoco Menus](https://github.com/tefra/navgoco)
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## Installation
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### via GitHub Pages remote theme
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The quickiest way to use Just The Docs is to use GitHub pages [remote theme](https://blog.github.com/2017-11-29-use-any-theme-with-github-pages/) feature in your `config.yml` file:
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```yaml
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remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
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```
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### via RubyGems:
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cd jekyll-bootstrap-theme
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Alternatively you can install it as a Ruby Gem (preferred way if you use GitLab).
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Add this line to your Jekyll site's Gemfile:
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```ruby
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gem "elixir-toolkit-theme"
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```
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And add this line to your Jekyll site's `_config.yml`:
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```yaml
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theme: elixir-toolkit-theme
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```
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docker run -it --rm -p 4000:4000 -v $PWD:/srv/jekyll jekyll/jekyll:latest /bin/bash -c "chmod a+w /srv/jekyll/Gemfile.lock && chmod 777 /srv/jekyll && jekyll serve -w"
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```
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This will start the docker container and serve the website locally.
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## Usage
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[View the documentation](https://elixir-belgium.github.io/elixir-toolkit-theme/) for usage information.
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## Deployment
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### Using GitHub pages
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This theme can be used to deploy the website using GitHub pages. Visit the [GitHub documentation](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/) to find out more about how to setup GitHub pages.
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### Locally using Jekyll
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1. If not already present on your machine, install ruby. Note that incompatibility issues may arise with ruby 3.0.0 (released 25.12.20) or newer versions.
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Additional information can be found at the following link: [https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll](https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll)
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### Using Docker
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If not already installed on your machine, install Docker. From the root of the `elixir-toolkit-theme` directory, run:
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```
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docker run -it --rm -p [::1]:4000:4000 -v $PWD:/srv/jekyll jekyll/jekyll:latest /bin/bash -c "chmod a+w /srv/jekyll/Gemfile.lock && chmod 777 /srv/jekyll && bundle install && bundle exec jekyll serve --host 0.0.0.0"
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```
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This will start the docker container and serve the website locally. Make sure the `.\_site` is not yet created to avoid permission errors.
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## This theme is known to be used in:
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- [RDMkit](https://rdmkit.elixir-europe.org/)
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- [RDMGuide](https://rdm.elixir-belgium.org/)
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- [Infectious Diseases Toolkit](https://www.infectious-diseases-toolkit.org/)
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- [Applied Bioinformatics and Biostatistics intranet page](https://intranet.psb.ugent.be/abb/)
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## Used packages
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This theme would not be possible without following open source projects:
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- [Bootstrap5](https://github.com/twbs/bootstrap) - As main CSS framework
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- [DataTables](https://github.com/DataTables/DataTablesSrc) - To generate tables that are sortable, searchable and contain pagination
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- [AnchorJS](https://github.com/bryanbraun/anchorjs) - Adds deep anchor links to the headings
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- [lunr.js](https://github.com/olivernn/lunr.js) - Main tool behind the search bar enabling content search
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- [jQuery](https://github.com/jquery/jquery) - A fast, small, and feature-rich JavaScript library for easy scripting
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- [jekyll-table-of-contents](https://github.com/ghiculescu/jekyll-table-of-contents) - Lightweight JS script to render the table of contents
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- [jQuery Navgoco Menus](https://github.com/tefra/navgoco) - Multi-level slide navigation with accordion effect
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- [Font-Awesome](https://github.com/FortAwesome/Font-Awesome) - The famous icon library
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- [flag-icons](https://github.com/lipis/flag-icons) - A curated collection of all country flags in SVG + css integration
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## License
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The theme is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
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{%- assign alllogos = site.data.affiliations %}
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<div class="row row-cols-2 row-cols-sm-3 row-cols-md-4 g-5 my-3">
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<div class="affiliation-tiles row row-cols-2 row-cols-sm-3 row-cols-md-4 g-5 my-3">
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{%- assign filtered_logos = alllogos | where: "type", include.type %}
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{%- for affiliation in filtered_logos %}
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{%- if affiliation.image_url and affiliation.expose == true %}
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<div class="col">
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<div class="card h-100 border-0">
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<div class="my-auto">
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{% if affiliation.url %}<a href="{{ affiliation.url }}">{% endif %}<img class="
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{% if affiliation.url %}<a href="{{ affiliation.url }}">{% endif %}<img class="rounded" src="{{ affiliation.image_url | relative_url }}" alt="{{ affiliation.name }}">{%- if affiliation.url %}</a>{% endif %}
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</div>
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</div>
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</div>
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data/_includes/head.html
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<meta property="og:description" content="{{ site.description }}" />
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<meta property="og:image" content="//{{site.github.url | remove: 'https://' | remove: 'http://'}}/assets/img/apple-touch-icon.png" />
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<meta name="apple-mobile-web-app-title" content="{{site.title}}">
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<meta name="msapplication-TileColor" content="#{{site.theme_variables.theme_color}}">
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<meta name="theme-color" content="#{{site.theme_variables.theme_color}}">
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<meta name="msapplication-TileColor" content="#{{site.theme_variables.theme_color | default: 0d6efd }}">
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<meta name="theme-color" content="#{{site.theme_variables.theme_color | default: 0d6efd }}">
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{%- if page.search_exclude == true and page.url != "/index.html" %}
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<meta name="robots" content="noindex" />
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{%- endif %}
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<link rel="icon" type="image/png" sizes="32x32" href="{{ 'assets/img/favicon-32x32.png' | relative_url }}">
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<link rel="icon" type="image/png" sizes="16x16" href="{{ 'assets/img/favicon-16x16.png' | relative_url }}">
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<link rel="manifest" href="{{ 'assets/img/site.webmanifest' | relative_url }}">
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<link rel="mask-icon" href="{{ 'assets/img/safari-pinned-tab.svg' | relative_url }}" color="#{{site.theme_variables.theme_color}}">
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<link rel="mask-icon" href="{{ 'assets/img/safari-pinned-tab.svg' | relative_url }}" color="#{{site.theme_variables.theme_color | default: 0d6efd }}">
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<link rel="shortcut icon" href="{{ 'assets/img/favicon.ico' | relative_url }}">
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<!-- Schema.org metadata -->
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{% include schemasorg.html %}
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data/_includes/sidebar.html
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{{ page.sidebar | capitalize | replace: "_", " " }} menu <i title="navbar-toggler" class="fa fa-bars ms-2"></i>
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</button>
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<nav class="collapse" id="side-nav" aria-label="Side navigation">
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</li>
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{%- endif %}
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{%- if sidebar.title or sidebar.version %}
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{%- if sidebar.title_url %}
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{%- if page.url == sidebar.title_url %}
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<a class="btn hover-primary text-start d-block mb-1 sidebar-title active" href="{{ sidebar.title_url | relative_url }}">{{sidebar.title}} {{sidebar.version}}</a>
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{%- else %}
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<a class="btn hover-primary text-start d-block mb-1 sidebar-title" href="{{ sidebar.title_url | relative_url }}">{{sidebar.title}} {{sidebar.version}}</a>
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{%- endif %}
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{%- else %}
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<a class="btn text-start d-block mb-1 sidebar-title disabled" aria-disabled="true">{{sidebar.title}} {{sidebar.version}}</a>
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{%- endif %}
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{%- endif %}
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<ul class="list-unstyled mb-4 mb-lg-0">
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{%- for folder in sidebar.subitems %}
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{%- if page.url == folder.url %}
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<li class="active{%- if folder.hr %} mt-3{% endif %}">
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data/_layouts/page.html
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{%- else %}
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<h1>{{ page.title }}
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{%- endif %}
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{%- if site.theme_variables.github_buttons.edit_me or site.theme_variables.github_buttons.open_issue or site.theme_variables.github_buttons.history or site.theme_variables.github_buttons.edit_me == nil or site.theme_variables.github_buttons.open_issue == nil or site.theme_variables.github_buttons.history == nil %}
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<div class="btn-group">
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{%- if site.theme_variables.github_buttons.edit_me or site.theme_variables.github_buttons.edit_me == nil %}
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{%- if page.custom-editme %}
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<a role="button" data-bs-toggle="tooltip" title="Propose changes to the content of this page on {{site.theme_variables.git_host | default: 'GitHub' }}" href="{{site.github.repository_url}}/blob/{{site.github.source.branch}}/{{page.custom-editme}}" class="btn btn-sm hover-primary text-primary"><i class="fas fa-pencil-alt"></i></a>
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{%- else %}
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<a role="button" data-bs-toggle="tooltip" title="Propose changes to this page on {{site.theme_variables.git_host | default: 'GitHub' }}" href="{{site.github.repository_url}}/blob/{{site.github.source.branch}}/{{page.path}}" class="btn btn-sm hover-primary text-primary"><i class="fas fa-pencil-alt"></i></a>
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{%- endif %}
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{%- endif %}
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{%- if site.theme_variables.github_buttons.open_issue or site.theme_variables.github_buttons.open_issue == nil %}
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<a role="button" data-bs-toggle="tooltip" title="Report an issue" href="{{site.github.repository_url}}/issues/new?title={{'Issue on page: ' | url_encode }}{{page.title | url_encode }}&body={{'I would like to report an issue on the ' | url_encode }}{{page.title | url_encode }}{{' page at `'| url_encode }}{{page.url | url_encode }}{{'`. Description of the issue:' | url_encode }}" class="btn btn-sm hover-primary text-primary"><i class="fas fa-exclamation"></i></a>
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{%- endif %}
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{%- if site.theme_variables.github_buttons.history or site.theme_variables.github_buttons.history == nil %}
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<a role="button" data-bs-toggle="tooltip" title="Check out the history of this page" href="{{site.github.repository_url}}/commits/{{site.github.source.branch}}/{{page.path}}" class="btn btn-sm hover-primary text-primary"><i class="fas fa-history"></i></a>
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{%- endif %}
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</div>
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{%- endif %}
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</h1>
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{%- endif %}
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{%- if page.summary %}
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data/assets/css/main.scss
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a:not(.btn):hover {
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text-decoration: underline;
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overflow-wrap: break-word;
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word-wrap: break-word;
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-ms-word-break: break-all;
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word-break: break-word;
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}
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ol li,
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@@ -271,7 +275,7 @@ header .navbar {
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background-color: $sidebar-bg-active;
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}
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ul
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#side-nav>ul {
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> li:not(.sidebar-title) > a {
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background-color: $sidebar-bg;
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color: $sidebar-color;
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data/assets/img/site.webmanifest
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---
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layout: none
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3
|
+
permalink: assets/img/site.webmanifest
|
|
4
|
+
---
|
|
1
5
|
{
|
|
2
6
|
"name": "",
|
|
3
7
|
"short_name": "",
|
|
@@ -13,7 +17,7 @@
|
|
|
13
17
|
"type": "image/png"
|
|
14
18
|
}
|
|
15
19
|
],
|
|
16
|
-
"theme_color": "#
|
|
20
|
+
"theme_color": "#{{ site.theme_variables.theme_color | default: '0d6efd' }}",
|
|
17
21
|
"background_color": "#ffffff",
|
|
18
22
|
"display": "standalone"
|
|
19
23
|
}
|
data/assets/js/main.js
CHANGED
|
@@ -31,7 +31,7 @@ $(document).ready(function external_new_window() {
|
|
|
31
31
|
*/
|
|
32
32
|
$(document).ready(function () {
|
|
33
33
|
// Initialize navgoco with default options
|
|
34
|
-
$("#
|
|
34
|
+
$("#side-nav>ul").navgoco({
|
|
35
35
|
caretHtml: '',
|
|
36
36
|
accordion: true,
|
|
37
37
|
openClass: 'active', // open
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: elixir-toolkit-theme
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.
|
|
4
|
+
version: 1.7.2
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- bedroesb
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2022-03-
|
|
11
|
+
date: 2022-03-14 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: jekyll
|