diff --git a/_config.yml b/_config.yml index 75deef9..8a9dee0 100644 --- a/_config.yml +++ b/_config.yml @@ -217,10 +217,10 @@ exclude: - "package*.json" jekyll-archives: - enabled: [categories, tags] + enabled: [categories, tags, tutorials] layouts: category: category tag: tag permalinks: tag: /tags/:name/ - category: /categories/:name/ + category: /tutorials/:name/ diff --git a/_layouts/archives.html b/_layouts/archives.html new file mode 100644 index 0000000..4f7ad7d --- /dev/null +++ b/_layouts/archives.html @@ -0,0 +1,35 @@ +--- +layout: page +# The Archives of posts. +--- + +{% include lang.html %} + +{% assign df_strftime_m = site.data.locales[lang].df.archives.strftime | default: '/ %m' %} +{% assign df_dayjs_m = site.data.locales[lang].df.archives.dayjs | default: '/ MM' %} + +
+ {% for post in site.posts %} + {% assign cur_year = post.date | date: '%Y' %} + + {% if cur_year != last_year %} + {% unless forloop.first %}{% endunless %} + + + {{ '{% endif %} + {% endfor %} +
diff --git a/_layouts/categories.html b/_layouts/categories.html new file mode 100644 index 0000000..0515097 --- /dev/null +++ b/_layouts/categories.html @@ -0,0 +1,138 @@ +--- +layout: page +# All the Categories of posts +--- + +{% include lang.html %} + +{% assign HEAD_PREFIX = 'h_' %} +{% assign LIST_PREFIX = 'l_' %} + +{% assign group_index = 0 %} + +{% assign sort_categories = site.categories | sort %} + +{% for category in sort_categories %} + {% assign category_name = category | first %} + {% assign posts_of_category = category | last %} + {% assign first_post = posts_of_category | first %} + + {% if category_name == first_post.categories[0] %} + {% assign sub_categories = '' | split: '' %} + + {% for post in posts_of_category %} + {% assign second_category = post.categories[1] %} + {% if second_category %} + {% unless sub_categories contains second_category %} + {% assign sub_categories = sub_categories | push: second_category %} + {% endunless %} + {% endif %} + {% endfor %} + + {% assign sub_categories = sub_categories | sort %} + {% assign sub_categories_size = sub_categories | size %} + +
+ +
+ + + + {% capture _category_url %}/categories/{{ category_name | slugify | url_encode }}/{% endcapture %} + {{ category_name }} + + + {% assign top_posts_size = site.categories[category_name] | size %} + + {% if sub_categories_size > 0 %} + {{ sub_categories_size }} + {% if sub_categories_size > 1 %} + {{ + site.data.locales[lang].categories.category_measure.plural + | default: site.data.locales[lang].categories.category_measure + }} + {% else %} + {{ + site.data.locales[lang].categories.category_measure.singular + | default: site.data.locales[lang].categories.category_measure + }} + {% endif -%} + , + {% endif %} + + {{ top_posts_size }} + + {% if top_posts_size > 1 %} + {{ + site.data.locales[lang].categories.post_measure.plural + | default: site.data.locales[lang].categories.post_measure + }} + {% else %} + {{ + site.data.locales[lang].categories.post_measure.singular + | default: site.data.locales[lang].categories.post_measure + }} + {% endif %} + + + + + {% if sub_categories_size > 0 %} + + + + {% else %} + + + + {% endif %} +
+ + + + {% if sub_categories_size > 0 %} +
+ +
+ {% endif %} +
+ + + {% assign group_index = group_index | plus: 1 %} + {% endif %} +{% endfor %} diff --git a/_layouts/category.html b/_layouts/category.html new file mode 100644 index 0000000..b064f27 --- /dev/null +++ b/_layouts/category.html @@ -0,0 +1,24 @@ +--- +layout: page +# The Category layout +--- + +{% include lang.html %} + +
+

+ + {{ page.title }} + {{ page.posts | size }} +

+ + +
diff --git a/_layouts/compress.html b/_layouts/compress.html new file mode 100644 index 0000000..2779e92 --- /dev/null +++ b/_layouts/compress.html @@ -0,0 +1,10 @@ +--- +# Jekyll layout that compresses HTML +# v3.2.0 +# http://jch.penibelst.de/ +# © 2014–2015 Anatol Broder +# MIT License +--- + +{% capture _LINE_FEED %} +{% endcapture %}{% if site.compress_html.ignore.envs contains jekyll.environment or site.compress_html.ignore.envs == "all" or page.compress_html == false %}{{ content }}{% else %}{% capture _content %}{{ content }}{% endcapture %}{% assign _profile = site.compress_html.profile %}{% if site.compress_html.endings == "all" %}{% assign _endings = "html head body li dt dd optgroup option colgroup caption thead tbody tfoot tr td th" | split: " " %}{% else %}{% assign _endings = site.compress_html.endings %}{% endif %}{% for _element in _endings %}{% capture _end %}{% endcapture %}{% assign _content = _content | remove: _end %}{% endfor %}{% if _profile and _endings %}{% assign _profile_endings = _content | size | plus: 1 %}{% endif %}{% for _element in site.compress_html.startings %}{% capture _start %}<{{ _element }}>{% endcapture %}{% assign _content = _content | remove: _start %}{% endfor %}{% if _profile and site.compress_html.startings %}{% assign _profile_startings = _content | size | plus: 1 %}{% endif %}{% if site.compress_html.comments == "all" %}{% assign _comments = "" | split: " " %}{% else %}{% assign _comments = site.compress_html.comments %}{% endif %}{% if _comments.size == 2 %}{% capture _comment_befores %}.{{ _content }}{% endcapture %}{% assign _comment_befores = _comment_befores | split: _comments.first %}{% for _comment_before in _comment_befores %}{% if forloop.first %}{% continue %}{% endif %}{% capture _comment_outside %}{% if _carry %}{{ _comments.first }}{% endif %}{{ _comment_before }}{% endcapture %}{% capture _comment %}{% unless _carry %}{{ _comments.first }}{% endunless %}{{ _comment_outside | split: _comments.last | first }}{% if _comment_outside contains _comments.last %}{{ _comments.last }}{% assign _carry = false %}{% else %}{% assign _carry = true %}{% endif %}{% endcapture %}{% assign _content = _content | remove_first: _comment %}{% endfor %}{% if _profile %}{% assign _profile_comments = _content | size | plus: 1 %}{% endif %}{% endif %}{% assign _pre_befores = _content | split: "" %}{% assign _pres_after = "" %}{% if _pres.size != 0 %}{% if site.compress_html.blanklines %}{% assign _lines = _pres.last | split: _LINE_FEED %}{% capture _pres_after %}{% for _line in _lines %}{% assign _trimmed = _line | split: " " | join: " " %}{% if _trimmed != empty or forloop.last %}{% unless forloop.first %}{{ _LINE_FEED }}{% endunless %}{{ _line }}{% endif %}{% endfor %}{% endcapture %}{% else %}{% assign _pres_after = _pres.last | split: " " | join: " " %}{% endif %}{% endif %}{% capture _content %}{{ _content }}{% if _pre_before contains "" %}{% endif %}{% unless _pre_before contains "" and _pres.size == 1 %}{{ _pres_after }}{% endunless %}{% endcapture %}{% endfor %}{% if _profile %}{% assign _profile_collapse = _content | size | plus: 1 %}{% endif %}{% if site.compress_html.clippings == "all" %}{% assign _clippings = "html head title base link meta style body article section nav aside h1 h2 h3 h4 h5 h6 hgroup header footer address p hr blockquote ol ul li dl dt dd figure figcaption main div table caption colgroup col tbody thead tfoot tr td th" | split: " " %}{% else %}{% assign _clippings = site.compress_html.clippings %}{% endif %}{% for _element in _clippings %}{% assign _edges = " ;; ;" | replace: "e", _element | split: ";" %}{% assign _content = _content | replace: _edges[0], _edges[1] | replace: _edges[2], _edges[3] | replace: _edges[4], _edges[5] %}{% endfor %}{% if _profile and _clippings %}{% assign _profile_clippings = _content | size | plus: 1 %}{% endif %}{{ _content }}{% if _profile %}
Step Bytes
raw {{ content | size }}{% if _profile_endings %}
endings {{ _profile_endings }}{% endif %}{% if _profile_startings %}
startings {{ _profile_startings }}{% endif %}{% if _profile_comments %}
comments {{ _profile_comments }}{% endif %}{% if _profile_collapse %}
collapse {{ _profile_collapse }}{% endif %}{% if _profile_clippings %}
clippings {{ _profile_clippings }}{% endif %}
{% endif %}{% endif %} diff --git a/_layouts/default.html b/_layouts/default.html new file mode 100644 index 0000000..a55bfef --- /dev/null +++ b/_layouts/default.html @@ -0,0 +1,86 @@ +--- +layout: compress +--- + + + +{% include origin-type.html %} + +{% include lang.html %} + +{% if site.theme_mode %} + {% capture prefer_mode %}data-mode="{{ site.theme_mode }}"{% endcapture %} +{% endif %} + + + + {% include head.html %} + + + {% include sidebar.html lang=lang %} + +
+
+ {% include topbar.html lang=lang %} + +
+
+ {% if layout.refactor or layout.layout == 'default' %} + {% include refactor-content.html content=content lang=lang %} + {% else %} + {{ content }} + {% endif %} +
+ + + +
+ +
+ +
+ {% for _include in layout.tail_includes %} + {% assign _include_path = _include | append: '.html' %} + {% include {{ _include_path }} lang=lang %} + {% endfor %} + + {% include_cached footer.html lang=lang %} +
+
+ + {% include_cached search-results.html lang=lang %} +
+ + +
+ +
+ + {% if site.pwa.enabled %} + {% include_cached notification.html lang=lang %} + {% endif %} + + + + {% for _include in layout.script_includes %} + {% assign _include_path = _include | append: '.html' %} + {% include {{ _include_path }} %} + {% endfor %} + + {% include_cached search-loader.html lang=lang %} + + diff --git a/_layouts/home.html b/_layouts/home.html new file mode 100644 index 0000000..b1b4c02 --- /dev/null +++ b/_layouts/home.html @@ -0,0 +1,139 @@ +--- +layout: default +refactor: true +--- + +{% include lang.html %} + +{% assign all_pinned = site.posts | where: 'pin', 'true' %} +{% assign all_normal = site.posts | where_exp: 'item', 'item.pin != true and item.hidden != true' %} + +{% assign posts = '' | split: '' %} + + + +{% assign visible_start = paginator.page | minus: 1 | times: paginator.per_page %} +{% assign visible_end = visible_start | plus: paginator.per_page %} + +{% if all_pinned.size > visible_start %} + {% if all_pinned.size > visible_end %} + {% assign pinned_size = paginator.per_page %} + {% else %} + {% assign pinned_size = all_pinned.size | minus: visible_start %} + {% endif %} + + {% for i in (visible_start..all_pinned.size) limit: pinned_size %} + {% assign posts = posts | push: all_pinned[i] %} + {% endfor %} +{% else %} + {% assign pinned_size = 0 %} +{% endif %} + + + +{% assign normal_size = paginator.posts | size | minus: pinned_size %} + +{% if normal_size > 0 %} + {% if pinned_size > 0 %} + {% assign normal_start = 0 %} + {% else %} + {% assign normal_start = visible_start | minus: all_pinned.size %} + {% endif %} + + {% assign normal_end = normal_start | plus: normal_size | minus: 1 %} + + {% for i in (normal_start..normal_end) %} + {% assign posts = posts | push: all_normal[i] %} + {% endfor %} +{% endif %} + +
+ + {% if paginator.page == 1 %} +
+
+

Welcome to BIGr Documentation!

+
+

+ This R package contains the functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. + Here you will find all the documentation, tutorials, and latest updates for the Breeding Insight Genomics R Package (BIGr). +

+

+ Please use the tabs above to navigate to our tutorials or check the FAQ. The most recent posts and updates are listed below. +

+
+
+
+ {% endif %} + {% for post in posts %} +
+ + {% assign card_body_col = '12' %} + + {% if post.image %} + {% assign src = post.image.path | default: post.image %} + {% unless src contains '//' %} + {% assign src = post.media_subpath | append: '/' | append: src | replace: '//', '/' %} + {% endunless %} + + {% assign alt = post.image.alt | xml_escape | default: 'Preview Image' %} + + {% assign lqip = null %} + + {% if post.image.lqip %} + {% capture lqip %}lqip="{{ post.image.lqip }}"{% endcapture %} + {% endif %} + +
+ {{ alt }} +
+ + {% assign card_body_col = '7' %} + {% endif %} + +
+
+

{{ post.title }}

+ +
+

{% include post-description.html %}

+
+ + + +
+ +
+
+
+ {% endfor %} +
+ + +{% if paginator.total_pages > 1 %} + {% include post-paginator.html %} +{% endif %} diff --git a/_layouts/page.html b/_layouts/page.html new file mode 100644 index 0000000..32d6582 --- /dev/null +++ b/_layouts/page.html @@ -0,0 +1,20 @@ +--- +layout: default +--- + +{% include lang.html %} + +
+ {% if page.layout == 'page' or page.collection == 'tabs' %} + {% assign tab_key = page.title | downcase %} + {% assign title = site.data.locales[lang].tabs[tab_key] | default: page.title %} +

+ {{ title }} +

+
+ {{ content }} +
+ {% else %} + {{ content }} + {% endif %} +
diff --git a/_layouts/post.html b/_layouts/post.html new file mode 100644 index 0000000..336773f --- /dev/null +++ b/_layouts/post.html @@ -0,0 +1,179 @@ +--- +layout: default +refactor: true +panel_includes: + - toc +tail_includes: + - related-posts + - post-nav +script_includes: + - comment +--- + +{% include lang.html %} + +{% include toc-status.html %} + +
+
+

{{ page.title }}

+ {% if page.description %} +

{{ page.description }}

+ {% endif %} + + +
+ + {% if enable_toc %} + + + + + +
+
{{- page.title -}}
+ +
+
+
+ {% endif %} + +
+ {{ content }} +
+ +
+ + {% if page.categories.size > 0 %} + + {% endif %} + + + {% if page.tags.size > 0 %} + + {% endif %} + +
+
+ {% if site.data.locales[lang].copyright.license.template %} + {% capture _replacement %} + + {{ site.data.locales[lang].copyright.license.name }} + + {% endcapture %} + + {{ site.data.locales[lang].copyright.license.template | replace: ':LICENSE_NAME', _replacement }} + {% endif %} +
+ + {% include post-sharing.html lang=lang %} +
+ +
+ +
diff --git a/_layouts/tag.html b/_layouts/tag.html new file mode 100644 index 0000000..d766d09 --- /dev/null +++ b/_layouts/tag.html @@ -0,0 +1,23 @@ +--- +layout: page +# The layout for Tag page +--- + +{% include lang.html %} + +
+

+ + {{ page.title }} + {{ page.posts | size }} +

+
    + {% for post in page.posts %} +
  • + {{ post.title }} + + {% include datetime.html date=post.date class='text-muted small text-nowrap' lang=lang %} +
  • + {% endfor %} +
+
diff --git a/_layouts/tags.html b/_layouts/tags.html new file mode 100644 index 0000000..7800ca0 --- /dev/null +++ b/_layouts/tags.html @@ -0,0 +1,22 @@ +--- +layout: page +# All the Tags of posts. +--- + +
+ {% assign tags = '' | split: '' %} + {% for t in site.tags %} + {% assign tags = tags | push: t[0] %} + {% endfor %} + + {% assign sorted_tags = tags | sort_natural %} + + {% for t in sorted_tags %} +
+ + {{ t -}} + {{ site.tags[t].size }} + +
+ {% endfor %} +
diff --git a/_layouts/tutorials.html b/_layouts/tutorials.html new file mode 100644 index 0000000..f7648aa --- /dev/null +++ b/_layouts/tutorials.html @@ -0,0 +1,138 @@ +--- +layout: page +# All the Categories of posts +--- + +{% include lang.html %} + +{% assign HEAD_PREFIX = 'h_' %} +{% assign LIST_PREFIX = 'l_' %} + +{% assign group_index = 0 %} + +{% assign sort_categories = site.categories | sort %} + +{% for category in sort_categories %} + {% assign category_name = category | first %} + {% assign posts_of_category = category | last %} + {% assign first_post = posts_of_category | first %} + + {% if category_name == first_post.categories[0] %} + {% assign sub_categories = '' | split: '' %} + + {% for post in posts_of_category %} + {% assign second_category = post.categories[1] %} + {% if second_category %} + {% unless sub_categories contains second_category %} + {% assign sub_categories = sub_categories | push: second_category %} + {% endunless %} + {% endif %} + {% endfor %} + + {% assign sub_categories = sub_categories | sort %} + {% assign sub_categories_size = sub_categories | size %} + +
+ +
+ + + + {% capture _category_url %}/tutorials/{{ category_name | slugify | url_encode }}/{% endcapture %} + {{ category_name }} + + + {% assign top_posts_size = site.categories[category_name] | size %} + + {% if sub_categories_size > 0 %} + {{ sub_categories_size }} + {% if sub_categories_size > 1 %} + {{ + site.data.locales[lang].categories.category_measure.plural + | default: site.data.locales[lang].categories.category_measure + }} + {% else %} + {{ + site.data.locales[lang].categories.category_measure.singular + | default: site.data.locales[lang].categories.category_measure + }} + {% endif -%} + , + {% endif %} + + {{ top_posts_size }} + + {% if top_posts_size > 1 %} + {{ + site.data.locales[lang].categories.post_measure.plural + | default: site.data.locales[lang].categories.post_measure + }} + {% else %} + {{ + site.data.locales[lang].categories.post_measure.singular + | default: site.data.locales[lang].categories.post_measure + }} + {% endif %} + + + + + {% if sub_categories_size > 0 %} + + + + {% else %} + + + + {% endif %} +
+ + + + {% if sub_categories_size > 0 %} +
+
    + {% for sub_category in sub_categories %} +
  • + + + {% capture _sub_ctg_url %}/tutorials/{{ sub_category | slugify | url_encode }}/{% endcapture %} + {{ sub_category }} + + {% assign posts_size = site.categories[sub_category] | size %} + + {{ posts_size }} + + {% if posts_size > 1 %} + {{ + site.data.locales[lang].categories.post_measure.plural + | default: site.data.locales[lang].categories.post_measure + }} + {% else %} + {{ + site.data.locales[lang].categories.post_measure.singular + | default: site.data.locales[lang].categories.post_measure + }} + {% endif %} + +
  • + {% endfor %} +
+
+ {% endif %} +
+ + + {% assign group_index = group_index | plus: 1 %} + {% endif %} +{% endfor %} diff --git a/_site/404.html b/_site/404.html index d560d1f..139a2cf 100644 --- a/_site/404.html +++ b/_site/404.html @@ -231,7 +231,7 @@