diff --git a/Makefile b/Makefile new file mode 100644 index 000000000..f99651e0c --- /dev/null +++ b/Makefile @@ -0,0 +1,2 @@ +_config.yml: _config_header.yml registry/ontologies.yml + cat $^ > $@ diff --git a/_config_header.yml b/_config_header.yml new file mode 100644 index 000000000..4a650935b --- /dev/null +++ b/_config_header.yml @@ -0,0 +1,6 @@ +name: Uberon +markdown: redcarpet +pygments: true +baseurl: / +imgurl: /images +speciesAOs: [xao, zfa] diff --git a/_includes/JB/analytics b/_includes/JB/analytics new file mode 100644 index 000000000..2bb4c8028 --- /dev/null +++ b/_includes/JB/analytics @@ -0,0 +1,20 @@ +{% include JB/is_production %} + +{% if is_production and site.JB.analytics.provider and page.JB.analytics != false %} + +{% case site.JB.analytics.provider %} +{% when "gauges" %} + {% include JB/analytics-providers/gauges %} +{% when "google" %} + {% include JB/analytics-providers/google %} +{% when "getclicky" %} + {% include JB/analytics-providers/getclicky %} +{% when "mixpanel" %} + {% include JB/analytics-providers/mixpanel %} +{% when "piwik" %} + {% include JB/analytics-providers/piwik %} +{% when "custom" %} + {% include custom/analytics %} +{% endcase %} + +{% endif %} diff --git a/_includes/JB/analytics-providers/gauges b/_includes/JB/analytics-providers/gauges new file mode 100644 index 000000000..b793ff100 --- /dev/null +++ b/_includes/JB/analytics-providers/gauges @@ -0,0 +1,13 @@ + diff --git a/_includes/JB/analytics-providers/getclicky b/_includes/JB/analytics-providers/getclicky new file mode 100644 index 000000000..e9462f4f6 --- /dev/null +++ b/_includes/JB/analytics-providers/getclicky @@ -0,0 +1,12 @@ + + diff --git a/_includes/JB/analytics-providers/google b/_includes/JB/analytics-providers/google new file mode 100644 index 000000000..9014866a4 --- /dev/null +++ b/_includes/JB/analytics-providers/google @@ -0,0 +1,11 @@ + \ No newline at end of file diff --git a/_includes/JB/analytics-providers/google-universal b/_includes/JB/analytics-providers/google-universal new file mode 100644 index 000000000..834f2eec6 --- /dev/null +++ b/_includes/JB/analytics-providers/google-universal @@ -0,0 +1,9 @@ + \ No newline at end of file diff --git a/_includes/JB/analytics-providers/mixpanel b/_includes/JB/analytics-providers/mixpanel new file mode 100644 index 000000000..4406eb048 --- /dev/null +++ b/_includes/JB/analytics-providers/mixpanel @@ -0,0 +1,11 @@ + \ No newline at end of file diff --git a/_includes/JB/analytics-providers/piwik b/_includes/JB/analytics-providers/piwik new file mode 100755 index 000000000..077a373a4 --- /dev/null +++ b/_includes/JB/analytics-providers/piwik @@ -0,0 +1,10 @@ + \ No newline at end of file diff --git a/_includes/JB/categories_list b/_includes/JB/categories_list new file mode 100644 index 000000000..83be2e290 --- /dev/null +++ b/_includes/JB/categories_list @@ -0,0 +1,37 @@ +{% comment %}{% endcomment %} + +{% if site.JB.categories_list.provider == "custom" %} + {% include custom/categories_list %} +{% else %} + {% if categories_list.first[0] == null %} + {% for category in categories_list %} +
  • + {{ category | join: "/" }} {{ site.categories[category].size }} +
  • + {% endfor %} + {% else %} + {% for category in categories_list %} +
  • + {{ category[0] | join: "/" }} {{ category[1].size }} +
  • + {% endfor %} + {% endif %} +{% endif %} +{% assign categories_list = nil %} \ No newline at end of file diff --git a/_includes/JB/comments b/_includes/JB/comments new file mode 100644 index 000000000..eec2e1e75 --- /dev/null +++ b/_includes/JB/comments @@ -0,0 +1,18 @@ +{% if site.JB.comments.provider and page.comments != false %} + +{% case site.JB.comments.provider %} +{% when "disqus" %} + {% include JB/comments-providers/disqus %} +{% when "livefyre" %} + {% include JB/comments-providers/livefyre %} +{% when "intensedebate" %} + {% include JB/comments-providers/intensedebate %} +{% when "facebook" %} + {% include JB/comments-providers/facebook %} +{% when "duoshuo" %} + {% include JB/comments-providers/duoshuo %} +{% when "custom" %} + {% include custom/comments %} +{% endcase %} + +{% endif %} \ No newline at end of file diff --git a/_includes/JB/comments-providers/disqus b/_includes/JB/comments-providers/disqus new file mode 100644 index 000000000..634310030 --- /dev/null +++ b/_includes/JB/comments-providers/disqus @@ -0,0 +1,15 @@ +
    + + +blog comments powered by Disqus diff --git a/_includes/JB/comments-providers/duoshuo b/_includes/JB/comments-providers/duoshuo new file mode 100644 index 000000000..90865a07c --- /dev/null +++ b/_includes/JB/comments-providers/duoshuo @@ -0,0 +1,14 @@ + +
    + + diff --git a/_includes/JB/comments-providers/facebook b/_includes/JB/comments-providers/facebook new file mode 100644 index 000000000..e1d3debe8 --- /dev/null +++ b/_includes/JB/comments-providers/facebook @@ -0,0 +1,9 @@ +
    + +
    \ No newline at end of file diff --git a/_includes/JB/comments-providers/intensedebate b/_includes/JB/comments-providers/intensedebate new file mode 100644 index 000000000..233ce3410 --- /dev/null +++ b/_includes/JB/comments-providers/intensedebate @@ -0,0 +1,6 @@ + + diff --git a/_includes/JB/comments-providers/livefyre b/_includes/JB/comments-providers/livefyre new file mode 100644 index 000000000..704b80392 --- /dev/null +++ b/_includes/JB/comments-providers/livefyre @@ -0,0 +1,6 @@ + + \ No newline at end of file diff --git a/_includes/JB/feedburner b/_includes/JB/feedburner new file mode 100644 index 000000000..6dba60352 --- /dev/null +++ b/_includes/JB/feedburner @@ -0,0 +1,3 @@ +{% if site.author.feedburner != null %} + +{% endif %} diff --git a/_includes/JB/file_exists b/_includes/JB/file_exists new file mode 100644 index 000000000..f40080f1e --- /dev/null +++ b/_includes/JB/file_exists @@ -0,0 +1,26 @@ +{% comment %}{% endcomment %} + +{% assign file_exists_result = false %} + +{% if include.file %} + {% for static_file in site.static_files %} + {% if static_file.path == include.file %} + {% assign file_exists_result = true %} + {% break %} + {% endif %} + {% endfor %} +{% endif %} diff --git a/_includes/JB/gist b/_includes/JB/gist new file mode 100644 index 000000000..38a5b1ca0 --- /dev/null +++ b/_includes/JB/gist @@ -0,0 +1,19 @@ +{% comment %}{% endcomment %} + +
    + + +
    diff --git a/_includes/JB/is_production b/_includes/JB/is_production new file mode 100644 index 000000000..3548f8c3d --- /dev/null +++ b/_includes/JB/is_production @@ -0,0 +1,39 @@ +{% capture jbcache %}{% comment %} + + Determine whether or not the site is being built in a production environment. + + Parameters: + None. + + Returns: + is_production: [true|false] + jb_prod_env: [development|github|other] + + Examples: + + {% include JB/is_production %} + + {% if is_production != true %} +

    This is Private

    +

    I love to watch television in my undies. Don't tell anyone!

    + {% endif %} + +

    This is Public

    +

    I have no unusual quirks.

    + +{% endcomment %} + +{% assign is_production = false %} +{% assign jb_prod_env = "development" %} + +{% if jekyll.environment != "development" %} + {% assign is_production = true %} + {% assign jb_prod_env = jekyll.environment %} +{% endif %} + +{% if site.github %} + {% assign is_production = true %} + {% assign jb_prod_env = "github" %} +{% endif %} + +{% endcapture %}{% assign jbcache = nil %} \ No newline at end of file diff --git a/_includes/JB/liquid_raw b/_includes/JB/liquid_raw new file mode 100644 index 000000000..da2d3590f --- /dev/null +++ b/_includes/JB/liquid_raw @@ -0,0 +1,32 @@ +{% comment%}{% endcomment%} + +{% if site.JB.liquid_raw.provider == "custom" %} + {% include custom/liquid_raw %} +{% else %} +
    {{text | replace:"|.", "{" | replace:".|", "}" | replace:">", ">" | replace:"<", "<" }}
    +{% endif %} +{% assign text = nil %} \ No newline at end of file diff --git a/_includes/JB/pages_list b/_includes/JB/pages_list new file mode 100644 index 000000000..42f827a8c --- /dev/null +++ b/_includes/JB/pages_list @@ -0,0 +1,39 @@ +{% comment %}{% endcomment %} + +{% if site.JB.pages_list.provider == "custom" %} + {% include custom/pages_list %} +{% else %} + {% for node in pages_list %} + {% if node.title != null %} + {% if group == null or group == node.group %} + {% if page.url == node.url %} +
  • {{node.title}}
  • + {% else %} +
  • {{node.title}}
  • + {% endif %} + {% endif %} + {% endif %} + {% endfor %} +{% endif %} +{% assign pages_list = nil %} +{% assign group = nil %} \ No newline at end of file diff --git a/_includes/JB/posts_collate b/_includes/JB/posts_collate new file mode 100644 index 000000000..f612ade87 --- /dev/null +++ b/_includes/JB/posts_collate @@ -0,0 +1,55 @@ +{% comment %}{% endcomment %} + +{% if site.JB.posts_collate.provider == "custom" %} + {% include custom/posts_collate %} +{% else %} + {% for post in posts_collate %} + {% capture this_year %}{{ post.date | date: "%Y" }}{% endcapture %} + {% capture this_month %}{{ post.date | date: "%B" }}{% endcapture %} + {% capture next_year %}{{ post.previous.date | date: "%Y" }}{% endcapture %} + {% capture next_month %}{{ post.previous.date | date: "%B" }}{% endcapture %} + + {% if forloop.first %} +

    {{this_year}}

    +

    {{this_month}}

    + + {% else %} + {% if this_year != next_year %} + +

    {{next_year}}

    +

    {{next_month}}

    + +

    {{next_month}}

    +