Update version to 0.1.5, rebuild docs

akoyabio · Jan 25, 2019 · 29f50bc · 29f50bc
1 parent 3a3a509
commit 29f50bc
Show file tree

Hide file tree

Showing 55 changed files with 142 additions and 115 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: phenoptrReports
 Title: Create reports using Phenoptics data
-Version: 0.1.4.9000
+Version: 0.1.5
 Date: 2018-11-05
 Authors@R: c(
     person("Kent S", "Johnson", role = c("aut", "cre"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,5 @@
-# phenoptrReports 0.1.4.9000
+# phenoptrReports 0.1.5
+**2019-01-25**
 
 New features:
 - The "Merge cell seg files" addin now supports searching sub-directories

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html
diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
@@ -65,7 +65,7 @@ summary {
 
 /* Typographic tweaking ---------------------------------*/
 
-.contents h1.page-header {
+.contents .page-header {
   margin-top: calc(-60px + 1em);
 }
 

diff --git a/docs/pkgdown.js b/docs/pkgdown.js
@@ -25,6 +25,10 @@
     for (var i = 0; i < links.length; i++) {
       if (links[i].getAttribute("href") === "#")
         continue;
+      // Ignore external links
+      if (links[i].host !== location.host)
+        continue;
+
       var nav_path = paths(links[i].pathname);
 
       var length = prefix_length(nav_path, cur_path);
@@ -52,13 +56,14 @@
     return(pieces);
   }
 
+  // Returns -1 if not found
   function prefix_length(needle, haystack) {
     if (needle.length > haystack.length)
-      return(0);
+      return(-1);
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return(needle.length === 0 ? 0 : -1);
     }
 
     for (var i = 0; i < haystack.length; i++) {

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
 pandoc: 1.19.2.1
-pkgdown: 1.2.0
+pkgdown: 1.3.0
 pkgdown_sha: ~
 articles:
   analysis: analysis.html

diff --git a/docs/reference/add_tissue_category_totals.html b/docs/reference/add_tissue_category_totals.html
diff --git a/docs/reference/addin_10_merge.html b/docs/reference/addin_10_merge.html
diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html
diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html
diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html
diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html