Prep for release: bump version, rebuild docs, cleanup

akoyabio · Aug 18, 2021 · 529e16e · 529e16e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: phenoptrReports
 Title: Create reports using Phenoptics data
-Version: 0.2.13.9000
-Date: 2021-06-10
+Version: 0.3.0
+Date: 2021-08-18
 Authors@R: c(
     person("Kent S", "Johnson", role = c("aut", "cre"),
            email = "kjohnson@akoyabio.com"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,15 +1,16 @@
-# phenoptrReports 0.2.13.9000
-
-Staining consistency report:
-- New addin creates a report showing mean expression of a selected marker
-  across multiple samples.
+# phenoptrReports 0.3.0
+**2021-08-18**
 
 Mean of top 20 / bottom 10 addin:
 - New addin helps to evaluate whether the staining quality is
   likely to produce good unmixing. See 
   https://akoyabio.github.io/phenoptrReports/articles/top_20_bottom_10_report.html
   for details.
 
+Staining consistency report:
+- New addin creates a report showing mean expression of a selected marker
+  across multiple samples.
+
 Analysis addin:
 - Fix problem computing mean expression for phenotypes with formulas 
   in their definition #47

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -20,6 +20,10 @@ navbar:
           href: articles/spatial_map_viewer.html
         - text: "Unmixing quality report"
           href: articles/unmixing_quality_report.html
+        - text: "Mean of top 20 / bottom 10 cells report"
+          href: articles/top_20_bottom_10_report.html
+        - text: "Staining consistency report"
+          href: articles/staining_consistency_report.html
     - text: "Reference"
       href: reference/index.html
   right:
@@ -83,8 +87,9 @@ reference:
   - title: Data reporting - HTML
     desc: These functions write analysis results to HTML reports.
     contents:
-      - unmixing_quality_report
       - component_levels_report
+      - staining_consistency_report
+      - unmixing_quality_report
       - write_summary_report
   - title: Data reporting - Excel and Word
     desc: These functions write analysis results to Excel worksheets

diff --git a/docs/404.html b/docs/404.html
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/analysis_files/header-attrs-2.9/header-attrs.js b/docs/articles/analysis_files/header-attrs-2.9/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/component_levels_report.html b/docs/articles/component_levels_report.html
diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html
diff --git a/docs/articles/consolidation_files/header-attrs-2.9/header-attrs.js b/docs/articles/consolidation_files/header-attrs-2.9/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});