Bump version to 0.2.10 and rebuild docs

akoyabio · Nov 11, 2020 · 995fc78 · 995fc78
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: phenoptrReports
 Title: Create reports using Phenoptics data
-Version: 0.2.9.1
-Date: 2020-08-22
+Version: 0.2.10
+Date: 2020-11-11
 Authors@R: c(
     person("Kent S", "Johnson", role = c("aut", "cre"),
            email = "kjohnson@akoyabio.com"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# phenoptrReports 0.2.10
+**2020-11-11**
+
+Consolidate and summarize addin:
+- Reduce memory use to allow consolidation of larger files
+
+Bug fixes:
+- Nearest neighbor and count within summaries work correctly 
+  if detailed data is not requested.
+- Correctly double-escape *all* backslashes in the slide id prefix.
+- Improved error checks and error messages
+
 # phenoptrReports 0.2.9
 **2020-08-22**
 

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-2.3/header-attrs.js b/docs/articles/analysis_files/header-attrs-2.3/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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html
diff --git a/docs/articles/consolidation_files/header-attrs-2.3/header-attrs.js b/docs/articles/consolidation_files/header-attrs-2.3/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/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/index.html b/docs/articles/index.html
diff --git a/docs/articles/spatial_map_viewer.html b/docs/articles/spatial_map_viewer.html
diff --git a/docs/articles/spatial_map_viewer_files/header-attrs-2.3/header-attrs.js b/docs/articles/spatial_map_viewer_files/header-attrs-2.3/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]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html
diff --git a/docs/articles/unmixing_quality_report_files/header-attrs-2.3/header-attrs.js b/docs/articles/unmixing_quality_report_files/header-attrs-2.3/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/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/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.yml b/docs/pkgdown.yml
@@ -1,12 +1,12 @@
-pandoc: 2.7.3
+pandoc: 2.9.2.1
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   analysis: analysis.html
   consolidation: consolidation.html
   spatial_map_viewer: spatial_map_viewer.html
   unmixing_quality_report: unmixing_quality_report.html
-last_built: 2020-09-22T19:27Z
+last_built: 2020-11-11T20:35Z
 urls:
   reference: http://akoyabio.github.io/phenoptrReports/reference
   article: http://akoyabio.github.io/phenoptrReports/articles

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_35_spatial_map_viewer.html b/docs/reference/addin_35_spatial_map_viewer.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
diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html
diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html
diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html
diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html
diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html
diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html
diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html
diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html