Merge branch 'develop' into releases/Release_2_11_3_Branch

diff --git a/RELEASE b/RELEASE
index cfbbf93..a5d5f52 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_3_Branch
-jalview.version=2.11.3.0
+jalview.version=2.11.3.1

diff --git a/build.gradle b/build.gradle
index 011be67..3b81404 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -2240,9 +2240,9 @@ task getdownImages() {
   dependsOn getdownImagesProcess
 }
 
-task getdownWebsite() {
+task getdownWebsiteBuild() {
   group = "distribution"
-  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
+  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer. No digest is created."
 
   dependsOn getdownImages
   if (buildDist) {
@@ -2354,7 +2354,7 @@ task getdownWebsite() {
           from s
           into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
         }
-        getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+        getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}"
       }
     }
 
@@ -2496,7 +2496,9 @@ task getdownDigestDir(type: JavaExec) {
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
-  dependsOn getdownWebsite
+
+  dependsOn getdownWebsiteBuild
+
   doFirst {
     classpath = files(getdownLauncher)
   }
@@ -2529,12 +2531,19 @@ task getdown() {
   }
 }
 
+task getdownWebsite {
+  group = "distribution"
+  description = "A task to create the whole getdown channel website dir including digest file"
+
+  dependsOn getdownWebsiteBuild
+  dependsOn getdownDigest
+}
 
 task getdownArchiveBuild() {
   group = "distribution"
   description = "Put files in the archive dir to go on the website"
 
-  dependsOn getdownWebsite
+  dependsOn getdownWebsiteBuild
 
   def v = "v${JALVIEW_VERSION_UNDERSCORES}"
   def vDir = "${getdownArchiveDir}/${v}"

diff --git a/help/markdown/releases/release-2_11_3_1.md b/help/markdown/releases/release-2_11_3_1.md
new file mode 100644 (file)
index 0000000..23f6abf
--- /dev/null
+++ b/help/markdown/releases/release-2_11_3_1.md
@@ -0,0 +1,16 @@
+---
+version: 2.11.3.1
+date: 2023-11-30
+channel: "release"
+---
+
+## New Features
+
+- <!-- JAL-4243 --> bio.tools record for jalview updated and synced with json in source release
+
+## Issues Resolved
+
+- <!-- JAL-4340 --> Getdown does not preserve executable permission of jalview.sh file when it gets updated
+
+### New Known Issues
+

diff --git a/utils/biotools/Jalview.json b/utils/biotools/Jalview.json
index 69aa95c..760eaa7 100644 (file)
--- a/utils/biotools/Jalview.json
+++ b/utils/biotools/Jalview.json
@@ -5,7 +5,7 @@
   "biotoolsID": "Jalview",
   "biotoolsCURIE": "biotools:Jalview",
   "version": [
-    "2.11.2.7"
+    "2.11.3.0"
   ],
   "relation": [
     {
@@ -233,11 +233,12 @@
           ]
         }
       ],
-      "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\n\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);"
+      "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);"
     }
   ],
   "toolType": [
-    "Desktop application"
+    "Desktop application",
+    "Command-line tool"
   ],
   "topic": [
     {
@@ -255,6 +256,9 @@
     "Mac"
   ],
   "license": "GPL-3.0",
+  "collectionID": [
+    "ELIXIR-UK"
+  ],
   "maturity": "Mature",
   "cost": "Free of charge",
   "accessibility": "Open access",
@@ -363,7 +367,7 @@
         "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench",
         "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).",
         "date": "2009-05-07T00:00:00Z",
-        "citationCount": 5999,
+        "citationCount": 6209,
         "authors": [
           {
             "name": "Waterhouse A.M."
@@ -403,7 +407,7 @@
   ],
   "owner": "ben_s",
   "additionDate": "2019-02-13T17:01:40Z",
-  "lastUpdate": "2023-07-22T09:24:44.755337Z",
+  "lastUpdate": "2023-11-16T19:51:39.349417Z",
   "editPermission": {
     "type": "group",
     "authors": [