From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 2 Nov 2023 16:02:07 +0000 (+0000)
Subject: JAL-4090 release notes for JAL-4304,JAL-4305 and JAL-3783 and marking JAL-4323 as... 
X-Git-Tag: Release_2_11_4_0~114
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3cf308115d0ad959d36e81f5cc5e9254b69b79e6;p=jalview.git

JAL-4090 release notes for JAL-4304,JAL-4305 and JAL-3783 and marking JAL-4323 as known issue (groovy scripts colourschemes and file formats)
---

diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md
index f7e7b88..f3888cf 100644
--- a/help/markdown/releases/release-2_11_3_0.md
+++ b/help/markdown/releases/release-2_11_3_0.md
@@ -60,6 +60,7 @@ channel: "release"
 - <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
 - <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
 - <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
+- <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
 
 ### Development and Deployment
 - <!-- JAL-4054 --> Installers built with install4j10
@@ -92,6 +93,7 @@ channel: "release"
 - <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
 - <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running
 - <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
+- <!-- JAL-3783 --> Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy
 
 ## New Known defects
 - <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
@@ -103,7 +105,7 @@ channel: "release"
 - <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
 - <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
 - <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
-
+- <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line