From 3cf308115d0ad959d36e81f5cc5e9254b69b79e6 Mon Sep 17 00:00:00 2001 From: James Procter Date: Thu, 2 Nov 2023 16:02:07 +0000 Subject: [PATCH] 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) --- help/markdown/releases/release-2_11_3_0.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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" - Reduce number of database crossreferences shown in tooltip - Drag and drop feature colours file on an alignment to quickly apply feature settings - Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button +- Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly. ### Development and Deployment - Installers built with install4j10 @@ -92,6 +93,7 @@ channel: "release" - SLF4J produces an error to STDERR at Jalview startup due to missing class - macOS Dock and KDE taskbar names Jalview icon "java" when running - HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2)) +- 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 - 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" - Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export - Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x) - Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation - +- scripts adding new fileformats or colourschemes do not work when run via command line -- 1.7.10.2