From 0a3e026928c7e25c16958bbabfe142d0b0a2dbbd Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 26 Jul 2024 17:02:24 +0100 Subject: [PATCH] JAL-4418 updated release notes and release date to 13 august 2024 --- help/markdown/releases/release-2_11_4_0.md | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/help/markdown/releases/release-2_11_4_0.md b/help/markdown/releases/release-2_11_4_0.md index 0d4017a..43ad48a 100644 --- a/help/markdown/releases/release-2_11_4_0.md +++ b/help/markdown/releases/release-2_11_4_0.md @@ -1,22 +1,38 @@ --- version: 2.11.4.0 -date: 2024-06-30 +date: 2024-08-13 channel: "develop" --- ## New Features +- Calculate PASiMap projection for sequences - ported by Thomas Morell ( U. Konstanz) - Consensus secondary structure visualization for alignments +- Show data source for 'reference annotation' from 3D structure (e.g. Secondary Structure) - Calculate tree or PCA using secondary structure annotation -- Calculate PASiMap projection for sequences - ported by Thomas Morell ( U. Konstanz) - allow adjustment of gap opening, extension, and score model for built in pairwise alignment - +- Jalview sensibly handles opening or a drag'n'drop of several .features, .annotations and .newick files onto an alignment + ### development and deployment +- Add a command-line wrapper script to macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) +- Redirect stdout and stderr to file when launched from getdown +- Add error message when launched directly from Jalview Installer DMG volume +- Allow jalview auto-updates to download to and work from separate user-space directory +- Gradle build with install4j launchers +- Implement in Jalview (and getdown for JVL) the use of specific scheme names for different channels (e.g. jalviewd://) +- integrate OSX codesigning scripts in jalview's repository +- fixed inconsistencies in test suite on different platforms ## Issues Resolved - +- jalview does not fetch from a URL containing a redirect +- HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import +- launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console +- Possible "Zip Slip Vulnerability" in getdown +- jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for --gui and --headless when using certain .jalview_properties +- Release installer DMG does not display the background image +- Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible ### New Known Issues -- 1.7.10.2