JAL-4090 fix up release notes and what’s new (inc removing 2.11.2 cruft from template)

diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md
index 01a54f6..80f8cf4 100644 (file)
--- a/help/markdown/releases/release-2_11_3_0.md
+++ b/help/markdown/releases/release-2_11_3_0.md
@@ -1,40 +1,31 @@
 ---
 version: 2.11.3.0
-date: 2023-07-19
+date: 2023-10-03
 channel: "release"
 ---
 
 ## New Features
 - <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
-- <!-- JAL-4054 --> Installers built with install4j10
-- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
-- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else
-
+- <!-- JAL-3416 --> Jalview now uses a standard 'look and feel' (FlatLaf) on Linux, OSX and everywhere else
 - <!-- JAL-4019 --> Ambiguous Base Colourscheme
 - <!-- JAL-4061 --> Find can search sequence features' type and description
 - <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
 - <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu
 - <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
 - <!-- JAL-4190 --> Pressing escape in tree panel clears any current selection
-
 - <!-- JAL-4089 --> Use selected columns for superposition
 - <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
-
 - <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
 - <!-- JAL-4273 --> Visible adjuster marks to grab and adjust annotation panel height and id width
 - <!-- JAL-4260 --> Adjustable ID margin when alignment is wrapped
-
 - <!-- JAL-4274 --> Command line options and configurable bitmap export preferences for height, width and scale factor
 
 ### Improved support for working with computationally determined models
-
 - <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
 - <!-- JAL-4095 --> Interactive picking of low pAE score regions
 - <!-- JAL-4027 --> contact matrix datatype in Jalview
 - <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
-
 - <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
-
 - <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
 - <!-- JAL-4123 --> GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted
 - <!-- JAL-3914 --> Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
@@ -43,17 +34,17 @@ channel: "release"
 - <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
 - <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
 
-
 ### Jalview on the command line
-
 - <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation.
+- <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
 - <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
 - <!-- JAL-244 --> Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs
 - <!-- JAL-901 --> Specify alignment title on import via --title argument
+- <!-- JAL-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
+- Add a command line option to set Jalview properties for this session only
+- Add a command line option to suppress opening the startup file for this session
 
 ### Other improvements
-
-
 - <!-- JAL-4250 --> Secondary structure annotation glyphs are rendered anti-aliasing when enabled
 - <!-- JAL-325 --> Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track
 - <!-- JAL-4253 --> Lower line of the sequence group border does not align with vertical and background residue box
@@ -61,38 +52,18 @@ channel: "release"
 - <!-- JAL-3119 --> Name of alignment and view included in overview window's title
 - <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
 - <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
-
-- <!-- JAL-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
-Add a command line option to set Jalview properties for this session only
-Add a command line option to suppress opening the startup file for this session
-
-
-JAL-4187        Powershell launcher script fails when given no arguments with the old ArgsParser
-
-known issue ? <!-- JAL-4127    --> 'Reload' for a jalview project results in all windows being duplicated
-
-
-- <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
 - <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
 - <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
 - <!-- JAL-4206 --> Relative files added to recent files list via import from command line are selected when Jalview opened from same location
-
-
-       
-## Still in progress (delete on release)
-
-- <!-- JAL-2382 --> Import and display sequence-associated contact predictions in CASP-RR format
-- <!-- JAL-2349 --> Contact prediction visualisation
-- <!-- JAL-2348 --> modularise annotation renderer
+- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
 
 ### Development and Deployment
-
+- <!-- JAL-4054 --> Installers built with install4j10
 - <!-- JAL-4167 --> Create separate gradle test task for some tests
 - <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
 - <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
 - <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
 
-
 ## Issues Resolved
 - <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
 - <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
@@ -116,10 +87,10 @@ known issue ? <!-- JAL-4127        --> 'Reload' for a jalview project results in all wi
 - <!-- 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))
 
-
 ## New Known defects
 - <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
 - <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
+- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
 - <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
 - <!-- 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)

diff --git a/help/markdown/whatsnew/whatsnew-2_11_3_0.md b/help/markdown/whatsnew/whatsnew-2_11_3_0.md
index cf91e3a..b6c1b0d 100644 (file)
--- a/help/markdown/whatsnew/whatsnew-2_11_3_0.md
+++ b/help/markdown/whatsnew/whatsnew-2_11_3_0.md
@@ -1,4 +1,4 @@
-The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold's standard Blue-Orange-Red confidence colourscheme, and a host of minor improvements and bug fixes.
+The 2.11.3 Jalview release features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold's standard Blue-Orange-Red confidence colourscheme, and a host of [minor improvements and bug fixes](releases.html#Jalview.2.11.3.0)
 
 **Interactive exploration of AlphaFold Predicted Alignment Error Matrices**
 

diff --git a/help/templates/whatsNew.html b/help/templates/whatsNew.html
index 70deea4..301ea4b 100755 (executable)
--- a/help/templates/whatsNew.html
+++ b/help/templates/whatsNew.html
@@ -27,69 +27,5 @@
     <strong>Welcome to Jalview Version __VERSION__ (released __DISPLAY_DATE__)!!</strong><br/>
   </p>
 __WHATS_NEW__
-  <p>
-    The 2.11.2 release series provides support for two popular 3D
-    structure visualisation tools, new features for discovery of 3D
-    structures, improved platform integration and a new command line
-    tool allowing Jalview to be more easily called from scripts.</p>
-
-  <p>
-    <strong>View predicted protein structures via 3D-Beacons</strong> <br>
-    Jalview 2.11.2's <a href="features/structurechooser.html">Structure
-      Chooser includes a client for the 3D-Beacons Network</a>. Launched in
-    2021, the 3D-Beacons network (<a
-      href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
-    provides a central point for the retrieval of predicted and observed
-    3D structures for sequences in Uniprot, including homology models
-    from Swiss-model and deep learning based predictions from the EBI's
-    Alphafold database (Orengo et al. 2020, <a
-      href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
-  </p>
-
-  <p>
-    <strong>Support for viewing structures with ChimeraX and
-      Pymol</strong><br> Jalview's 3D structure viewer system has been
-    re-architected to allow easier integration of external structure
-    viewers, and takes advantage of the strucViz2 Chimera communications
-    library developed by Scooter Morris (<a
-      href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
-    The <a href="features/preferences.html#structure">Structures
-      Preferences tab</a> provides new options allowing ChimeraX and
-    Pymol to be used for visualising external 3D structures. Views
-    from all structure viewers are saved in Jalview Projects, allowing
-    them to be shared with others using Jalview 2.11.2 or later,
-    providing they have the same viewer installed and configured to be
-    used with Jalview.<br/><br/>Jalview
-    2.11.2 has been tested with <strong>Pymol 2.5.0 (community)</strong> and <strong>2.5.2
-    (incentive)</strong>. For <strong>ChimeraX, we recommend using v1.3 or later</strong>.
-  </p>
-  <p>Other highlights include:</p>
-  <ul>
-    <li>Import of annotated DNA and RNA loci via GenBank and EMBL
-      style flatfile</li>
-    <li><strong>Easier configuration of <a
-        href="features/preferences.html#startup">Jalview's memory
-          allocation</a></strong></li>
-    <li>Scripts for <a href="features/commandline.html">running
-        Jalview via the command line</a> on macOS, Linux/Unix and Windows.
-    </li>
-  </ul>
-
-
-  <p>
-      For the full details, see <a
-        href="releases.html#Jalview.2.11.2">the Jalview 2.11.2 series
-        release notes</a>.
-    </p>
-  <p>
-    <strong>Known Issues</strong> <br />The following known issues will
-    be addressed in a minor patch release.
-  
-  <ul>
-    <li>Display of RESNUM sequence features are not suppressed when
-      structures associated with a sequence are viewed with an external
-      viewer (Regression from 2.11.1 series)</li>
-  </ul>
-    <p></p>
 </body>
 </html>