All Activity

Merge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_develop

Took Issues Resolved (1 issue) from releases.html 2.11.2.3 row and put

in help/markdown/releases/release-2_11_2_3.md

and regenerated releases.html with

gradle releasesTemplates

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    /help/markdown/releases/release-2_11_2_3.md
JAL-4014 4 gecos colour schemes added to help documentation

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    /help/help/html/colourSchemes/gecos-blossom.html
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    /help/help/html/colourSchemes/gecos-flower.html
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    /help/help/html/colourSchemes/gecos-ocean.html
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    /help/help/html/menus/alignmentMenu.html
Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3

JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3

JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !

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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
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    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j8lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
JWS-128 patch out log4j references in the compbio.FileUtil class, and corresponding calls to methods in the JABAWS client and engine code.

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    /compbio-utils/compbio/util/FileUtil.java
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    /engine/compbio/engine/client/Util.java
Merge branch 'releases/Release_2_11_2_Branch'

JAL-4004 cosmetic improvements for Java documentation renderer

JAL-4004 gradle task releasesTemplates now part of main build dependency tree. Improvements to releases.html.

JAL-4004 working templates and generated whatsNew.html and releases.html file for both browser and Doc viewer

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    /help/help/html/releases.html
JAL-4004 remove stray empty h3 headers

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    /help/markdown/releases/release-2_10_3.md
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    /help/markdown/releases/temp
JAL-4004 gradle releasesTemplates builds releases.html

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    /help/help/html/releases.html
JAL-4004 Temporary mechanism to add JalviewJS link for selected versions to hugo website

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    /utils/hugo/jalviewjs.txt
JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time in release date header

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    /utils/hugo/old_jvl.txt
JAL-4004 Now generating hugo files from help/markdown/...

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    /help/templates/whatsNew.html
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    /utils/hugo/old_task_to_extract_markdown_from_old_releases_html.txt
JAL-4004 existing releases-VERSION.md files and releases.html template

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    /help/markdown/releases/release-2_0.md
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    /help/markdown/releases/release-2_01.md
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    /help/markdown/releases/release-2_1.md
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    /help/markdown/releases/release-2_10_0.md
  1. … 42 more files in changeset.
JAL-4004 locations for markdown to go into whatsnew.html, releases.html and Version-VERSION/_index.md

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    /help/markdown/whatsnew/whatsnew-2_10_2b2.md
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    /help/markdown/whatsnew/whatsnew-2_11_0.md
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    /help/markdown/whatsnew/whatsnew-2_11_1_0.md
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JAL-3989 improved parsing and formatting now using flex CSS layout for columns

JAL-1544 minor errors in releases.html and one missing version (2.8.2b1)

JAL-3989 small improvements to output markdown

JAL-3989 add in issue shortcodes to the archive version page changes list

JAL-1544 version number typo, probably copy and paste

JAL-3989 Populate template files for hugo build: archive version files including changes from releases.html, and installers data file

JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/... This is better in multiple ways including collating files needed for the hugo website and website docroot.

JAL-3989 Independent creation of JSON installer sections

JAL-3978 clean up unnecessary local variables for JALVIEW_VERSION_UNDERSCORES

JAL-3989 Changed to using com.google.common.hash for SHA256 sum, for gradle 7 compatibility

Merge branch 'develop' into improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store

Merge branch 'develop' into merge/JAL-3978+JAL-3553+develop+JAL-3989

Merge branch 'develop' into task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup