build.gradle

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JAL-3753 avoid appending unreplaced html content in help pages

JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

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JAL-3553 added filesize to json

JAL-3553 now creating a json file for use on website. It's easier to parse all the info here than on the website!

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JAL-3923 JAL-3878 disable clover for CI builds

JAL-3553 copy sha256sums to a versioned filename too when created

JAL-3553 improve the labels in install4j's output.txt and make a versioned filename output-JALVIEW_VERSION.txt

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JAL-3830 install4j9 tries to parse and can't cope with the hyphens and filename format of the jre-VERSION-OS-ARCH.tar.gz JRE tar files, so using underscores in symbolic links

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JAL-3907 adjusted download_jdks.sh and download_jres.sh scripts to use adoptium and added Java 17 download. Added JAVA_VERSION=17 as a gradle build property option.

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JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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JAL-3874 attempt to add source jars to eclipse through buildship

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JAL-3871 replaced Jmol with zip -F version fo Jmol and added excludeDuplicates flags to build.gradle

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JAL-3850 fixed full class name

JAL-3850 using reflection for SimpleHttpFileServerFactory

JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

Merge branch 'develop' into improvement/JAL-3830_macOS_bundle_wrapper

JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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JAL-3633 getdown reads jalview_properties for proxy settings

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JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

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JAL-3830 add the windows bash script to getdown files and install4j installers

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JAL-3830 improved bash scripts. Added powershell script. Needs testing

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JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

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JAL-3830 install4j adds script to Jalview.app/Contents/MacOS/jalview but we need install4j9 to make it executable

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