build.gradle

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JAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate entries in the tarball

Append git.hash and git.branch to RELEASE file stored in tarball. When compiling, if not in git repo use git.branch and git.hash from RELEASE file.

JAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)

JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2

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JAL-3830 fix broken/buggy install4j9 setting of executeSetupApp=false still running setupApp

JAL-3830 temporarily disable the setup screen for OSX dmgs until we can properly document its use

JAL-3823 JAL-3830 update gradle plugin for install4j to 9.0.6

JAL-3553: Create working getdown appbase and jvl file(s) for each old version of Jalview
JAL-3553: Create working getdown appbase and jvl file(s) for each old version of Jalview
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application

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Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop

Conflicts:

src/jalview/bin/MemorySetting.java

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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-3850 fixed full class name

JAL-3850 using reflection for SimpleHttpFileServerFactory

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-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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