gradle.properties

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Merge branch 'develop' into task/JAL-3796_notarization_no_uninstaller

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Merge branch 'develop' into task/JAL-3796_notarization

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JAL-3796 update to Install4j 8.0.10 and add config for code notarization

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JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

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JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

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JAL-3789 First attempt for configurable property to look at

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JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

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JAL-3594 New way for build.gradle to override properties with channel based properties files. Starting to tidy up some old image files

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Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

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JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

JAL-3753 JAL-3754 first rejig

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JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest. This key is completely ignored by the getdown-launcher. Looks in j8/j11digestonly.

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JAL-3658 Now only making cores from utils/jalviewjs/classlists/*.txt

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Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

gradle.properties

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/structures/JalviewStructureDisplayI.java

src/jalview/appletgui/AppletJmol.java

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/rbvi/chimera/AtomSpecModel.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AppJmol.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/gui/StructureViewerBase.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/jmol/JmolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/structures/models/AAStructureBindingModelTest.java

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JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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JAL-3225 small fixes for building within Eclipse

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JAL-3225 small fixes for building within Eclipse

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JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity

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JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity

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JAL-3541 selectively merged build.gradle and gradle.properties

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JAL-3541 Added mem setting and jvmArgs for cloverReporting

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JAL-3541 Added mem setting and jvmArgs for cloverReporting

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JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.

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JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.

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JAL-3602 Added configuration for enforced use of UTF-8 for creating the core js files and also in the closure-compiler.

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