jalview

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JAL-3847 Add some dependencies that gradle 7 mildly complains about

JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984

Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop

JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..

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    /src/jalview/gui/TextColourChooser.java
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3983 update release notes for JAL-3973

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

Merge branch 'bug/JAL-3973_source_tarball_not_building' into develop

JAL-3983 release 2.11.2.1 date and release notes

JAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after JvOptionPane action.

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    /src/jalview/gui/FeatureEditor.java
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-3746 bump release date to 10th March - after UoD network maintenance

JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

JAL-3746 JAL-3841 fix README typo

JAL-3746 more docs tweaking and release notes

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    /help/help/html/features/preferences.html
Merge branch 'spike/try_spotless_JAL-3438' into develop

JAL-3746 apply copyright to tests

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    /test/jalview/bin/HiDPISettingTest1.java
  1. … 59 more files in changeset.
JAL-3746 apply copyright to source

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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/fts/api/StructureFTSRestClientI.java
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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /src/jalview/gui/ChimeraXViewFrame.java
  1. … 31 more files in changeset.
JAL-3438 spotless for 2.11.2.0

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    /src/com/stevesoft/pat/ChangeRule.java
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    /src/com/stevesoft/pat/Ctrl.java
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    /src/com/stevesoft/pat/FastBracket.java
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    /src/com/stevesoft/pat/Regex.java
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    /src/com/stevesoft/pat/RegexWriter.java
  1. … 647 more files in changeset.
JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

JAL-3108 updated Ensembl client and model species names

JAL-3746 new release date for 2.11.2

JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes

Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop

JAL-3103 updated help doc to remove default browser choice

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    /help/help/html/features/preferences.html
JAL-3103 Removed code and unused widgets for defaultBrowser

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    /src/jalview/jbgui/GPreferences.java