Ben Soares <b.soares@dundee.ac.uk>: Author Summary
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GDBI › #21 | 3 months ago |
JAL-4186 fixed a test
JAL-4186 fix dialog. broken in JalviewJS
JAL-4186 attempts to work in jalviewjs, still not working
JAL-4186 Turn JvOptionPane Callable<Void> handlers back into Runnable for jalviewjs (now working)
|
Testless build |
| JB › GPC › #241 | 1 day ago |
JAL-4265 Use ColourUtils.parseColourString() for consistency with the rest of Jalview (and it's better). Change documentation to match new hexstring format
JAL-4265 Use ColorUtils.parseColourString() and adjust documentation to use un-hashed hex-string for consistency with other Jalview uses of parseColourString(). When adding 2 structures and 2 structureimages I am now getting a NPE for String[] files = getStructureFiles(); in AAStructureBindingModel, and when using bgcolour for the first structureimage, losing the residues in the second structure image. Will need to investigate when I'm back
|
Testless build |
| JB › GJB › #337 | 1 day ago |
JAL-4265 Use ColorUtils.parseColourString() and adjust documentation to use un-hashed hex-string for consistency with other Jalview uses of parseColourString(). When adding 2 structures and 2 structureimages I am now getting a NPE for String[] files = getStructureFiles(); in AAStructureBindingModel, and when using bgcolour for the first structureimage, losing the residues in the second structure image. Will need to investigate when I'm back
JAL-4265 Use ColourUtils.parseColourString() for consistency with the rest of Jalview (and it's better). Change documentation to match new hexstring format
|
Testless build |
| JB › GDB › #558 | 1 day ago |
JAL-4265 Use ColorUtils.parseColourString() and adjust documentation to use un-hashed hex-string for consistency with other Jalview uses of parseColourString(). When adding 2 structures and 2 structureimages I am now getting a NPE for String[] files = getStructureFiles(); in AAStructureBindingModel, and when using bgcolour for the first structureimage, losing the residues in the second structure image. Will need to investigate when I'm back
JAL-4265 Use ColourUtils.parseColourString() for consistency with the rest of Jalview (and it's better). Change documentation to match new hexstring format
|
1674 passed |
| JB › GDC › #169 | 1 week ago |
JAL-4001 corrected analytics message labels
|
Testless build |
| JB › GDC › #168 | 2 weeks ago |
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-4255 better grammar
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
JAL-3830 Take account of --gui taking precedence over --headless
JAL-629 Fix --structureimage and options
JAL-3820 add java and java.exe from JAVAHOME to list of likely JVMs
JAL-629 STDOUT documentation. Opt.STDOUT narrower option. Fix for subvals and STDOUT detection.
Merge branch 'bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'features/r2_11_2_alphafold/JAL-629' into develop
JAL-4255 Updated THIRDPARTYLIBS
JAL-244 testing without AlignFrame for --wrap
JAL-629 Much better way of dealing with list of filenames/URLs without an --open argument. Added tests for these and fixed multiple STDOUT files.
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-629 Small buglet with getting --seqid
JAL-244 Allow wrap manual adjustments to be smaller than the actual id widths.
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-629 Save structure frames in project files when opened and saved in headless mode
JAL-4160 JAL-3830 Improvements to the jalview.sh bash script especially when not in .app bundle on mac.
Merge branch 'improvement/JAL-4212_remove_macos_test_java_icons' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-629 Method to use for printStackTrace
JAL-244 Fixed idWidth labels in headless mode for non-wrap alignments
JAL-629 more tests for stdout
Merge branch 'develop' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-4001 remove stray --headless mode analytic
Merge branch 'task/JAL-4001_Plausible_API' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
JAL-3830 Look for --headless mode and add -Djava.awt.headless=true to java invocation to remove icon from dock in macos
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-4212 set no-macos-java-icon property if on macos in the testTasks
JAL-244 Allow adjusting Id column width in wrap mode. Set Id column width in gui and image output with --wrap mode.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-3830 Remove dock icon for -h too
JAL-4206 Use All Known Alignment Files as default until a file is loaded
JAL-4214 Make modal internal frame disappear when main menu clicked on linux to avoid a hanging bug
JAL-4214 Linux only: Disable menus when internal modal is open but allow menu accelerators to go through
JAL-629 Add accessors for argParser and bootstrapArgs
JAL-244 Adjust wrapped alignment widths to always maintain a visible wrapped sequence width (and also avoid zero divisions)
JAL-244 Fix mismatched vertical positioning of sequences and their labels in wrap mode with margin adjustment enabled
JAL-244 Fix window size narrow adjustment not becoming a manual adjustment clash
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-244 Changes to Annotation labels width now adjusts the overall idWidth if larger than the alignment idWidth. Will not shrink the width if a manual adjustment has been made. Can be overridden by preference. Also fixed buglet of scroll bar not adjusting with manual changes to idWidth.
Merge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-244 test files
JAL-3416 Don't forget java bin in the correct java home
JAL-244 Fix buglet with automatic change in id column width not being recorded. More tests includeing wrapped format.
JAL-244 More accurate width calculation, allow increased id width adjustment after manual adjustment
JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console.errPrintln. Fix command line tests. Add test for STDOUT output file.
Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-4242 null check on getValue() return
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-4255 Added slf4j-nop jar and upgraded to last 1.x release
JAL-4214 Close modal internal frame if JRootPane activity detected. Problem with re-opened modal internal frame afterwards
Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
JAL-629 Avoid hidden options dialog when saving in headless mode
JAL-629 Default to FASTA if no format given for output to STDOUT
JAL-244 Avoid working on the Ids Graphics object when we don't mean to
Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
JAL-3416 flatlaf and flatlaf-extras 3.2 jars
Merge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
Merge branch 'develop' into improvement/JAL-4212_remove_macos_test_java_icons
Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-3416 Remove full height separators between new curved tabs
JAL-629 Enable output to STDOUT when specifying output filename as '-'. Must check other output is suppressed.
JAL-3830 JAL-3421 Conda launch script for 2.11.3 and new CLI with OS compatibility from installer launch script
JAL-4026 if relative path in recently opened exists from PWD, use it.
JAL-244 More control of automatic idWidth adjustments. Added tests.
JAL-244 Added light grey marks to indicate regions to resize the margins
Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode
Merge branch 'develop' into merge/big_merge_of_bens_stuff_before_2_11_3_0
JAL-629 Move more stdout messages to stderr when outputting file to stdout
Merge branch 'develop' into improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf
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Testless build |
| JB › GTC › #6 | 1 month ago |
JAL-4001 Added a genuine client_id (from gtag). Added /debug/mp/collect with response content
JAL-4513 now re-add the SwingUtilities.invokeAndWait() with minimal sleep
JAL-4001 Only send defaultParams for application_launch event
JAL-4001 Added a random id to User-Agent to ensure separate visits recorded in Plausible. Changed default URL to self-hosted site
JAL-4001 Check --nousagestats before doing analytics in headless mode
JAL-4001 Trying to see extra information in GA dashboard
JAL-3599 increase real and virtual time chrome runs for to 60s (in real-time this is still about 3s)
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
JAL-3599 Cater for macOS. ScheduledExecutor timeout implemented
JAL-3599 Updated default eclipse to 'latest' and made jalviewjsLaunchTest timeouts a bit more flexible
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
JAL-4513 add a SwingUtilities.invokeAndWait() to see what happens
JAL-3599 gradle tasks to test JalviewJS launches in a chrome or chromium browser
JAL-4001 Plausible class
JAL-4513 move comments
Merge branch 'develop' into task/JAL-4001_Plausible_API
JAL-3599 Tidyup for all OS to use ScheduledExecutor
Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
JAL-4019 corrected to '>' to '>=' for percentage comparisons
JAL-3599 --no-sandbox --disable-gpu and Thorium flatpak on build server
JAL-4001 Working Plausible analytics
JAL-4001 change Plausible discovery URL
JAL-4001 Added 'installation' property.
JAL-4513 reduce wait to invoke fail
JAL-3416 FlatLaf SystemInfo failing in JalviewJS. Look and Feel not relevant to JalviewJS so setLookAndFeel commented out for j2s with @j2sIgnore
JAL-4001 Remove jgoogleanalytics code and jar
JAL-4001 Rationalise user-agent string into HttpUtils
JAL-4001 Fix default API url
JAL-4001 Added useful props information
JAL-4001 rename the init method
JAL-4001 Added lookup to https://www.jalview.org/config/analytics/url to check API base url. Changed terminology to match Plausible API
JAL-4001 Change wording from google to plausible or generic analytics
JAL-3599 Cater for macOS. --timeout not working yet
JAL-3599 More stderr/stdout output to logs when failed
JAL-3599 Not redirecting STDOUT or STDERR just for build server debuggin
JAL-3599 replaced a build dependency for jalviewjsLaunchTest
JAL-3599 Deliberate NPE to see if build plan fails
JAL-4001 remove headless code from analytics
JAL-4001 Remove analytics for --headless mode
JAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest. Change jalviewjsLaunchTest to only stop the task (not trigger a failure) if chrome not found. Remove deliberate NPE.
JAL-4001 Add a _geo=1 to query string and JSON. Add a headless flag to path and JSON, and send analytics in headless mode if USAGESTATS=true.
JAL-3599 More stderr/stdout output to logs when anything
JAL-4001 Changed for Java 8 compatibility
JAL-3599 fixed placement of 'First Run' file for chromium profile
JAL-3599 STDOUT and STDERR saved and sent to System.out/err
JAL-4001 make page_location the same encoding as the old jgoogleanalytics
|
Testless build |
| JB › GGR › #7 | 6 months ago |
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
JAL-629 Add debug messages for more failing tests
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args
JAL-629 test fixing
JAL-629 refactoring TFType. Remove i18n identification of annotation.
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.
JAL-1988 Add a sleep to file save test to give time for file to save
JAL-629 nf-core sample alignment files and a2m versions
JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.
JAL-3416 Fix file permissions on bundled macOS JREs
JAL-629 "updated" json-simple
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
JAL-3416 No longer needed
JAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents' for mac JRE bundles for install4j (not strictly used, but might be in the future).
JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold
JAL-629 fix a PAEMatrix casting error
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-629 make sequence id key 'seqid'
JAL-629 better test fixes. --props=... instead of --debug
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-4125 Spanish translations
JAL-629 fixed a Log4j test by adding --debug arg
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
JAL-4118 remove unnecessary sleep from QuitHandlerTest
JAL-629 example files from nf-core
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
JAL-629 helper eclipse CLI run
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI in Linux and Java 8 - Some GUI parts unusable
Merge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels
JAL-3416 remove a missed panel titlebar icon in TreePanel
JAL-3416 More explicit setting of FlatLaf macOS theme
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
|
Testless build |
| JB › GDI › #11 | 7 months ago |
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
JAL-3416 Added logoIcon to quit (and potentially other) dialogs
JAL-4019 Clarification of position on 'X' in help text
JAL-4019 Put original test back
JAL-3416 make flatlaf default for linux
JAL-4125 Spanish translations
JAL-4019 Help pages for Nucleotide Ambiguity colour scheme
JAL-4064 Download JRE/JDKs from Azul if not os/arch combination not available from Adoptium
JAL-3416 Fix file permissions on bundled macOS JREs
JAL-1988 Add a sleep to file save test to give time for file to save
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-4054 Altered file association templates and generated install4j xml and Info.plist snippets.
JAL-4019 small but important corrections to array order, and X colour
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
JAL-4118 remove unnecessary sleep from QuitHandlerTest
JAL-3416 More explicit setting of FlatLaf macOS theme
JAL-4064 re-added bundled macOS JREs as Filesets, which is the only way to get them in the DMG where we want them
JAL-3416 Remove all JFrame/JInternalFrame icons (set to null)
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
JAL-4019 improvement to short sequence nucleotide detection, and some tidying of unused parameters
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
JAL-4101 Updated Rfam* tests
JAL-3416 Add necessary logo to non-internal Frames
JAL-3416 Start to add JInternalFrame icons (to replace default java Duke icon in frame decoration)
JAL-3416 File Chooser iconified, JvOptionPanes iconified, other internal frames and dialogs iconified
JAL-4019 Nucleotide Ambiguity Colour Scheme added. Test for nucleotide sequence adapted to recognise nucleotide sequences with (more than 15%) ambiguity codes. Two tests fixed.
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
JAL-3416 remove a missed panel titlebar icon in TreePanel
JAL-4019 attribution to Suzanne
JAL-3416 Add necessary logo to non-internal Frames
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
JAL-4064 tidying build.gradle
JAL-3416 More JInternalFrame icons
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
JAL-4101 Updated Rfam* tests
JAL-4101 Updated DEFAULT_RFAM_BASEURL
JAL-4019 Make diagnostic message debug level
JAL-4064 Cleaned up file sets in install4j template. New media installers for AARCH64 JVMs for macOS and Linux in install4j template. New variables passed to install4j by gradle.
JAL-1988 JAL-3772 Tidying of unspecified Callable declarations. Use SwingUtilities.getAncestorOfClass()
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
JAL-3416 No longer needed
JAL-1988 JAL-3772 Change default alignmentviewport saved status and set to true when loaded from file
JAL-4019 finalised a boolean option and tidied some comments
JAL-4064 JAL-4054 Combined install4j10 template with new architectures. Added scheme associations for macOS.
JAL-4019 Added tests for new Nucleotide sequence detection
JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.
JAL-4019 small colour fix for X in the documentation
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
JAL-4101 Updated DEFAULT_RFAM_BASEURL
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Testless build |
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GGR › #7 | 6 months ago |
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
JAL-629 Add debug messages for more failing tests
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args
JAL-629 test fixing
JAL-629 refactoring TFType. Remove i18n identification of annotation.
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.
JAL-1988 Add a sleep to file save test to give time for file to save
JAL-629 nf-core sample alignment files and a2m versions
JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.
JAL-3416 Fix file permissions on bundled macOS JREs
JAL-629 "updated" json-simple
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
JAL-3416 No longer needed
JAL-4064 JAL-4054 Corrected the tgz top-level dir from './Contents' to 'Contents' for mac JRE bundles for install4j (not strictly used, but might be in the future).
JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file.
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold
JAL-629 fix a PAEMatrix casting error
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-629 make sequence id key 'seqid'
JAL-629 better test fixes. --props=... instead of --debug
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
JAL-4125 Spanish translations
JAL-629 fixed a Log4j test by adding --debug arg
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
JAL-4118 remove unnecessary sleep from QuitHandlerTest
JAL-629 example files from nf-core
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
JAL-629 helper eclipse CLI run
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI in Linux and Java 8 - Some GUI parts unusable
Merge branch 'develop' into improvement/JAL-4111_suffixed_DEVELOP_channels
JAL-3416 remove a missed panel titlebar icon in TreePanel
JAL-3416 More explicit setting of FlatLaf macOS theme
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
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Testless build |
| Build | Completed | Code commits | Tests |
|---|