Ben Soares <b.soares@dundee.ac.uk>: Author Summary

Builds triggered by Ben Soares <b.soares@dundee.ac.uk>

Builds triggered by an author are those builds which contains changes committed by the author.
5
1 (20%)
4 (80%)

Breakages and fixes

Broken means the build has failed but the previous build was successful.
Fixed means that the build was successful but the previous build has failed.
1 (20% of all builds triggered)
0 (0% of all builds triggered)
-1
Build Completed Code commits Tests
JB › GDBI › #21 9 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 › GDC › #188 1 month ago
JAL-4290 Add method to allow for specific settings. Revert setting show annotations.
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' of https://source.jalview.org/git/jalview into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
JAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file
Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
JAL-4290 incorrect usage of main()
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
JAL-4367 Limit right and top adjustments
JAL-4290 Fix image comparison between gui and headless output.  Images are now the same
JAL-4373 Setting the jvmmempc and jvmmemmax strings from the Arg.getName() for consistency. Updated some comments.
JAL-4290 Set structureSelectionManager settings more generically and when no desktop exists
JAL-4290 Move some annotation visibility settings to after opening a structure. Set synchronously if in headless mode.
JAL-4290 Fixed one test
JAL-4290 not quite working tests
JAL-4290 fixed tests
JAL-4373 Fix Main-Class and other attribute settings in the shadowJar manifest. It requires a 'dummy' Jar task with the correct settings.
Testless build
JB › GDC › #187 2 months ago
JAL-4353 helper method and test for primary/secondary and auxiliary arguments with --structure pdb0 --structureimage png0a --bgcolour col0a --structureimagepng0b --bgcolour col0b --structure pdb1 --...
JAL-4353 bigger tighter test
JAL-4353 Preserve the user given 'linkedId' with ArgValue, to help with deciding if user deliberately set a wildcard linkedId (or --all), to inform value of sub-args.
JAL-4353 Add a 'random' colour to produce a random colour.
JAL-4353 re-used random color code
JAL-4353 Add secondary Types for Args, for STRUCTUREIMAGE Type and restrict structureimages between structures on the same open alignment
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' of https://source.jalview.org/git/jalview into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
Testless build
JB › GGR › #7 11 months ago
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
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
JAL-4064 JAL-4054 Correct names of mac arch installer DMG files
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
Merge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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 1 year 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-1988 JAL-3772 Fixes highlighted by tests
JAL-4019 Put original test back
JAL-3416 make flatlaf default for linux
JAL-4125 Spanish translations
JAL-1988 JAL-3776 Formatting JvOptionPane
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 merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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
Merge branch 'merge/JAL-4054+JAL-4064' into ben-big-merge
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-1988 JAL-3772 Allow other window closing dialogs to cancel quit handling
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-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
JAL-3416 Add necessary logo to non-internal Frames
JAL-1988 JAL-3772 Moving packages to somewhere more obvious (jbgui -> gui)
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
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution of JalviewFileChooser and JvOptionPane
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-1988 JAL-3772 Tests for various quitting scenarios
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.
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into ben-big-merge
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-1988 JAL-3772 Test for FORCE_QUIT whilst saving a file
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Testless build
Build Completed Code commits Tests
JB › GGR › #7 11 months ago
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
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
JAL-4064 JAL-4054 Correct names of mac arch installer DMG files
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
Merge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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
Build Completed Code commits Tests