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

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.

All builds triggered 3

Failed builds 1 (33%)

Successful jobs 2 (67%)

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.

Broken by author 1 (33% of all builds triggered)

Fixed by author 0 (0% of all builds triggered)

Difference of fixes and breaks -1

Build	Completed	Code commits	Tests
JB › GGR › #7	1 week ago	details 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 › GDC › #141	1 month ago	details JAL-629 Allow attachment of pAE file to a particular sequence Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629 JAL-629 fix opening files JAL-629 Add debug messages for more failing tests JAL-629 null check, fixed tests! JAL-629 make sequence id key 'seqid' JAL-629 stray code deleted JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument JAL-629 Doing things with the command line arguments JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups JAL-629 implementation of --tempfac options JAL-629 refactoring TFType. Remove i18n identification of annotation. JAL-629 test fixing JAL-629 fixed a Log4j test by adding --debug arg 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-629 Open Structure Viewer from cmdline JAL-629 helper eclipse CLI run JAL-629 fix a PAEMatrix casting error Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629 JAL-629 better test fixes. --props=... instead of --debug JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single threaded in headless mode. Delete an editor temp file. JAL-629 move SubId to more logical place. Attempt removal of annotations in a better way (commented out). JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args JAL-629 added Alphafold cif, pdb and PAE json files to examples/AlphaFold JAL-629 Add image output and quit JAL-629 "updated" json-simple JAL-629 nf-core sample alignment files and a2m versions JAL-629 example files from nf-core	Testless build
JB › GDI › #11	1 month ago	details 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	1 week ago	details 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