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 11

Failed builds 3 (27%)

Successful jobs 8 (73%)

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 3 (27% of all builds triggered)

Fixed by author 4 (36% of all builds triggered)

Difference of fixes and breaks 1

Build	Completed	Code commits	Tests
JB › GDBI › #21	1 year ago	details 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 › GTC › #15	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GDC › #214	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GDL › #67	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GPC › #349	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GDB › #697	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	1803 passed
JB › GJB › #470	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GTC › #14	2 weeks ago	details JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest() JAL-4474 Added -Force option to all Get-Item calls in Readlink-f function in jalview.ps1 JAL-4487 Escape backslash file separators when looking for file globs. Fixed a CLI and a debugging NPE. JAL-4485 Extra debugging for Chimera/X and PyMol launches JAL-4485 Extracted the whitelist/blacklist fileglob finding code into FileUtils for more generic use JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist if version is not in the blacklist JAL-4485 Not using whitelist, just file glob and blacklist JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding. JAL-4485 Better var name and using FileUtils method in StructureManager JAL-4485 Path fix for macOS Applications	Testless build
JB › GDC › #213	2 weeks ago	details JAL-4485 Not using whitelist, just file glob and blacklist JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding. JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist if version is not in the blacklist JAL-4487 Escape backslash file separators when looking for file globs. Fixed a CLI and a debugging NPE. JAL-4485 Better var name and using FileUtils method in StructureManager JAL-4485 Path fix for macOS Applications JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest() JAL-4485 Extra debugging for Chimera/X and PyMol launches JAL-4485 Extracted the whitelist/blacklist fileglob finding code into FileUtils for more generic use JAL-4474 Added -Force option to all Get-Item calls in Readlink-f function in jalview.ps1	Testless build
JB › GGR › #7	1 year 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
JB › GTC › #14	2 weeks ago	details JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest() JAL-4474 Added -Force option to all Get-Item calls in Readlink-f function in jalview.ps1 JAL-4487 Escape backslash file separators when looking for file globs. Fixed a CLI and a debugging NPE. JAL-4485 Extra debugging for Chimera/X and PyMol launches JAL-4485 Extracted the whitelist/blacklist fileglob finding code into FileUtils for more generic use JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist if version is not in the blacklist JAL-4485 Not using whitelist, just file glob and blacklist JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding. JAL-4485 Better var name and using FileUtils method in StructureManager JAL-4485 Path fix for macOS Applications	Testless build
JB › GDC › #213	2 weeks ago	details JAL-4485 Not using whitelist, just file glob and blacklist JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding. JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist if version is not in the blacklist JAL-4487 Escape backslash file separators when looking for file globs. Fixed a CLI and a debugging NPE. JAL-4485 Better var name and using FileUtils method in StructureManager JAL-4485 Path fix for macOS Applications JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest() JAL-4485 Extra debugging for Chimera/X and PyMol launches JAL-4485 Extracted the whitelist/blacklist fileglob finding code into FileUtils for more generic use JAL-4474 Added -Force option to all Get-Item calls in Readlink-f function in jalview.ps1	Testless build
JB › GGR › #7	1 year 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
JB › GTC › #15	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GDC › #214	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GDL › #67	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build
JB › GPC › #349	2 weeks ago	details JAL-4482 make the dummy whatsNew.html file HTML with an #experimental named anchor	Testless build