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.
8
1 (12%)
7 (88%)

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 (12% of all builds triggered)
0 (0% of all builds triggered)
-1
Build Completed Code commits Tests
JB › GDBI › #21 1 year 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 › #217 5 days ago
JAL-4001 Added useful props information
JAL-4001 Dynamic API_BASE_URL lookup at https://www.jalview.org/config/analytics/url. Change more terminology.  Add 'installation' property.
JAL-4001 Fix default API url
JAL-4001 remove headless code from analytics
JAL-4001 Release_2_11_2 branch with Plausible analytics
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 change Plausible discovery URL
Testless build
JB › GTC › #17 1 week ago
JAL-4001 Release_2_11_2 branch with Plausible analytics
JAL-4001 remove headless code from analytics
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 Fix default API url
JAL-4001 Dynamic API_BASE_URL lookup at https://www.jalview.org/config/analytics/url. Change more terminology.  Add 'installation' property.
JAL-4001 change Plausible discovery URL
JAL-4001 Added useful props information
Testless build
JB › GDC › #216 2 weeks ago
Merge branch 'develop' into bug/JAL-4477_unmapped_filename_characters
Changed getdown file.getCanonicalPath() and file.mkdirs to use FileUtils helper methods
JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this).
JAL-4477 Using FileUtils.mkdirs(file) instead of file.mkdirs() in getdown and FileUtils
JAL-4477 Change to Files.createDirectories(). Adding sun.jnu.encoding=UTF-8 to install4j and getdown launches
JAL-4477 Re-work install4j and getdown to use the installer.appdir first or installer.original_appdir if installer.appdir doesn't exist. Fix FileUtils to workj with getdown.
JAL-4477 install4j 11 template
JAL-4477 Forcing UTF-8 system properties through install4j launch and getdown launch. Works with Java 11 when 'Worldwide language' support is set.
JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this). Recompile.
Merge branch 'bug/JAL-4477_unmapped_filename_characters' into JAL-4474_jalview.ps1_not_working
Testless build
JB › GDB › #703 3 weeks ago
Merge branch 'bug/JAL-4477_unmapped_filename_characters' into JAL-4474_jalview.ps1_not_working
1814 passed
JB › GDB › #702 3 weeks ago
JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this). Recompile.
JAL-4477 Re-work install4j and getdown to use the installer.appdir first or installer.original_appdir if installer.appdir doesn't exist. Fix FileUtils to workj with getdown.
JAL-4477 Forcing UTF-8 system properties through install4j launch and getdown launch. Works with Java 11 when 'Worldwide language' support is set.
Changed getdown file.getCanonicalPath() and file.mkdirs to use FileUtils helper methods
JAL-4477 Change to Files.createDirectories(). Adding sun.jnu.encoding=UTF-8 to install4j and getdown launches
JAL-4477 install4j 11 template
JAL-4477 Using FileUtils.mkdirs(file) instead of file.mkdirs() in getdown and FileUtils
JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this).
Merge branch 'develop' into bug/JAL-4477_unmapped_filename_characters
1814 passed
JB › GGR › #7 1 year 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 1 year 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