Ben Soares <b.soares@dundee.ac.uk>: Author Summary
| Build | Completed | Code commits | Tests |
|---|---|---|---|
| JB › GDBI › #21 | 4 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 › #170 | 6 days ago |
JAL-629 updated tests
JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTIID and Opt.MULTI to Opt.MULTIVALUE. Remove filename value open* as trigger for applying an output file to all globbed files opened in the last --open, and make it the default option for globbed files opened. Adjust 2 test data for removed 'open*'.
JAL-629 Added/corrected/tidied documentation
Merge branch 'develop' into feature/JAL-4274_configurable_bitmap_export_preferences
JAL-4277 fixed and improved tests
JAL-4250 Fixed blue arrows in drawStemAnnot()
JAL-4284 JAL-4285 Deal with output files/images consistently with --overwrite check. Gather batch process errors together to output at the end of processing.
JAL-4285 JAL-4262 Added a scrollable dialog to display errors. Moved old-style CLI warning so it appears above Jalview desktop.
JAL-4262 Dialog for GUI and WARN for CLI of old style arguments, or mixed arguments \(with exit\). Changed Jalview.exit to use an enum for exit code to avoid collisions.
JAL-4274 Use Cache BITMAP_* if no other image restrictions given
JAL-4277 Corrected choice of all or last opened linkedIds. Better wildcard syntactic sugar for output files. Fixed all tests for new defaults.
JAL-4262 Make an excepetion for STDOUT filename in old style arguments detection
JAL-4265 Added --bgcolour for --structureimage output. Saves and restores Jmol state before and after colour changes and export. Added 'set antialiasdisplay on' by default for all Jmol viewers.
JAL-4274 comments to help follow the tests
JAL-4277 No longer using getCanonicalPath() for parent dir -- fix test
Merge branch 'develop' into bug/JAL-4277_dirname_substitution_always_absolute
JAL-4274 Tests for BIS defaults and overrides
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 Change to use JmolCommands
Merge branch 'improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed' into bug/JAL-4277_dirname_substitution_always_absolute
JAL-4277 --mkdirs with cautious refusal for paths with ..
JAL-629 Allow multiple structure images for multiple structure files for the one alignment. Add a {structurebasename} etc and {m} substitution which must be handled differently (on the fly) to other substitutions.
JAL-4285 Better checkFiles processing. Better dialog.
JAL-4265 Added saveState and restoreState to interface with no-op methods in abstract class
Merge branch 'bug/JAL-4277_dirname_substitution_always_absolute' into improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
JAL-629 Make arguments appear correctly using all non-breaking hyphens
JAL-4269 Now using --width, --height, --scale for both --image and --structureimage. Multiple --image and --structureimage can be specified with --imagecolour allowing changes of colour. --width etc only apply to that particular image.
JAL-629 Add link and example for BioJS image output
JAL-629 Fix a test and omit an incorrect error message for structureviewer=none
JAL-4265 Use ColourUtils.parseColourString() for consistency with the rest of Jalview (and it's better). Change documentation to match new hexstring format
JAL-4262 Allow HTML in the dialog box for link to CLI documentation
JAL-4262 Made deprecation warning properly modal
JAL-629 Explanation of \{m\} in case anyone actually wants it
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Testless build |
| JB › GTC › #6 | 2 months 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
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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
|
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
|
Testless build |
| Build | Completed | Code commits | Tests |
|---|