jalview.git
21 months agoJAL-3280 Fixed the version checking URL formulation (getdown build_properties) for... Develop-2_11_2_0-d20201215
Ben Soares [Mon, 14 Dec 2020 23:18:04 +0000 (23:18 +0000)]
JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

21 months agoJAL-3783 Reverting to using groovy-all-2.4.12-indy.jar to fix serious problem with...
Ben Soares [Mon, 14 Dec 2020 17:56:17 +0000 (17:56 +0000)]
JAL-3783 Reverting to using groovy-all-2.4.12-indy.jar to fix serious problem with Groovy console using shadowJar

21 months agoJAL-3628 Test for doubly saved single backup file scheme
Ben Soares [Mon, 14 Dec 2020 17:24:03 +0000 (17:24 +0000)]
JAL-3628 Test for doubly saved single backup file scheme

21 months agoJAL-3594 Allow setting of getdownappbase and getdowndistdir properties for DEVELOP...
Ben Soares [Mon, 14 Dec 2020 16:12:59 +0000 (16:12 +0000)]
JAL-3594 Allow setting of getdownappbase and getdowndistdir properties for DEVELOP channel, and change DEVELOP version to be VERSION-dDATE instead of VERSION-develop.  dDATE will help users know when Jalview Develop applicaiton updated

21 months agoJAL-3280 Test for remote release build_properties file version check
Ben Soares [Wed, 2 Sep 2020 17:25:40 +0000 (18:25 +0100)]
JAL-3280 Test for remote release build_properties file version check

21 months agoJAL-3280 fixes after CR-JAL-241. Now only checking release build_properties.
Ben Soares [Tue, 1 Sep 2020 16:45:21 +0000 (17:45 +0100)]
JAL-3280 fixes after CR-JAL-241. Now only checking release build_properties.

21 months agoJAL-3280 Pass appbase and appdir from getdown to jalvew. Check appbase (defaults...
Ben Soares [Mon, 31 Aug 2020 17:38:15 +0000 (18:38 +0100)]
JAL-3280 Pass appbase and appdir from getdown to jalvew. Check appbase (defaults to release appbase) for build_properties VERSION insteadl of jnlp file.

21 months agoJAL-3594 Defintely want SplashScreen to appear in the Desktop window otherwise it...
Ben Soares [Fri, 11 Dec 2020 20:27:19 +0000 (20:27 +0000)]
JAL-3594 Defintely want SplashScreen to appear in the Desktop window otherwise it might not be closeable

21 months agoJAL-3594 Changed building.md to describe -PCHANNEL=JALVIEWJS and JALVIEWJS-TEST
Ben Soares [Fri, 11 Dec 2020 17:19:16 +0000 (17:19 +0000)]
JAL-3594 Changed building.md to describe -PCHANNEL=JALVIEWJS and JALVIEWJS-TEST

21 months agoJAL-3594 Changed building.md to reflect change of name of channel_properties to chann...
Ben Soares [Fri, 11 Dec 2020 17:14:26 +0000 (17:14 +0000)]
JAL-3594 Changed building.md to reflect change of name of channel_properties to channel.props

21 months agoJAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/chann...
Ben Soares [Fri, 11 Dec 2020 17:02:36 +0000 (17:02 +0000)]
JAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/channels dir for jalviewjs and jalviewjs-release

21 months agoJAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS
Ben Soares [Fri, 11 Dec 2020 16:34:53 +0000 (16:34 +0000)]
JAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS

21 months agoMerge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop
Ben Soares [Thu, 10 Dec 2020 19:56:14 +0000 (19:56 +0000)]
Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

21 months agoJAL-3594 Better Jalview Develop banner
Ben Soares [Thu, 10 Dec 2020 19:53:55 +0000 (19:53 +0000)]
JAL-3594 Better Jalview Develop banner

21 months agoJAL-3594 Documentation added to building.md for using the utils/channels/... folders
Ben Soares [Thu, 10 Dec 2020 10:49:44 +0000 (10:49 +0000)]
JAL-3594 Documentation added to building.md for using the utils/channels/... folders

21 months agoMerge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop
Ben Soares [Thu, 10 Dec 2020 10:05:25 +0000 (10:05 +0000)]
Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

21 months agoMerge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609...
Ben Soares [Thu, 10 Dec 2020 09:56:09 +0000 (09:56 +0000)]
Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into develop

21 months agoJAL-3594 Improved About banners for develop and test-release
Ben Soares [Wed, 9 Dec 2020 20:21:03 +0000 (20:21 +0000)]
JAL-3594 Improved About banners for develop and test-release

21 months agoJAL-3594 Images for splash screen
Ben Soares [Wed, 9 Dec 2020 18:23:02 +0000 (18:23 +0000)]
JAL-3594 Images for splash screen

21 months agoJAL-3594 JAL-3728 Added taskbar icons to desktop and Java console. Changed "Jalview...
Ben Soares [Wed, 9 Dec 2020 13:57:08 +0000 (13:57 +0000)]
JAL-3594 JAL-3728 Added taskbar icons to desktop and Java console. Changed "Jalview" to "app_name" in various appropriate places

21 months agoMerge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609...
Ben Soares [Tue, 8 Dec 2020 20:42:31 +0000 (20:42 +0000)]
Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into merge/JAL-3594_and_new_develop_issues

21 months agoJAL-3594 Change main window title
Ben Soares [Tue, 8 Dec 2020 18:17:35 +0000 (18:17 +0000)]
JAL-3594 Change main window title

21 months agoJAL-3594 DMG fixes
Ben Soares [Tue, 8 Dec 2020 00:56:02 +0000 (00:56 +0000)]
JAL-3594 DMG fixes

21 months agoJAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test...
Ben Soares [Mon, 7 Dec 2020 21:22:01 +0000 (21:22 +0000)]
JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

21 months agoJAL-3754 Fixed jar task creating strange dir because of outputs.file()
Ben Soares [Mon, 7 Dec 2020 13:29:39 +0000 (13:29 +0000)]
JAL-3754 Fixed jar task creating strange dir because of outputs.file()

21 months agoJAL-3754 Fixed jar task creating strange dir because of outputs.file()
Ben Soares [Mon, 7 Dec 2020 13:29:39 +0000 (13:29 +0000)]
JAL-3754 Fixed jar task creating strange dir because of outputs.file()

22 months agoJAL-3594 Default values for channel properties defined in code as fallback
Ben Soares [Sat, 5 Dec 2020 21:17:33 +0000 (21:17 +0000)]
JAL-3594 Default values for channel properties defined in code as fallback

22 months agoJAL-3594 Added rotating logo png
Ben Soares [Fri, 4 Dec 2020 18:52:37 +0000 (18:52 +0000)]
JAL-3594 Added rotating logo png

22 months agoJAL-3754 fixed a problem with jar task creating a stray dir when building merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch
Ben Soares [Fri, 4 Dec 2020 18:31:32 +0000 (18:31 +0000)]
JAL-3754 fixed a problem with jar task creating a stray dir when building

22 months agoJAL-3775 added the Platform.isLinux() check for test HiDPISetting2
Ben Soares [Fri, 4 Dec 2020 17:59:13 +0000 (17:59 +0000)]
JAL-3775 added the Platform.isLinux() check for test HiDPISetting2

22 months agoJAL-3594 New jalview.util.ChannelProperties to get/cache values and images used in...
Ben Soares [Fri, 4 Dec 2020 17:16:39 +0000 (17:16 +0000)]
JAL-3594 New jalview.util.ChannelProperties to get/cache values and images used in the application. Starting to tidy images in resources/images.

22 months agoJAL-3594 Generating GIMP XCF files for getdown and new release getdown images
Ben Soares [Fri, 4 Dec 2020 11:09:12 +0000 (11:09 +0000)]
JAL-3594 Generating GIMP XCF files for getdown and new release getdown images

22 months agoJAL-3594 Release images and channel properties
Ben Soares [Fri, 4 Dec 2020 00:56:40 +0000 (00:56 +0000)]
JAL-3594 Release images and channel properties

22 months agoJAL-3594 New way for build.gradle to override properties with channel based propertie...
Ben Soares [Thu, 3 Dec 2020 22:51:23 +0000 (22:51 +0000)]
JAL-3594 New way for build.gradle to override properties with channel based properties files. Starting to tidy up some old image files

22 months agoJAL-3594 new logos, icons and cosmetics for getdown and install4j
Ben Soares [Wed, 2 Dec 2020 14:01:25 +0000 (14:01 +0000)]
JAL-3594 new logos, icons and cosmetics for getdown and install4j

22 months agoJAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL...
Ben Soares [Fri, 18 Sep 2020 11:09:36 +0000 (12:09 +0100)]
JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

22 months agoMerge branch 'develop' into merge/develop_and_rebase_squashed_merge_JAL-3628+JAL...
Ben Soares [Tue, 1 Dec 2020 15:03:56 +0000 (15:03 +0000)]
Merge branch 'develop' into merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch

22 months agoJAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No...
Ben Soares [Tue, 1 Dec 2020 14:57:16 +0000 (14:57 +0000)]
JAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No real functionality change.

22 months agoJAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting
Ben Soares [Tue, 1 Dec 2020 14:52:26 +0000 (14:52 +0000)]
JAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting

22 months agoJAL-3609 JAL-3775 Refactoring a bit of jalview.bin.HiDPISetting so screen display...
Ben Soares [Tue, 1 Dec 2020 14:34:06 +0000 (14:34 +0000)]
JAL-3609 JAL-3775 Refactoring a bit of jalview.bin.HiDPISetting so screen display can be mocked in tests by Mockito

22 months agoJAL-3775 Adding Mockito jars for tests. Needed for HiDPISettingTest1
Ben Soares [Tue, 1 Dec 2020 14:30:28 +0000 (14:30 +0000)]
JAL-3775 Adding Mockito jars for tests.  Needed for HiDPISettingTest1

22 months agoJAL-3660 Fix for specified output format when using command line arg to convert a...
Ben Soares [Fri, 27 Nov 2020 17:24:08 +0000 (17:24 +0000)]
JAL-3660 Fix for specified output format when using command line arg to convert a file

22 months agoJAL-3530 Added a -nowebservicediscovery command line argument.
Ben Soares [Tue, 1 Dec 2020 14:25:55 +0000 (14:25 +0000)]
JAL-3530 Added a -nowebservicediscovery command line argument.

22 months agoJAL-3660 Fix for specified output format when using command line arg to convert a...
Ben Soares [Fri, 27 Nov 2020 17:24:08 +0000 (17:24 +0000)]
JAL-3660 Fix for specified output format when using command line arg to convert a file

22 months agoJAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval...
Jim Procter [Thu, 24 Sep 2020 13:36:17 +0000 (14:36 +0100)]
JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)

22 months agoJAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as...
Ben Soares [Wed, 23 Sep 2020 22:41:36 +0000 (23:41 +0100)]
JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as 

22 months agoJAL-3775 Re-compiled Getdown jars
Ben Soares [Fri, 13 Nov 2020 18:10:54 +0000 (18:10 +0000)]
JAL-3775 Re-compiled Getdown jars

22 months agoJAL-3775 Eclipse re-formatting commit
Ben Soares [Fri, 13 Nov 2020 18:09:28 +0000 (18:09 +0000)]
JAL-3775 Eclipse re-formatting commit

22 months agoJAL-3633 last minute refinement so password box doesn't get focus all the time
Ben Soares [Thu, 30 Jul 2020 12:53:23 +0000 (13:53 +0100)]
JAL-3633 last minute refinement so password box doesn't get focus all the time

22 months agoJAL-3633 Apply (proxy) button enabled when needed
Ben Soares [Thu, 30 Jul 2020 11:06:29 +0000 (12:06 +0100)]
JAL-3633 Apply (proxy) button enabled when needed

22 months agoJAL-3633 Help documentation updated
Ben Soares [Thu, 30 Jul 2020 11:05:49 +0000 (12:05 +0100)]
JAL-3633 Help documentation updated

22 months agoJAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview...
Ben Soares [Wed, 29 Jul 2020 18:48:02 +0000 (19:48 +0100)]
JAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview-JS, Most NPE fixes for tests

22 months agoJAL-3275 JAL-3633: JAL-3275 Turned Preferences into a Singleton that checks renews...
Ben Soares [Wed, 29 Jul 2020 11:44:24 +0000 (12:44 +0100)]
JAL-3275 JAL-3633: JAL-3275 Turned Preferences into a Singleton that checks renews if it's been closed.  Removed some debugging for JAL-3633. Added focus/highlight to proxy password box when needed. Forced WS lookup wheb proxy settings changed.

22 months agoJAL-3633 Set proxy preferences before web calls in jalview.bin.Jalview. Fixed call...
Ben Soares [Mon, 27 Jul 2020 19:31:16 +0000 (20:31 +0100)]
JAL-3633 Set proxy preferences before web calls in jalview.bin.Jalview. Fixed call to open Preferences->Connections with message when required.

22 months agoJAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab...
Ben Soares [Sat, 25 Jul 2020 23:41:42 +0000 (00:41 +0100)]
JAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab when proxy password needed

22 months agoJAL-3633 Added Proxy Authentication credentials in Preferences and set via java.net...
Ben Soares [Wed, 22 Jul 2020 18:40:59 +0000 (19:40 +0100)]
JAL-3633 Added Proxy Authentication credentials in Preferences and set via java.net.Authenticator

22 months agoJAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet
Ben Soares [Tue, 21 Jul 2020 19:47:18 +0000 (20:47 +0100)]
JAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet

22 months agoJAL-3633 label.proxy_server -> label.proxy_servers
Ben Soares [Tue, 21 Jul 2020 11:41:31 +0000 (12:41 +0100)]
JAL-3633 label.proxy_server -> label.proxy_servers

22 months agoJAL-3633 Remember system set proxy properties. Add options in Preferences for No...
Ben Soares [Sun, 12 Jul 2020 23:31:13 +0000 (00:31 +0100)]
JAL-3633 Remember system set proxy properties. Add options in Preferences for No proxy, system proxy, or custom proxy servers.

22 months agoJAL-3633 pass getdown proxy settings in proxy.txt on to Jalview
Ben Soares [Thu, 9 Jul 2020 14:57:19 +0000 (15:57 +0100)]
JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview

22 months agoJAL-3633 ensure check both http:// or https:// for urls
Ben Soares [Wed, 8 Jul 2020 16:01:32 +0000 (17:01 +0100)]
JAL-3633 ensure check both  or https:// for urls

22 months agoJAL-3628 Error when saving alert box has been moved in develop for JS, adding Platfor...
Ben Soares [Thu, 12 Nov 2020 14:27:51 +0000 (14:27 +0000)]
JAL-3628 Error when saving alert box has been moved in develop for JS, adding Platform.isHeadless test to new isSaveAlignmentSuccessful method.

22 months agoJAL-3676 More explicit tooltip about resetting log level on Console close. Also clari...
Ben Soares [Fri, 14 Aug 2020 12:01:06 +0000 (13:01 +0100)]
JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

22 months agoJAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed...
Ben Soares [Wed, 12 Aug 2020 12:48:57 +0000 (13:48 +0100)]
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.

22 months agoJAL-3628 Fixed oddly worded and non-formatted error popups when saving fails
Ben Soares [Tue, 7 Jul 2020 00:30:23 +0000 (01:30 +0100)]
JAL-3628 Fixed oddly worded and non-formatted error popups when saving fails

22 months agoJAL-3676 improvement for visual selection of console text - fg color change if required
Ben Soares [Mon, 6 Jul 2020 14:54:52 +0000 (15:54 +0100)]
JAL-3676 improvement for visual selection of console text - fg color change if required

22 months agoJAL-3676 code review -- added non-listed Level into dropdown list
Ben Soares [Thu, 2 Jul 2020 14:36:41 +0000 (15:36 +0100)]
JAL-3676 code review -- added non-listed Level into dropdown list

22 months agoJAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console
Ben Soares [Tue, 30 Jun 2020 15:04:00 +0000 (16:04 +0100)]
JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console

22 months agoJAL-3628 Fix for slightly incorrect boolean usage to determine success when rolling...
Ben Soares [Mon, 6 Jul 2020 14:43:37 +0000 (15:43 +0100)]
JAL-3628 Fix for slightly incorrect boolean usage to determine success when rolling backup files

22 months agoJAL-3628 Even more Cache.log.debug statements
Ben Soares [Mon, 6 Jul 2020 13:48:59 +0000 (14:48 +0100)]
JAL-3628 Even more Cache.log.debug statements

22 months agoJAL-3628 More Cache.log.debug statements
Ben Soares [Sat, 4 Jul 2020 12:17:42 +0000 (13:17 +0100)]
JAL-3628 More Cache.log.debug statements

23 months agoJAL-3628 Changed other calls to renameTo to use BackupFiles.moveFileToFile
Ben Soares [Mon, 15 Jun 2020 19:22:29 +0000 (20:22 +0100)]
JAL-3628 Changed other calls to renameTo to use BackupFiles.moveFileToFile

23 months agoJAL-3628 Changed all file1.renameTo(file2) calls to Files.move(path1,path2,REPLACE_EX...
Ben Soares [Mon, 8 Jun 2020 23:49:34 +0000 (00:49 +0100)]
JAL-3628 Changed all file1.renameTo(file2) calls to Files.move(path1,path2,REPLACE_EXISTING) in jalview.io.BackupFiles. This fixes a problem in Windows with renameTo when destination file already exists.

23 months agoJAL-3609 formatting save after cherry-picks
Ben Soares [Fri, 6 Nov 2020 17:05:48 +0000 (17:05 +0000)]
JAL-3609 formatting save after cherry-picks

23 months agoJAL-3609 Allow pass-through of setHiDPIScale property to tests via (e.g.) gradle...
Ben Soares [Wed, 1 Jul 2020 14:37:35 +0000 (15:37 +0100)]
JAL-3609 Allow pass-through of setHiDPIScale property to tests via (e.g.) gradle test -Ptest_HiDPIScale=2

23 months agoJAL-3609 Report when scale setting used.
Ben Soares [Sun, 21 Jun 2020 00:24:10 +0000 (01:24 +0100)]
JAL-3609 Report when scale setting used.

23 months agoJAL-3609 New auto-scale 'formula' for linux HiDPI. Tested to work for UHD screen...
Ben Soares [Sun, 21 Jun 2020 00:23:37 +0000 (01:23 +0100)]
JAL-3609 New auto-scale 'formula' for linux HiDPI.  Tested to work for UHD screen in various OS display settings.

23 months agoJAL-3609 corrected maxdimension to mindimension. Adjusted tallscreen limit
soares [Fri, 22 May 2020 11:56:04 +0000 (12:56 +0100)]
JAL-3609 corrected maxdimension to mindimension. Adjusted tallscreen limit

23 months agoJAL-3609 removed debugging prints
Ben Soares [Wed, 20 May 2020 17:25:34 +0000 (18:25 +0100)]
JAL-3609 removed debugging prints

23 months agoJAL-3609 changed property names to something more palatable and catered for portrait...
Ben Soares [Tue, 19 May 2020 19:32:27 +0000 (20:32 +0100)]
JAL-3609 changed property names to something more palatable and catered for portrait screens

23 months agoJAL-3609 system properties to force a scale, or automatically choose based on OS...
Ben Soares [Tue, 19 May 2020 17:15:01 +0000 (18:15 +0100)]
JAL-3609 system properties to force a scale, or automatically choose based on OS, Screen DPI and Screen height in pixels

23 months agoJAL-3609 Added a -DforceHiDPISetting=true option mainly for testing, and updated...
Ben Soares [Tue, 19 May 2020 00:38:58 +0000 (01:38 +0100)]
JAL-3609 Added a -DforceHiDPISetting=true option mainly for testing, and updated getdown HiDPISetting

23 months agoJAL-3608 cherry pick of 92cb745e7
Ben Soares [Thu, 5 Nov 2020 16:01:23 +0000 (16:01 +0000)]
JAL-3608 cherry pick of 92cb745e7

23 months agoJAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html...
Ben Soares [Thu, 29 Oct 2020 14:26:45 +0000 (14:26 +0000)]
JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

23 months agoJAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename
Ben Soares [Thu, 29 Oct 2020 14:19:51 +0000 (14:19 +0000)]
JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

23 months agoJAL-3760 fix tests for changed behaviour
Jim Procter [Tue, 29 Sep 2020 15:41:39 +0000 (16:41 +0100)]
JAL-3760 fix tests for changed behaviour

23 months agoJAL-3760 refactor nucleotide proportion test to per-sequence and return false if...
Jim Procter [Tue, 29 Sep 2020 14:26:34 +0000 (15:26 +0100)]
JAL-3760 refactor nucleotide proportion test to per-sequence and return false if any sequence appears protein-like

23 months agoMerge branch 'portforward/JAL-3765_patch_to_2112' into develop
Jim Procter [Wed, 28 Oct 2020 16:04:52 +0000 (16:04 +0000)]
Merge branch 'portforward/JAL-3765_patch_to_2112' into develop

23 months agoJAL-3765 fix test
Jim Procter [Tue, 20 Oct 2020 16:23:30 +0000 (17:23 +0100)]
JAL-3765 fix test

23 months agofix for JAL-3765
Jim Procter [Tue, 20 Oct 2020 16:13:33 +0000 (17:13 +0100)]
fix for JAL-3765

23 months agoJAL-3248 Added step to create the eclipse files before project import. Noted non...
Ben Soares [Wed, 28 Oct 2020 12:18:59 +0000 (12:18 +0000)]
JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

23 months agoMerge branch 'develop' into blocker/JAL-3611_space_character_in_jalview_install_path
Ben Soares [Thu, 15 Oct 2020 14:01:19 +0000 (15:01 +0100)]
Merge branch 'develop' into blocker/JAL-3611_space_character_in_jalview_install_path

2 years agoJAL-3753 ensure correct dependencies for shadowJar task bug/JAL-3753_resources_duplicated_in_jalview_jar
Ben Soares [Mon, 28 Sep 2020 15:57:51 +0000 (16:57 +0100)]
JAL-3753 ensure correct dependencies for shadowJar task

2 years agoMerge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar
Ben Soares [Mon, 28 Sep 2020 11:12:47 +0000 (12:12 +0100)]
Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

2 years agoJAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by...
Ben Soares [Fri, 25 Sep 2020 08:39:02 +0000 (09:39 +0100)]
JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

2 years agoJAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...
Ben Soares [Thu, 24 Sep 2020 17:16:17 +0000 (18:16 +0100)]
JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

2 years agoMerge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar
Ben Soares [Wed, 23 Sep 2020 16:19:01 +0000 (17:19 +0100)]
Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

2 years agoJAL-3477 Added 10k leeway to amount of memory reserved for OS test for float rounding...
Ben Soares [Wed, 23 Sep 2020 15:49:00 +0000 (16:49 +0100)]
JAL-3477 Added 10k leeway to amount of memory reserved for OS test for float rounding errors (needed to fix failing test)

2 years agoJAL-3753 Resources seen in tests and appropriate filters now being used as file opt...
Ben Soares [Wed, 23 Sep 2020 15:48:01 +0000 (16:48 +0100)]
JAL-3753 Resources seen in tests and appropriate filters now being used as file opt-in rather than opt-out.

2 years agoMerge branch 'merge_review/JAL-3490_2_11_2_develop' into develop
Jim Procter [Mon, 21 Sep 2020 11:01:51 +0000 (12:01 +0100)]
Merge branch 'merge_review/JAL-3490_2_11_2_develop' into develop