Ben Soares [Tue, 5 Apr 2022 11:25:37 +0000 (12:25 +0100)]
JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places
Ben Soares [Mon, 4 Apr 2022 11:01:22 +0000 (12:01 +0100)]
JAL-3989 fix a build date once in build.gradle, not each time getDate() is called.
Ben Soares [Thu, 31 Mar 2022 17:52:55 +0000 (18:52 +0100)]
Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop
Ben Soares [Thu, 31 Mar 2022 17:18:40 +0000 (18:18 +0100)]
Merge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_archive_dir
Jim Procter [Wed, 30 Mar 2022 17:35:07 +0000 (18:35 +0100)]
Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop
Jim Procter [Wed, 30 Mar 2022 16:32:19 +0000 (17:32 +0100)]
JAL-3976 fix mock PDBFTS query & responses
Jim Procter [Wed, 30 Mar 2022 15:56:41 +0000 (16:56 +0100)]
JAL-3983 known issue note for JAL-3984
Jim Procter [Wed, 30 Mar 2022 15:54:33 +0000 (16:54 +0100)]
JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984
Jim Procter [Wed, 30 Mar 2022 15:52:27 +0000 (16:52 +0100)]
Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop
Jim Procter [Wed, 30 Mar 2022 15:51:44 +0000 (16:51 +0100)]
JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..
Ben Soares [Tue, 15 Mar 2022 17:13:01 +0000 (17:13 +0000)]
JAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after JvOptionPane action.
Jim Procter [Wed, 30 Mar 2022 15:15:43 +0000 (16:15 +0100)]
JAL-3983 update release notes for JAL-3973
Jim Procter [Wed, 30 Mar 2022 15:12:51 +0000 (16:12 +0100)]
JAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate entries in the tarball
Jim Procter [Wed, 30 Mar 2022 14:49:09 +0000 (15:49 +0100)]
Merge branch 'bug/JAL-3973_source_tarball_not_building' into develop
Jim Procter [Wed, 30 Mar 2022 14:45:01 +0000 (15:45 +0100)]
JAL-3983 release 2.11.2.1 date and release notes
Jim Procter [Wed, 23 Mar 2022 12:22:41 +0000 (12:22 +0000)]
JAL-3976 skip entries with null values when analyzing
Jim Procter [Wed, 23 Mar 2022 12:22:15 +0000 (12:22 +0000)]
JAL-3976 update tests
Ben Soares [Fri, 18 Mar 2022 18:12:17 +0000 (18:12 +0000)]
JAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict with getAppbaseBuildProperties(). Added an if around fetching build_properties to avoid failing to fetch local file appbase.
Ben Soares [Fri, 18 Mar 2022 16:55:46 +0000 (16:55 +0000)]
JAL-3978 Getdown add getdownappbase property to launched Jalview
Ben Soares [Fri, 18 Mar 2022 16:55:17 +0000 (16:55 +0000)]
JAL-3978 New tasks to build archive 'old' dir with appropriate getdown resources, JVL file and digest
Ben Soares [Wed, 16 Mar 2022 17:29:56 +0000 (17:29 +0000)]
JAL-3978 task stub and getdown splash screens
Ben Soares [Sun, 13 Mar 2022 21:00:24 +0000 (21:00 +0000)]
Append git.hash and git.branch to RELEASE file stored in tarball. When compiling, if not in git repo use git.branch and git.hash from RELEASE file.
Ben Soares [Fri, 11 Mar 2022 09:31:57 +0000 (09:31 +0000)]
JAL-3973 This fixes the gradle build when not in a git repo. (Part 1 of the issue)
Jalview Development Admin [Thu, 10 Mar 2022 17:40:40 +0000 (17:40 +0000)]
Merge branch 'master' into releases/Release_2_11_2_Branch
Jalview Development Admin [Thu, 10 Mar 2022 01:34:08 +0000 (01:34 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jalview Development Admin [Thu, 10 Mar 2022 01:29:53 +0000 (01:29 +0000)]
JAL-3746 bump release date to 10th March - after UoD network maintenance
Jalview Development Admin [Thu, 10 Mar 2022 01:28:58 +0000 (01:28 +0000)]
JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(
Jim Procter [Wed, 9 Mar 2022 17:31:53 +0000 (17:31 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jalview Development Admin [Wed, 9 Mar 2022 16:51:38 +0000 (16:51 +0000)]
JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert
Jim Procter [Wed, 9 Mar 2022 10:12:18 +0000 (10:12 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 10:11:56 +0000 (10:11 +0000)]
JAL-3746 JAL-3841 fix README typo
Jim Procter [Wed, 9 Mar 2022 08:14:14 +0000 (08:14 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 9 Mar 2022 08:09:45 +0000 (08:09 +0000)]
JAL-3746 more docs tweaking and release notes
Jim Procter [Wed, 9 Mar 2022 07:59:03 +0000 (07:59 +0000)]
Merge branch 'spike/try_spotless_JAL-3438' into develop
Jim Procter [Tue, 8 Mar 2022 21:58:37 +0000 (21:58 +0000)]
JAL-3746 apply copyright to tests
Jim Procter [Tue, 8 Mar 2022 21:56:25 +0000 (21:56 +0000)]
JAL-3746 apply copyright to source
Jim Procter [Tue, 8 Mar 2022 21:30:05 +0000 (21:30 +0000)]
JAL-3438 spotless for 2.11.2.0
Jim Procter [Tue, 8 Mar 2022 20:40:15 +0000 (20:40 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 8 Mar 2022 20:39:47 +0000 (20:39 +0000)]
JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes
Jim Procter [Tue, 8 Mar 2022 18:53:09 +0000 (18:53 +0000)]
JAL-3108 updated Ensembl client and model species names
Jim Procter [Tue, 8 Mar 2022 18:18:56 +0000 (18:18 +0000)]
JAL-3746 new release date for 2.11.2
Jim Procter [Tue, 8 Mar 2022 18:13:27 +0000 (18:13 +0000)]
JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes
Jim Procter [Tue, 8 Mar 2022 17:41:04 +0000 (17:41 +0000)]
Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop
Ben Soares [Tue, 8 Mar 2022 12:26:28 +0000 (12:26 +0000)]
JAL-3103 updated help doc to remove default browser choice
Ben Soares [Tue, 8 Mar 2022 12:14:45 +0000 (12:14 +0000)]
JAL-3103 Removed code and unused widgets for defaultBrowser
Ben Soares [Tue, 8 Mar 2022 12:03:11 +0000 (12:03 +0000)]
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods
Ben Soares [Tue, 8 Mar 2022 00:39:04 +0000 (00:39 +0000)]
JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS
Ben Soares [Tue, 8 Mar 2022 00:34:55 +0000 (00:34 +0000)]
JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2
Jim Procter [Mon, 7 Mar 2022 20:12:04 +0000 (20:12 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 7 Mar 2022 20:07:36 +0000 (20:07 +0000)]
JAL-3647 release notes for JAL-1842 JAL-3509 JAL-3881, JAL-3884 JAL-3632 JAL-3633 and report JAL-3764 as a known issue
Jim Procter [Mon, 7 Mar 2022 17:52:44 +0000 (17:52 +0000)]
JAL-3685 - two single quotes when replacements are present in i18n message
Ben Soares [Mon, 7 Mar 2022 17:51:47 +0000 (17:51 +0000)]
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
Jim Procter [Fri, 4 Mar 2022 17:19:40 +0000 (17:19 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 4 Mar 2022 17:19:17 +0000 (17:19 +0000)]
JAL-3647 release notes for hdpi/laf scaling JAL-3608 JAL-3609 JAL-3552
Jim Procter [Fri, 4 Mar 2022 16:38:01 +0000 (16:38 +0000)]
JAL-3746 structure mapping preference docs for JAL-3817
Jim Procter [Fri, 5 Feb 2021 17:03:12 +0000 (17:03 +0000)]
JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.
Jim Procter [Fri, 5 Feb 2021 17:05:03 +0000 (17:05 +0000)]
JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository
Jim Procter [Fri, 5 Feb 2021 17:07:18 +0000 (17:07 +0000)]
JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences
Jim Procter [Fri, 5 Feb 2021 17:07:54 +0000 (17:07 +0000)]
JAL-3746 JAL-3814 don’t automatically launch the news browser when the desktop is first opened
Jim Procter [Fri, 5 Feb 2021 17:01:09 +0000 (17:01 +0000)]
JAL-3746 JAL-3814 NONEWS property
Jim Procter [Fri, 4 Mar 2022 15:57:52 +0000 (15:57 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 4 Mar 2022 15:41:06 +0000 (15:41 +0000)]
JAL-3608 JAL-3830 tweaked the what’s new text and updated helpTOC
Jim Procter [Fri, 4 Mar 2022 15:26:25 +0000 (15:26 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 4 Mar 2022 15:26:03 +0000 (15:26 +0000)]
JAL-3608 JAL-3830 simplified command line docs a bit
Jim Procter [Fri, 4 Mar 2022 14:36:11 +0000 (14:36 +0000)]
Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs' into develop
Ben Soares [Fri, 4 Mar 2022 13:48:54 +0000 (13:48 +0000)]
JAL-3830 added command line to whatsnew and releases
Ben Soares [Fri, 4 Mar 2022 13:38:29 +0000 (13:38 +0000)]
JAL-3830 Added new command line usage to docs
Ben Soares [Fri, 4 Mar 2022 12:19:35 +0000 (12:19 +0000)]
JAL-3608 added to LaF documentation
Ben Soares [Thu, 3 Mar 2022 15:38:47 +0000 (15:38 +0000)]
JAL-3830 fix broken/buggy install4j9 setting of executeSetupApp=false still running setupApp
Jim Procter [Wed, 2 Mar 2022 20:51:16 +0000 (20:51 +0000)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 2 Mar 2022 20:50:54 +0000 (20:50 +0000)]
Merge branch 'bug/JAL-3962_awt_dll_problem' into develop
Jim Procter [Wed, 2 Mar 2022 20:50:02 +0000 (20:50 +0000)]
JAL-3746 release notes for JAL-3867
Jim Procter [Wed, 2 Mar 2022 18:12:13 +0000 (18:12 +0000)]
JAL-3746 release note for JAL-3907 building Jalview with j17
Jim Procter [Wed, 2 Mar 2022 18:09:45 +0000 (18:09 +0000)]
JAL-3746 release note for JAL-3618 Vaqua config so app directories can be opened
Jim Procter [Wed, 2 Mar 2022 17:59:33 +0000 (17:59 +0000)]
Merge branch 'benreview/JAL-3691_for_2_11_2_getdownrebuilds' into develop
Jim Procter [Wed, 2 Mar 2022 17:55:41 +0000 (17:55 +0000)]
JAL-3594 release notes and mention jalview develop app in release notes
Jim Procter [Wed, 2 Mar 2022 17:49:37 +0000 (17:49 +0000)]
Release notes for JAL—3728 - waiting for ben to sign off or leave issue open
Jim Procter [Wed, 2 Mar 2022 17:28:55 +0000 (17:28 +0000)]
JAL-3208 release notes and docs for setprop
Jim Procter [Wed, 2 Mar 2022 17:10:06 +0000 (17:10 +0000)]
JAL-3746 release notes and cli arg docs for JAL-3530
Ben Soares [Wed, 2 Mar 2022 17:00:48 +0000 (17:00 +0000)]
JAL-3691 bumped the version to 1.8.3-1.2.12 in source and libraries
Jim Procter [Wed, 2 Mar 2022 16:14:59 +0000 (16:14 +0000)]
JAL-3746 release notes JAL-3391 JAL-3829 improved 3dbeacons docs, including documenting ‘best’ and ‘multiple best’ options in 3D-beacons
Jim Procter [Wed, 2 Mar 2022 15:58:48 +0000 (15:58 +0000)]
JAL-3746 release notes for JAL-3929
Jim Procter [Wed, 2 Mar 2022 15:11:20 +0000 (15:11 +0000)]
JAL-3746 more what’s new
Jim Procter [Wed, 2 Mar 2022 15:10:53 +0000 (15:10 +0000)]
JAL-3619 fix up error messages and try to bail quietly if the viewer doesn’t open
Jim Procter [Wed, 2 Mar 2022 14:49:56 +0000 (14:49 +0000)]
JAL-3619 fix up warning message and minimal patch to make sure failed-to-launch viewers tidy up after themselves.
Ben Soares [Wed, 2 Mar 2022 14:39:32 +0000 (14:39 +0000)]
JAL-3962 Added jre/bin and dist folders to the native library path to try and fix the awt.dll problem
Ben Soares [Wed, 2 Mar 2022 14:38:34 +0000 (14:38 +0000)]
JAL-3130 updated download_jres.sh
Jim Procter [Wed, 2 Mar 2022 14:22:56 +0000 (14:22 +0000)]
JAL-3746 what’s new..
Jim Procter [Wed, 2 Mar 2022 13:05:39 +0000 (13:05 +0000)]
JAL-3746 release notes for JAL-3202 (JalviewJS)
Jim Procter [Wed, 2 Mar 2022 12:30:53 +0000 (12:30 +0000)]
JAL-3746 update release date and release notes/docs for JAL-1260, JAL-3821, JAL-3144, JAL-2226
Jim Procter [Mon, 28 Feb 2022 18:57:07 +0000 (18:57 +0000)]
JAL-3746 more what’s new and release notes
Jim Procter [Mon, 28 Feb 2022 18:30:02 +0000 (18:30 +0000)]
JAL-3503 2.11.2.0 release notes and docs
Jim Procter [Mon, 28 Feb 2022 17:57:49 +0000 (17:57 +0000)]
JAL-3746 JAL-3551 update pymol docs and what’s new text
Jim Procter [Mon, 28 Feb 2022 11:59:28 +0000 (11:59 +0000)]
JAL-3746 document -no-annotation cli arg
Jalview Development Admin [Wed, 23 Feb 2022 18:55:37 +0000 (18:55 +0000)]
Merge branch 'improvement/JAL-3830_install4j9_macos_setup_application' of source.jalview.org/git/jalview into improvement/JAL-3830_install4j9_macos_setup_application
Jalview Development Admin [Wed, 23 Feb 2022 18:54:57 +0000 (18:54 +0000)]
JAL-3830 temporarily disable the setup screen for OSX dmgs until we can properly document its use
Jalview Development Admin [Wed, 23 Feb 2022 17:23:42 +0000 (17:23 +0000)]
JAL-3796 additional steps for notarization
Jim Procter [Thu, 17 Feb 2022 17:28:24 +0000 (17:28 +0000)]
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
Jim Procter [Thu, 17 Feb 2022 17:15:38 +0000 (17:15 +0000)]
JAL-3551 patch superpose test for additional undo dis/enable commands
Jim Procter [Thu, 17 Feb 2022 17:10:50 +0000 (17:10 +0000)]
JAL-3823 JAL-3830 update gradle plugin for install4j to 9.0.6
git://source.jalview.org / jalview.git / log