Jim Procter [Tue, 5 Jul 2022 21:53:03 +0000 (22:53 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Jul 2022 21:52:27 +0000 (22:52 +0100)]
JAL-4012 release date bump and JAL-4004 tweak to include current version in generated whatsNew.html
Jim Procter [Mon, 4 Jul 2022 14:59:58 +0000 (15:59 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Mon, 4 Jul 2022 14:58:04 +0000 (15:58 +0100)]
JAL-4012 updated release date and whats new for 2.11.2.3
Jim Procter [Fri, 1 Jul 2022 13:12:45 +0000 (14:12 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 1 Jul 2022 13:08:52 +0000 (14:08 +0100)]
JAL-4012 tweak release notes wording for legacy.uniprot
Jim Procter [Fri, 1 Jul 2022 12:55:20 +0000 (13:55 +0100)]
Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop
Jim Procter [Fri, 1 Jul 2022 12:44:40 +0000 (13:44 +0100)]
JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new
Jim Procter [Thu, 30 Jun 2022 16:37:02 +0000 (17:37 +0100)]
JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)
Ben Soares [Tue, 28 Jun 2022 12:32:51 +0000 (13:32 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop
Ben Soares [Tue, 28 Jun 2022 12:31:55 +0000 (13:31 +0100)]
JAL-1988 Don't put Quit in the File menu if there's a handler for it
Ben Soares [Thu, 23 Jun 2022 15:02:46 +0000 (16:02 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop
Ben Soares [Thu, 23 Jun 2022 14:28:46 +0000 (15:28 +0100)]
JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void
Ben Soares [Fri, 17 Jun 2022 16:10:52 +0000 (17:10 +0100)]
JAL-3027 Avoid FlatLAF Desktop class is JalviewJS
Jim Procter [Wed, 15 Jun 2022 15:17:59 +0000 (16:17 +0100)]
JAL-4012 release notes for JAL-1988,JAL-3416
Jim Procter [Wed, 15 Jun 2022 14:54:56 +0000 (15:54 +0100)]
JAL-1988 JAL-3416 avoid unnecessary static flag
Jim Procter [Wed, 15 Jun 2022 14:54:19 +0000 (15:54 +0100)]
JAL-3418 JAL-1988 don’t need java version check anymore
Jim Procter [Wed, 15 Jun 2022 14:41:53 +0000 (15:41 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop
Ben Soares [Mon, 13 Jun 2022 17:32:22 +0000 (18:32 +0100)]
JAL-1988 Hack to ensure Quit dialog box is moved to front
Ben Soares [Mon, 13 Jun 2022 17:14:11 +0000 (18:14 +0100)]
JAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop. Use result to not add About and Preferences to normal menus.
Ben Soares [Mon, 13 Jun 2022 16:22:52 +0000 (17:22 +0100)]
Merge branch 'develop' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
Ben Soares [Mon, 13 Jun 2022 15:20:12 +0000 (16:20 +0100)]
JAL-4004 Fix missing whatsNew.html when not building with RELEASE channel set
Jim Procter [Mon, 13 Jun 2022 11:24:07 +0000 (12:24 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option
Jim Procter [Mon, 13 Jun 2022 11:22:31 +0000 (12:22 +0100)]
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler
Ben Soares [Mon, 13 Jun 2022 10:43:35 +0000 (11:43 +0100)]
JAL-3416 remove flat as default for linux
Ben Soares [Mon, 13 Jun 2022 10:20:50 +0000 (11:20 +0100)]
JAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system to set APQhandler for both J9+ and now Java 8
Ben Soares [Mon, 13 Jun 2022 10:18:31 +0000 (11:18 +0100)]
JAL-3416 Added some mac specific FlatLAF settings. Note this is not the default macOS LaF, this is only when -Dlaf=flat is set on a mac when running Jalview
Ben Soares [Mon, 13 Jun 2022 10:17:04 +0000 (11:17 +0100)]
JAL-3416 updated FlatLAF libraries to 2.3. Added the flatlaf-extras library
Jim Procter [Thu, 9 Jun 2022 13:37:56 +0000 (14:37 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 9 Jun 2022 13:25:39 +0000 (14:25 +0100)]
JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation
Jim Procter [Thu, 9 Jun 2022 13:07:04 +0000 (14:07 +0100)]
Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop
Jim Procter [Thu, 9 Jun 2022 13:03:55 +0000 (14:03 +0100)]
JAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore
Jim Procter [Thu, 9 Jun 2022 11:37:18 +0000 (12:37 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 9 Jun 2022 11:35:26 +0000 (12:35 +0100)]
JAL-4014 release notes for JAL-4026 patches
Jim Procter [Thu, 9 Jun 2022 11:16:08 +0000 (12:16 +0100)]
JAL-4026 increase timeouts for command line ops
Jim Procter [Thu, 9 Jun 2022 10:20:22 +0000 (11:20 +0100)]
JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them
Jim Procter [Thu, 9 Jun 2022 09:38:44 +0000 (10:38 +0100)]
JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.
Jim Procter [Thu, 9 Jun 2022 07:18:31 +0000 (08:18 +0100)]
JAL-4026 update the viewport’s wrapped width after calculating it
Jim Procter [Wed, 8 Jun 2022 15:32:14 +0000 (16:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Wed, 8 Jun 2022 14:17:16 +0000 (15:17 +0100)]
JAL-4014 release notes for JAL-4023 and JAL-4024
Jim Procter [Wed, 8 Jun 2022 14:11:27 +0000 (15:11 +0100)]
Merge branch 'improvement/JAL-4023_snotation_for_trees' into develop
Jim Procter [Wed, 8 Jun 2022 14:11:01 +0000 (15:11 +0100)]
Merge branch 'patch/JAL-4024_jumpScrollHang' into develop
Jim Procter [Wed, 8 Jun 2022 14:04:44 +0000 (15:04 +0100)]
JAL-4012 what’s new and release notes (in the new styleee!) for JAL-4004, JAL-3989 and JAL-3553
Jim Procter [Wed, 8 Jun 2022 13:42:48 +0000 (14:42 +0100)]
JAL-4004 delete temporary file mistakenly checked in
Jim Procter [Wed, 8 Jun 2022 13:01:17 +0000 (14:01 +0100)]
Merge branch 'issues/JAL-3553+JAL-3978+JAL-3989+JAL-4004_merged_with_develop' into develop
Jim Procter [Wed, 8 Jun 2022 12:10:42 +0000 (13:10 +0100)]
JAL-4024 only render partially when new view overlaps with last rendered annotation panel view
Ben Soares [Tue, 7 Jun 2022 13:14:53 +0000 (14:14 +0100)]
JAL-4020 class formatting
Ben Soares [Tue, 7 Jun 2022 09:13:29 +0000 (10:13 +0100)]
JAL-4020 added the \Scripts\pymol.exe. to the pathList
Ben Soares [Mon, 6 Jun 2022 18:56:53 +0000 (19:56 +0100)]
JAL-4020 Added the +2 arg for PyMOLWin.exe allowing older versions of PyMOL
Ben Soares [Mon, 6 Jun 2022 16:00:03 +0000 (17:00 +0100)]
JAL-4020 updated tests
Ben Soares [Mon, 6 Jun 2022 15:35:08 +0000 (16:35 +0100)]
JAL-4020 class reformatting
Ben Soares [Mon, 6 Jun 2022 13:54:43 +0000 (14:54 +0100)]
JAL-4020 Added path search for global installation path and older version installation paths
Jim Procter [Mon, 6 Jun 2022 13:09:01 +0000 (14:09 +0100)]
JAL-4023 use %g for distances (scientific notation for very small or large values)
Ben Soares [Mon, 6 Jun 2022 13:03:50 +0000 (14:03 +0100)]
JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places starting with default install dir. Added a new version (1.3) to ChimeraX
Jim Procter [Mon, 6 Jun 2022 11:22:03 +0000 (12:22 +0100)]
JAL-4023 store distances as doubles
Ben Soares [Thu, 12 May 2022 15:06:59 +0000 (16:06 +0100)]
Merge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_develop
Took Issues Resolved (1 issue) from releases.html 2.11.2.3 row and put
in help/markdown/releases/release-2_11_2_3.md
and regenerated releases.html with
gradle releasesTemplates
Jim Procter [Wed, 11 May 2022 14:50:10 +0000 (15:50 +0100)]
Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3
Jim Procter [Wed, 11 May 2022 12:44:36 +0000 (13:44 +0100)]
JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3
Jim Procter [Tue, 10 May 2022 16:56:51 +0000 (17:56 +0100)]
JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !
Jalview Development Admin [Tue, 10 May 2022 11:17:28 +0000 (12:17 +0100)]
Merge branch 'releases/Release_2_11_2_Branch'
Ben Soares [Tue, 10 May 2022 09:06:38 +0000 (10:06 +0100)]
JAL-4004 cosmetic improvements for Java documentation renderer
Ben Soares [Mon, 9 May 2022 22:21:27 +0000 (23:21 +0100)]
JAL-4004 gradle task releasesTemplates now part of main build dependency tree. Improvements to releases.html.
Ben Soares [Mon, 9 May 2022 22:19:45 +0000 (23:19 +0100)]
JAL-4004 working templates and generated whatsNew.html and releases.html file for both browser and Doc viewer
Ben Soares [Mon, 9 May 2022 21:58:46 +0000 (22:58 +0100)]
JAL-4004 remove stray empty h3 headers
Ben Soares [Mon, 9 May 2022 18:23:06 +0000 (19:23 +0100)]
JAL-4004 gradle releasesTemplates builds releases.html
Ben Soares [Mon, 9 May 2022 11:27:27 +0000 (12:27 +0100)]
JAL-4004 Temporary mechanism to add JalviewJS link for selected versions to hugo website
Ben Soares [Mon, 9 May 2022 10:33:27 +0000 (11:33 +0100)]
JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time in release date header
Ben Soares [Thu, 5 May 2022 16:02:39 +0000 (17:02 +0100)]
JAL-4004 Now generating hugo files from help/markdown/...
Ben Soares [Wed, 4 May 2022 13:45:07 +0000 (14:45 +0100)]
JAL-4004 existing releases-VERSION.md files and releases.html template
Ben Soares [Wed, 4 May 2022 00:18:03 +0000 (01:18 +0100)]
JAL-4004 locations for markdown to go into whatsnew.html, releases.html and Version-VERSION/_index.md
Ben Soares [Tue, 3 May 2022 11:35:42 +0000 (12:35 +0100)]
JAL-3989 improved parsing and formatting now using flex CSS layout for columns
Ben Soares [Tue, 3 May 2022 11:35:04 +0000 (12:35 +0100)]
JAL-1544 minor errors in releases.html and one missing version (2.8.2b1)
Ben Soares [Fri, 29 Apr 2022 12:29:17 +0000 (13:29 +0100)]
JAL-3989 small improvements to output markdown
Ben Soares [Thu, 28 Apr 2022 13:47:55 +0000 (14:47 +0100)]
JAL-3989 add in issue shortcodes to the archive version page changes list
Ben Soares [Wed, 27 Apr 2022 22:41:20 +0000 (23:41 +0100)]
JAL-1544 version number typo, probably copy and paste
Ben Soares [Wed, 27 Apr 2022 22:39:34 +0000 (23:39 +0100)]
JAL-3989 Populate template files for hugo build: archive version files including changes from releases.html, and installers data file
Ben Soares [Mon, 25 Apr 2022 19:32:54 +0000 (20:32 +0100)]
JAL-3989 moved getdown build dirs to build/website/docroot/getdown/CHANNEL, build/website/docroot/old/VERSION and build/getdown/files, and files for hugo into build/website/hugo/... This is better in multiple ways including collating files needed for the hugo website and website docroot.
Ben Soares [Mon, 25 Apr 2022 16:58:56 +0000 (17:58 +0100)]
JAL-3989 Independent creation of JSON installer sections
Ben Soares [Mon, 25 Apr 2022 14:03:49 +0000 (15:03 +0100)]
JAL-3978 clean up unnecessary local variables for JALVIEW_VERSION_UNDERSCORES
Ben Soares [Fri, 22 Apr 2022 15:17:09 +0000 (16:17 +0100)]
JAL-3989 Changed to using com.google.common.hash for SHA256 sum, for gradle 7 compatibility
Ben Soares [Thu, 21 Apr 2022 19:24:35 +0000 (20:24 +0100)]
Merge branch 'develop' into merge/JAL-3978+JAL-3553+develop+JAL-3989
Jim Procter [Tue, 19 Apr 2022 14:04:00 +0000 (15:04 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 19 Apr 2022 14:03:23 +0000 (15:03 +0100)]
JAL-3992 bump version and report updates in 2.11.2.2 release notes
Jim Procter [Tue, 19 Apr 2022 14:02:17 +0000 (15:02 +0100)]
Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop
Jim Procter [Tue, 19 Apr 2022 13:57:56 +0000 (14:57 +0100)]
Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop
Jim Procter [Mon, 18 Apr 2022 13:49:47 +0000 (14:49 +0100)]
JAL-3997 check for tooltip being null before checking equivalence to last tooltip string
Jim Procter [Mon, 18 Apr 2022 12:27:14 +0000 (13:27 +0100)]
Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm
Jim Procter [Mon, 18 Apr 2022 11:51:59 +0000 (12:51 +0100)]
JAL-3992 fix path
Jim Procter [Sat, 16 Apr 2022 12:36:06 +0000 (13:36 +0100)]
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files
Jim Procter [Wed, 13 Apr 2022 15:13:40 +0000 (16:13 +0100)]
JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode
Jim Procter [Tue, 5 Apr 2022 19:48:38 +0000 (20:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 19:44:48 +0000 (20:44 +0100)]
JAL-3990 release notes and what’s new
Jim Procter [Tue, 5 Apr 2022 17:50:33 +0000 (18:50 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 17:37:11 +0000 (18:37 +0100)]
JAL-3981 patch tests and remove errant imports
Jim Procter [Tue, 5 Apr 2022 17:15:28 +0000 (18:15 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 5 Apr 2022 17:14:52 +0000 (18:14 +0100)]
JAL-3990 gradle spotlessApply
Jim Procter [Tue, 5 Apr 2022 17:12:13 +0000 (18:12 +0100)]
JAL-3990 release notes for 2.11.2.1 patch release
Jim Procter [Tue, 5 Apr 2022 16:57:40 +0000 (17:57 +0100)]
Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop
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.
git://source.jalview.org / jalview.git / log