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 14:03:23 +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.
Jim Procter [Thu, 31 Mar 2022 22:11:44 +0000 (23:11 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 31 Mar 2022 19:44:49 +0000 (20:44 +0100)]
JAL-3983 release note for JAL-3985
Jim Procter [Thu, 31 Mar 2022 19:42:53 +0000 (20:42 +0100)]
Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop
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 [Thu, 31 Mar 2022 14:17:46 +0000 (15:17 +0100)]
JAL-3085 update tests and mock responses, new P0dtd1 testcase
Jim Procter [Thu, 31 Mar 2022 13:06:28 +0000 (14:06 +0100)]
JAL-3985 formatting
Jim Procter [Thu, 31 Mar 2022 13:06:04 +0000 (14:06 +0100)]
JAL-3985 split PDB id queries into multiple queries so server doesn’t 414
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 [Fri, 25 Mar 2022 14:31:18 +0000 (14:31 +0000)]
JAL-3980 JAL-3979 TODOs
Jim Procter [Fri, 25 Mar 2022 14:30:17 +0000 (14:30 +0000)]
JAL-3980 defensive copy - inefficient but fixes bug
Jim Procter [Fri, 25 Mar 2022 14:16:21 +0000 (14:16 +0000)]
JAL-3981 Additional line breaks - sort of helps
Jim Procter [Thu, 24 Mar 2022 17:02:10 +0000 (17:02 +0000)]
JAL-3981 strategic newlines to help speed up Java's html parser
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
git://source.jalview.org / jalview.git / log