Jim Procter [Wed, 11 Sep 2024 14:44:03 +0000 (15:44 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 11 Sep 2024 14:34:09 +0000 (15:34 +0100)]
JAL-4418 JAL-4428,JAL-4421,JAL-3393 release notes
Jim Procter [Wed, 11 Sep 2024 14:29:08 +0000 (15:29 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Jim Procter [Wed, 11 Sep 2024 14:25:52 +0000 (15:25 +0100)]
JAL-4428 codesign jnilibs
Jim Procter [Wed, 11 Sep 2024 14:25:21 +0000 (15:25 +0100)]
JAL-4428 informational output (possibly needs verbosity control)
Jim Procter [Wed, 11 Sep 2024 14:24:54 +0000 (15:24 +0100)]
JAL-4428 giving another XXX
Jim Procter [Wed, 11 Sep 2024 14:23:46 +0000 (15:23 +0100)]
JAL-4428 add some XXXX for mktemp -t
Ben Soares [Wed, 11 Sep 2024 10:21:07 +0000 (11:21 +0100)]
JAL-4428 Fixes to -z's and mktemp
Jim Procter [Tue, 10 Sep 2024 16:21:35 +0000 (17:21 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 10 Sep 2024 16:17:17 +0000 (17:17 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Jim Procter [Tue, 10 Sep 2024 15:25:27 +0000 (16:25 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Tue, 10 Sep 2024 15:24:26 +0000 (16:24 +0100)]
JAL-4454 allow channels to pick up most recent 'whatsNew' and releasenotes for their associated version
Jim Procter [Mon, 9 Sep 2024 17:13:49 +0000 (18:13 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Mon, 9 Sep 2024 17:12:06 +0000 (18:12 +0100)]
JAL-4418 initial pasimap documentation and updated release notes for recent merges
Jim Procter [Mon, 9 Sep 2024 14:37:16 +0000 (15:37 +0100)]
JAL-4418 postpone release to Thursday 12th Sept 2024
Jim Procter [Tue, 3 Sep 2024 14:08:47 +0000 (15:08 +0100)]
JAL-4386 remove magic string in registerScoreModel...
Jim Procter [Mon, 2 Sep 2024 16:53:11 +0000 (17:53 +0100)]
JAL-4418 fix linkCheck
Jim Procter [Mon, 2 Sep 2024 16:47:59 +0000 (17:47 +0100)]
JAL-4418 release 10th September
Jim Procter [Mon, 2 Sep 2024 16:46:56 +0000 (17:46 +0100)]
Merge branch 'documentation/JAL-4418_2_11_4_0_docs' into develop
Jim Procter [Mon, 2 Sep 2024 16:46:49 +0000 (17:46 +0100)]
Merge branch 'feature/JAL-4446_cancellable_pasimap_etal' into develop
Jim Procter [Mon, 2 Sep 2024 16:34:02 +0000 (17:34 +0100)]
JAL-4418 first pass at updating docs with pasimap, ssconservation, etc
Jim Procter [Thu, 29 Aug 2024 15:39:04 +0000 (16:39 +0100)]
JAL-4446 improved reporting of progress, and transition between cancelable and non-cancelable phases of pasimap calculation
Jim Procter [Thu, 29 Aug 2024 13:19:37 +0000 (14:19 +0100)]
JAL-4446 refactor progress listener handler code for reuse
Jim Procter [Thu, 29 Aug 2024 12:46:37 +0000 (13:46 +0100)]
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
Jim Procter [Wed, 28 Aug 2024 13:20:37 +0000 (14:20 +0100)]
JAL-4418 tweak release notes for JAL-4328
Jim Procter [Wed, 28 Aug 2024 13:19:34 +0000 (14:19 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Wed, 28 Aug 2024 12:54:18 +0000 (13:54 +0100)]
JAL-3631 Allow use of ~/ for unixBinDir specified in response.varfile
Ben Soares [Wed, 28 Aug 2024 12:17:06 +0000 (13:17 +0100)]
JAL-3631 Allow unixBinDir (where a symbolic link gets made) to be set in response.varfile. If it's not set or empty then the usual (dynamic) default will be ascertained. Disallow reading in certain variables from the response.varfile that would just mess up the installation if changed.
Ben Soares [Wed, 28 Aug 2024 11:41:37 +0000 (12:41 +0100)]
JAL-3631 Configuration tweaks if using the response.varfile
Ben Soares [Wed, 28 Aug 2024 10:53:00 +0000 (11:53 +0100)]
JAL-3631 Adjustments to allow setting the Advanced options in the response.varfile. Also big improvement on setting sys.fileAssociation.launchers automatically so only sys.fileAssociation.extensions needs to be set in a response.varfile.
Ben Soares [Mon, 26 Aug 2024 18:36:56 +0000 (19:36 +0100)]
JAL-3631 Fix interpolatove quotation marks in grep in jalview.sh. Fix some folder name trailing slash checks in macos_install_jalview.sh, add ditto -v and more informative output.
Ben Soares [Mon, 26 Aug 2024 18:31:43 +0000 (19:31 +0100)]
JAL-3631 Fix interpolative quotation marks in new grep
Jim Procter [Mon, 26 Aug 2024 16:50:33 +0000 (17:50 +0100)]
Merge branch 'jims/JAL-4420_review_redo' into develop
Ben Soares [Mon, 26 Aug 2024 16:44:30 +0000 (17:44 +0100)]
JAL-3631 When appdir/jre can't be found, look for the installer.appdir found in installer.properties (if it exists) and use jre dir in installer.appdir
Ben Soares [Mon, 26 Aug 2024 16:43:29 +0000 (17:43 +0100)]
JAL-3631 Create an installer.properties file in the userappdir
Jim Procter [Mon, 26 Aug 2024 16:33:02 +0000 (17:33 +0100)]
JAL-4418 JAL-4420 is experimental feature
Jim Procter [Mon, 26 Aug 2024 16:30:37 +0000 (17:30 +0100)]
JAL-4420 new drag'n'drop behaviour is now an 'Experimental Feature'
Jim Procter [Mon, 26 Aug 2024 15:34:49 +0000 (16:34 +0100)]
JAL-4420 report exceptions raised during a drop rather than swallowing them
Jim Procter [Mon, 26 Aug 2024 14:18:44 +0000 (15:18 +0100)]
JAL-4418 release notes for JAL-4398 and rejigged order a bit
Jim Procter [Mon, 26 Aug 2024 13:55:10 +0000 (14:55 +0100)]
Merge branch 'bug/JAL-4398_Window_menu_font_rendering' into develop
Jim Procter [Fri, 23 Aug 2024 14:49:48 +0000 (15:49 +0100)]
Merge branch 'develop' into bug/JAL-4449_ensembl_sequence_retrieval_broken
Jim Procter [Fri, 23 Aug 2024 14:48:26 +0000 (15:48 +0100)]
JAL-4449 signed off and also updated Ensembl REST API version after fixing the EnsemblGene BRAF query test: JAL-3018
Jim Procter [Fri, 23 Aug 2024 14:10:07 +0000 (15:10 +0100)]
JAL-4418 JAL-3064 JAL-4111 release notes
Ben Soares [Thu, 22 Aug 2024 16:44:04 +0000 (17:44 +0100)]
JAL-4449 Changed HttpUtils.followConnection(conn0) to return conn0 unused when there is not a redirect from http to https, otherwise to return a new unused connection directly to the new https URL
Jim Procter [Thu, 22 Aug 2024 16:22:47 +0000 (17:22 +0100)]
JAL-4418 JAL-4450 known issue for 2.11.4 and 2.11.3.3
Jim Procter [Thu, 22 Aug 2024 13:50:20 +0000 (14:50 +0100)]
JAL-4418 JAL-4100 ncrna genbank as known issue
Ben Soares [Mon, 19 Aug 2024 16:33:16 +0000 (17:33 +0100)]
JAL-4428 README.md file for sign_and_stapled_dmg.sh
Jim Procter [Mon, 19 Aug 2024 16:13:24 +0000 (17:13 +0100)]
JAL-789 limit applicable score models to substitution matrix based ones
Ben Soares [Mon, 19 Aug 2024 16:08:12 +0000 (17:08 +0100)]
JAL-3631 Change macos-install-jalview.sh to use ditto instead of Localise function vars.
Jim Procter [Mon, 19 Aug 2024 16:03:29 +0000 (17:03 +0100)]
JAL-4446 allow progress bar to become indeterminate after pairwise alignment step
Jim Procter [Mon, 19 Aug 2024 15:12:56 +0000 (16:12 +0100)]
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
Ben Soares [Mon, 19 Aug 2024 09:30:42 +0000 (10:30 +0100)]
JAL-4428 localise function vars. Add -q -q option. Fix detaching volumes for cleanup -C
Ben Soares [Sun, 18 Aug 2024 23:50:05 +0000 (00:50 +0100)]
JAL-4428 More coherent command line options and better 'running command' stdout management
Ben Soares [Sat, 17 Aug 2024 00:57:55 +0000 (01:57 +0100)]
JAL-4428 Added in stapling into (now) sign_and_staple_dmg.sh. Some other small improvements to the script.
Ben Soares [Fri, 16 Aug 2024 17:36:32 +0000 (18:36 +0100)]
JAL-4428 sign_dmg.sh with bells on
Ben Soares [Fri, 16 Aug 2024 11:06:50 +0000 (12:06 +0100)]
JAL-3631 Fix EnvConfig.getUserAppdir() in getdown when running the getdown-launcher.jar update
Ben Soares [Thu, 15 Aug 2024 20:31:02 +0000 (21:31 +0100)]
JAL-3631 Create a jalview_x_update link in appdir/bin alongside jalview_x in install4j wizard
Ben Soares [Thu, 15 Aug 2024 20:18:52 +0000 (21:18 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Tue, 13 Aug 2024 17:50:44 +0000 (18:50 +0100)]
JAL-4111 Remove unnecessary dependency on gradle-imagemagick plugin, as causing problems in repo on Windows
Ben Soares [Mon, 12 Aug 2024 13:03:25 +0000 (14:03 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Thu, 8 Aug 2024 09:35:43 +0000 (10:35 +0100)]
JAL-3631 Better messaging and a root check on updating the --installation
Ben Soares [Thu, 8 Aug 2024 09:27:27 +0000 (10:27 +0100)]
JAL-3631 Change name of update link in DMGs. Correct wrong message in macos installer script. Adding build_properties and channel.props into hidden folder on DMG. I'm sure they will be useful!
Jim Procter [Wed, 7 Aug 2024 16:48:14 +0000 (17:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Wed, 7 Aug 2024 16:31:16 +0000 (17:31 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Jim Procter [Wed, 7 Aug 2024 16:16:25 +0000 (17:16 +0100)]
JAL-4447 standardised title formula for reporting score model and other parameters for pairwise alignment, PCA, tree, and Pasimap
Jim Procter [Wed, 7 Aug 2024 14:11:40 +0000 (15:11 +0100)]
JAL-4446 reuse lasteta value
Jim Procter [Wed, 7 Aug 2024 14:11:03 +0000 (15:11 +0100)]
JAL-4159 JAL-789 report pasimap and pairwise alignment parameters in window title
Jim Procter [Wed, 7 Aug 2024 14:09:55 +0000 (15:09 +0100)]
JAL-4159 suppress pairwise alignment display options when not available from pasimap
Jim Procter [Wed, 7 Aug 2024 14:07:51 +0000 (15:07 +0100)]
JAL-4446 better reporting of ETA estimation - particularly for large alignments
Ben Soares [Tue, 6 Aug 2024 23:50:30 +0000 (00:50 +0100)]
JAL-3631 Made bespoke command line arguments for console or unattended installs only (i.e. not GUI install mode), and work consistently with macos-install-jalview.sh
Ben Soares [Tue, 6 Aug 2024 19:13:17 +0000 (20:13 +0100)]
JAL-3631 Added install4j installer command line options -a -u -U and -S to match the macos-install-jalview.sh script
Ben Soares [Tue, 6 Aug 2024 18:02:25 +0000 (19:02 +0100)]
JAL-3631 Important change to Execution Level in Windows. Some disabled attempts at File Association Reset.
Ben Soares [Tue, 6 Aug 2024 14:08:33 +0000 (15:08 +0100)]
JAL-3631 Short sleep added to 100% progress on installer wizard
Ben Soares [Tue, 6 Aug 2024 12:29:17 +0000 (13:29 +0100)]
JAL-3631 An attempt to add a Reset to defaults button on the File Associations screen, but no joy (yet). Useful changes to customizedIds left in
Jim Procter [Tue, 6 Aug 2024 11:06:49 +0000 (12:06 +0100)]
JAL-4446 avoid NPE when progress bar message is null
Ben Soares [Tue, 6 Aug 2024 11:05:37 +0000 (12:05 +0100)]
JAL-3631 Some small but important changes to run_other_script.ps1
Ben Soares [Mon, 5 Aug 2024 22:49:05 +0000 (23:49 +0100)]
JAL-3631 JAL-4444 Change way we add the jalview_x and jalview_x_update PS1 and BAT files, moved into build.gradle and removed from install4j. Add title icon to install4j.
Ben Soares [Mon, 5 Aug 2024 22:46:03 +0000 (23:46 +0100)]
JAL-3631 Icons for installer wizard title bar
Ben Soares [Mon, 5 Aug 2024 18:21:16 +0000 (19:21 +0100)]
JAL-3631 update.ps1 has fixed Readlink-f function, works across platforms
Ben Soares [Mon, 5 Aug 2024 18:20:46 +0000 (19:20 +0100)]
JAL-3631 Revert the Jalview installer icon back to the Jalview icon
Jim Procter [Mon, 5 Aug 2024 17:42:04 +0000 (18:42 +0100)]
JAL-1551 source formatting and header
Jim Procter [Mon, 5 Aug 2024 17:41:40 +0000 (18:41 +0100)]
JAL-4446 .. missing methods for cancellable pasimap
Jim Procter [Mon, 5 Aug 2024 17:40:18 +0000 (18:40 +0100)]
JAL-4446 cancellable Pasimap - still need to make the actual pasimap CCA calculation cancellable and report progress
Jim Procter [Mon, 5 Aug 2024 17:39:23 +0000 (18:39 +0100)]
JAL-4446 calculate and report PaSiMap ETA in progress bar
Jim Procter [Mon, 5 Aug 2024 17:01:47 +0000 (18:01 +0100)]
JAL-4446 allow progress bar message to be changed whilst progress continues & todo re desktop's custom progress implementation
Jim Procter [Mon, 5 Aug 2024 15:17:48 +0000 (16:17 +0100)]
JAL-1551 apply GPLv3 for source files
Jim Procter [Mon, 5 Aug 2024 15:14:37 +0000 (16:14 +0100)]
JAL-1551 gradle spotlessApply and doc tweaks
Ben Soares [Mon, 5 Aug 2024 14:40:17 +0000 (15:40 +0100)]
JAL-3631 Adjustment to wizard size (was too big in Windows) and add 'Administrator mode' label to installation progress screen
Jim Procter [Mon, 5 Aug 2024 11:48:54 +0000 (12:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Mon, 5 Aug 2024 11:48:39 +0000 (12:48 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Fri, 2 Aug 2024 16:49:18 +0000 (17:49 +0100)]
JAL-3631 made Readlink-f work in powershell. Need to test once more in Windows\!
Jim Procter [Fri, 2 Aug 2024 15:48:46 +0000 (16:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_4_Branch
Jim Procter [Fri, 2 Aug 2024 15:47:31 +0000 (16:47 +0100)]
JAL-4418 release note for JAL-3063 doc/jalview-projects.md
Jim Procter [Fri, 2 Aug 2024 15:41:03 +0000 (16:41 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Fri, 2 Aug 2024 15:06:22 +0000 (16:06 +0100)]
JAL-3631 update.sh script fixed to work in Windows (11)
Ben Soares [Thu, 1 Aug 2024 19:57:51 +0000 (20:57 +0100)]
JAL-3631 Administrator mode label on all screens of wizard
Ben Soares [Thu, 1 Aug 2024 16:24:00 +0000 (17:24 +0100)]
JAL-3631 Added a test for a specified update and a usage line. update.ps1 tested on macos
Ben Soares [Thu, 1 Aug 2024 15:34:01 +0000 (16:34 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Thu, 1 Aug 2024 15:33:39 +0000 (16:33 +0100)]
JAL-3631 Small change to update.sh. update.ps1 NOT COMPLETED YET
Ben Soares [Thu, 1 Aug 2024 15:15:11 +0000 (16:15 +0100)]
JAL-3631 Remove a debug echo