jalview.git
9 days agoJAL-4454 allow channels to pick up most recent 'whatsNew' and releasenotes for their...
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

10 days agoJAL-4418 initial pasimap documentation and updated release notes for recent merges
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

10 days agoJAL-4418 postpone release to Thursday 12th Sept 2024
Jim Procter [Mon, 9 Sep 2024 14:37:16 +0000 (15:37 +0100)]
JAL-4418 postpone release to Thursday 12th Sept 2024

2 weeks agoJAL-4386 remove magic string in registerScoreModel...
Jim Procter [Tue, 3 Sep 2024 14:08:47 +0000 (15:08 +0100)]
JAL-4386 remove magic string in registerScoreModel...

2 weeks agoJAL-4418 fix linkCheck documentation/JAL-4418_2_11_4_0_docs
Jim Procter [Mon, 2 Sep 2024 16:53:11 +0000 (17:53 +0100)]
JAL-4418 fix linkCheck

2 weeks agoJAL-4418 release 10th September
Jim Procter [Mon, 2 Sep 2024 16:47:59 +0000 (17:47 +0100)]
JAL-4418 release 10th September

2 weeks agoMerge branch 'documentation/JAL-4418_2_11_4_0_docs' into develop
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

2 weeks agoMerge branch 'feature/JAL-4446_cancellable_pasimap_etal' 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

2 weeks agoJAL-4418 first pass at updating docs with pasimap, ssconservation, etc
Jim Procter [Mon, 2 Sep 2024 16:34:02 +0000 (17:34 +0100)]
JAL-4418 first pass at updating docs with pasimap, ssconservation, etc

3 weeks agoJAL-4446 improved reporting of progress, and transition between cancelable and non... feature/JAL-4446_cancellable_pasimap_etal
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

3 weeks agoJAL-4446 refactor progress listener handler code for reuse
Jim Procter [Thu, 29 Aug 2024 13:19:37 +0000 (14:19 +0100)]
JAL-4446 refactor progress listener handler code for reuse

3 weeks agoMerge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
Jim Procter [Thu, 29 Aug 2024 12:46:37 +0000 (13:46 +0100)]
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal

3 weeks agoJAL-4418 tweak release notes for JAL-4328
Jim Procter [Wed, 28 Aug 2024 13:20:37 +0000 (14:20 +0100)]
JAL-4418 tweak release notes for JAL-4328

3 weeks agoMerge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into...
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

3 weeks agoJAL-3631 Allow use of ~/ for unixBinDir specified in response.varfile feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Wed, 28 Aug 2024 12:54:18 +0000 (13:54 +0100)]
JAL-3631 Allow use of ~/ for unixBinDir specified in response.varfile

3 weeks agoJAL-3631 Allow unixBinDir (where a symbolic link gets made) to be set in response...
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.

3 weeks agoJAL-3631 Configuration tweaks if using the response.varfile
Ben Soares [Wed, 28 Aug 2024 11:41:37 +0000 (12:41 +0100)]
JAL-3631 Configuration tweaks if using the response.varfile

3 weeks agoJAL-3631 Adjustments to allow setting the Advanced options in 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.

3 weeks agoJAL-3631 Fix interpolatove quotation marks in grep in jalview.sh. Fix some folder...
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.

3 weeks agoJAL-3631 Fix interpolative quotation marks in new grep
Ben Soares [Mon, 26 Aug 2024 18:31:43 +0000 (19:31 +0100)]
JAL-3631 Fix interpolative quotation marks in new grep

3 weeks agoMerge branch 'jims/JAL-4420_review_redo' into develop
Jim Procter [Mon, 26 Aug 2024 16:50:33 +0000 (17:50 +0100)]
Merge branch 'jims/JAL-4420_review_redo' into develop

3 weeks agoJAL-3631 When appdir/jre can't be found, look for the installer.appdir found in insta...
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

3 weeks agoJAL-3631 Create an installer.properties file in the userappdir
Ben Soares [Mon, 26 Aug 2024 16:43:29 +0000 (17:43 +0100)]
JAL-3631 Create an installer.properties file in the userappdir

3 weeks agoJAL-4418 JAL-4420 is experimental feature jims/JAL-4420_review_redo
Jim Procter [Mon, 26 Aug 2024 16:33:02 +0000 (17:33 +0100)]
JAL-4418 JAL-4420 is experimental feature

3 weeks agoJAL-4420 new drag'n'drop behaviour is now an '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'

3 weeks agoJAL-4420 report exceptions raised during a drop rather than swallowing them
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

3 weeks agoJAL-4418 release notes for JAL-4398 and rejigged order a bit
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

3 weeks agoMerge branch 'bug/JAL-4398_Window_menu_font_rendering' into develop
Jim Procter [Mon, 26 Aug 2024 13:55:10 +0000 (14:55 +0100)]
Merge branch 'bug/JAL-4398_Window_menu_font_rendering' into develop

3 weeks agoMerge branch 'develop' into bug/JAL-4449_ensembl_sequence_retrieval_broken
Jim Procter [Fri, 23 Aug 2024 14:49:48 +0000 (15:49 +0100)]
Merge branch 'develop' into bug/JAL-4449_ensembl_sequence_retrieval_broken

3 weeks agoJAL-4449 signed off and also updated Ensembl REST API version after fixing the Ensemb...
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

3 weeks agoJAL-4418 JAL-3064 JAL-4111 release notes
Jim Procter [Fri, 23 Aug 2024 14:10:07 +0000 (15:10 +0100)]
JAL-4418 JAL-3064 JAL-4111 release notes

4 weeks agoJAL-4449 Changed HttpUtils.followConnection(conn0) to return conn0 unused when there...
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

4 weeks agoJAL-4418 JAL-4450 known issue for 2.11.4 and 2.11.3.3
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

4 weeks agoJAL-4418 JAL-4100 ncrna genbank as known issue
Jim Procter [Thu, 22 Aug 2024 13:50:20 +0000 (14:50 +0100)]
JAL-4418 JAL-4100 ncrna genbank as known issue

4 weeks agoJAL-789 limit applicable score models to substitution matrix based ones
Jim Procter [Mon, 19 Aug 2024 16:13:24 +0000 (17:13 +0100)]
JAL-789 limit applicable score models to substitution matrix based ones

4 weeks agoJAL-3631 Change macos-install-jalview.sh to use ditto instead of rsync. Localise...
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.

4 weeks agoJAL-4446 allow progress bar to become indeterminate after pairwise alignment step
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

4 weeks agoMerge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
Jim Procter [Mon, 19 Aug 2024 15:12:56 +0000 (16:12 +0100)]
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal

5 weeks agoJAL-3631 Fix EnvConfig.getUserAppdir() in getdown when running the getdown-launcher...
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

5 weeks agoJAL-3631 Create a jalview_x_update link in appdir/bin alongside jalview_x in install4...
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

5 weeks agoMerge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_di...
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

5 weeks agoJAL-4111 Remove unnecessary dependency on gradle-imagemagick plugin, as causing probl...
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

5 weeks agoMerge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_di...
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

6 weeks agoJAL-3631 Better messaging and a root check on updating the --installation
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

6 weeks agoJAL-3631 Change name of update link in DMGs. Correct wrong message in macos installer...
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!

6 weeks agoMerge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into...
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

6 weeks agoJAL-4447 standardised title formula for reporting score model and other parameters...
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

6 weeks agoJAL-4446 reuse lasteta value
Jim Procter [Wed, 7 Aug 2024 14:11:40 +0000 (15:11 +0100)]
JAL-4446 reuse lasteta value

6 weeks agoJAL-4159 JAL-789 report pasimap and pairwise alignment parameters in window title
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

6 weeks agoJAL-4159 suppress pairwise alignment display options when not available from pasimap
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

6 weeks agoJAL-4446 better reporting of ETA estimation - particularly for large alignments
Jim Procter [Wed, 7 Aug 2024 14:07:51 +0000 (15:07 +0100)]
JAL-4446 better reporting of ETA estimation - particularly for large alignments

6 weeks agoJAL-3631 Made bespoke command line arguments for console or unattended installs only...
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

6 weeks agoJAL-3631 Added install4j installer command line options -a -u -U and -S to match...
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

6 weeks agoJAL-3631 Important change to Execution Level in Windows. Some disabled attempts at...
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.

6 weeks agoJAL-3631 Short sleep added to 100% progress on installer wizard
Ben Soares [Tue, 6 Aug 2024 14:08:33 +0000 (15:08 +0100)]
JAL-3631 Short sleep added to 100% progress on installer wizard

6 weeks agoJAL-3631 An attempt to add a Reset to defaults button on the File Associations screen...
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

6 weeks agoJAL-4446 avoid NPE when progress bar message is null
Jim Procter [Tue, 6 Aug 2024 11:06:49 +0000 (12:06 +0100)]
JAL-4446 avoid NPE when progress bar message is null

6 weeks agoJAL-3631 Some small but important changes to run_other_script.ps1
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

6 weeks agoJAL-3631 JAL-4444 Change way we add the jalview_x and jalview_x_update PS1 and BAT...
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.

6 weeks agoJAL-3631 Icons for installer wizard title bar
Ben Soares [Mon, 5 Aug 2024 22:46:03 +0000 (23:46 +0100)]
JAL-3631 Icons for installer wizard title bar

6 weeks agoJAL-3631 update.ps1 has fixed Readlink-f function, works across platforms
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

6 weeks agoJAL-3631 Revert the Jalview installer icon back to the Jalview icon
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

6 weeks agoJAL-1551 source formatting and header
Jim Procter [Mon, 5 Aug 2024 17:42:04 +0000 (18:42 +0100)]
JAL-1551 source formatting and header

6 weeks agoJAL-4446 .. missing methods for cancellable pasimap
Jim Procter [Mon, 5 Aug 2024 17:41:40 +0000 (18:41 +0100)]
JAL-4446 .. missing methods for cancellable pasimap

6 weeks agoJAL-4446 cancellable Pasimap - still need to make the actual pasimap CCA calculation...
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

6 weeks agoJAL-4446 calculate and report PaSiMap ETA in progress bar
Jim Procter [Mon, 5 Aug 2024 17:39:23 +0000 (18:39 +0100)]
JAL-4446 calculate and report PaSiMap ETA in progress bar

6 weeks agoJAL-4446 allow progress bar message to be changed whilst progress continues & todo...
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

6 weeks agoJAL-1551 apply GPLv3 for source files
Jim Procter [Mon, 5 Aug 2024 15:17:48 +0000 (16:17 +0100)]
JAL-1551 apply GPLv3 for source files

6 weeks agoJAL-1551 gradle spotlessApply and doc tweaks
Jim Procter [Mon, 5 Aug 2024 15:14:37 +0000 (16:14 +0100)]
JAL-1551 gradle spotlessApply and doc tweaks

6 weeks agoJAL-3631 Adjustment to wizard size (was too big in Windows) and add 'Administrator...
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

6 weeks agoMerge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into...
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

6 weeks agoJAL-3631 made Readlink-f work in powershell. Need to test once more in Windows\!
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\!

6 weeks agoJAL-4418 release note for JAL-3063 doc/jalview-projects.md
Jim Procter [Fri, 2 Aug 2024 15:47:31 +0000 (16:47 +0100)]
JAL-4418 release note for JAL-3063 doc/jalview-projects.md

6 weeks agoMerge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into...
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

6 weeks agoJAL-3631 update.sh script fixed to work in Windows (11)
Ben Soares [Fri, 2 Aug 2024 15:06:22 +0000 (16:06 +0100)]
JAL-3631 update.sh script fixed to work in Windows (11)

7 weeks agoJAL-3631 Administrator mode label on all screens of wizard
Ben Soares [Thu, 1 Aug 2024 19:57:51 +0000 (20:57 +0100)]
JAL-3631 Administrator mode label on all screens of wizard

7 weeks agoJAL-3631 Added a test for a specified update and a usage line. update.ps1 tested...
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

7 weeks agoMerge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_di...
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

7 weeks agoJAL-3631 Small change to update.sh. update.ps1 NOT COMPLETED YET
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

7 weeks agoJAL-3631 Remove a debug echo
Ben Soares [Thu, 1 Aug 2024 15:15:11 +0000 (16:15 +0100)]
JAL-3631 Remove a debug echo

7 weeks agoJAL-4445 - increase the fileglob expected counts
Jim Procter [Thu, 1 Aug 2024 15:14:15 +0000 (16:14 +0100)]
JAL-4445 - increase the fileglob expected counts

7 weeks agoJAL-3631 Convert both CLASSPATHS in update.sh
Ben Soares [Thu, 1 Aug 2024 14:40:56 +0000 (15:40 +0100)]
JAL-3631 Convert both CLASSPATHS in update.sh

7 weeks agoJAL-3631 Separated jalview.sh and update.sh, and included in install4j installer...
Ben Soares [Thu, 1 Aug 2024 14:30:15 +0000 (15:30 +0100)]
JAL-3631 Separated jalview.sh and update.sh, and included in install4j installer and macos DMG.

7 weeks agoMerge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into...
Jim Procter [Thu, 1 Aug 2024 13:57:32 +0000 (14:57 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop

7 weeks agoJAL-3631 Changes to bash launcher to allow headless updates to user-space or installa...
Ben Soares [Wed, 31 Jul 2024 15:38:42 +0000 (16:38 +0100)]
JAL-3631 Changes to bash launcher to allow headless updates to user-space or installation. Added some of this functionality to Powershell (work in progress).  The update functionality is to be separated out to update.sh.

7 weeks agoJAL-3631 Add a (by-passable) confirmation and improved output to the macos-install...
Ben Soares [Wed, 31 Jul 2024 15:37:17 +0000 (16:37 +0100)]
JAL-3631 Add a (by-passable) confirmation and improved output to the macos-install-jalview.sh script, with some corrections

7 weeks agoJAL-3631 Changes to Getdown to call getdown-launcher.jar update without launching...
Ben Soares [Wed, 31 Jul 2024 15:36:01 +0000 (16:36 +0100)]
JAL-3631 Changes to Getdown to call getdown-launcher.jar update without launching Jalview for both installation and user-space

7 weeks agoJAL-3631 Correction to a comment in build.gradle
Ben Soares [Wed, 31 Jul 2024 15:33:03 +0000 (16:33 +0100)]
JAL-3631 Correction to a comment in build.gradle

7 weeks agoJAL-3631 Add --updateuser and --updateinstallation to the jalview.sh script: This...
Ben Soares [Mon, 29 Jul 2024 18:44:49 +0000 (19:44 +0100)]
JAL-3631 Add --updateuser and --updateinstallation to the jalview.sh script: This runs getdown in headless mode to run update of either user or installation appdir without launching Jalview

7 weeks agoJAL-3631 Small corrections
Ben Soares [Mon, 29 Jul 2024 18:43:25 +0000 (19:43 +0100)]
JAL-3631 Small corrections

7 weeks agoJAL-3631 Getdown acknowledges in output when only performing an update
Ben Soares [Mon, 29 Jul 2024 18:42:47 +0000 (19:42 +0100)]
JAL-3631 Getdown acknowledges in output when only performing an update

7 weeks agoJAL-3631 Ensure the DMG default vmoptions.txt has the commented properties
Ben Soares [Mon, 29 Jul 2024 18:06:45 +0000 (19:06 +0100)]
JAL-3631 Ensure the DMG default vmoptions.txt has the commented properties

7 weeks agoJAL-3631 Add PID to console info - only available in Java 9+
Ben Soares [Mon, 29 Jul 2024 18:04:49 +0000 (19:04 +0100)]
JAL-3631 Add PID to console info - only available in Java 9+

7 weeks agoJAL-4443 patch out pasimap in GUI for JalviewJS and note some lines causing java2scri...
Jim Procter [Mon, 29 Jul 2024 16:35:38 +0000 (17:35 +0100)]
JAL-4443 patch out pasimap in GUI for JalviewJS and note some lines causing java2script issues

7 weeks agoJAL-3631 Added an --update option to the jalview.sh launcher (does not launch, just...
Ben Soares [Fri, 26 Jul 2024 16:50:10 +0000 (17:50 +0100)]
JAL-3631 Added an --update option to the jalview.sh launcher (does not launch, just updates).  Combining the update script with this as there's a lot of work to make this shell script Linux/macOS/Cygwin/WSL compliant that doesn't need to be duplicated.  PS1 still to do.

7 weeks agoJAL-4418 updated release notes and release date to 13 august 2024
Jim Procter [Fri, 26 Jul 2024 16:02:24 +0000 (17:02 +0100)]
JAL-4418 updated release notes and release date to 13 august 2024

7 weeks agoMerge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into...
Jim Procter [Fri, 26 Jul 2024 15:25:34 +0000 (16:25 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop

7 weeks agoMerge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Jim Procter [Fri, 26 Jul 2024 15:23:06 +0000 (16:23 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop

7 weeks agoJAL-3631 Added verbose and quiet options, and matched vmoptions with installer. Prove...
Ben Soares [Fri, 26 Jul 2024 14:39:41 +0000 (15:39 +0100)]
JAL-3631 Added verbose and quiet options, and matched vmoptions with installer. Provenance of options added.

7 weeks agoJAL-3631 Some minor bugfixes to the install4j installer and word changes to match...
Ben Soares [Fri, 26 Jul 2024 14:38:28 +0000 (15:38 +0100)]
JAL-3631 Some minor bugfixes to the install4j installer and word changes to match macos-install-jalview.sh