Build: #2 was successful Changes by Gitlab User
Code commits
Jalview Git
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Gitlab User 47cde5d652a565b540c345825c638fc4c167c4d7
Merge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_text' into develop
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Gitlab User e87c7127294709e3eb3f6e2ee6582c6a6890d788 m
JAL-4454 make sure 2.11.4.0-test is stripped - *for reals*
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Gitlab User 50cf1b0f1c8ca0f99f35c33fb5f6556a200ef057 m
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Gitlab User d9bc459a175e6fc2d3806adfa71aea35e59027a9 m
Merge branch 'bug/JAL-4460_alignment_save_as_format_not_registering' into develop
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Gitlab User 96e15273c58ad93f09a18d52e7eadcf6901012aa m
JAL-4454 make sure 2.11.4.0-test is stripped
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Ben Soares <b.soares@dundee.ac.uk> 8003658d5abb83eb5d42a1a7b957b0686c852a26 m
JAL-4460 In save as, set format from file extension if a multi-format file filter is selected
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Ben Soares <b.soares@dundee.ac.uk> 983bf691df367eef3dff83ec809bb236f7e021af m
JAL-4460 Don't add .aln for an 'All known formats...' filename
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Ben Soares <b.soares@dundee.ac.uk> 4dd649b088b13205d9eff79b494158d67c63dc16 m
JAL-4460 Update currentFileFormat /after/ new format selection
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Gitlab User 4d60d8b917a3cfe7202c9ff2e301eeb5e14ff1be m
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Gitlab User 4da518baaf1ad5a8e19243e8fe98cbb162d797f9 m
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
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Gitlab User e428c76d94fdfb3c8d3783b62c14ef555e693adc m
JAL-4428 codesign jnilibs
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Gitlab User 8b9105836b3e771c2bad52b567a8cbdad2404cfa m
JAL-4428 informational output (possibly needs verbosity control)
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Gitlab User 6ca157ff447d81c2f38fc17b51cffa484afed9ba m
JAL-4428 giving another XXX
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Gitlab User 7513043ef659cee485e54ec0939c64a36cd031cc m
JAL-4428 add some XXXX for mktemp -t
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Ben Soares <b.soares@dundee.ac.uk> 619551ed8a68b6f9d5cedd08cc67945150cc9d9d m
JAL-4428 Fixes to -z's and mktemp
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Gitlab User 2ab8dec60f0beca5e33ba4c9f348c45227d0ffd1 m
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
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Gitlab User 08ed00519c5f652f91e8403ae1ea2790a479394f m
JAL-4454 allow channels to pick up most recent 'whatsNew' and releasenotes for their associated version
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Gitlab User 84393a0dcdd5056f3b75b28ecce838c409d9b6ff m
JAL-4418 initial pasimap documentation and updated release notes for recent merges
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Gitlab User bcd1fb33af892cbbaea5162e7a9da57e385d9e8a m
JAL-4418 postpone release to Thursday 12th Sept 2024
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Gitlab User 8a347b5268314778b49c80737058679cb3ec4827 m
JAL-4386 remove magic string in registerScoreModel...
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Gitlab User e7bfd7141229e93961d676431233487da4e7789b m
JAL-4418 fix linkCheck
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Gitlab User e937933118a48e607805629f9581c6fd6d274a33 m
JAL-4418 release 10th September
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Gitlab User e386ab351a5fae6088dc95e3be00cc70c17d8cee m
Merge branch 'documentation/JAL-4418_2_11_4_0_docs' into develop
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Gitlab User 3296f8cb9d9f4c9f01f197e971ff625cd3be3ed7 m
Merge branch 'feature/JAL-4446_cancellable_pasimap_etal' into develop
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Gitlab User 69e9cb3c4b9297c19411876e32604822f7f909de m
JAL-4418 first pass at updating docs with pasimap, ssconservation, etc
- help/help/help.jhm (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/helpTOC.xml (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/calculations/calculations.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/calculations/pasimap.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/calculations/protssconsensus.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/calculations/tree.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/alignmentMenu.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/alwannotation.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/alwannotationpanel.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/alwcalculate.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/alwcolour.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/alwformat.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/desktopMenu.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/help/html/menus/wsmenu.html (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
- help/markdown/whatsnew/whatsnew-2_11_4_0.md (version 69e9cb3c4b9297c19411876e32604822f7f909de) (diffs)
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Gitlab User f40edd5d97571d331bd03489ef67858bbb2595bf m
JAL-4446 improved reporting of progress, and transition between cancelable and non-cancelable phases of pasimap calculation
- src/jalview/analysis/PaSiMap.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
- src/jalview/gui/PaSiMapPanel.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
- src/jalview/gui/PairwiseAlignPanel.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
- src/jalview/gui/ProgressBar.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
- src/jalview/viewmodel/PaSiMapModel.java (version f40edd5d97571d331bd03489ef67858bbb2595bf) (diffs)
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Gitlab User 30c13c1638967753f7b1f9c880a92cc7308b1278 m
JAL-4446 refactor progress listener handler code for reuse
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Gitlab User 6ec1491ad65b1a0d63eff8277677a8ecd5ab354d m
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
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Ben Soares <b.soares@dundee.ac.uk> 518abfdf0b3d2028617b781219086ad932c6f40a m
JAL-4428 README.md file for sign_and_stapled_dmg.sh
- utils/osx_signing/README (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
- utils/osx_signing/README.md (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
- utils/osx_signing/README.old (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
- utils/osx_signing/staple_dmg.sh (version 518abfdf0b3d2028617b781219086ad932c6f40a) (diffs)
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Gitlab User e69db6fc850b0e89328bb2dbc3d371930fa6c595 m
JAL-789 limit applicable score models to substitution matrix based ones
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Gitlab User 23eabe997df728d46b1333cbfd01407acba70908 m
JAL-4446 allow progress bar to become indeterminate after pairwise alignment step
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Gitlab User 695d7f4c7259087a58d01bdf3bbddd11aa59de79 m
Merge branch 'develop' into feature/JAL-4446_cancellable_pasimap_etal
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Ben Soares <b.soares@dundee.ac.uk> 44a4e6d8ab25553d72ddbb214f3fc8abfb9dd3a0 m
JAL-4428 localise function vars. Add -q -q option. Fix detaching volumes for cleanup -C
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Ben Soares <b.soares@dundee.ac.uk> 08791dd0d5c3293554d3d65ba41a22d2954edf81 m
JAL-4428 More coherent command line options and better 'running command' stdout management
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Ben Soares <b.soares@dundee.ac.uk> 3264c552a4fe29835a10f38ca92244253f305bb0 m
JAL-4428 Added in stapling into (now) sign_and_staple_dmg.sh. Some other small improvements to the script.
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Ben Soares <b.soares@dundee.ac.uk> 8204755d1364be5cfbdbb1695803e8c1f2ea24f6 m
JAL-4428 sign_dmg.sh with bells on
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Gitlab User a51b5f709d28d8a25a3c2c4596cbe086aa34ea43 m
JAL-4447 standardised title formula for reporting score model and other parameters for pairwise alignment, PCA, tree, and Pasimap
- src/jalview/gui/AlignFrame.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/CalculationChooser.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/PCAPanel.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/PaSiMapPanel.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
- src/jalview/gui/PairwiseAlignPanel.java (version a51b5f709d28d8a25a3c2c4596cbe086aa34ea43) (diffs)
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Gitlab User a74f2604de0825eeeeda41158e9b9c1a32a2dd3c m
JAL-4446 reuse lasteta value
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Gitlab User 11cfa06b3572d711c3441c965e6340abcf20a4a2 m
JAL-4159 JAL-789 report pasimap and pairwise alignment parameters in window title
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Gitlab User 0c8213058cfc306cf459355543bcb93c546047dc m
JAL-4159 suppress pairwise alignment display options when not available from pasimap
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Gitlab User 39ef2c483d62e04129703d6acff8a594cc7e9b16 m
JAL-4446 better reporting of ETA estimation - particularly for large alignments
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Gitlab User df8c5515d51b26ef229cd2916a30d6a27f46c236 m
JAL-4446 avoid NPE when progress bar message is null
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Gitlab User 1a09df2fbacbdaf9a76ee5fe3b25925742bc78d9 m
JAL-4446 .. missing methods for cancellable pasimap
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Gitlab User 2f15cb2f6239cf3a51d2528f5f873273cdcc7936 m
JAL-4446 cancellable Pasimap - still need to make the actual pasimap CCA calculation cancellable and report progress
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Gitlab User 01dd0eed037513b5b2dbcd499dfd0cdd957cf0bd m
JAL-4446 calculate and report PaSiMap ETA in progress bar
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Gitlab User 84126942cf15bed4109e81345e2412425cfa48ed m
JAL-4446 allow progress bar message to be changed whilst progress continues & todo re desktop's custom progress implementation
- src/jalview/gui/AlignFrame.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/Desktop.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/IProgressIndicator.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/PCAPanel.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/PaSiMapPanel.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/ProgressBar.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/StructureChooser.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)
- src/jalview/gui/WebserviceInfo.java (version 84126942cf15bed4109e81345e2412425cfa48ed) (diffs)