James Procter <j.procter@dundee.ac.uk>: Author Summary

Builds triggered by James Procter <j.procter@dundee.ac.uk>

Builds triggered by an author are those builds which contains changes committed by the author.
11
1 (9%)
10 (91%)

Breakages and fixes

Broken means the build has failed but the previous build was successful.
Fixed means that the build was successful but the previous build has failed.
1 (9% of all builds triggered)
0 (0% of all builds triggered)
-1
Build Completed Code commits Tests
JB › GDBI › #21 9 months ago
Merge branch 'bug/JAL-4186_space_in_sequence_name_causes_empty_modal' into develop
Testless build
JB › GDC › #188 1 month ago
Merge branch 'bug/JAL-4290_headless_alignment_figure_with_sse' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
JAL-4353 wait for files to be written fully before comparing size with older file
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
Merge branch 'develop' into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
JAL-4369 uniprotkb - try to avoid another redirect response
JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations.Worker to run jalview as a separate process to verify headless alignment image export should be same size as when launched with —gui
Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' into develop
JAL-4353 singleThread all tests
Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop
Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into develop
JAL-4356 update release notes for 2.11.3.3
JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is in progress
JAL-4369 use rest.uniprot.org as fetch domain t pu# Please enter the commit message for your changes. Lines starting
JAL-4356 release notes
Testless build
JB › GPC › #286 1 month ago
JAL-4356 release notes
Testless build
JB › GDB › #621 1 month ago
JAL-4356 release notes
1696 passed
JB › GPC › #285 1 month ago
JAL-4356 update release notes for 2.11.3.3
Testless build
JB › GJB › #400 1 month ago
JAL-4356 release notes
Testless build
JB › GDB › #620 1 month ago
JAL-4356 update release notes for 2.11.3.3
1696 passed
JB › GJB › #399 1 month ago
JAL-4356 update release notes for 2.11.3.3
Testless build
JB › GDC › #187 2 months ago
Merge branch 'bug/JAL-2934proportionalScrolling' into develop
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop
JAL-4353 wait for files to be written fully before comparing size with older file
Merge branch 'bug/JAL-2934proportionalScrolling' into develop
Merge branch 'develop' into bug/JAL-2934proportionalScrolling
JAL-4217 don’t try and export an image when Jmol is also trying to repaint
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
JAL-4353 failing test
Merge branch 'develop' into bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment
JAL-4353 fix assert that successive test output files get bigger in structureImageOutputTest and argFilesGlobAndSubstitutionsTest
JAL-4217 singleThread all tests
Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment' into develop
JAL-4356 update release notes
Testless build
JB › GGR › #7 11 months ago
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
JAL-3858 construct a PAE direct from float array
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Passing test for JAL-4127 failing on the JAL-1713 branch
JAL-4090 Release 2.11.3.0 release notes and version bump
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
JAL-629 don’t complain for Unary args
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-4095 slightly better threshold setting and todos for improvement
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
JAL-1551 source formatting
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-629 labelled breaks are frowned upon by everyone
JAL-3858 new MatrixType JAX-RI POJO
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
 Conflicts:
        src/jalview/bin/Jalview.java
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
 Conflicts:
        src/jalview/bin/Jalview.java
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
JAL-3858 simple test for PAE matrix recovery
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alphafold/JAL-629
JAL-1551 remove temp file in src
JAL-629 make sure we show GUI when not driven programmatically
JAL-4095 magic fill behaviour is PAE specific
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
Testless build
Build Completed Code commits Tests
JB › GGR › #7 11 months ago
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4133 store/restore alignment view’s charWidth and charHeight in Jalview project
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
JAL-3858 construct a PAE direct from float array
JAL-3858 JAL-2381 allow different linear shading schemes for selected/non-selected regions of contact matrix heat map
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Passing test for JAL-4127 failing on the JAL-1713 branch
JAL-4090 Release 2.11.3.0 release notes and version bump
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type, with actual matrix type stored in calcId
JAL-629 don’t complain for Unary args
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
JAL-4095 slightly better threshold setting and todos for improvement
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
JAL-1551 source formatting
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
JAL-629 labelled breaks are frowned upon by everyone
JAL-3858 new MatrixType JAX-RI POJO
JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset sequence annotation. Rudimentary tests.
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
 Conflicts:
        src/jalview/bin/Jalview.java
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
JAL-629 don’t trash user’s system property file when adjusting settings to process CL args
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
 Conflicts:
        src/jalview/bin/Jalview.java
Merge branch 'develop' into feature/JAL-1713_overviewInProject
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
JAL-3858 simple test for PAE matrix recovery
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into features/r2_11_2_alphafold/JAL-629
JAL-1551 remove temp file in src
JAL-629 make sure we show GUI when not driven programmatically
JAL-4095 magic fill behaviour is PAE specific
JAL-629 don’t carry on Jalview.main if we’ve already processed command line args another way
Testless build
Build Completed Code commits Tests