jalview

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Commits this week: 9
Total Committers: 73
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Commits this week: 9

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Wednesday 26 Jan
11:41 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
11:41 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)

Options
    • -1
    • +1
    /test/jalview/bin/CommandLineOperations.java
11:33 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
11:32 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763 release notes

Options
    • -0
    • +3
    /help/help/html/releases.html
11:26 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'merge/develop_task/JAL-3763_newDatasetForCds' into develop

Options
7:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)

Options
    • -1
    • +1
    /test/jalview/bin/CommandLineOperations.java
7:36 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

Options
    • -55
    • +41
    /src/jalview/analysis/AlignmentUtils.java
    • -2
    • +4
    /src/jalview/datamodel/SearchResults.java
    • -1
    • +6
    /src/jalview/gui/PopupMenu.java
    • -53
    • +53
    /src/jalview/util/MappingUtils.java
    • -7
    • +7
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
    • -3
    • +4
    /test/jalview/util/MapListTest.java
    • -2
    • +114
    /test/jalview/util/MappingUtilsTest.java
6:34 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
6:32 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'releases/Release_2_11_1_Branch'

Options
Tuesday 18 Jan
12:24 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

Options
    • -7
    • +9
    /help/help/html/releases.html
11:44 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 errant heading in release notes..

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    • +11
    /help/help/html/releases.html
8:14 am

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

Options
Monday 17 Jan
12:50 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3703 patch Windows save file test for 2.11.1 codebase

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    • -4
    • +4
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
12:39 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

Options
12:38 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 fix issues in release notes

Options
    • -1
    • +1
    /help/help/html/releases.html
12:36 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release

Options
    • -6
    • +18
    /help/help/html/releases.html
12:24 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 bump version and update release notes - release set for Tuesday 18th January 2022

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    • +1
    /RELEASE
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    • +1
    /help/help/html/releases.html
    • -6
    • +5
    /help/help/html/whatsNew.html
12:20 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 update release notes for JAL-3702,JAL-3935 in 2.11.1.7 release

Options
    • -5
    • +10
    /help/help/html/releases.html
11:57 am

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
11:54 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 possible release date 1st Feb 2022

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    • +10
    /help/help/html/releases.html
11:54 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 Release notes for patch JAL-3702 JAL-3915

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    • -9
    • +6
    /help/help/html/releases.html
11:45 am

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails' into develop

Options
Wednesday 12 Jan
12:32 pm

Ben Soares

JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

Options
    • -1
    • +2
    /test/jalview/io/BackupFilesTest.java
    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
12:32 pm

Ben Soares

JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

Options
    • -1
    • +7
    /test/jalview/io/BackupFilesTest.java
    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
Tuesday 11 Jan
8:13 pm

Ben Soares

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

Options
    • -2
    • +19
    /src/jalview/io/AlignFile.java
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    • +8
    /src/jalview/io/FastaFile.java
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    • +3
    /src/jalview/io/FeaturesFile.java
8:13 pm

Ben Soares

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

Options
    • -2
    • +19
    /src/jalview/io/AlignFile.java
    • -3
    • +8
    /src/jalview/io/FastaFile.java
    • -1
    • +3
    /src/jalview/io/FeaturesFile.java
    • -2
    • +2
    /src/jalview/io/FileParse.java
4:04 pm

Ben Soares

close filehandles straight after parse, without setting an error

Conflicts:

src/jalview/project/Jalview2XML.java

(locale aware PDBID string compare)

Options
    • -7
    • +8
    /src/jalview/io/AlignFile.java
    • -3
    • +5
    /src/jalview/project/Jalview2XML.java
4:04 pm

Ben Soares

close filehandles straight after parse, without setting an error

Options
    • -7
    • +8
    /src/jalview/io/AlignFile.java
    • -4
    • +4
    /src/jalview/project/Jalview2XML.java
2:45 pm

Ben Soares

JAL-3937 update releases.html

Options
    • -1
    • +16
    /help/help/html/releases.html
Monday 10 Jan
8:58 pm

Ben Soares

JAL-3937 enable AIA download of intermediate certificates when needed

Options
    • -0
    • +3
    /src/jalview/bin/Jalview.java