Build #5

Jalview Test RELEASE Channel build

Build: #5 was successful

Job: Default Job was successful

Stages & jobs

  1. Default Stage

Code commits

Jalview Gitlab

  • Gitlab User

    Gitlab User a66e20be839021308667d6b9cfd5110ede25ac1a

    Merge branch 'development/Release_2_11_5_Branch' into releases/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User d96cd12c18b602f601a84a1a90774e5a203fa154 m

    JAL-4617 'whats new' for 2.11.5.1 and update fileformat docs for .a3m

    • help/markdown/whatsnew/whatsnew-2_11_5_1.md (version d96cd12c18b602f601a84a1a90774e5a203fa154)
    • help/help/html/io/fileformats.html (version d96cd12c18b602f601a84a1a90774e5a203fa154)
  • Gitlab User

    Gitlab User 867df43eea5552fcff91729cc98aa6ab6d1f21f3

    Merge branch 'development/Release_2_11_5_Branch' into releases/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User 26e5206fcd793334724fa4f2127ff956d994ef72 m

    JAL-4602 JAL-4617 release notes & docs for autohiding of global ss consensus for just one provider

    • help/markdown/releases/release-2_11_5_1.md (version 26e5206fcd793334724fa4f2127ff956d994ef72)
  • Gitlab User

    Gitlab User d0a286713116c07f50d958c9c9e06dfa29e3d494 m

    JAL-4602 JAL-4617 release notes & docs for autohiding of global ss consensus for just one provider

    • help/help/html/calculations/protssconsensus.html (version d0a286713116c07f50d958c9c9e06dfa29e3d494)
  • Gitlab User

    Gitlab User 89d8c1d5df9f40af9bd27e1591837ad9532a67a2 m

    Merge branch 'feature/JAL-4602_Hide_All_SS_consensus_for_single_provider' into development/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User b0fd08a15bfaff92e5d6c81412f82b5902ac284e m

    JAL-4617 release notes for JAL-4626,JAL-835

    • help/markdown/releases/release-2_11_5_1.md (version b0fd08a15bfaff92e5d6c81412f82b5902ac284e)
  • Gitlab User

    Gitlab User f78fcddb036b7af746d360ab4253c44958640ff4 m

    Merge branch 'feature/JAL-835_hhsuite_a3m_support' into development/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User ca386e6bc36dc5a22b753f9a7417b26e1f5ea349 m

    Merge branch 'patch/JAL-4626_alphafoldVersionTracker' into development/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User 2c607230589b9dd93f77cf07e9e7c0004f23a9a5 m

    JAL-4617 release notes for JAL-4606 JAL-4521

    • help/markdown/releases/release-2_11_5_1.md (version 2c607230589b9dd93f77cf07e9e7c0004f23a9a5)
    • .settings/org.eclipse.buildship.core.prefs (version 2c607230589b9dd93f77cf07e9e7c0004f23a9a5)
  • Renia Correya

    Renia Correya 4a5185652a9c0450b46184af8a5fb7233e8b707f m

    JAL-4606 Bug fix for Jmol incorrect path interpretation on windows

    • src/jalview/structure/StructureSelectionManager.java (version 4a5185652a9c0450b46184af8a5fb7233e8b707f)
  • Renia Correya

    Renia Correya e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d m

    JAL-4602 Hide 'All' ss consensus annotation when one type is available

    • src/jalview/workers/SecondaryStructureConsensusThread.java (version e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d)
    • src/jalview/viewmodel/AlignmentViewport.java (version e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d)
    • src/jalview/gui/AlignFrame.java (version e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d)
  • Gitlab User

    Gitlab User 377f1f52a15db66fd5768669a50bfda03250a6c7 m

    Merge branch 'development/Release_2_11_5_Branch' into patch/JAL-4626_alphafoldVersionTracker

  • Gitlab User

    Gitlab User 9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616 m

    JAL-4626 pick up AF_VERSION when first referred to

    • test/jalview/ws/dbsources/EBIAlphaFoldTest.java (version 9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616)
    • src/jalview/ws/dbsources/EBIAlfaFold.java (version 9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616)
  • Ben Soares

    Ben Soares f306b783e2b09b813cffc5c6cd4bab2c46d74f12 m

    Merge branch 'feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss' into 'development/Release_2_11_5_Branch'
    JAL-4521 Allow tree calculation for one sequence multiple structure

    See merge request jalview/jalview!23

  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 9369deda21dc14b2f5921ce5208142e89f295600 m

    Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch

  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 0d10b35174aa38a4a48c5965e683dabe47dcd553 m

    JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set.  This was causing jalview.util.Log4jTest.testLog4j to fail.  Neatened the args in that test to use '--' to prevent mixed argstyle warning.

    • test/jalview/util/Log4jTest.java (version 0d10b35174aa38a4a48c5965e683dabe47dcd553)
    • src/jalview/bin/Jalview.java (version 0d10b35174aa38a4a48c5965e683dabe47dcd553)
  • Renia Correya

    Renia Correya e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3 m

    JAL-4521 Allow tree calculation for SS for 1 seq and muliple structures
    Allow calculation dialog/score model to be selected for secondary
    structure when working with 1 sequence + many structures.

    • src/jalview/gui/CalculationChooser.java (version e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3)
    • src/jalview/gui/AlignFrame.java (version e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3)
    • resources/lang/Messages.properties (version e3c46fcd8ca84107f389e7e5bf51d3fc4f10dbc3)
  • Gitlab User

    Gitlab User 1e51a6fea55e3be2947e7bcd5018494754acb92b m

    JAL-835 hook in A3mFile as an importable type and recognise filenames that have .a3m suffixes as an A3m file

    • src/jalview/io/IdentifyFile.java (version 1e51a6fea55e3be2947e7bcd5018494754acb92b)
  • Gitlab User

    Gitlab User 754034afa3c6d7859c83cd9d6f2c8f11276e6cef m

    JAL-835 support a3m file import

    • src/jalview/io/FileFormat.java (version 754034afa3c6d7859c83cd9d6f2c8f11276e6cef)
    • src/jalview/io/FastaFile.java (version 754034afa3c6d7859c83cd9d6f2c8f11276e6cef)
    • src/jalview/io/A3mFile.java (version 754034afa3c6d7859c83cd9d6f2c8f11276e6cef)
  • Gitlab User

    Gitlab User 407915ca3bba33d94b3529b49b52175efdc71dce m

    Merge branch 'development/Release_2_11_5_Branch' into feature/JAL-835_hhsuite_a3m_support

  • Gitlab User

    Gitlab User 3bf9d58d0cd1b768503f644d8126520f565af95e m

    JAL-4243 JAL-4617 release notes for bio-tools record update

    • help/markdown/releases/release-2_11_5_1.md (version 3bf9d58d0cd1b768503f644d8126520f565af95e)
  • Gitlab User

    Gitlab User 665ae4644ceccd2ff2d5e70181c6baa189f3797d m

    Merge branch 'update/JAL-4243_biotools_json_record' into development/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User 94dd8e493d9351cfeb5a07c4a13583aa225cf21a m

    JAL-4607 release notes for 2.11.5.1 (JAL-4617)

    • help/markdown/releases/release-2_11_5_1.md (version 94dd8e493d9351cfeb5a07c4a13583aa225cf21a)
  • Gitlab User

    Gitlab User 28d0eb545da3936b9c0fda00bd49eea577a1ebee m

    Merge branch 'improvement/JAL-4607_install4j_dark_mode_background_colour' into development/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User 7875d21f5c728fc242817aa1020e2cff18e41300 m

    JAL-4604 plus JAL-4617 release notes and version bump

    • help/markdown/whatsnew/whatsnew-2_11_5_1.md (version 7875d21f5c728fc242817aa1020e2cff18e41300)
    • help/markdown/releases/release-2_11_5_1.md (version 7875d21f5c728fc242817aa1020e2cff18e41300)
  • Gitlab User

    Gitlab User 33005ea58c7b9583772afb479c7f3289f932d0d3 m

    Merge branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' into development/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User de404214a47d594b38f4d5ce869e357f3a36ff6b m

    JAL-835 enhanced ShiftList to support a3m insert expansion via AlignmentUtils.a3mToMSA and provided a groovy script PoC

    • test/jalview/util/ShiftListTest.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
    • test/jalview/analysis/AlignmentUtilsTests.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
    • src/jalview/util/ShiftList.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
    • src/jalview/analysis/AlignmentUtils.java (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
    • examples/testdata/query.a3m.fa (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
    • examples/testdata/query.a3m (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
    • examples/groovy/a3mtoFasta.groovy (version de404214a47d594b38f4d5ce869e357f3a36ff6b)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> c662cdbcf8253d09fe5f7215ba99385e9e9be2ae m

    JAL-4607 minor changes required for install4j 11.0.5 gradle plugin

    • build.gradle (version c662cdbcf8253d09fe5f7215ba99385e9e9be2ae)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 6221773ca9538a097b31b1d6f53097774c2485a1 m

    JAL-4607 Fix background colour of install4j wizard in dark mode, with update to 11.0.5

    • utils/install4j/install4j11_template.install4j (version 6221773ca9538a097b31b1d6f53097774c2485a1)
    • build.gradle (version 6221773ca9538a097b31b1d6f53097774c2485a1)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 01b48f04818d683d5d0f90d7833ae0c6d4191a8c m

    JAL-4604 Allow getdown to use its own version in jar comparison

    • src/jalview/util/LaunchUtils.java (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • j8lib/getdown-core.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • j11lib/getdown-core.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • getdown/lib/getdown-launcher.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • getdown/lib/getdown-launcher-local.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
    • getdown/lib/getdown-core.jar (version 01b48f04818d683d5d0f90d7833ae0c6d4191a8c)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 473e3dd1153b3493888e8841a5fec30eed205b92 m

    JAL-4604 removed a line marked REMOVE THIS LINE

    • j8lib/getdown-core.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
    • j11lib/getdown-core.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
    • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 473e3dd1153b3493888e8841a5fec30eed205b92)
    • getdown/lib/getdown-launcher.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
    • getdown/lib/getdown-launcher-local.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
    • getdown/lib/getdown-core.jar (version 473e3dd1153b3493888e8841a5fec30eed205b92)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> c7ec2412ae67d38a9306a4f68e946b8eeecabff2 m

    JAL-4604 This needed for some old installations. Normally set in getdown separately

    • gradle.properties (version c7ec2412ae67d38a9306a4f68e946b8eeecabff2)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 4659cdba6eac42181072c7437e2f2742a2333cb3 m

    JAL-4604 Now ensure non-buggy arguments are passed as-is

    • j8lib/getdown-core.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • j11lib/getdown-core.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • getdown/lib/getdown-launcher.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • getdown/lib/getdown-launcher-local.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
    • getdown/lib/getdown-core.jar (version 4659cdba6eac42181072c7437e2f2742a2333cb3)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 28fb06e0e3779a4a52075ac7957a8d953256bfef m

    JAL-4604 Ensure getdownappdir is now set and passed through. Some indentation fixes in getdown...Application.java

    • src/jalview/bin/Jalview.java (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
    • j8lib/getdown-core.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
    • j11lib/getdown-core.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
    • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
    • getdown/lib/getdown-launcher.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
    • getdown/lib/getdown-launcher-local.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
    • getdown/lib/getdown-core.jar (version 28fb06e0e3779a4a52075ac7957a8d953256bfef)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> b4309df8f01a5abf9d7d73cea76b1f9b9aa3a3f6 m

    JAL-4604 Check for old install4j set property for appdir to swap in new getdown-launcher.jar

    • src/jalview/bin/Jalview.java (version b4309df8f01a5abf9d7d73cea76b1f9b9aa3a3f6)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 7feb4abf2fc4dd85712b5824af621206ca5603eb m

    JAL-4604 Changes to getdown/LaunchUtils to fix the arguments bug, and also detect being launched with the spurious arguments and remove them

    • src/jalview/util/LaunchUtils.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • j8lib/getdown-core.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • j11lib/getdown-core.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • getdown/lib/getdown-launcher.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • getdown/lib/getdown-launcher-local.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
    • getdown/lib/getdown-core.jar (version 7feb4abf2fc4dd85712b5824af621206ca5603eb)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> ba4e65d505f158f9a0397a6b669b392155ca1cb8 m

    JAL-4604 Bug in LaunchUtils not removing previous 'appbase' 'appid' arguments

    • src/jalview/util/LaunchUtils.java (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
    • j8lib/getdown-core.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
    • j11lib/getdown-core.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
    • getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
    • getdown/lib/getdown-launcher.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
    • getdown/lib/getdown-launcher-local.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
    • getdown/lib/getdown-core.jar (version ba4e65d505f158f9a0397a6b669b392155ca1cb8)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> ce46f05124d94cb4f54117bc98e9a295b4c1199d m

    JAL-4604 getdown upgrade bug avert in GetdownApp.java

    • src/jalview/util/StringUtils.java (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • j8lib/getdown-core.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • j11lib/getdown-core.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • help/markdown/whatsnew/whatsnew-2_11_5_1.md (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • help/markdown/releases/release-2_11_5_1.md (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/mvn_cmd (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/launcher/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/core/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/src/getdown/ant/pom.xml (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/lib/getdown-launcher.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/lib/getdown-launcher-local.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/lib/getdown-core.jar (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/lib/JVL_VERSION (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • getdown/lib/FJVL_VERSION (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
    • RELEASE (version ce46f05124d94cb4f54117bc98e9a295b4c1199d)
  • Ben Soares <b.soares@dundee.ac.uk>

    Ben Soares <b.soares@dundee.ac.uk> 59b555ddd49df7b78598773826980346e320f232 m

    JAL-4243 Bio.tools JSON record updated for 2.11.5.0 and added to Bio.tools

    • utils/biotools/Jalview.json (version 59b555ddd49df7b78598773826980346e320f232)
  • Gitlab User

    Gitlab User 86d2c844db19c23c7922b5fd103807d0d2469a66

    Merge branch 'development/Release_2_11_5_Branch' into releases/Release_2_11_5_Branch

  • Gitlab User

    Gitlab User 2c0064b6000a3666230f5f3ff75e356835e68bd2 m

    JAL-4531 updated resolved issues and knowndefects

    • help/markdown/releases/release-2_11_5_0.md (version 2c0064b6000a3666230f5f3ff75e356835e68bd2)