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Java 17 (draft) #8013

Closed
wants to merge 141 commits into from
Closed

Java 17 (draft) #8013

wants to merge 141 commits into from

Commits on Sep 6, 2022

  1. Attempt to build with Java 17 - WIP.

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  2. Upgrade gradle to 7.4.2.

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  3. Remove doclet code.

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  4. Oh yeah remove the doclet tests too.

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  5. Temporarily pretend we don't need SecurityManager.

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  6. Spark 3.3.0.

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  7. Suppress more deprecation warnings.

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  8. Remove guava lists.

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  9. Upgrade Scala - WIP.

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  10. More exports/opens clauses.

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  11. Revert problematic Scala upgrade.

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  12. Open java.lang.invoke.

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  13. Open sun.nio.fs.

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  14. Support changd avro API.

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  15. Upgrade jacoco for Java 17.

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  16. Add opens for jacoco.

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  17. Try running jacoco with --daemon.

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  18. Temporarily update .seg files for ModelSegmentsIntegrationTest.

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  19. Remove unused PosteriorSummary and friends.

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  20. I feel lucky.

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  21. Remove unnecessary github action job matrix entries.

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  22. Update job matrix for remaining tasks.

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  23. Fix expired google cloud key.

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  24. You have to update ALL the job matrix entires.

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  25. Update Docker file for google key.

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  26. Fix statement order.

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  27. Not sudo.

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  28. Pin commons-math3 to 3.5 and revert changes to expected files for Mod… 

    …elSegmentsIntegrationTest.
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  29. Check for failures with scala 11.

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  30. Revert "Check for failures with scala 11." 

    This reverts commit 0df59c4.
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  31. Update ModelSegmentsIntegration test using values resulting for commo… 

    …ns-math3-2.5 pinned.
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  32. Fix Docker build.

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  33. Temporarily disable all gatkDoc dependencies.

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  34. Fix docker java path, fix gradle dependency prereqs.

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  35. Fix docker second stage.

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  36. Update order.

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  37. Don't apt-upgrade again.

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  38. Update gatk script.

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  39. Oh there is another gradle file too.

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  40. Remove unnecessary and problematic non-test closure.

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  41. Update jvmargs.

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  42. Revert "Update jvmargs." 

    This reverts commit 0dffd93.
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  43. Move jmvargs.

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  44. Use open rather than export (--add-opens vs --add-export) for sun.nio.ch

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  45. Use folder of classes rather than separate jars for the docker tests.

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  46. Update docker build script.

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  47. Add docker trace.

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  48. Set file permissions.

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  49. TEMP change to pre-create testclass dir.

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  50. Fix ls command.

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  51. Update file perms.

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  52. More permissions.

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  53. More updates.

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  54. Move test classes dir so it is onwed by root.

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  55. Fix bad command.

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  56. Check files post extract.

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  57. Smarter logging.

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  58. Update file logging command.

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  59. Spill cromwell logs.

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  60. Fix last commit.

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  61. Fix the fix.

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  62. update find.

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  63. Try running the docker tests using an uber test jar.

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  64. Revert "Try running the docker tests using an uber test jar." 

    This reverts commit b370a50.
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  65. Try utf-8 encoding with flat classes.

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  66. Try filtering out the shapeless class entirely.

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  67. Set fileMode.

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  68. Try an alternative file copy task.

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  69. Exclude META_INF.

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  70. Set duplicatesStrategy.

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  71. Upgrade hadoop.

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  72. Add the shapeless filter.

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  73. Filter spire.

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  74. Update messages.

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  75. Use the correct classpath.

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  76. Restore (incorrect) isJavaNN call.

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  77. Add TODO comment.

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  78. Revert to multiple jars.

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  79. Update CP_DIR.

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  80. Try not caching.

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  81. Revert "Try not caching." 

    This reverts commit df915ed.
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  82. Temporarily revert missing io redirection fixes.

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  83. Revert unpackTestJars.

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  84. Export not open.

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  85. Use --add-opens instead of --add-exports.

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  86. More opens for spark test code.

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  87. Fix opens.

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  88. More opens.

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  89. Upgrade kryo.

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  90. Use older kryo.

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  91. More opens.

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  92. More opens.

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  93. Display jvm args.

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  94. Set args directly.

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  95. Remove jacoco jvm args.

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  96. Fix opens.

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  97. More opens.

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  98. Open java.lang.module.

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  99. Lambda serialization, try forcing jetty.

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  100. Upgrade gradle to 7.5.1.

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Commits on Sep 7, 2022

  1. Use gradle daemon.

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  2. Use newest jetty.

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  3. Update opens.

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  4. Revert jetty.

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  5. Updates for rebase post-UltimaGen.

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  6. Temp trace.

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Commits on Sep 12, 2022

  1. Update HC test with new result - this needs to be investigated.

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  2. Work around jetty jar issue.

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Commits on Sep 13, 2022

  1. Fix IO redirection in Dockerfile.

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  2. Trace output.

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  3. Change classpath order, disable gradle cache.

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Commits on Sep 14, 2022

  1. Restore gradle cache.

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  2. Alternate classpath order.

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  3. Debug cromwell.

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  4. Cromwell version 84.

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  5. Use debug level TRACE for cromwell.

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  6. Add opens for jacoco.

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  7. Fix missing comma.

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    cmnbroad committed Sep 14, 2022
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  8. Fix syntax error in gatk.

    @cmnbroad
    cmnbroad committed Sep 14, 2022
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  9. Add opens for gradle process jacoco task.

    @cmnbroad
    cmnbroad committed Sep 14, 2022
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  10. Stop using classesdir.

    @cmnbroad
    cmnbroad committed Sep 14, 2022
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  11. Restore classesDir.

    @cmnbroad
    cmnbroad committed Sep 14, 2022
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Commits on Sep 15, 2022

  1. Fix build dependencies.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  2. Debug class loader.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  3. Reorder classpath.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  4. Write to stderr.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  5. Revert to debug level info.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  6. Throw to debug.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  7. testImplementation dependencies.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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  8. Remove tracing code.

    @cmnbroad
    cmnbroad committed Sep 15, 2022
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Commits on Sep 19, 2022

  1. Increase test fork frequency.

    @cmnbroad
    cmnbroad committed Sep 19, 2022
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  2. Decrease test fork frequency.

    @cmnbroad
    cmnbroad committed Sep 19, 2022
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  3. Restore fork interval; relax test verbosity on docker tests.

    @cmnbroad
    cmnbroad committed Sep 19, 2022
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  4. Suppress info suppression.

    @cmnbroad
    cmnbroad committed Sep 19, 2022
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Commits on Sep 20, 2022

  1. Trace info.

    @cmnbroad
    cmnbroad committed Sep 20, 2022
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  2. Reduce test output noise.

    @cmnbroad
    cmnbroad committed Sep 20, 2022
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  3. Chang test order.

    @cmnbroad
    cmnbroad committed Sep 20, 2022
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  4. No parallel forks.

    @cmnbroad
    cmnbroad committed Sep 20, 2022
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  5. Revert naming.

    @cmnbroad
    cmnbroad committed Sep 20, 2022
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Commits on Sep 26, 2022

  1. Fix java version test.

    @cmnbroad
    cmnbroad committed Sep 26, 2022
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  2. Fix gradle Java tests.

    @cmnbroad
    cmnbroad committed Sep 26, 2022
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