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Java 17 and Spark 3.3.0. #8035

Merged
merged 36 commits into from
Mar 2, 2023
Merged

Java 17 and Spark 3.3.0. #8035

merged 36 commits into from
Mar 2, 2023

Commits on Feb 28, 2023

  1. Java 17/Spark 3.3.0.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  2. Move the --add-opens directives to the jar file.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  3. Fix bad dependency picked up in rebase.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  4. Repair README.md.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  5. changing non-Docker from 17 to 17.0.1+12

    @samuelklee @cmnbroad
    samuelklee authored and cmnbroad committed Feb 28, 2023
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  6. Update ModelSegments expected results for Java 17.0.1+12.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  7. Update scala to fix DirectBuffer access issue.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  8. Fix scala dependencies.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  9. Update Spark version.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  10. Repair manifest syntax.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  11. Clean up build aand test files.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  12. Java 17 doclets.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  13. Port gatkWDLGen doclet to Java 17.

    @cmnbroad
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  14. Update to Barclay 5.0.0.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  15. Rebase, resolve, clean up.

    @cmnbroad
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  16. Upgrade to Picard 3.0.0.

    @cmnbroad
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  17. Fix ClassFinder references.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  18. Remove javadoc command from WDLGen and TabCompletion test, since its … 

    …no longer needed in v17.
    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  19. Now on htsjdk 3.0.5.

    @cmnbroad
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  20. Remove obsolete jitpack.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  21. Remove obsolete (and unnecessary/problematic) langauge directive.

    @cmnbroad
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  22. Align java version.

    @cmnbroad
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  23. Revert "Update ModelSegments expected results for Java 17.0.1+12." 

    This reverts commit da3fbda.
    @cmnbroad
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  24. Capture documentation generation integration test output.

    @cmnbroad
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  25. Remove google cloud apt-key update.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  26. Code review comments, plus capture doc gen test output.

    @cmnbroad
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  27. Restore kryo version change.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  28. Make docgen smoke tests non-docker only.

    @cmnbroad
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  29. Remove unused scala version variable.

    @cmnbroad
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  30. Revert unnecessary debugging change to IntegrationTestSpec.

    @cmnbroad
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  31. Revert transient modifier from CachingIndexedFastaSequenceFile.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  32. One more -add-opens.

    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  33. And one more --add-opens.

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  34. Revert "And one more --add-opens." 

    This reverts commit 664a6ec.
    @cmnbroad
    cmnbroad committed Feb 28, 2023
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  35. Revert "One more -add-opens." 

    This reverts commit 4b90179.
    @cmnbroad
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  36. Revert "Revert transient modifier from CachingIndexedFastaSequenceFile." 

    This reverts commit c70582c.
    @cmnbroad
    cmnbroad committed Feb 28, 2023
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