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Java 17 (draft)#8013

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cmnbroad wants to merge 141 commits intomasterbroadinstitute/gatk:masterfrom cn_spark_3.3.0_rebasedbroadinstitute/gatk:cn_spark_3.3.0_rebasedCopy head branch name to clipboard

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Commits on Sep 6, 2022

• Attempt to build with Java 17 - WIP.

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• Upgrade gradle to 7.4.2.

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• Remove doclet code.

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• Oh yeah remove the doclet tests too.

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• Temporarily pretend we don't need SecurityManager.

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• Spark 3.3.0.

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• Suppress more deprecation warnings.

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• Remove guava lists.

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• Upgrade Scala - WIP.

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• More exports/opens clauses.

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• Revert problematic Scala upgrade.

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• Open java.lang.invoke.

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• Open sun.nio.fs.

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• Support changd avro API.

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• Upgrade jacoco for Java 17.

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• Add opens for jacoco.

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• Try running jacoco with --daemon.

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• Temporarily update .seg files for ModelSegmentsIntegrationTest.

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• Remove unused PosteriorSummary and friends.

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• I feel lucky.

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• Remove unnecessary github action job matrix entries.

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• Update job matrix for remaining tasks.

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• Fix expired google cloud key.

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• You have to update ALL the job matrix entires.

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• Update Docker file for google key.

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• Fix statement order.

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• Not sudo.

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• Pin commons-math3 to 3.5 and revert changes to expected files for ModelSegmentsIntegrationTest.

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• Check for failures with scala 11.

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• Revert "Check for failures with scala 11."

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• Update ModelSegmentsIntegration test using values resulting for commons-math3-2.5 pinned.

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• Fix Docker build.

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• Temporarily disable all gatkDoc dependencies.

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• Fix docker java path, fix gradle dependency prereqs.

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• Fix docker second stage.

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• Update order.

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• Don't apt-upgrade again.

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• Update gatk script.

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• Oh there is another gradle file too.

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• Remove unnecessary and problematic non-test closure.

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• Update jvmargs.

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• Revert "Update jvmargs."

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• Move jmvargs.

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

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

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• Update docker build script.

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• Add docker trace.

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• Set file permissions.

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• TEMP change to pre-create testclass dir.

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• Fix ls command.

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• Update file perms.

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• More permissions.

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• More updates.

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

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• Fix bad command.

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• Check files post extract.

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• Smarter logging.

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• Update file logging command.

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• Spill cromwell logs.

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• Fix last commit.

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• Fix the fix.

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• update find.

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

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

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• Try utf-8 encoding with flat classes.

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• Try filtering out the shapeless class entirely.

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• Set fileMode.

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• Try an alternative file copy task.

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• Exclude META_INF.

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• Set duplicatesStrategy.

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• Upgrade hadoop.

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• Add the shapeless filter.

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• Filter spire.

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• Update messages.

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• Use the correct classpath.

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• Restore (incorrect) isJavaNN call.

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• Add TODO comment.

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• Revert to multiple jars.

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• Update CP_DIR.

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• Try not caching.

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• Revert "Try not caching."

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• Temporarily revert missing io redirection fixes.

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• Revert unpackTestJars.

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• Export not open.

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

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• More opens for spark test code.

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• Fix opens.

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• More opens.

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• Upgrade kryo.

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• Use older kryo.

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• More opens.

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• More opens.

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• Display jvm args.

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• Set args directly.

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• Remove jacoco jvm args.

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• Fix opens.

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• More opens.

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• Open java.lang.module.

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• Lambda serialization, try forcing jetty.

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• Upgrade gradle to 7.5.1.

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Commits on Sep 7, 2022

• Use gradle daemon.

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• Use newest jetty.

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• Update opens.

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• Revert jetty.

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• Updates for rebase post-UltimaGen.

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• Temp trace.

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Commits on Sep 12, 2022

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

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• Work around jetty jar issue.

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Commits on Sep 13, 2022

• Fix IO redirection in Dockerfile.

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• Trace output.

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• Change classpath order, disable gradle cache.

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Commits on Sep 14, 2022

• Restore gradle cache.

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• Alternate classpath order.

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• Debug cromwell.

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• Cromwell version 84.

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• Use debug level TRACE for cromwell.

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• Add opens for jacoco.

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• Fix missing comma.

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• Fix syntax error in gatk.

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• Add opens for gradle process jacoco task.

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• Stop using classesdir.

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• Restore classesDir.

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Commits on Sep 15, 2022

• Fix build dependencies.

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• Debug class loader.

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• Reorder classpath.

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• Write to stderr.

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• Revert to debug level info.

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• Throw to debug.

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• testImplementation dependencies.

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• Remove tracing code.

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Commits on Sep 19, 2022

• Increase test fork frequency.

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• Decrease test fork frequency.

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• Restore fork interval; relax test verbosity on docker tests.

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• Suppress info suppression.

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Commits on Sep 20, 2022

• Trace info.

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• Reduce test output noise.

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• Chang test order.

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• No parallel forks.

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• Revert naming.

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Commits on Sep 26, 2022

• Fix java version test.

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• Fix gradle Java tests.

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