[ADAM-1093] Move to support Spark 2.0.0. #1123

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fnothaft commented Aug 24, 2016

Relies on bigdatagenomics/utils#78. Resolves #1093:

  • Clean up logging in VariantContextRDD
  • Add move_to_spark_2.sh script and CI hooks
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GitHub pull request #1123 of commit e4a539c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1123/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 21b7ba2 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1123/merge^{commit} # timeout=10Checking out Revision 21b7ba2 (origin/pr/1123/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 21b7ba24c1c10df6180d3744623bc081123c0aafFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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GitHub pull request #1123 of commit e4a539c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1123/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 21b7ba2 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1123/merge^{commit} # timeout=10Checking out Revision 21b7ba2 (origin/pr/1123/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 21b7ba24c1c10df6180d3744623bc081123c0aafFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh referenced this pull request Sep 7, 2016

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Release ADAM version 0.20.0 #1048

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Rebased. Once this passes tests, @heuermh or I can cut a release of bdg-utils, and then I'll update this PR with the non-snapshot coordinates.

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fnothaft commented Sep 7, 2016

Rebased. Once this passes tests, @heuermh or I can cut a release of bdg-utils, and then I'll update this PR with the non-snapshot coordinates.

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Hooray! I'll cut utils-0.2.8 upstream.

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fnothaft commented Sep 7, 2016

Hooray! I'll cut utils-0.2.8 upstream.

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Jenkins, retest this please.

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fnothaft commented Sep 7, 2016

Jenkins, retest this please.

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Just realized that Jenkins didn't run the 2.0.0 tests. Updated Jenkins, and kicked those off now!

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fnothaft commented Sep 7, 2016

Just realized that Jenkins didn't run the 2.0.0 tests. Updated Jenkins, and kicked those off now!

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utils 0.2.8 artifacts are available from Maven Central.

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heuermh commented Sep 8, 2016

utils 0.2.8 artifacts are available from Maven Central.

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We also need a move_to_spark_1.sh script and need to have this called near the end of release.sh.

I don't know what the spark packages zip file is, does that also need Spark 1.x and 2.x versions?

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heuermh commented Sep 8, 2016

We also need a move_to_spark_1.sh script and need to have this called near the end of release.sh.

I don't know what the spark packages zip file is, does that also need Spark 1.x and 2.x versions?

[ADAM-1093] Move to support Spark 2.0.0.
Relies on bigdatagenomics/utils#78. Resolves #1093:

* Clean up logging in VariantContextRDD
* Add move_to_spark_2.sh script and CI hooks
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Updated with the final release version for utils.

We also need a move_to_spark_1.sh script and need to have this called near the end of release.sh.

Actually, we don't! (That's what I like about the release scripts here.) We do all of the releases from maintenance branches, and only update the versions on the master branch, so the POMs on the master branch don't get touched.

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fnothaft commented Sep 8, 2016

Updated with the final release version for utils.

We also need a move_to_spark_1.sh script and need to have this called near the end of release.sh.

Actually, we don't! (That's what I like about the release scripts here.) We do all of the releases from maintenance branches, and only update the versions on the master branch, so the POMs on the master branch don't get touched.

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the POMs on the master branch don't get touched

Ah, ok. LGTM then.

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heuermh commented Sep 8, 2016

the POMs on the master branch don't get touched

Ah, ok. LGTM then.

@heuermh heuermh merged commit 97b801d into bigdatagenomics:master Sep 8, 2016

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Thank you, @fnothaft!

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heuermh commented Sep 8, 2016

Thank you, @fnothaft!

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