Cleanup on `org.bdgenomics.adam.algorithms.smithwaterman` package. #1056

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fnothaft commented Jun 26, 2016

  • Added documentation for all methods, values, classes, and constructors that were currently missing documentation.
  • Made SmithWatermanGapScoringFromFn class package private.
  • Refactored SmithWaterman and SmithWatermanGapScoringFromFn to be traits instead of abstract classes, which allowed for refactoring SmithWatermanConstantGapScoring to eliminate the singleton object.
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Test FAILed.
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Build result: FAILURE

GitHub pull request #1056 of commit 3551c1e 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/1056/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 44cbceb4e95940e51c0fcdf73412f15e8b19d11e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1056/merge^{commit} # timeout=10Checking out Revision 44cbceb4e95940e51c0fcdf73412f15e8b19d11e (origin/pr/1056/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 44cbceb4e95940e51c0fcdf73412f15e8b19d11eFirst 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.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1284/

Build result: FAILURE

GitHub pull request #1056 of commit 3551c1e 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/1056/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 44cbceb4e95940e51c0fcdf73412f15e8b19d11e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1056/merge^{commit} # timeout=10Checking out Revision 44cbceb4e95940e51c0fcdf73412f15e8b19d11e (origin/pr/1056/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 44cbceb4e95940e51c0fcdf73412f15e8b19d11eFirst 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.

Cleanup on `org.bdgenomics.adam.algorithms.smithwaterman` package.
* Added documentation for all methods, values, classes, and constructors that
  were currently missing documentation.
* Made `SmithWatermanGapScoringFromFn` class package private.
* Refactored `SmithWaterman` and `SmithWatermanGapScoringFromFn` to be traits
  instead of abstract classes, which allowed for refactoring
  `SmithWatermanConstantGapScoring` to eliminate the singleton object.
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1285/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1285/
Test PASSed.

@heuermh heuermh referenced this pull request Jun 27, 2016

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Release ADAM version 0.20.0 #1048

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heuermh Jun 27, 2016

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+1, pending further conversation about doc style, e.g. #1055 (comment)

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heuermh commented Jun 27, 2016

+1, pending further conversation about doc style, e.g. #1055 (comment)

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heuermh Jul 6, 2016

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Merged commit fdc5189.

Thank you, @fnothaft!

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heuermh commented Jul 6, 2016

Merged commit fdc5189.

Thank you, @fnothaft!

@heuermh heuermh closed this Jul 6, 2016

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