Update for bdg-formats code style changes

[heuermh]

No description provided.

[fnothaft]

LGTM! Can you resolve the conflicts?

[heuermh]

Don't see why there would be any.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #1126 of commit 43bd039.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 43bd039^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 43bd039 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1126/head^{commit} # timeout=10Checking out Revision 43bd039 (origin/pr/1126/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 43bd039b3b86d08e15e378e1335b72a0fb40ae14First 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]

Oh wait, there's a commit on the feature branch I didn't see before, d86f258. That won't work since bdg-formats HEAD builds as 0.9.1-SNAPSHOT.

[heuermh]

GIt can't seem to infer what I want to do when I use commands incorrectly

$ git rebase -i upstream/upgrade-to-bdg-formats-0.10.0
fatal: Needed a single revision
invalid upstream upstream/upgrade-to-bdg-formats-0.10.0

[heuermh]

That means I'm git stuck. 😦 Please advise.

[fnothaft]

Did you do git fetch upstream? What happens if you do git checkout upstream/upgrade-to-bdg-formats-0.10.0?

[heuermh]

Nope. Not realizing there were any commits on upgrade-to-bdg-formats-0.10.0 I branched from master.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #1126 of commit bf886c9 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/1126/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains fb78db3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1126/merge^{commit} # timeout=10Checking out Revision fb78db3 (origin/pr/1126/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f fb78db388ecbe43062fc423cab713ebf46296adeFirst 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]

Jenkins isn't getting the latest bdg-formats snapshot build. Do I have to mvn deploy a snapshot manually or is Jenkins supposed to be taking care of that automatically?

[fnothaft]

Jenkins isn't getting the latest bdg-formats snapshot build. Do I have to mvn deploy a snapshot manually or is Jenkins supposed to be taking care of that automatically?

Jenkins did get the latest bdg-formats snapshot. However! What Jenkins did not do, was build and deploy the snapshot after the last bdg-formats commit was pushed. There was an issue with the refspec for the bdg-formats master branch that caused the git polling hook to fail. The polling hook should run in 10 minutes; I'll trigger this build once Jenkins has pushed the bdg-formats snapshot.

[fnothaft]

Jenkins, test this please.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[heuermh]

Thanks. I'm not sure how to interpret the latest build matrix -- only some of the Jenkins build configurations got the right snapshot version?

[heuermh]

Jenkins, retest this please.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[heuermh]

Jenkins, test this please.

[AmplabJenkins]

Test PASSed.
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Test PASSed.

[heuermh]

Woot!

[jpdna]

LGTM - is this ready to merge?

[fnothaft]

LGTM

[heuermh]

is this ready to merge?

Yes, please

[fnothaft]

Thanks @heuermh! For these PRs against the topic branch, I'm just going to use the green merge button, since we'll eventually need to sort out the topic branch itself.

[heuermh]

Thanks!

[heuermh]

As far as topic branching goes, should I be merging commits from master here or will we resolve all of those when merging the topic branch?

[fnothaft]

I'm thinking that we should periodically rebase the 0.10.0 branch on master. To make it easier to tell when we've got a merge conflict, perhaps we should PR 0.10.0 against master? This way, we'll get a CI build whenever we push an update, and GitHub will tell us whenever we're out of date.

[fnothaft]

Opened #1135.