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[ADAM-1520] Bump to bdg-formats 0.11.0. #1523

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merged 1 commit into from May 26, 2017

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fnothaft commented May 12, 2017

Resolves #1520.

WIP; depends on bigdatagenomics/bdg-formats#136.

@heuermh I figured it'd be easier to finish this off than to explain on bigdatagenomics/bdg-formats#136 why said PR was necessary. ;)

@fnothaft fnothaft requested a review from heuermh May 12, 2017

@fnothaft fnothaft added this to the 0.23.0 milestone May 12, 2017

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Test FAILed.
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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1523/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains c026572 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1523/merge^{commit} # timeout=10Checking out Revision c026572 (origin/pr/1523/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f c026572862801077fab97041d99a0ef80edadc78First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1523/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains c026572 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1523/merge^{commit} # timeout=10Checking out Revision c026572 (origin/pr/1523/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f c026572862801077fab97041d99a0ef80edadc78First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented May 21, 2017

Jenkins, test this please.

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Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1523/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 45474de5849a159dc222730a748f452491d58ef3 # timeout=10Checking out Revision 45474de5849a159dc222730a748f452491d58ef3 (origin/pr/1523/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 45474de5849a159dc222730a748f452491d58ef3First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1523/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 45474de5849a159dc222730a748f452491d58ef3 # timeout=10Checking out Revision 45474de5849a159dc222730a748f452491d58ef3 (origin/pr/1523/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 45474de5849a159dc222730a748f452491d58ef3First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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coveralls May 22, 2017

Coverage Status

Coverage increased (+0.2%) to 82.209% when pulling ff75c70 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 2820e94 on bigdatagenomics:master.

coveralls commented May 22, 2017

Coverage Status

Coverage increased (+0.2%) to 82.209% when pulling ff75c70 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 2820e94 on bigdatagenomics:master.

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Test PASSed.
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Fragment,
Genotype,
NucleotideContigFragment,
RecordGroup => RecordGroupMetadata,

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Is this to minimize changes, or is there a collision with RecordGroup?

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Is this to minimize changes, or is there a collision with RecordGroup?

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Collision.

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Collision.

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Everywhere that it doesn't collide, I've renamed to RecordGroup.

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Everywhere that it doesn't collide, I've renamed to RecordGroup.

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@heuermh I think that this is good to go. I'll cut the bdg-formats release tomorrow unless you have objections.

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fnothaft commented May 24, 2017

@heuermh I think that this is good to go. I'll cut the bdg-formats release tomorrow unless you have objections.

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Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1523/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 821f4b6b00702242f94f439eb9bf97c4ffcfb3b0 # timeout=10Checking out Revision 821f4b6b00702242f94f439eb9bf97c4ffcfb3b0 (origin/pr/1523/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 821f4b6b00702242f94f439eb9bf97c4ffcfb3b0First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1523/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 821f4b6b00702242f94f439eb9bf97c4ffcfb3b0 # timeout=10Checking out Revision 821f4b6b00702242f94f439eb9bf97c4ffcfb3b0 (origin/pr/1523/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 821f4b6b00702242f94f439eb9bf97c4ffcfb3b0First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Oops! Clearly not quite done. Let me sort out the unit test failures and report back.

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fnothaft commented May 24, 2017

Oops! Clearly not quite done. Let me sort out the unit test failures and report back.

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coveralls May 24, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.943% when pulling e82b146 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 2820e94 on bigdatagenomics:master.

coveralls commented May 24, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.943% when pulling e82b146 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 2820e94 on bigdatagenomics:master.

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How about merge bigdatagenomics/bdg-formats#140 and then cut the bdg-formats 0.11.0 release? I can pick up the necessary changes to ADAM in #1505.

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heuermh commented May 24, 2017

How about merge bigdatagenomics/bdg-formats#140 and then cut the bdg-formats 0.11.0 release? I can pick up the necessary changes to ADAM in #1505.

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How about merge bigdatagenomics/bdg-formats#140 and then cut the bdg-formats 0.11.0 release? I can pick up the necessary changes to ADAM in #1505.

SGTM! I've merged bigdatagenomics/bdg-formats#140 upstream and will prep and cut the release later today.

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fnothaft commented May 24, 2017

How about merge bigdatagenomics/bdg-formats#140 and then cut the bdg-formats 0.11.0 release? I can pick up the necessary changes to ADAM in #1505.

SGTM! I've merged bigdatagenomics/bdg-formats#140 upstream and will prep and cut the release later today.

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coveralls May 26, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.943% when pulling b359da3 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 3ea4f18 on bigdatagenomics:master.

coveralls commented May 26, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.943% when pulling b359da3 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 3ea4f18 on bigdatagenomics:master.

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Coverage Status

Coverage decreased (-0.2%) to 81.848% when pulling b359da3 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 3ea4f18 on bigdatagenomics:master.

coveralls commented May 26, 2017

Coverage Status

Coverage decreased (-0.2%) to 81.848% when pulling b359da3 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 3ea4f18 on bigdatagenomics:master.

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Coverage Status

Coverage decreased (-0.1%) to 81.943% when pulling b359da3 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 3ea4f18 on bigdatagenomics:master.

coveralls commented May 26, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.943% when pulling b359da3 on fnothaft:issues/1520-bump-bdg-formats-0.11.0 into 3ea4f18 on bigdatagenomics:master.

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@heuermh heuermh merged commit fc3e5fd into bigdatagenomics:master May 26, 2017

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage decreased (-0.1%) to 81.943%
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Thank you, @fnothaft!

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heuermh commented May 26, 2017

Thank you, @fnothaft!

@heuermh heuermh added this to Completed in Release 0.23.0 May 30, 2017

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