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@samanvp samanvp commented Oct 31, 2019

Two issues needed to be fixed:

  • Replace all pip install commands with python -m pip install due to a new cloud-sdk:slim.
  • Add --region to all integrations tests due to new Apache Beam requires to send --region to all pipeline executions.

Note that this PR only fixes the build. We need to also enforce users to provide --region flag when running Variant Transforms. For more details refer to #525

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coveralls commented Oct 31, 2019

Pull Request Test Coverage Report for Build 1838

  • 0 of 2 (0.0%) changed or added relevant lines in 2 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage decreased (-0.01%) to 89.092%

Changes Missing Coverage Covered Lines Changed/Added Lines %
gcp_variant_transforms/testing/integration/run_tests_common.py 0 1 0.0%
gcp_variant_transforms/testing/integration/run_vcf_to_bq_tests.py 0 1 0.0%
Totals Coverage Status
Change from base Build 1815: -0.01%
Covered Lines: 7808
Relevant Lines: 8764

💛 - Coveralls

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@tneymanov tneymanov left a comment

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Again, I would had preferred updating all the tests, but for now this works. we can fix the build and update the tests to supply region explicitly prior to the release.

setup.py Outdated
'protobuf>=3.6.1',
'mmh3<2.6',
# Need to explicitly install v<=1.14.0. apache-beam requires
# google-cloud-pubsub 0.39.1, which relies on google-cloud-core<0.30dev,
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done.

run_presubmit.sh Outdated
pip install pylint
python -m pip install pylint
fi
pylint gcp_variant_transforms
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This may not be needed, but for consistency, maybe modify this to python -m pylint?

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done.

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Thanks Tural.

run_presubmit.sh Outdated
pip install pylint
python -m pip install pylint
fi
pylint gcp_variant_transforms
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done.

setup.py Outdated
'protobuf>=3.6.1',
'mmh3<2.6',
# Need to explicitly install v<=1.14.0. apache-beam requires
# google-cloud-pubsub 0.39.1, which relies on google-cloud-core<0.30dev,
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done.

@samanvp samanvp requested a review from kemp-google November 1, 2019 02:31
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@allieychen allieychen left a comment

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Thank you Saman, LGTM!

# A helper script for ensuring all checks pass before submitting any change.

echo ========== Running unit tests.
if [[ -z `which coverage` ]];then

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Just a general question: is it relatively fast to just install the tools required? eg, if this were apt, I'd just install everything rather than check/install.

Not something to change in this PR, just a general question about pip.

@samanvp samanvp merged commit 5044996 into googlegenomics:master Nov 4, 2019
@samanvp samanvp deleted the pip_fix2 branch November 22, 2019 04:59
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5 participants