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run :
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shell : bash -l {0}
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strategy :
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- matrix :
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- os : ["ubuntu-latest"]
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+ matrix :
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+ os : ["ubuntu-latest"]
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steps :
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- - uses : actions/checkout@v2
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+ - uses : actions/checkout@v4
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- uses : conda-incubator/setup-miniconda@v2
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with :
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activate-environment : test
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environment-file : kingfisher.yml
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python-version : 3.9
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auto-activate-base : false
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- mamba-version : " * "
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+ use-mamba : false
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channels : conda-forge,defaults,bioconda,masonite
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- run : |
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conda info
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env :
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NCBI_API_KEY : ${{ secrets.NCBI_API_KEY }}
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run : |
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- # ascp does not work in bare conda env, so don't run those tests. AWS cp also fails here (because it has not been setup, I think).
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- echo key is $NCBI_API_KEY && \
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- rm test/test_ena.py && \
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- pytest -v --timeout=600 -m 'not aws_cp'
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+ # ascp does not work in bare conda env, so don't run those tests. AWS cp also fails here (because it has not been setup, I think).
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+ echo key is $NCBI_API_KEY && \
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+ rm test/test_ena.py && \
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+ pytest -v --timeout=600 -m 'not aws_cp'
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