misc small fixes #877
misc small fixes #877
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…s reported an exception when keeping tmp files, even when there was none. added parse_cmd() and run_cmd() utils to cmd.py .
…ved preservation of tmp files on request
…nslow is specified
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Would it be better to break out these changes into separate PRs? Some are general fixes, some are general utils on which #854 relies. |
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What led to these changes, or what do they fix?
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These are useful for testing, if you want to run a command but also see the results of parsing its arguments, e.g. https://github.com/broadinstitute/viral-ngs/pull/854/files#diff-771ac3c0ea113ca9a6634523f4fb6893R273
Also calling run_cmd() is clearer than the current pattern of calling the parser manually then calling its func_main .
| @@ -11,6 +11,7 @@ env: | |||
| - PIP_DIR="$HOME/virtualenv" | |||
| - GATK_PATH="$CACHE_DIR" | |||
| - PYTHONIOENCODING=UTF8 | |||
| - PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils" | |||
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I had moved these travis env variables to the parts of the build matrix that actually use py.test... there are a bunch of other points in the build matrix that have nothing to do with pytest.
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Right; on the other hand, there are parts that don't use GATK_PATH either. There's a downside to having copies of the same complex line in several places -- the copies have to be kept in sync.
But if having PYTEST_ADDOPTS defined in jobs that don't use it might cause problems, I'll revert this change.
Misc small fixes. Factoring out parts of #854 not specific to kmer operations.