Add toil-lib dependency (resolves BD2KGenomics/toil#922)#434
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I like the +/- spread on this! Reviewing now. |
setup.py
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| url="https://github.com/BD2KGenomics/toil-scripts", | ||
| install_requires=[ | ||
| 'toil-lib==1.0.2', | ||
| 'tqdm==3.8.0', # FIXME: Remove once ADAM stops using it (superfluous import) |
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Small aside, but I think we can get rid of the tqdm requirement. I don't see it used anywhere in the codebase.
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That would be great
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Let's just remove it in this PR?
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Just dropped a few nits. Other than nits, LGTM! |
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Thanks @fnothaft! I'll address these now. |
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@fnothaft — found a blunder in toil-lib. I'll need to push 1.0.3 out before I can merge this, doing that now. |
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Blimey mate! A blunder! |
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@jvivian so now that this is merged, PRs that added to toil_scripts.tools or toil_scripts.lib should be split, right? E.g., #381 added to |
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That's a good question. I think the former option is what I'll do in the short term until a pipeline gets broken out into its own repo. Once a pipeline has broken up with its estranged lover toil-scripts, PRs can target the new repo with changes that complement the additions to toil-lib. PR against toil-lib > merge > bump toil-lib to new release > build release branch on jenkins to push to pypi > bump toil-lib to dev version > PR against toil-scripts | PR against pipeline-repo. |
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SGTM. I'm not planning to touch #381 for a while, so I'll hold off there. |
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