Closed juanesarango closed 3 years ago
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@@ Coverage Diff @@
## master #31 +/- ##
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Coverage ? 95.42%
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Files ? 7
Lines ? 350
Branches ? 0
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Hits ? 334
Misses ? 16
Partials ? 0
Impacted Files | Coverage Ξ | |
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toil_container/jobs.py | 95.71% <88.46%> (ΓΈ) |
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toil_container/__init__.py | 100.00% <100.00%> (ΓΈ) |
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toil_container/containers.py | 98.09% <100.00%> (ΓΈ) |
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toil_container/parsers.py | 100.00% <100.00%> (ΓΈ) |
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toil_container/utils.py | 73.17% <100.00%> (ΓΈ) |
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It's worth noting that toil just merged the addBatchSystemFactory
function as a public API again: https://github.com/DataBiosphere/toil/pull/3754. So we can revert one of my changes and go back to using it as soon as it's published. Could be done in a separate PR though.
@multimeric yes, I can roll back those changes. Will do this when toil makes a new release with the changes.
Thanks for asking the toil
team to add this back!
Following @multimeric contributions to upgrade
toil_container
to the latest toil version https://github.com/papaemmelab/toil_container/pull/29, this PR adds the following:custom_lsf
to be compatible withtoil >= 5.4.0
CustomLsf
tocustom_lsf
to keep new toil snake_case style forbatchSystem
options.coloredlogs
to improve logging with ansi outputdocker>=4.3
With contributions of @ddomenico