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🔧 toil feedback refactor #11

Merged
merged 26 commits into from
Feb 27, 2018
Merged

🔧 toil feedback refactor #11

merged 26 commits into from
Feb 27, 2018

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jsmedmar
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This refactor was motivated by feedback from DataBiosphere/toil#2064 (comment):

  • use subprocess32
  • use docker.from_env(version='auto')
  • fix the way workdir was mapped to /tmp on singularity containers
  • avoid shadowing of subprocess names def check_output and def check_call
  • avoid use of /dev/null

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codecov bot commented Feb 24, 2018

Codecov Report

Merging #11 into master will increase coverage by 6.09%.
The diff coverage is 100%.

Impacted file tree graph

@@           Coverage Diff            @@
##           master    #11      +/-   ##
========================================
+ Coverage    93.9%   100%   +6.09%     
========================================
  Files           4      5       +1     
  Lines         164    219      +55     
========================================
+ Hits          154    219      +65     
+ Misses         10      0      -10
Impacted Files Coverage Δ
toil_container/validators.py 100% <100%> (ø)
toil_container/jobs.py 100% <100%> (ø) ⬆️
toil_container/containers.py 100% <100%> (+5.55%) ⬆️
toil_container/exceptions.py 100% <100%> (ø) ⬆️
toil_container/parsers.py 100% <100%> (+8.57%) ⬆️

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@jsmedmar jsmedmar changed the title 💎 new version with toil feedback refactor 🔧 toil feedback refactor Feb 26, 2018
jsmedmar and others added 4 commits February 26, 2018 10:18
 🔧 short long description for pypi
fix wrong option passed to toil job
juanesarango
juanesarango previously approved these changes Feb 27, 2018
if os.name == "posix" and sys.version_info[0] < 3:
import subprocess32 as subprocess
else:
import subprocess

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Nice!

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got this from the subprocess32 github

@juanesarango juanesarango merged commit 2d474f3 into master Feb 27, 2018
@juanesarango juanesarango deleted the toil-feedback-refactor branch February 27, 2018 23:11
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2 participants