Code

Megamerge#4464

Code

Merged

adamnovak merged 37 commits intomasterDataBiosphere/toil:masterfrom megamergeDataBiosphere/toil:megamergeCopy head branch name to clipboardMay 5, 2023

Commits

Commits on Feb 3, 2023

• Update version_template.py

  DailyDreaming

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Commits on Feb 4, 2023

• Update version_template.py

  DailyDreaming

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• Update with fix.

  DailyDreaming

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Commits on Apr 21, 2023

• Catch 'Device or resource busy'

  

  jfennick

  authored and

  mr-c

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• Catch FileNotFoundError

  

  jfennick

  authored and

  mr-c

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• added @Retry to _readJobState

  

  jfennick

  authored and

  mr-c

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• Catch FileNotFoundError

  

  jfennick

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  mr-c

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Commits on Apr 26, 2023

• Allow ue of mesos roles (resolves #4455)

  stephanaime

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Commits on Apr 28, 2023

• Dont let --user-space-docker-cmd and --custom-net be mutually exclusive. Otherwise get this error, toil-cwl-runner: error: argument --user-space-docker-cmd: not allowed with argument --custom-net.

  

  misterbrandonwalker

  authored and

  mr-c

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• Update src/toil/cwl/cwltoil.py

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  misterbrandonwalker

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  mr-c

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  c4d84a0

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• Update src/toil/cwl/cwltoil.py

  Show description for 0646950
  

  misterbrandonwalker

  and

  mr-c

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Commits on May 2, 2023

• Change CWL internal job system to generic local job system

  adamnovak

  committed
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• Make all WDL jobs except running or attempting to run a task local

  adamnovak

  committed
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• Add a non-downloading file size implementation

  adamnovak

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• Satisfy MyPy

  adamnovak

  committed
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• Eliminate the old stack and adopt a slightly more controlled successor phase concept

  adamnovak

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• Appease MyPy

  adamnovak

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• Drop a lingering use of the old stack

  adamnovak

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• Get mini tests to pass

  adamnovak

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• Get WDL workflow to start

  adamnovak

  committed
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• Add debugging to show that jobs are missing from the registry

  adamnovak

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• Fix ordering to actually look at the right job

  adamnovak

  committed
  76c92ef

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• Quiet debugging

  adamnovak

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  88e2e6e

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• Change log message

  adamnovak

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  b7b4f68

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• Stop making unwanted changes

  adamnovak

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• Remove redundant and wrongly-typed check

  adamnovak

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Commits on May 4, 2023

• Get docker-compose from apt instead of pip where it fights Toil deps

  adamnovak

  committed
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• Ban urllib3 2.0+ until Docker module supports it

  adamnovak

  committed
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• Use docker-compose in the prebake

  adamnovak

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• Move Slurm tests to earlier stage

  adamnovak

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• Account for how docker compose plugin names containers

  adamnovak

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  7fc9b7f

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• Revert "Move Slurm tests to earlier stage"

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  adamnovak

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• Merge branch 'fix_docker_network' of https://github.com/misterbrandonwalker/toil into megamerge

  adamnovak

  committed
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• Merge branch 'robust_rmtree' of https://github.com/jfennick/toil into megamerge

  adamnovak

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• Merge branch 'issues/4455-support-mesos-roles' of https://github.com/stephanaime/toil into megamerge

  adamnovak

  committed
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• Undo unwanted version change

  adamnovak

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• Document new Mesos options and don't apply sort and high always

  adamnovak

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