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@DailyDreaming DailyDreaming released this 27 Mar 04:37
· 1492 commits to master since this release
releases/3.19.0
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Learn about vigilant mode.
  • Support for CWL s3 imports. #2522
  • Support for running custom init commands in docker (allowing auth in private dockers). #2561
  • Add --no-read-only option to the CWL runner. #2531
  • Add support for assuming roles. #2527
  • Added an adapter to allow Boto 2 to use credentials obtained via Boto 3. #2527
  • Add a flag for running CWL internal jobs on workers. #2524
  • Added CWL tests for http, https, and s3 file imports. #2234
  • Begin testing python3 in gitlab. #2518
  • Relegate pytest dependency to the dev reqs. #2508
  • WDL changes to enable resource usage. #2495
  • Sphinx and pathlib2 dependencies. #2490 #2493
  • Upgrade appliance to Ubuntu 16.04. #2480
  • Update cwltool from 1.0.20180820141117 -> 1.0.20181118133959 #2469
  • Add CWL's --preserve-entire-environment option. #2481
  • Bump minimum version of galaxy-lib (17.9.3 -> 17.9.9). #2476
  • Added all tutorial scripts to unit testing. #2426
  • More python3 support added. #2405
  • Update the CoreOS AMI. #2430
  • Simplify log creation in leader. #2423
  • Support for hardlinks and greater testing for toil status. #2402
  • Pymesos port. #2366 #2338
  • Use displayName for CWLJob to show stats in toil --stats. #2397

Bug Fixes

  • Import errors. #2558
  • Fix boto3 credentials for permanent credentials. #2549
  • Fix bug in Toil stats. #2513
  • Replace some str objects as real FileIDs. #2500
  • Remove linear-time bottleneck from Mesos batch system. #2498
  • Slurm and py3 fixes. #2494
  • Safeguard unintentional boto imports. #2489
  • Fix broken readthedocs build. #2485
  • Specify region in prometheus. #2437
  • Fixed bytestring-string tagging. #2472
  • LSF log job id on error. #2450
  • Fix massive slowdown when many jobs are running. #2439
  • Make ServiceManager stop blocking while (most) services are established. #2441
  • Default to bash on the leader node rather than sh. #2435
  • resource.getusage returns KB already, so dividing by 1024 yields MB. #2425
  • Recognize conda virtual envs. #2422

Thank you to our contributors: @mr-c, @arostamianfar, @adamnovak, @nikhil, @lamby, @gijzelaerr, @joelarmstrong, @markasbach, @davidjsherman, @psafont, @jsmedmar, @bencvdb, @emlys, @ionox0, @ibebio, @MarkFilus!

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