toil 6.1.0a1__py3-none-any.whl → 7.0.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (104) hide show
  1. toil/__init__.py +1 -232
  2. toil/batchSystems/abstractBatchSystem.py +41 -17
  3. toil/batchSystems/abstractGridEngineBatchSystem.py +79 -65
  4. toil/batchSystems/awsBatch.py +8 -8
  5. toil/batchSystems/cleanup_support.py +7 -3
  6. toil/batchSystems/contained_executor.py +4 -5
  7. toil/batchSystems/gridengine.py +1 -1
  8. toil/batchSystems/htcondor.py +5 -5
  9. toil/batchSystems/kubernetes.py +25 -11
  10. toil/batchSystems/local_support.py +3 -3
  11. toil/batchSystems/lsf.py +9 -9
  12. toil/batchSystems/mesos/batchSystem.py +4 -4
  13. toil/batchSystems/mesos/executor.py +3 -2
  14. toil/batchSystems/options.py +9 -0
  15. toil/batchSystems/singleMachine.py +11 -10
  16. toil/batchSystems/slurm.py +129 -16
  17. toil/batchSystems/torque.py +1 -1
  18. toil/bus.py +45 -3
  19. toil/common.py +56 -31
  20. toil/cwl/cwltoil.py +442 -371
  21. toil/deferred.py +1 -1
  22. toil/exceptions.py +1 -1
  23. toil/fileStores/abstractFileStore.py +69 -20
  24. toil/fileStores/cachingFileStore.py +6 -22
  25. toil/fileStores/nonCachingFileStore.py +6 -15
  26. toil/job.py +270 -86
  27. toil/jobStores/abstractJobStore.py +37 -31
  28. toil/jobStores/aws/jobStore.py +280 -218
  29. toil/jobStores/aws/utils.py +60 -31
  30. toil/jobStores/conftest.py +2 -2
  31. toil/jobStores/fileJobStore.py +3 -3
  32. toil/jobStores/googleJobStore.py +3 -4
  33. toil/leader.py +89 -38
  34. toil/lib/aws/__init__.py +26 -10
  35. toil/lib/aws/iam.py +2 -2
  36. toil/lib/aws/session.py +62 -22
  37. toil/lib/aws/utils.py +73 -37
  38. toil/lib/conversions.py +24 -1
  39. toil/lib/ec2.py +118 -69
  40. toil/lib/expando.py +1 -1
  41. toil/lib/generatedEC2Lists.py +8 -8
  42. toil/lib/io.py +42 -4
  43. toil/lib/misc.py +1 -3
  44. toil/lib/resources.py +57 -16
  45. toil/lib/retry.py +12 -5
  46. toil/lib/threading.py +29 -14
  47. toil/lib/throttle.py +1 -1
  48. toil/options/common.py +31 -30
  49. toil/options/wdl.py +5 -0
  50. toil/provisioners/__init__.py +9 -3
  51. toil/provisioners/abstractProvisioner.py +12 -2
  52. toil/provisioners/aws/__init__.py +20 -15
  53. toil/provisioners/aws/awsProvisioner.py +406 -329
  54. toil/provisioners/gceProvisioner.py +2 -2
  55. toil/provisioners/node.py +13 -5
  56. toil/server/app.py +1 -1
  57. toil/statsAndLogging.py +93 -23
  58. toil/test/__init__.py +27 -12
  59. toil/test/batchSystems/batchSystemTest.py +40 -33
  60. toil/test/batchSystems/batch_system_plugin_test.py +79 -0
  61. toil/test/batchSystems/test_slurm.py +22 -7
  62. toil/test/cactus/__init__.py +0 -0
  63. toil/test/cactus/test_cactus_integration.py +58 -0
  64. toil/test/cwl/cwlTest.py +245 -236
  65. toil/test/cwl/seqtk_seq.cwl +1 -1
  66. toil/test/docs/scriptsTest.py +11 -14
  67. toil/test/jobStores/jobStoreTest.py +40 -54
  68. toil/test/lib/aws/test_iam.py +2 -2
  69. toil/test/lib/test_ec2.py +1 -1
  70. toil/test/options/__init__.py +13 -0
  71. toil/test/options/options.py +37 -0
  72. toil/test/provisioners/aws/awsProvisionerTest.py +51 -34
  73. toil/test/provisioners/clusterTest.py +99 -16
  74. toil/test/server/serverTest.py +2 -2
  75. toil/test/src/autoDeploymentTest.py +1 -1
  76. toil/test/src/dockerCheckTest.py +2 -1
  77. toil/test/src/environmentTest.py +125 -0
  78. toil/test/src/fileStoreTest.py +1 -1
  79. toil/test/src/jobDescriptionTest.py +18 -8
  80. toil/test/src/jobTest.py +1 -1
  81. toil/test/src/realtimeLoggerTest.py +4 -0
  82. toil/test/src/workerTest.py +52 -19
  83. toil/test/utils/toilDebugTest.py +62 -4
  84. toil/test/utils/utilsTest.py +23 -21
  85. toil/test/wdl/wdltoil_test.py +49 -21
  86. toil/test/wdl/wdltoil_test_kubernetes.py +77 -0
  87. toil/toilState.py +68 -9
  88. toil/utils/toilDebugFile.py +1 -1
  89. toil/utils/toilDebugJob.py +153 -26
  90. toil/utils/toilLaunchCluster.py +12 -2
  91. toil/utils/toilRsyncCluster.py +7 -2
  92. toil/utils/toilSshCluster.py +7 -3
  93. toil/utils/toilStats.py +310 -266
  94. toil/utils/toilStatus.py +98 -52
  95. toil/version.py +11 -11
  96. toil/wdl/wdltoil.py +644 -225
  97. toil/worker.py +125 -83
  98. {toil-6.1.0a1.dist-info → toil-7.0.0.dist-info}/LICENSE +25 -0
  99. toil-7.0.0.dist-info/METADATA +158 -0
  100. {toil-6.1.0a1.dist-info → toil-7.0.0.dist-info}/RECORD +103 -96
  101. {toil-6.1.0a1.dist-info → toil-7.0.0.dist-info}/WHEEL +1 -1
  102. toil-6.1.0a1.dist-info/METADATA +0 -125
  103. {toil-6.1.0a1.dist-info → toil-7.0.0.dist-info}/entry_points.txt +0 -0
  104. {toil-6.1.0a1.dist-info → toil-7.0.0.dist-info}/top_level.txt +0 -0