toil 7.0.0__py3-none-any.whl → 8.0.0__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 (190) hide show
  1. toil/__init__.py +121 -83
  2. toil/batchSystems/__init__.py +1 -0
  3. toil/batchSystems/abstractBatchSystem.py +137 -77
  4. toil/batchSystems/abstractGridEngineBatchSystem.py +211 -101
  5. toil/batchSystems/awsBatch.py +237 -128
  6. toil/batchSystems/cleanup_support.py +22 -16
  7. toil/batchSystems/contained_executor.py +30 -26
  8. toil/batchSystems/gridengine.py +85 -49
  9. toil/batchSystems/htcondor.py +164 -87
  10. toil/batchSystems/kubernetes.py +622 -386
  11. toil/batchSystems/local_support.py +17 -12
  12. toil/batchSystems/lsf.py +132 -79
  13. toil/batchSystems/lsfHelper.py +13 -11
  14. toil/batchSystems/mesos/__init__.py +41 -29
  15. toil/batchSystems/mesos/batchSystem.py +288 -149
  16. toil/batchSystems/mesos/executor.py +77 -49
  17. toil/batchSystems/mesos/test/__init__.py +31 -23
  18. toil/batchSystems/options.py +38 -29
  19. toil/batchSystems/registry.py +53 -19
  20. toil/batchSystems/singleMachine.py +293 -123
  21. toil/batchSystems/slurm.py +489 -137
  22. toil/batchSystems/torque.py +46 -32
  23. toil/bus.py +141 -73
  24. toil/common.py +630 -359
  25. toil/cwl/__init__.py +1 -1
  26. toil/cwl/cwltoil.py +1114 -532
  27. toil/cwl/utils.py +17 -22
  28. toil/deferred.py +62 -41
  29. toil/exceptions.py +5 -3
  30. toil/fileStores/__init__.py +5 -5
  31. toil/fileStores/abstractFileStore.py +88 -57
  32. toil/fileStores/cachingFileStore.py +711 -247
  33. toil/fileStores/nonCachingFileStore.py +113 -75
  34. toil/job.py +988 -315
  35. toil/jobStores/abstractJobStore.py +387 -243
  36. toil/jobStores/aws/jobStore.py +727 -403
  37. toil/jobStores/aws/utils.py +161 -109
  38. toil/jobStores/conftest.py +1 -0
  39. toil/jobStores/fileJobStore.py +289 -151
  40. toil/jobStores/googleJobStore.py +137 -70
  41. toil/jobStores/utils.py +36 -15
  42. toil/leader.py +614 -269
  43. toil/lib/accelerators.py +115 -18
  44. toil/lib/aws/__init__.py +55 -28
  45. toil/lib/aws/ami.py +122 -87
  46. toil/lib/aws/iam.py +284 -108
  47. toil/lib/aws/s3.py +31 -0
  48. toil/lib/aws/session.py +193 -58
  49. toil/lib/aws/utils.py +238 -218
  50. toil/lib/bioio.py +13 -5
  51. toil/lib/compatibility.py +11 -6
  52. toil/lib/conversions.py +83 -49
  53. toil/lib/docker.py +131 -103
  54. toil/lib/ec2.py +322 -209
  55. toil/lib/ec2nodes.py +174 -106
  56. toil/lib/encryption/_dummy.py +5 -3
  57. toil/lib/encryption/_nacl.py +10 -6
  58. toil/lib/encryption/conftest.py +1 -0
  59. toil/lib/exceptions.py +26 -7
  60. toil/lib/expando.py +4 -2
  61. toil/lib/ftp_utils.py +217 -0
  62. toil/lib/generatedEC2Lists.py +127 -19
  63. toil/lib/humanize.py +6 -2
  64. toil/lib/integration.py +341 -0
  65. toil/lib/io.py +99 -11
  66. toil/lib/iterables.py +4 -2
  67. toil/lib/memoize.py +12 -8
  68. toil/lib/misc.py +65 -18
  69. toil/lib/objects.py +2 -2
  70. toil/lib/resources.py +19 -7
  71. toil/lib/retry.py +115 -77
  72. toil/lib/threading.py +282 -80
  73. toil/lib/throttle.py +15 -14
  74. toil/options/common.py +834 -401
  75. toil/options/cwl.py +175 -90
  76. toil/options/runner.py +50 -0
  77. toil/options/wdl.py +70 -19
  78. toil/provisioners/__init__.py +111 -46
  79. toil/provisioners/abstractProvisioner.py +322 -157
  80. toil/provisioners/aws/__init__.py +62 -30
  81. toil/provisioners/aws/awsProvisioner.py +980 -627
  82. toil/provisioners/clusterScaler.py +541 -279
  83. toil/provisioners/gceProvisioner.py +282 -179
  84. toil/provisioners/node.py +147 -79
  85. toil/realtimeLogger.py +34 -22
  86. toil/resource.py +137 -75
  87. toil/server/app.py +127 -61
  88. toil/server/celery_app.py +3 -1
  89. toil/server/cli/wes_cwl_runner.py +82 -53
  90. toil/server/utils.py +54 -28
  91. toil/server/wes/abstract_backend.py +64 -26
  92. toil/server/wes/amazon_wes_utils.py +21 -15
  93. toil/server/wes/tasks.py +121 -63
  94. toil/server/wes/toil_backend.py +142 -107
  95. toil/server/wsgi_app.py +4 -3
  96. toil/serviceManager.py +58 -22
  97. toil/statsAndLogging.py +148 -64
  98. toil/test/__init__.py +263 -179
  99. toil/test/batchSystems/batchSystemTest.py +438 -195
  100. toil/test/batchSystems/batch_system_plugin_test.py +18 -7
  101. toil/test/batchSystems/test_gridengine.py +173 -0
  102. toil/test/batchSystems/test_lsf_helper.py +67 -58
  103. toil/test/batchSystems/test_slurm.py +93 -47
  104. toil/test/cactus/test_cactus_integration.py +20 -22
  105. toil/test/cwl/cwlTest.py +271 -71
  106. toil/test/cwl/measure_default_memory.cwl +12 -0
  107. toil/test/cwl/not_run_required_input.cwl +29 -0
  108. toil/test/cwl/scatter_duplicate_outputs.cwl +40 -0
  109. toil/test/docs/scriptsTest.py +60 -34
  110. toil/test/jobStores/jobStoreTest.py +412 -235
  111. toil/test/lib/aws/test_iam.py +116 -48
  112. toil/test/lib/aws/test_s3.py +16 -9
  113. toil/test/lib/aws/test_utils.py +5 -6
  114. toil/test/lib/dockerTest.py +118 -141
  115. toil/test/lib/test_conversions.py +113 -115
  116. toil/test/lib/test_ec2.py +57 -49
  117. toil/test/lib/test_integration.py +104 -0
  118. toil/test/lib/test_misc.py +12 -5
  119. toil/test/mesos/MesosDataStructuresTest.py +23 -10
  120. toil/test/mesos/helloWorld.py +7 -6
  121. toil/test/mesos/stress.py +25 -20
  122. toil/test/options/options.py +7 -2
  123. toil/test/provisioners/aws/awsProvisionerTest.py +293 -140
  124. toil/test/provisioners/clusterScalerTest.py +440 -250
  125. toil/test/provisioners/clusterTest.py +81 -42
  126. toil/test/provisioners/gceProvisionerTest.py +174 -100
  127. toil/test/provisioners/provisionerTest.py +25 -13
  128. toil/test/provisioners/restartScript.py +5 -4
  129. toil/test/server/serverTest.py +188 -141
  130. toil/test/sort/restart_sort.py +137 -68
  131. toil/test/sort/sort.py +134 -66
  132. toil/test/sort/sortTest.py +91 -49
  133. toil/test/src/autoDeploymentTest.py +140 -100
  134. toil/test/src/busTest.py +20 -18
  135. toil/test/src/checkpointTest.py +8 -2
  136. toil/test/src/deferredFunctionTest.py +49 -35
  137. toil/test/src/dockerCheckTest.py +33 -26
  138. toil/test/src/environmentTest.py +20 -10
  139. toil/test/src/fileStoreTest.py +538 -271
  140. toil/test/src/helloWorldTest.py +7 -4
  141. toil/test/src/importExportFileTest.py +61 -31
  142. toil/test/src/jobDescriptionTest.py +32 -17
  143. toil/test/src/jobEncapsulationTest.py +2 -0
  144. toil/test/src/jobFileStoreTest.py +74 -50
  145. toil/test/src/jobServiceTest.py +187 -73
  146. toil/test/src/jobTest.py +120 -70
  147. toil/test/src/miscTests.py +19 -18
  148. toil/test/src/promisedRequirementTest.py +82 -36
  149. toil/test/src/promisesTest.py +7 -6
  150. toil/test/src/realtimeLoggerTest.py +6 -6
  151. toil/test/src/regularLogTest.py +71 -37
  152. toil/test/src/resourceTest.py +80 -49
  153. toil/test/src/restartDAGTest.py +36 -22
  154. toil/test/src/resumabilityTest.py +9 -2
  155. toil/test/src/retainTempDirTest.py +45 -14
  156. toil/test/src/systemTest.py +12 -8
  157. toil/test/src/threadingTest.py +44 -25
  158. toil/test/src/toilContextManagerTest.py +10 -7
  159. toil/test/src/userDefinedJobArgTypeTest.py +8 -5
  160. toil/test/src/workerTest.py +33 -16
  161. toil/test/utils/toilDebugTest.py +70 -58
  162. toil/test/utils/toilKillTest.py +4 -5
  163. toil/test/utils/utilsTest.py +239 -102
  164. toil/test/wdl/wdltoil_test.py +789 -148
  165. toil/test/wdl/wdltoil_test_kubernetes.py +37 -23
  166. toil/toilState.py +52 -26
  167. toil/utils/toilConfig.py +13 -4
  168. toil/utils/toilDebugFile.py +44 -27
  169. toil/utils/toilDebugJob.py +85 -25
  170. toil/utils/toilDestroyCluster.py +11 -6
  171. toil/utils/toilKill.py +8 -3
  172. toil/utils/toilLaunchCluster.py +251 -145
  173. toil/utils/toilMain.py +37 -16
  174. toil/utils/toilRsyncCluster.py +27 -14
  175. toil/utils/toilSshCluster.py +45 -22
  176. toil/utils/toilStats.py +75 -36
  177. toil/utils/toilStatus.py +226 -119
  178. toil/utils/toilUpdateEC2Instances.py +3 -1
  179. toil/version.py +11 -11
  180. toil/wdl/utils.py +5 -5
  181. toil/wdl/wdltoil.py +3513 -1052
  182. toil/worker.py +269 -128
  183. toil-8.0.0.dist-info/METADATA +173 -0
  184. toil-8.0.0.dist-info/RECORD +253 -0
  185. {toil-7.0.0.dist-info → toil-8.0.0.dist-info}/WHEEL +1 -1
  186. toil-7.0.0.dist-info/METADATA +0 -158
  187. toil-7.0.0.dist-info/RECORD +0 -244
  188. {toil-7.0.0.dist-info → toil-8.0.0.dist-info}/LICENSE +0 -0
  189. {toil-7.0.0.dist-info → toil-8.0.0.dist-info}/entry_points.txt +0 -0
  190. {toil-7.0.0.dist-info → toil-8.0.0.dist-info}/top_level.txt +0 -0

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