toil 6.1.0a1__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 (193) hide show
  1. toil/__init__.py +122 -315
  2. toil/batchSystems/__init__.py +1 -0
  3. toil/batchSystems/abstractBatchSystem.py +173 -89
  4. toil/batchSystems/abstractGridEngineBatchSystem.py +272 -148
  5. toil/batchSystems/awsBatch.py +244 -135
  6. toil/batchSystems/cleanup_support.py +26 -16
  7. toil/batchSystems/contained_executor.py +31 -28
  8. toil/batchSystems/gridengine.py +86 -50
  9. toil/batchSystems/htcondor.py +166 -89
  10. toil/batchSystems/kubernetes.py +632 -382
  11. toil/batchSystems/local_support.py +20 -15
  12. toil/batchSystems/lsf.py +134 -81
  13. toil/batchSystems/lsfHelper.py +13 -11
  14. toil/batchSystems/mesos/__init__.py +41 -29
  15. toil/batchSystems/mesos/batchSystem.py +290 -151
  16. toil/batchSystems/mesos/executor.py +79 -50
  17. toil/batchSystems/mesos/test/__init__.py +31 -23
  18. toil/batchSystems/options.py +46 -28
  19. toil/batchSystems/registry.py +53 -19
  20. toil/batchSystems/singleMachine.py +296 -125
  21. toil/batchSystems/slurm.py +603 -138
  22. toil/batchSystems/torque.py +47 -33
  23. toil/bus.py +186 -76
  24. toil/common.py +664 -368
  25. toil/cwl/__init__.py +1 -1
  26. toil/cwl/cwltoil.py +1136 -483
  27. toil/cwl/utils.py +17 -22
  28. toil/deferred.py +63 -42
  29. toil/exceptions.py +5 -3
  30. toil/fileStores/__init__.py +5 -5
  31. toil/fileStores/abstractFileStore.py +140 -60
  32. toil/fileStores/cachingFileStore.py +717 -269
  33. toil/fileStores/nonCachingFileStore.py +116 -87
  34. toil/job.py +1225 -368
  35. toil/jobStores/abstractJobStore.py +416 -266
  36. toil/jobStores/aws/jobStore.py +863 -477
  37. toil/jobStores/aws/utils.py +201 -120
  38. toil/jobStores/conftest.py +3 -2
  39. toil/jobStores/fileJobStore.py +292 -154
  40. toil/jobStores/googleJobStore.py +140 -74
  41. toil/jobStores/utils.py +36 -15
  42. toil/leader.py +668 -272
  43. toil/lib/accelerators.py +115 -18
  44. toil/lib/aws/__init__.py +74 -31
  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 +214 -39
  49. toil/lib/aws/utils.py +287 -231
  50. toil/lib/bioio.py +13 -5
  51. toil/lib/compatibility.py +11 -6
  52. toil/lib/conversions.py +104 -47
  53. toil/lib/docker.py +131 -103
  54. toil/lib/ec2.py +361 -199
  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 +5 -3
  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 +141 -15
  66. toil/lib/iterables.py +4 -2
  67. toil/lib/memoize.py +12 -8
  68. toil/lib/misc.py +66 -21
  69. toil/lib/objects.py +2 -2
  70. toil/lib/resources.py +68 -15
  71. toil/lib/retry.py +126 -81
  72. toil/lib/threading.py +299 -82
  73. toil/lib/throttle.py +16 -15
  74. toil/options/common.py +843 -409
  75. toil/options/cwl.py +175 -90
  76. toil/options/runner.py +50 -0
  77. toil/options/wdl.py +73 -17
  78. toil/provisioners/__init__.py +117 -46
  79. toil/provisioners/abstractProvisioner.py +332 -157
  80. toil/provisioners/aws/__init__.py +70 -33
  81. toil/provisioners/aws/awsProvisioner.py +1145 -715
  82. toil/provisioners/clusterScaler.py +541 -279
  83. toil/provisioners/gceProvisioner.py +282 -179
  84. toil/provisioners/node.py +155 -79
  85. toil/realtimeLogger.py +34 -22
  86. toil/resource.py +137 -75
  87. toil/server/app.py +128 -62
  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 +224 -70
  98. toil/test/__init__.py +282 -183
  99. toil/test/batchSystems/batchSystemTest.py +460 -210
  100. toil/test/batchSystems/batch_system_plugin_test.py +90 -0
  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 +110 -49
  104. toil/test/cactus/__init__.py +0 -0
  105. toil/test/cactus/test_cactus_integration.py +56 -0
  106. toil/test/cwl/cwlTest.py +496 -287
  107. toil/test/cwl/measure_default_memory.cwl +12 -0
  108. toil/test/cwl/not_run_required_input.cwl +29 -0
  109. toil/test/cwl/scatter_duplicate_outputs.cwl +40 -0
  110. toil/test/cwl/seqtk_seq.cwl +1 -1
  111. toil/test/docs/scriptsTest.py +69 -46
  112. toil/test/jobStores/jobStoreTest.py +427 -264
  113. toil/test/lib/aws/test_iam.py +118 -50
  114. toil/test/lib/aws/test_s3.py +16 -9
  115. toil/test/lib/aws/test_utils.py +5 -6
  116. toil/test/lib/dockerTest.py +118 -141
  117. toil/test/lib/test_conversions.py +113 -115
  118. toil/test/lib/test_ec2.py +58 -50
  119. toil/test/lib/test_integration.py +104 -0
  120. toil/test/lib/test_misc.py +12 -5
  121. toil/test/mesos/MesosDataStructuresTest.py +23 -10
  122. toil/test/mesos/helloWorld.py +7 -6
  123. toil/test/mesos/stress.py +25 -20
  124. toil/test/options/__init__.py +13 -0
  125. toil/test/options/options.py +42 -0
  126. toil/test/provisioners/aws/awsProvisionerTest.py +320 -150
  127. toil/test/provisioners/clusterScalerTest.py +440 -250
  128. toil/test/provisioners/clusterTest.py +166 -44
  129. toil/test/provisioners/gceProvisionerTest.py +174 -100
  130. toil/test/provisioners/provisionerTest.py +25 -13
  131. toil/test/provisioners/restartScript.py +5 -4
  132. toil/test/server/serverTest.py +188 -141
  133. toil/test/sort/restart_sort.py +137 -68
  134. toil/test/sort/sort.py +134 -66
  135. toil/test/sort/sortTest.py +91 -49
  136. toil/test/src/autoDeploymentTest.py +141 -101
  137. toil/test/src/busTest.py +20 -18
  138. toil/test/src/checkpointTest.py +8 -2
  139. toil/test/src/deferredFunctionTest.py +49 -35
  140. toil/test/src/dockerCheckTest.py +32 -24
  141. toil/test/src/environmentTest.py +135 -0
  142. toil/test/src/fileStoreTest.py +539 -272
  143. toil/test/src/helloWorldTest.py +7 -4
  144. toil/test/src/importExportFileTest.py +61 -31
  145. toil/test/src/jobDescriptionTest.py +46 -21
  146. toil/test/src/jobEncapsulationTest.py +2 -0
  147. toil/test/src/jobFileStoreTest.py +74 -50
  148. toil/test/src/jobServiceTest.py +187 -73
  149. toil/test/src/jobTest.py +121 -71
  150. toil/test/src/miscTests.py +19 -18
  151. toil/test/src/promisedRequirementTest.py +82 -36
  152. toil/test/src/promisesTest.py +7 -6
  153. toil/test/src/realtimeLoggerTest.py +10 -6
  154. toil/test/src/regularLogTest.py +71 -37
  155. toil/test/src/resourceTest.py +80 -49
  156. toil/test/src/restartDAGTest.py +36 -22
  157. toil/test/src/resumabilityTest.py +9 -2
  158. toil/test/src/retainTempDirTest.py +45 -14
  159. toil/test/src/systemTest.py +12 -8
  160. toil/test/src/threadingTest.py +44 -25
  161. toil/test/src/toilContextManagerTest.py +10 -7
  162. toil/test/src/userDefinedJobArgTypeTest.py +8 -5
  163. toil/test/src/workerTest.py +73 -23
  164. toil/test/utils/toilDebugTest.py +103 -33
  165. toil/test/utils/toilKillTest.py +4 -5
  166. toil/test/utils/utilsTest.py +245 -106
  167. toil/test/wdl/wdltoil_test.py +818 -149
  168. toil/test/wdl/wdltoil_test_kubernetes.py +91 -0
  169. toil/toilState.py +120 -35
  170. toil/utils/toilConfig.py +13 -4
  171. toil/utils/toilDebugFile.py +44 -27
  172. toil/utils/toilDebugJob.py +214 -27
  173. toil/utils/toilDestroyCluster.py +11 -6
  174. toil/utils/toilKill.py +8 -3
  175. toil/utils/toilLaunchCluster.py +256 -140
  176. toil/utils/toilMain.py +37 -16
  177. toil/utils/toilRsyncCluster.py +32 -14
  178. toil/utils/toilSshCluster.py +49 -22
  179. toil/utils/toilStats.py +356 -273
  180. toil/utils/toilStatus.py +292 -139
  181. toil/utils/toilUpdateEC2Instances.py +3 -1
  182. toil/version.py +12 -12
  183. toil/wdl/utils.py +5 -5
  184. toil/wdl/wdltoil.py +3913 -1033
  185. toil/worker.py +367 -184
  186. {toil-6.1.0a1.dist-info → toil-8.0.0.dist-info}/LICENSE +25 -0
  187. toil-8.0.0.dist-info/METADATA +173 -0
  188. toil-8.0.0.dist-info/RECORD +253 -0
  189. {toil-6.1.0a1.dist-info → toil-8.0.0.dist-info}/WHEEL +1 -1
  190. toil-6.1.0a1.dist-info/METADATA +0 -125
  191. toil-6.1.0a1.dist-info/RECORD +0 -237
  192. {toil-6.1.0a1.dist-info → toil-8.0.0.dist-info}/entry_points.txt +0 -0
  193. {toil-6.1.0a1.dist-info → toil-8.0.0.dist-info}/top_level.txt +0 -0
toil-6.1.0a1.dist-info/RECORD DELETED
@@ -1,237 +0,0 @@
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