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
toil/lib/throttle.py CHANGED
@@ -47,23 +47,23 @@ class LocalThrottle:
47
47
  configured minimum interval has passed since the last time this method returned True in
48
48
  the current thread) or False otherwise.
49
49
  """
50
- now = time.time( )
50
+ now = time.time()
51
51
  last_invocation = self.per_thread.last_invocation
52
52
  if last_invocation is not None:
53
53
  interval = now - last_invocation
54
54
  if interval < self.min_interval:
55
55
  if wait:
56
56
  remainder = self.min_interval - interval
57
- time.sleep( remainder )
57
+ time.sleep(remainder)
58
58
  else:
59
59
  return False
60
60
  self.per_thread.last_invocation = now
61
61
  return True
62
62
 
63
- def __call__( self, function ):
64
- def wrapper( *args, **kwargs ):
65
- self.throttle( )
66
- return function( *args, **kwargs )
63
+ def __call__(self, function):
64
+ def wrapper(*args, **kwargs):
65
+ self.throttle()
66
+ return function(*args, **kwargs)
67
67
 
68
68
  return wrapper
69
69
 
@@ -146,18 +146,19 @@ class throttle:
146
146
  def __init__(self, min_interval: Union[int, float]) -> None:
147
147
  self.min_interval = min_interval
148
148
 
149
- def __enter__( self ):
150
- self.start = time.time( )
149
+ def __enter__(self):
150
+ self.start = time.time()
151
151
 
152
- def __exit__( self, exc_type, exc_val, exc_tb ):
152
+ def __exit__(self, exc_type, exc_val, exc_tb):
153
153
  if exc_type is None:
154
- duration = time.time( ) - self.start
154
+ duration = time.time() - self.start
155
155
  remainder = self.min_interval - duration
156
156
  if remainder > 0:
157
- time.sleep( remainder )
157
+ time.sleep(remainder)
158
158
 
159
- def __call__( self, function ):
160
- def wrapper( *args, **kwargs ):
159
+ def __call__(self, function):
160
+ def wrapper(*args, **kwargs):
161
161
  with self:
162
- return function( *args, **kwargs )
162
+ return function(*args, **kwargs)
163
+
163
164
  return wrapper