toil 9.1.2__py3-none-any.whl → 9.2.0__py3-none-any.whl

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Files changed (155) hide show
  1. toil/__init__.py +5 -9
  2. toil/batchSystems/abstractBatchSystem.py +23 -22
  3. toil/batchSystems/abstractGridEngineBatchSystem.py +17 -12
  4. toil/batchSystems/awsBatch.py +8 -8
  5. toil/batchSystems/cleanup_support.py +4 -4
  6. toil/batchSystems/contained_executor.py +3 -3
  7. toil/batchSystems/gridengine.py +3 -4
  8. toil/batchSystems/htcondor.py +5 -5
  9. toil/batchSystems/kubernetes.py +65 -63
  10. toil/batchSystems/local_support.py +2 -3
  11. toil/batchSystems/lsf.py +6 -7
  12. toil/batchSystems/mesos/batchSystem.py +11 -7
  13. toil/batchSystems/mesos/test/__init__.py +1 -2
  14. toil/batchSystems/options.py +9 -10
  15. toil/batchSystems/registry.py +3 -7
  16. toil/batchSystems/singleMachine.py +8 -11
  17. toil/batchSystems/slurm.py +49 -38
  18. toil/batchSystems/torque.py +3 -4
  19. toil/bus.py +36 -34
  20. toil/common.py +129 -89
  21. toil/cwl/cwltoil.py +857 -729
  22. toil/cwl/utils.py +44 -35
  23. toil/fileStores/__init__.py +3 -1
  24. toil/fileStores/abstractFileStore.py +28 -30
  25. toil/fileStores/cachingFileStore.py +8 -8
  26. toil/fileStores/nonCachingFileStore.py +10 -21
  27. toil/job.py +159 -158
  28. toil/jobStores/abstractJobStore.py +68 -69
  29. toil/jobStores/aws/jobStore.py +249 -213
  30. toil/jobStores/aws/utils.py +13 -24
  31. toil/jobStores/fileJobStore.py +28 -22
  32. toil/jobStores/googleJobStore.py +21 -17
  33. toil/jobStores/utils.py +3 -7
  34. toil/leader.py +14 -14
  35. toil/lib/accelerators.py +6 -4
  36. toil/lib/aws/__init__.py +9 -10
  37. toil/lib/aws/ami.py +33 -19
  38. toil/lib/aws/iam.py +6 -6
  39. toil/lib/aws/s3.py +259 -157
  40. toil/lib/aws/session.py +76 -76
  41. toil/lib/aws/utils.py +51 -43
  42. toil/lib/checksum.py +19 -15
  43. toil/lib/compatibility.py +3 -2
  44. toil/lib/conversions.py +45 -18
  45. toil/lib/directory.py +29 -26
  46. toil/lib/docker.py +93 -99
  47. toil/lib/dockstore.py +77 -50
  48. toil/lib/ec2.py +39 -38
  49. toil/lib/ec2nodes.py +11 -4
  50. toil/lib/exceptions.py +8 -5
  51. toil/lib/ftp_utils.py +9 -14
  52. toil/lib/generatedEC2Lists.py +161 -20
  53. toil/lib/history.py +141 -97
  54. toil/lib/history_submission.py +163 -72
  55. toil/lib/io.py +27 -17
  56. toil/lib/memoize.py +2 -1
  57. toil/lib/misc.py +15 -11
  58. toil/lib/pipes.py +40 -25
  59. toil/lib/plugins.py +12 -8
  60. toil/lib/resources.py +1 -0
  61. toil/lib/retry.py +32 -38
  62. toil/lib/threading.py +12 -12
  63. toil/lib/throttle.py +1 -2
  64. toil/lib/trs.py +113 -51
  65. toil/lib/url.py +14 -23
  66. toil/lib/web.py +7 -2
  67. toil/options/common.py +18 -15
  68. toil/options/cwl.py +2 -2
  69. toil/options/runner.py +9 -5
  70. toil/options/wdl.py +1 -3
  71. toil/provisioners/__init__.py +9 -9
  72. toil/provisioners/abstractProvisioner.py +22 -20
  73. toil/provisioners/aws/__init__.py +20 -14
  74. toil/provisioners/aws/awsProvisioner.py +10 -8
  75. toil/provisioners/clusterScaler.py +19 -18
  76. toil/provisioners/gceProvisioner.py +2 -3
  77. toil/provisioners/node.py +11 -13
  78. toil/realtimeLogger.py +4 -4
  79. toil/resource.py +5 -5
  80. toil/server/app.py +2 -2
  81. toil/server/cli/wes_cwl_runner.py +11 -11
  82. toil/server/utils.py +18 -21
  83. toil/server/wes/abstract_backend.py +9 -8
  84. toil/server/wes/amazon_wes_utils.py +3 -3
  85. toil/server/wes/tasks.py +3 -5
  86. toil/server/wes/toil_backend.py +17 -21
  87. toil/server/wsgi_app.py +3 -3
  88. toil/serviceManager.py +3 -4
  89. toil/statsAndLogging.py +12 -13
  90. toil/test/__init__.py +33 -24
  91. toil/test/batchSystems/batchSystemTest.py +12 -11
  92. toil/test/batchSystems/batch_system_plugin_test.py +3 -5
  93. toil/test/batchSystems/test_slurm.py +38 -24
  94. toil/test/cwl/conftest.py +5 -6
  95. toil/test/cwl/cwlTest.py +194 -78
  96. toil/test/cwl/download_file_uri.json +6 -0
  97. toil/test/cwl/download_file_uri_no_hostname.json +6 -0
  98. toil/test/docs/scripts/tutorial_staging.py +1 -0
  99. toil/test/jobStores/jobStoreTest.py +9 -7
  100. toil/test/lib/aws/test_iam.py +1 -3
  101. toil/test/lib/aws/test_s3.py +1 -1
  102. toil/test/lib/dockerTest.py +9 -9
  103. toil/test/lib/test_ec2.py +12 -11
  104. toil/test/lib/test_history.py +4 -4
  105. toil/test/lib/test_trs.py +16 -14
  106. toil/test/lib/test_url.py +7 -6
  107. toil/test/lib/url_plugin_test.py +12 -18
  108. toil/test/provisioners/aws/awsProvisionerTest.py +10 -8
  109. toil/test/provisioners/clusterScalerTest.py +2 -5
  110. toil/test/provisioners/clusterTest.py +1 -3
  111. toil/test/server/serverTest.py +13 -4
  112. toil/test/sort/restart_sort.py +2 -6
  113. toil/test/sort/sort.py +3 -8
  114. toil/test/src/deferredFunctionTest.py +7 -7
  115. toil/test/src/environmentTest.py +1 -2
  116. toil/test/src/fileStoreTest.py +5 -5
  117. toil/test/src/importExportFileTest.py +5 -6
  118. toil/test/src/jobServiceTest.py +22 -14
  119. toil/test/src/jobTest.py +121 -25
  120. toil/test/src/miscTests.py +5 -7
  121. toil/test/src/promisedRequirementTest.py +8 -7
  122. toil/test/src/regularLogTest.py +2 -3
  123. toil/test/src/resourceTest.py +5 -8
  124. toil/test/src/restartDAGTest.py +5 -6
  125. toil/test/src/resumabilityTest.py +2 -2
  126. toil/test/src/retainTempDirTest.py +3 -3
  127. toil/test/src/systemTest.py +3 -3
  128. toil/test/src/threadingTest.py +1 -1
  129. toil/test/src/workerTest.py +1 -2
  130. toil/test/utils/toilDebugTest.py +6 -4
  131. toil/test/utils/toilKillTest.py +1 -1
  132. toil/test/utils/utilsTest.py +15 -14
  133. toil/test/wdl/wdltoil_test.py +247 -124
  134. toil/test/wdl/wdltoil_test_kubernetes.py +2 -2
  135. toil/toilState.py +2 -3
  136. toil/utils/toilDebugFile.py +3 -8
  137. toil/utils/toilDebugJob.py +1 -2
  138. toil/utils/toilLaunchCluster.py +1 -2
  139. toil/utils/toilSshCluster.py +2 -0
  140. toil/utils/toilStats.py +19 -24
  141. toil/utils/toilStatus.py +11 -14
  142. toil/version.py +10 -10
  143. toil/wdl/wdltoil.py +313 -209
  144. toil/worker.py +18 -12
  145. {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/METADATA +11 -14
  146. {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/RECORD +150 -153
  147. {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/WHEEL +1 -1
  148. toil/test/cwl/staging_cat.cwl +0 -27
  149. toil/test/cwl/staging_make_file.cwl +0 -25
  150. toil/test/cwl/staging_workflow.cwl +0 -43
  151. toil/test/cwl/zero_default.cwl +0 -61
  152. toil/test/utils/ABCWorkflowDebug/ABC.txt +0 -1
  153. {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/entry_points.txt +0 -0
  154. {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/licenses/LICENSE +0 -0
  155. {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/top_level.txt +0 -0
toil/lib/aws/iam.py CHANGED
@@ -3,7 +3,7 @@ import json
3
3
  import logging
4
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  from collections import defaultdict
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  from functools import lru_cache
6
- from typing import TYPE_CHECKING, Any, Optional, Union
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+ from typing import TYPE_CHECKING, Any, Union
7
7
 
8
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  import boto3
9
9
  from botocore.exceptions import ClientError
@@ -64,7 +64,7 @@ AllowedActionCollection = dict[str, dict[str, list[str]]]
64
64
 
65
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  @retry(errors=[AWSServerErrors])
66
66
  def delete_iam_instance_profile(
67
- instance_profile_name: str, region: Optional[str] = None, quiet: bool = True
67
+ instance_profile_name: str, region: str | None = None, quiet: bool = True
68
68
  ) -> None:
69
69
  iam_resource = session.resource("iam", region_name=region)
70
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  instance_profile = iam_resource.InstanceProfile(instance_profile_name)
@@ -81,7 +81,7 @@ def delete_iam_instance_profile(
81
81
 
82
82
  @retry(errors=[AWSServerErrors])
83
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  def delete_iam_role(
84
- role_name: str, region: Optional[str] = None, quiet: bool = True
84
+ role_name: str, region: str | None = None, quiet: bool = True
85
85
  ) -> None:
86
86
  """
87
87
  Deletes an AWS IAM role. Any separate policies are detached from the role, and any inline policies are deleted.
@@ -119,7 +119,7 @@ def create_iam_role(
119
119
  role_name: str,
120
120
  assume_role_policy_document: str,
121
121
  policies: dict[str, Any],
122
- region: Optional[str] = None,
122
+ region: str | None = None,
123
123
  ) -> str:
124
124
  """
125
125
  Creates an AWS IAM role. Any separate policies are detached from the role, and any inline policies are deleted.
@@ -336,7 +336,7 @@ def allowed_actions_roles(
336
336
 
337
337
 
338
338
  def collect_policy_actions(
339
- policy_documents: list[Union[str, "PolicyDocumentDictTypeDef"]]
339
+ policy_documents: list[Union[str, "PolicyDocumentDictTypeDef"]],
340
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  ) -> AllowedActionCollection:
341
341
  """
342
342
  Collect all of the actions allowed by the given policy documents into one AllowedActionCollection.
@@ -478,7 +478,7 @@ def get_policy_permissions(region: str) -> AllowedActionCollection:
478
478
 
479
479
 
480
480
  @lru_cache
481
- def get_aws_account_num() -> Optional[str]:
481
+ def get_aws_account_num() -> str | None:
482
482
  """
483
483
  Returns AWS account num
484
484
  """