toil 8.2.0__py3-none-any.whl → 9.0.0__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 (47) hide show
  1. toil/batchSystems/registry.py +15 -118
  2. toil/common.py +20 -1
  3. toil/cwl/cwltoil.py +80 -37
  4. toil/cwl/utils.py +103 -3
  5. toil/jobStores/abstractJobStore.py +11 -236
  6. toil/jobStores/aws/jobStore.py +2 -1
  7. toil/jobStores/fileJobStore.py +2 -1
  8. toil/jobStores/googleJobStore.py +7 -4
  9. toil/lib/accelerators.py +1 -1
  10. toil/lib/generatedEC2Lists.py +81 -19
  11. toil/lib/misc.py +1 -1
  12. toil/lib/plugins.py +106 -0
  13. toil/lib/url.py +320 -0
  14. toil/options/cwl.py +13 -1
  15. toil/options/runner.py +17 -10
  16. toil/options/wdl.py +12 -1
  17. toil/provisioners/aws/awsProvisioner.py +25 -2
  18. toil/server/app.py +12 -6
  19. toil/server/cli/wes_cwl_runner.py +2 -2
  20. toil/server/wes/abstract_backend.py +21 -43
  21. toil/server/wes/toil_backend.py +2 -2
  22. toil/test/__init__.py +2 -2
  23. toil/test/batchSystems/batchSystemTest.py +2 -9
  24. toil/test/batchSystems/batch_system_plugin_test.py +7 -0
  25. toil/test/cwl/cwlTest.py +181 -8
  26. toil/test/docs/scriptsTest.py +2 -1
  27. toil/test/lib/test_url.py +69 -0
  28. toil/test/lib/url_plugin_test.py +105 -0
  29. toil/test/provisioners/aws/awsProvisionerTest.py +1 -1
  30. toil/test/provisioners/clusterTest.py +15 -2
  31. toil/test/provisioners/gceProvisionerTest.py +1 -1
  32. toil/test/server/serverTest.py +78 -36
  33. toil/test/wdl/md5sum/md5sum-gs.json +1 -1
  34. toil/test/wdl/testfiles/read_file.wdl +18 -0
  35. toil/test/wdl/testfiles/url_to_optional_file.wdl +2 -1
  36. toil/test/wdl/wdltoil_test.py +74 -125
  37. toil/utils/toilSshCluster.py +23 -0
  38. toil/utils/toilUpdateEC2Instances.py +1 -0
  39. toil/version.py +9 -9
  40. toil/wdl/wdltoil.py +182 -314
  41. toil/worker.py +11 -6
  42. {toil-8.2.0.dist-info → toil-9.0.0.dist-info}/METADATA +23 -23
  43. {toil-8.2.0.dist-info → toil-9.0.0.dist-info}/RECORD +47 -42
  44. {toil-8.2.0.dist-info → toil-9.0.0.dist-info}/WHEEL +1 -1
  45. {toil-8.2.0.dist-info → toil-9.0.0.dist-info}/entry_points.txt +0 -0
  46. {toil-8.2.0.dist-info → toil-9.0.0.dist-info}/licenses/LICENSE +0 -0
  47. {toil-8.2.0.dist-info → toil-9.0.0.dist-info}/top_level.txt +0 -0
toil/utils/toilUpdateEC2Instances.py CHANGED
@@ -1,3 +1,4 @@
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+ #!/usr/bin/env python3
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  # Copyright (C) 2015-2021 Regents of the University of California
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  #
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  # Licensed under the Apache License, Version 2.0 (the "License");
toil/version.py CHANGED
@@ -1,13 +1,13 @@
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- baseVersion = '8.2.0'
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+ baseVersion = '9.0.0'
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  cgcloudVersion = '1.6.0a1.dev393'
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- version = '8.2.0-3efbe6f84b89a1eeab1d7b5913bbd01084d6490e'
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- cacheTag = 'cache-local-py3.10'
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- mainCacheTag = 'cache-master-py3.10'
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- distVersion = '8.2.0'
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- exactPython = 'python3.10'
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- python = 'python3.10'
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- dockerTag = '8.2.0-3efbe6f84b89a1eeab1d7b5913bbd01084d6490e-py3.10'
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- currentCommit = '3efbe6f84b89a1eeab1d7b5913bbd01084d6490e'
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+ version = '9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c'
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+ cacheTag = 'cache-local-py3.9'
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+ mainCacheTag = 'cache-master-py3.9'
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+ distVersion = '9.0.0'
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+ exactPython = 'python3.9'
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+ python = 'python3.9'
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+ dockerTag = '9.0.0-fa1e35a17670e1927036914ca624bfd591f8349c-py3.9'
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+ currentCommit = 'fa1e35a17670e1927036914ca624bfd591f8349c'
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  dockerRegistry = 'quay.io/ucsc_cgl'
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  dockerName = 'toil'
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  dirty = False