toil 8.1.0b1__py3-none-any.whl → 8.2.0__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.
- toil/__init__.py +0 -35
- toil/batchSystems/abstractBatchSystem.py +1 -1
- toil/batchSystems/abstractGridEngineBatchSystem.py +1 -1
- toil/batchSystems/awsBatch.py +1 -1
- toil/batchSystems/cleanup_support.py +1 -1
- toil/batchSystems/kubernetes.py +53 -7
- toil/batchSystems/local_support.py +1 -1
- toil/batchSystems/mesos/batchSystem.py +13 -8
- toil/batchSystems/mesos/test/__init__.py +3 -2
- toil/batchSystems/singleMachine.py +1 -1
- toil/batchSystems/slurm.py +27 -26
- toil/bus.py +5 -3
- toil/common.py +39 -11
- toil/cwl/cwltoil.py +1 -1
- toil/job.py +64 -49
- toil/jobStores/abstractJobStore.py +24 -3
- toil/jobStores/fileJobStore.py +25 -1
- toil/jobStores/googleJobStore.py +104 -30
- toil/leader.py +9 -0
- toil/lib/accelerators.py +3 -1
- toil/lib/aws/utils.py.orig +504 -0
- toil/lib/bioio.py +1 -1
- toil/lib/docker.py +252 -91
- toil/lib/dockstore.py +11 -3
- toil/lib/exceptions.py +5 -3
- toil/lib/history.py +87 -13
- toil/lib/history_submission.py +23 -9
- toil/lib/io.py +34 -22
- toil/lib/misc.py +7 -1
- toil/lib/resources.py +2 -1
- toil/lib/threading.py +11 -10
- toil/options/common.py +8 -0
- toil/options/wdl.py +11 -0
- toil/server/api_spec/LICENSE +201 -0
- toil/server/api_spec/README.rst +5 -0
- toil/server/cli/wes_cwl_runner.py +2 -1
- toil/test/__init__.py +275 -115
- toil/test/batchSystems/batchSystemTest.py +227 -205
- toil/test/batchSystems/test_slurm.py +27 -0
- toil/test/cactus/pestis.tar.gz +0 -0
- toil/test/conftest.py +7 -0
- toil/test/cwl/2.fasta +11 -0
- toil/test/cwl/2.fastq +12 -0
- toil/test/cwl/conftest.py +1 -1
- toil/test/cwl/cwlTest.py +999 -867
- toil/test/cwl/directory/directory/file.txt +15 -0
- toil/test/cwl/download_directory_file.json +4 -0
- toil/test/cwl/download_directory_s3.json +4 -0
- toil/test/cwl/download_file.json +6 -0
- toil/test/cwl/download_http.json +6 -0
- toil/test/cwl/download_https.json +6 -0
- toil/test/cwl/download_s3.json +6 -0
- toil/test/cwl/download_subdirectory_file.json +5 -0
- toil/test/cwl/download_subdirectory_s3.json +5 -0
- toil/test/cwl/empty.json +1 -0
- toil/test/cwl/mock_mpi/fake_mpi.yml +8 -0
- toil/test/cwl/mock_mpi/fake_mpi_run.py +42 -0
- toil/test/cwl/optional-file-exists.json +6 -0
- toil/test/cwl/optional-file-missing.json +6 -0
- toil/test/cwl/preemptible_expression.json +1 -0
- toil/test/cwl/revsort-job-missing.json +6 -0
- toil/test/cwl/revsort-job.json +6 -0
- toil/test/cwl/s3_secondary_file.json +16 -0
- toil/test/cwl/seqtk_seq_job.json +6 -0
- toil/test/cwl/stream.json +6 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.dat +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f0 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f1 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f1i +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f2 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f2_TSM0 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f3 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f3_TSM0 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f4 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f4_TSM0 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.f5 +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.info +0 -0
- toil/test/cwl/test_filename_conflict_resolution.ms/table.lock +0 -0
- toil/test/cwl/whale.txt +16 -0
- toil/test/docs/scripts/example_alwaysfail.py +38 -0
- toil/test/docs/scripts/example_alwaysfail_with_files.wdl +33 -0
- toil/test/docs/scripts/example_cachingbenchmark.py +117 -0
- toil/test/docs/scripts/stagingExampleFiles/in.txt +1 -0
- toil/test/docs/scripts/stagingExampleFiles/out.txt +2 -0
- toil/test/docs/scripts/tutorial_arguments.py +23 -0
- toil/test/docs/scripts/tutorial_debugging.patch +12 -0
- toil/test/docs/scripts/tutorial_debugging_hangs.wdl +126 -0
- toil/test/docs/scripts/tutorial_debugging_works.wdl +129 -0
- toil/test/docs/scripts/tutorial_docker.py +20 -0
- toil/test/docs/scripts/tutorial_dynamic.py +24 -0
- toil/test/docs/scripts/tutorial_encapsulation.py +28 -0
- toil/test/docs/scripts/tutorial_encapsulation2.py +29 -0
- toil/test/docs/scripts/tutorial_helloworld.py +15 -0
- toil/test/docs/scripts/tutorial_invokeworkflow.py +27 -0
- toil/test/docs/scripts/tutorial_invokeworkflow2.py +30 -0
- toil/test/docs/scripts/tutorial_jobfunctions.py +22 -0
- toil/test/docs/scripts/tutorial_managing.py +29 -0
- toil/test/docs/scripts/tutorial_managing2.py +56 -0
- toil/test/docs/scripts/tutorial_multiplejobs.py +25 -0
- toil/test/docs/scripts/tutorial_multiplejobs2.py +21 -0
- toil/test/docs/scripts/tutorial_multiplejobs3.py +22 -0
- toil/test/docs/scripts/tutorial_promises.py +25 -0
- toil/test/docs/scripts/tutorial_promises2.py +30 -0
- toil/test/docs/scripts/tutorial_quickstart.py +22 -0
- toil/test/docs/scripts/tutorial_requirements.py +44 -0
- toil/test/docs/scripts/tutorial_services.py +45 -0
- toil/test/docs/scripts/tutorial_staging.py +45 -0
- toil/test/docs/scripts/tutorial_stats.py +64 -0
- toil/test/lib/aws/test_iam.py +3 -1
- toil/test/lib/dockerTest.py +205 -122
- toil/test/lib/test_history.py +101 -77
- toil/test/provisioners/aws/awsProvisionerTest.py +12 -9
- toil/test/provisioners/clusterTest.py +4 -4
- toil/test/provisioners/gceProvisionerTest.py +16 -14
- toil/test/sort/sort.py +4 -1
- toil/test/src/busTest.py +17 -17
- toil/test/src/deferredFunctionTest.py +145 -132
- toil/test/src/importExportFileTest.py +71 -63
- toil/test/src/jobEncapsulationTest.py +27 -28
- toil/test/src/jobServiceTest.py +149 -133
- toil/test/src/jobTest.py +219 -211
- toil/test/src/miscTests.py +66 -60
- toil/test/src/promisedRequirementTest.py +163 -169
- toil/test/src/regularLogTest.py +24 -24
- toil/test/src/resourceTest.py +82 -76
- toil/test/src/restartDAGTest.py +51 -47
- toil/test/src/resumabilityTest.py +24 -19
- toil/test/src/retainTempDirTest.py +60 -57
- toil/test/src/systemTest.py +17 -13
- toil/test/src/threadingTest.py +29 -32
- toil/test/utils/ABCWorkflowDebug/B_file.txt +1 -0
- toil/test/utils/ABCWorkflowDebug/debugWorkflow.py +204 -0
- toil/test/utils/ABCWorkflowDebug/mkFile.py +16 -0
- toil/test/utils/ABCWorkflowDebug/sleep.cwl +12 -0
- toil/test/utils/ABCWorkflowDebug/sleep.yaml +1 -0
- toil/test/utils/toilDebugTest.py +117 -102
- toil/test/utils/toilKillTest.py +54 -53
- toil/test/utils/utilsTest.py +303 -229
- toil/test/wdl/lint_error.wdl +9 -0
- toil/test/wdl/md5sum/empty_file.json +1 -0
- toil/test/wdl/md5sum/md5sum-gs.json +1 -0
- toil/test/wdl/md5sum/md5sum.1.0.wdl +32 -0
- toil/test/wdl/md5sum/md5sum.input +1 -0
- toil/test/wdl/md5sum/md5sum.json +1 -0
- toil/test/wdl/md5sum/md5sum.wdl +25 -0
- toil/test/wdl/miniwdl_self_test/inputs-namespaced.json +1 -0
- toil/test/wdl/miniwdl_self_test/inputs.json +1 -0
- toil/test/wdl/miniwdl_self_test/self_test.wdl +40 -0
- toil/test/wdl/standard_library/as_map.json +16 -0
- toil/test/wdl/standard_library/as_map_as_input.wdl +23 -0
- toil/test/wdl/standard_library/as_pairs.json +7 -0
- toil/test/wdl/standard_library/as_pairs_as_input.wdl +23 -0
- toil/test/wdl/standard_library/ceil.json +3 -0
- toil/test/wdl/standard_library/ceil_as_command.wdl +16 -0
- toil/test/wdl/standard_library/ceil_as_input.wdl +16 -0
- toil/test/wdl/standard_library/collect_by_key.json +1 -0
- toil/test/wdl/standard_library/collect_by_key_as_input.wdl +23 -0
- toil/test/wdl/standard_library/cross.json +11 -0
- toil/test/wdl/standard_library/cross_as_input.wdl +19 -0
- toil/test/wdl/standard_library/flatten.json +7 -0
- toil/test/wdl/standard_library/flatten_as_input.wdl +18 -0
- toil/test/wdl/standard_library/floor.json +3 -0
- toil/test/wdl/standard_library/floor_as_command.wdl +16 -0
- toil/test/wdl/standard_library/floor_as_input.wdl +16 -0
- toil/test/wdl/standard_library/keys.json +8 -0
- toil/test/wdl/standard_library/keys_as_input.wdl +24 -0
- toil/test/wdl/standard_library/length.json +7 -0
- toil/test/wdl/standard_library/length_as_input.wdl +16 -0
- toil/test/wdl/standard_library/length_as_input_with_map.json +7 -0
- toil/test/wdl/standard_library/length_as_input_with_map.wdl +17 -0
- toil/test/wdl/standard_library/length_invalid.json +3 -0
- toil/test/wdl/standard_library/range.json +3 -0
- toil/test/wdl/standard_library/range_0.json +3 -0
- toil/test/wdl/standard_library/range_as_input.wdl +17 -0
- toil/test/wdl/standard_library/range_invalid.json +3 -0
- toil/test/wdl/standard_library/read_boolean.json +3 -0
- toil/test/wdl/standard_library/read_boolean_as_command.wdl +17 -0
- toil/test/wdl/standard_library/read_float.json +3 -0
- toil/test/wdl/standard_library/read_float_as_command.wdl +17 -0
- toil/test/wdl/standard_library/read_int.json +3 -0
- toil/test/wdl/standard_library/read_int_as_command.wdl +17 -0
- toil/test/wdl/standard_library/read_json.json +3 -0
- toil/test/wdl/standard_library/read_json_as_output.wdl +31 -0
- toil/test/wdl/standard_library/read_lines.json +3 -0
- toil/test/wdl/standard_library/read_lines_as_output.wdl +31 -0
- toil/test/wdl/standard_library/read_map.json +3 -0
- toil/test/wdl/standard_library/read_map_as_output.wdl +31 -0
- toil/test/wdl/standard_library/read_string.json +3 -0
- toil/test/wdl/standard_library/read_string_as_command.wdl +17 -0
- toil/test/wdl/standard_library/read_tsv.json +3 -0
- toil/test/wdl/standard_library/read_tsv_as_output.wdl +31 -0
- toil/test/wdl/standard_library/round.json +3 -0
- toil/test/wdl/standard_library/round_as_command.wdl +16 -0
- toil/test/wdl/standard_library/round_as_input.wdl +16 -0
- toil/test/wdl/standard_library/size.json +3 -0
- toil/test/wdl/standard_library/size_as_command.wdl +17 -0
- toil/test/wdl/standard_library/size_as_output.wdl +36 -0
- toil/test/wdl/standard_library/stderr.json +3 -0
- toil/test/wdl/standard_library/stderr_as_output.wdl +30 -0
- toil/test/wdl/standard_library/stdout.json +3 -0
- toil/test/wdl/standard_library/stdout_as_output.wdl +30 -0
- toil/test/wdl/standard_library/sub.json +3 -0
- toil/test/wdl/standard_library/sub_as_input.wdl +17 -0
- toil/test/wdl/standard_library/sub_as_input_with_file.wdl +17 -0
- toil/test/wdl/standard_library/transpose.json +6 -0
- toil/test/wdl/standard_library/transpose_as_input.wdl +18 -0
- toil/test/wdl/standard_library/write_json.json +6 -0
- toil/test/wdl/standard_library/write_json_as_command.wdl +17 -0
- toil/test/wdl/standard_library/write_lines.json +7 -0
- toil/test/wdl/standard_library/write_lines_as_command.wdl +17 -0
- toil/test/wdl/standard_library/write_map.json +6 -0
- toil/test/wdl/standard_library/write_map_as_command.wdl +17 -0
- toil/test/wdl/standard_library/write_tsv.json +6 -0
- toil/test/wdl/standard_library/write_tsv_as_command.wdl +17 -0
- toil/test/wdl/standard_library/zip.json +12 -0
- toil/test/wdl/standard_library/zip_as_input.wdl +19 -0
- toil/test/wdl/test.csv +3 -0
- toil/test/wdl/test.tsv +3 -0
- toil/test/wdl/testfiles/croo.wdl +38 -0
- toil/test/wdl/testfiles/drop_files.wdl +62 -0
- toil/test/wdl/testfiles/drop_files_subworkflow.wdl +13 -0
- toil/test/wdl/testfiles/empty.txt +0 -0
- toil/test/wdl/testfiles/not_enough_outputs.wdl +33 -0
- toil/test/wdl/testfiles/random.wdl +66 -0
- toil/test/wdl/testfiles/string_file_coercion.json +1 -0
- toil/test/wdl/testfiles/string_file_coercion.wdl +35 -0
- toil/test/wdl/testfiles/test.json +4 -0
- toil/test/wdl/testfiles/test_boolean.txt +1 -0
- toil/test/wdl/testfiles/test_float.txt +1 -0
- toil/test/wdl/testfiles/test_int.txt +1 -0
- toil/test/wdl/testfiles/test_lines.txt +5 -0
- toil/test/wdl/testfiles/test_map.txt +2 -0
- toil/test/wdl/testfiles/test_string.txt +1 -0
- toil/test/wdl/testfiles/url_to_file.wdl +13 -0
- toil/test/wdl/testfiles/url_to_optional_file.wdl +13 -0
- toil/test/wdl/testfiles/vocab.json +1 -0
- toil/test/wdl/testfiles/vocab.wdl +66 -0
- toil/test/wdl/testfiles/wait.wdl +34 -0
- toil/test/wdl/wdl_specification/type_pair.json +23 -0
- toil/test/wdl/wdl_specification/type_pair_basic.wdl +36 -0
- toil/test/wdl/wdl_specification/type_pair_with_files.wdl +36 -0
- toil/test/wdl/wdl_specification/v1_spec.json +1 -0
- toil/test/wdl/wdl_specification/v1_spec_declaration.wdl +39 -0
- toil/test/wdl/wdltoil_test.py +680 -407
- toil/test/wdl/wdltoil_test_kubernetes.py +2 -2
- toil/version.py +9 -9
- toil/wdl/wdltoil.py +336 -123
- {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/METADATA +5 -4
- toil-8.2.0.dist-info/RECORD +439 -0
- {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/WHEEL +1 -1
- toil-8.1.0b1.dist-info/RECORD +0 -259
- {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/entry_points.txt +0 -0
- {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info/licenses}/LICENSE +0 -0
- {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/top_level.txt +0 -0
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@@ -20,7 +20,7 @@ class WDLKubernetesClusterTest(AbstractClusterTest):
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Ensure WDL works on the Kubernetes batchsystem.
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"""
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def __init__(self, name):
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def __init__(self, name: str) -> None:
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self.clusterName = "wdl-integration-test-" + str(uuid4())
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# t2.medium is the minimum t2 instance that permits Kubernetes
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def test_wdl_kubernetes_cluster(self):
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def test_wdl_kubernetes_cluster(self) -> None:
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"""
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Test that a wdl workflow works on a kubernetes cluster. Launches a cluster with 1 worker. This runs a wdl
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workflow that performs an image pull on the worker.
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toil/version.py
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baseVersion = '8.
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baseVersion = '8.2.0'
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cgcloudVersion = '1.6.0a1.dev393'
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version = '8.
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cacheTag = 'cache-local-py3.
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mainCacheTag = 'cache-master-py3.
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distVersion = '8.
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exactPython = 'python3.
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python = 'python3.
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dockerTag = '8.
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currentCommit = '
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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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dockerTag = '8.2.0-3efbe6f84b89a1eeab1d7b5913bbd01084d6490e-py3.10'
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currentCommit = '3efbe6f84b89a1eeab1d7b5913bbd01084d6490e'
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dockerRegistry = 'quay.io/ucsc_cgl'
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dockerName = 'toil'
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dirty = False
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