toil 6.0.0__py3-none-any.whl → 6.1.0__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/batchSystems/abstractBatchSystem.py +19 -4
- toil/batchSystems/abstractGridEngineBatchSystem.py +22 -22
- toil/batchSystems/cleanup_support.py +7 -3
- toil/batchSystems/lsf.py +7 -7
- toil/batchSystems/slurm.py +85 -14
- toil/bus.py +38 -0
- toil/common.py +20 -18
- toil/cwl/cwltoil.py +81 -63
- toil/exceptions.py +1 -1
- toil/fileStores/abstractFileStore.py +53 -4
- toil/fileStores/cachingFileStore.py +4 -20
- toil/fileStores/nonCachingFileStore.py +5 -14
- toil/job.py +46 -30
- toil/jobStores/abstractJobStore.py +21 -23
- toil/jobStores/aws/utils.py +5 -4
- toil/jobStores/fileJobStore.py +1 -1
- toil/leader.py +17 -14
- toil/lib/conversions.py +19 -0
- toil/lib/generatedEC2Lists.py +8 -8
- toil/lib/io.py +28 -2
- toil/lib/resources.py +8 -1
- toil/lib/threading.py +27 -12
- toil/options/common.py +5 -7
- toil/options/wdl.py +5 -0
- toil/provisioners/abstractProvisioner.py +8 -0
- toil/statsAndLogging.py +36 -8
- toil/test/batchSystems/test_slurm.py +21 -6
- toil/test/cactus/__init__.py +0 -0
- toil/test/cactus/test_cactus_integration.py +58 -0
- toil/test/cwl/cwlTest.py +243 -151
- toil/test/docs/scriptsTest.py +2 -2
- toil/test/jobStores/jobStoreTest.py +7 -5
- toil/test/lib/test_ec2.py +1 -1
- toil/test/options/__init__.py +13 -0
- toil/test/options/options.py +37 -0
- toil/test/provisioners/clusterTest.py +9 -8
- toil/test/utils/toilDebugTest.py +1 -1
- toil/test/utils/utilsTest.py +3 -3
- toil/test/wdl/wdltoil_test.py +91 -16
- toil/utils/toilDebugFile.py +1 -1
- toil/utils/toilStats.py +309 -266
- toil/utils/toilStatus.py +1 -1
- toil/version.py +9 -9
- toil/wdl/wdltoil.py +341 -189
- toil/worker.py +31 -16
- {toil-6.0.0.dist-info → toil-6.1.0.dist-info}/METADATA +6 -7
- {toil-6.0.0.dist-info → toil-6.1.0.dist-info}/RECORD +51 -47
- {toil-6.0.0.dist-info → toil-6.1.0.dist-info}/LICENSE +0 -0
- {toil-6.0.0.dist-info → toil-6.1.0.dist-info}/WHEEL +0 -0
- {toil-6.0.0.dist-info → toil-6.1.0.dist-info}/entry_points.txt +0 -0
- {toil-6.0.0.dist-info → toil-6.1.0.dist-info}/top_level.txt +0 -0
toil/utils/toilStatus.py
CHANGED
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@@ -82,7 +82,7 @@ class ToilStatus:
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with job.getLogFileHandle(self.jobStore) as fH:
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# TODO: This looks intended to be machine-readable, but the format is
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# unspecified and no escaping is done. But keep these tags around.
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-
print(StatsAndLogging.formatLogStream(fH,
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+
print(StatsAndLogging.formatLogStream(fH, stream_name=f"LOG_FILE_OF_JOB:{job} LOG:"))
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else:
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print(f"LOG_FILE_OF_JOB: {job} LOG: Job has no log file")
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toil/version.py
CHANGED
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@@ -1,13 +1,13 @@
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baseVersion = '6.
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+
baseVersion = '6.1.0'
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cgcloudVersion = '1.6.0a1.dev393'
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version = '6.
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cacheTag = 'cache-local-py3.
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mainCacheTag = 'cache-master-py3.
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distVersion = '6.
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exactPython = 'python3.
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python = 'python3.
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dockerTag = '6.
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currentCommit = '
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version = '6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f'
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cacheTag = 'cache-local-py3.10'
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mainCacheTag = 'cache-master-py3.10'
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distVersion = '6.1.0'
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exactPython = 'python3.10'
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python = 'python3.10'
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dockerTag = '6.1.0-3f9cba3766e52866ea80d0934498f8c8f3129c3f-py3.10'
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currentCommit = '3f9cba3766e52866ea80d0934498f8c8f3129c3f'
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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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