toil 5.12.0__py3-none-any.whl → 6.1.0a1__py3-none-any.whl

toil/worker.py

@@ -11,7 +11,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-import argparse
 import base64
 import copy
 import json
@@ -29,6 +28,8 @@ import traceback
 from contextlib import contextmanager
 from typing import Any, Callable, Iterator, List, Optional
 
+from configargparse import ArgParser
+
 from toil import logProcessContext
 from toil.common import Config, Toil, safeUnpickleFromStream
 from toil.cwl.utils import (CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION,
@@ -222,7 +223,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     #Setup the temporary directories.
     ##########################################
     # Dir to put all this worker's temp files in.
-    assert config.workflowID is not None
+    if config.workflowID is None:
+        raise RuntimeError("The worker workflow ID was never set.")
     toilWorkflowDir = Toil.getLocalWorkflowDir(config.workflowID, config.workDir)
     # Dir to put lock files in, ideally not on NFS.
     toil_coordination_dir = Toil.get_local_workflow_coordination_dir(config.workflowID, config.workDir, config.coordination_dir)
@@ -250,8 +252,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
     if redirectOutputToLogFile:
         # Announce that we are redirecting logging, and where it will now go.
-        # This is important if we are trying to manually trace a faulty worker invocation.
-        logger.info("Redirecting logging to %s", tempWorkerLogPath)
+        # This is only important if we are trying to manually trace a faulty worker invocation.
+        logger.debug("Redirecting logging to %s", tempWorkerLogPath)
         sys.stdout.flush()
         sys.stderr.flush()
 
@@ -345,7 +347,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             if next(jobDesc.successorsAndServiceHosts(), None) is not None:
                 logger.debug("Checkpoint has failed; restoring")
                 # Reduce the try count
-                assert jobDesc.remainingTryCount >= 0
+                if jobDesc.remainingTryCount < 0:
+                    raise RuntimeError("The try count of the job cannot be negative.")
                 jobDesc.remainingTryCount = max(0, jobDesc.remainingTryCount - 1)
                 jobDesc.restartCheckpoint(jobStore)
             # Otherwise, the job and successors are done, and we can cleanup stuff we couldn't clean
@@ -371,7 +374,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             logger.info("Working on job %s", jobDesc)
 
             if jobDesc.command is not None:
-                assert jobDesc.command.startswith("_toil ")
+                if not jobDesc.command.startswith("_toil "):
+                    raise RuntimeError("Job command must start with '_toil' before being converted to an executable command.")
                 logger.debug("Got a command to run: %s" % jobDesc.command)
                 # Load the job. It will use the same JobDescription we have been using.
                 job = Job.loadJob(jobStore, jobDesc)
@@ -402,6 +406,10 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                             # versions of Cactus.
                             job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
 
+                            # When the executor for the job finishes it will
+                            # kick off a commit with the command link to the
+                            # job body cut.
+
                 # Accumulate messages from this job & any subsequent chained jobs
                 statsDict.workers.logsToMaster += fileStore.loggingMessages
 
@@ -426,7 +434,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
                 logger.info("Not chaining from job %s", jobDesc)
 
-                # TODO: Somehow the commit happens even if we don't start it here.
+                # No need to commit because the _executor context manager did it.
 
                 break
 
@@ -434,15 +442,16 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
             ##########################################
             # We have a single successor job that is not a checkpoint job. We
-            # reassign the ID of the current JobDescription to the successor.
-            # We can then delete the successor JobDescription (under its old
-            # ID) in the jobStore, as it is wholly incorporated into the
-            # current one.
+            # reassign the ID of the current JobDescription to the successor,
+            # and take responsibility for both jobs' associated files in the
+            # combined job.
             ##########################################
 
             # Make sure nothing has gone wrong and we can really chain
-            assert jobDesc.memory >= successor.memory
-            assert jobDesc.cores >= successor.cores
+            if jobDesc.memory < successor.memory:
+                raise RuntimeError("Cannot chain jobs. A job's memory cannot be less than it's successor.")
+            if jobDesc.cores < successor.cores:
+                raise RuntimeError("Cannot chain jobs. A job's cores cannot be less than it's successor.")
 
             # Save the successor's original ID, so we can clean it (and its
             # body) up after we finish executing it.
@@ -455,12 +464,6 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             successor.replace(jobDesc)
             jobDesc = successor
 
-            # Problem: successor's job body is a file that will be cleaned up
-            # when we delete the successor job by ID. We can't just move it. So
-            # we need to roll up the deletion of the successor job by ID with
-            # the deletion of the job ID we're currently working on.
-            jobDesc.jobsToDelete.append(successorID)
-
             # Clone the now-current JobDescription (which used to be the successor).
             # TODO: Why??? Can we not?
             jobDesc = copy.deepcopy(jobDesc)
@@ -476,15 +479,6 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             # This will update the job once the previous job is done updating
             fileStore.startCommit(jobState=True)
 
-            # Clone the current job description again, so that further updates
-            # to it (such as new successors being added when it runs) occur
-            # after the commit process we just kicked off, and aren't committed
-            # early or partially.
-            jobDesc = copy.deepcopy(jobDesc)
-            # Bump its version since saving will do that too and we don't want duplicate versions.
-            jobDesc.pre_update_hook()
-
-
             logger.debug("Starting the next job")
 
         ##########################################
@@ -638,7 +632,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     # This must happen after the log file is done with, else there is no place to put the log
     if (not jobAttemptFailed) and jobDesc.is_subtree_done():
         # We can now safely get rid of the JobDescription, and all jobs it chained up
-        for otherID in jobDesc.jobsToDelete:
+        for otherID in jobDesc.merged_jobs:
             jobStore.delete_job(otherID)
         jobStore.delete_job(str(jobDesc.jobStoreID))
 
@@ -647,7 +641,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     else:
         return 0
 
-def parse_args(args: List[str]) -> argparse.Namespace:
+def parse_args(args: List[str]) -> Any:
     """
     Parse command-line arguments to the worker.
     """
@@ -656,7 +650,7 @@ def parse_args(args: List[str]) -> argparse.Namespace:
     args = args[1:]
 
     # Make the parser
-    parser = argparse.ArgumentParser()
+    parser = ArgParser()
 
     # Now add all the options to it
 

{toil-5.12.0.dist-info → toil-6.1.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: toil
-Version: 5.12.0
+Version: 6.1.0a1
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -16,10 +16,10 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Astronomy
@@ -28,91 +28,98 @@ Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: System :: Distributed Computing
 Classifier: Topic :: Utilities
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 License-File: LICENSE
-Requires-Dist: dill (<0.4,>=0.3.2)
-Requires-Dist: requests (<3,>=2)
-Requires-Dist: docker (<6,>=3.7.2)
-Requires-Dist: urllib3 (<2.0.0,>=1.26.0)
-Requires-Dist: python-dateutil
-Requires-Dist: psutil (<6,>=3.0.1)
-Requires-Dist: py-tes (<1,>=0.4.2)
 Requires-Dist: PyPubSub (<5,>=4.0.3)
 Requires-Dist: addict (<2.5,>=2.2.1)
-Requires-Dist: pytz (>=2012)
+Requires-Dist: configargparse (<2,>=1.7)
+Requires-Dist: dill (<0.4,>=0.3.2)
+Requires-Dist: docker (<8,>=3.7.2)
 Requires-Dist: enlighten (<2,>=1.5.2)
-Requires-Dist: typing-extensions
+Requires-Dist: psutil (<6,>=3.0.1)
+Requires-Dist: python-dateutil
+Requires-Dist: pytz (>=2012)
+Requires-Dist: pyyaml (<7,>=6)
+Requires-Dist: requests (<3,>=2)
+Requires-Dist: ruamel.yaml.string (>=0.1.1)
+Requires-Dist: ruamel.yaml (>=0.15)
+Requires-Dist: typing-extensions (<5,>=4.6.2)
+Requires-Dist: urllib3 (<3,>=1.26.0)
 Provides-Extra: all
-Requires-Dist: boto (<3,>=2.48.0) ; extra == 'all'
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] (<2,>=1.28.3.post2) ; extra == 'all'
-Requires-Dist: mypy-boto3-iam (<2,>=1.28.3.post2) ; extra == 'all'
-Requires-Dist: moto (<5,>=4.1.11) ; extra == 'all'
-Requires-Dist: cwltool (==3.1.20230601100705) ; extra == 'all'
-Requires-Dist: schema-salad (<9,>=8.4.20230128170514) ; extra == 'all'
-Requires-Dist: galaxy-tool-util ; extra == 'all'
-Requires-Dist: ruamel.yaml (<=0.17.21,>=0.15) ; extra == 'all'
-Requires-Dist: ruamel.yaml.clib (>=0.2.6) ; extra == 'all'
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 Requires-Dist: CacheControl[filecache] ; extra == 'all'
-Requires-Dist: pynacl (<2,>=1.4.0) ; extra == 'all'
 Requires-Dist: apache-libcloud (<3,>=2.2.1) ; extra == 'all'
-Requires-Dist: google-cloud-storage (<=2.8.0,>=2) ; extra == 'all'
+Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] (<2,>=1.28.3.post2) ; extra == 'all'
+Requires-Dist: boto (<3,>=2.48.0) ; extra == 'all'
+Requires-Dist: celery (<6,>=5.1.0) ; extra == 'all'
+Requires-Dist: connexion[swagger-ui] (<3,>=2.10.0) ; extra == 'all'
+Requires-Dist: cwltool (==3.1.20240112164112) ; extra == 'all'
+Requires-Dist: flask-cors (==4.0.0) ; extra == 'all'
+Requires-Dist: flask (<3,>=2.0) ; extra == 'all'
+Requires-Dist: galaxy-tool-util (<23) ; extra == 'all'
+Requires-Dist: galaxy-util (<23) ; extra == 'all'
 Requires-Dist: google-auth (<3,>=2.18.1) ; extra == 'all'
-Requires-Dist: kubernetes (<22,>=12.0.1) ; extra == 'all'
+Requires-Dist: google-cloud-storage (<=2.8.0,>=2) ; extra == 'all'
+Requires-Dist: gunicorn (==21.2.0) ; extra == 'all'
+Requires-Dist: idna (>=2) ; extra == 'all'
 Requires-Dist: kubernetes-stubs (==v22.6.0post1) ; extra == 'all'
-Requires-Dist: types-urllib3 ; extra == 'all'
+Requires-Dist: kubernetes (<22,>=12.0.1) ; extra == 'all'
+Requires-Dist: miniwdl (==1.11.1) ; extra == 'all'
+Requires-Dist: moto (<5,>=4.1.11) ; extra == 'all'
+Requires-Dist: mypy-boto3-iam (<2,>=1.28.3.post2) ; extra == 'all'
+Requires-Dist: networkx (!=2.8.1,<4) ; extra == 'all'
+Requires-Dist: pynacl (<2,>=1.4.0) ; extra == 'all'
+Requires-Dist: ruamel.yaml.clib (>=0.2.6) ; extra == 'all'
+Requires-Dist: ruamel.yaml (<0.18.4,>=0.15) ; extra == 'all'
+Requires-Dist: ruamel.yaml (<=0.18.3,>=0.15) ; extra == 'all'
+Requires-Dist: schema-salad (<9,>=8.4.20230128170514) ; extra == 'all'
 Requires-Dist: types-PyYAML ; extra == 'all'
-Requires-Dist: idna (>=2) ; extra == 'all'
-Requires-Dist: pymesos (<0.4,>=0.3.15) ; extra == 'all'
-Requires-Dist: miniwdl (==1.10.0) ; extra == 'all'
+Requires-Dist: types-urllib3 ; extra == 'all'
 Requires-Dist: wdlparse (==0.1.0) ; extra == 'all'
-Requires-Dist: connexion[swagger-ui] (<3,>=2.10.0) ; extra == 'all'
-Requires-Dist: flask (<3,>=2.0) ; extra == 'all'
 Requires-Dist: werkzeug (<3,>=2.0) ; extra == 'all'
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 Requires-Dist: wes-service (<5,>=4.0.0) ; extra == 'all'
-Requires-Dist: ruamel.yaml (<0.17.22,>=0.15) ; extra == 'all'
+Requires-Dist: pymesos (<0.4,>=0.3.15) ; (python_version < "3.11") and extra == 'all'
+Requires-Dist: graphlib-backport (==1.0) ; (python_version < "3.9") and extra == 'all'
 Provides-Extra: aws
-Requires-Dist: boto (<3,>=2.48.0) ; extra == 'aws'
 Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] (<2,>=1.28.3.post2) ; extra == 'aws'
-Requires-Dist: mypy-boto3-iam (<2,>=1.28.3.post2) ; extra == 'aws'
+Requires-Dist: boto (<3,>=2.48.0) ; extra == 'aws'
 Requires-Dist: moto (<5,>=4.1.11) ; extra == 'aws'
+Requires-Dist: mypy-boto3-iam (<2,>=1.28.3.post2) ; extra == 'aws'
 Provides-Extra: cwl
-Requires-Dist: cwltool (==3.1.20230601100705) ; extra == 'cwl'
-Requires-Dist: schema-salad (<9,>=8.4.20230128170514) ; extra == 'cwl'
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-Requires-Dist: ruamel.yaml.clib (>=0.2.6) ; extra == 'cwl'
-Requires-Dist: networkx (<2.8.9,>=2) ; extra == 'cwl'
 Requires-Dist: CacheControl[filecache] ; extra == 'cwl'
+Requires-Dist: cwltool (==3.1.20240112164112) ; extra == 'cwl'
+Requires-Dist: galaxy-tool-util (<23) ; extra == 'cwl'
+Requires-Dist: galaxy-util (<23) ; extra == 'cwl'
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+Requires-Dist: ruamel.yaml.clib (>=0.2.6) ; extra == 'cwl'
+Requires-Dist: ruamel.yaml (<=0.18.3,>=0.15) ; extra == 'cwl'
+Requires-Dist: schema-salad (<9,>=8.4.20230128170514) ; extra == 'cwl'
 Provides-Extra: encryption
 Requires-Dist: pynacl (<2,>=1.4.0) ; extra == 'encryption'
 Provides-Extra: google
 Requires-Dist: apache-libcloud (<3,>=2.2.1) ; extra == 'google'
-Requires-Dist: google-cloud-storage (<=2.8.0,>=2) ; extra == 'google'
 Requires-Dist: google-auth (<3,>=2.18.1) ; extra == 'google'
+Requires-Dist: google-cloud-storage (<=2.8.0,>=2) ; extra == 'google'
 Provides-Extra: htcondor
 Requires-Dist: htcondor (<11,>=10.2.0.post1) ; (sys_platform!="darwin") and extra == 'htcondor'
 Provides-Extra: kubernetes
-Requires-Dist: kubernetes (<22,>=12.0.1) ; extra == 'kubernetes'
+Requires-Dist: idna (>=2) ; extra == 'kubernetes'
 Requires-Dist: kubernetes-stubs (==v22.6.0post1) ; extra == 'kubernetes'
-Requires-Dist: types-urllib3 ; extra == 'kubernetes'
+Requires-Dist: kubernetes (<22,>=12.0.1) ; extra == 'kubernetes'
 Requires-Dist: types-PyYAML ; extra == 'kubernetes'
-Requires-Dist: idna (>=2) ; extra == 'kubernetes'
+Requires-Dist: types-urllib3 ; extra == 'kubernetes'
 Provides-Extra: mesos
-Requires-Dist: pymesos (<0.4,>=0.3.15) ; extra == 'mesos'
+Requires-Dist: pymesos (<0.4,>=0.3.15) ; (python_version < "3.11") and extra == 'mesos'
 Provides-Extra: server
+Requires-Dist: celery (<6,>=5.1.0) ; extra == 'server'
 Requires-Dist: connexion[swagger-ui] (<3,>=2.10.0) ; extra == 'server'
+Requires-Dist: flask-cors (==4.0.0) ; extra == 'server'
 Requires-Dist: flask (<3,>=2.0) ; extra == 'server'
+Requires-Dist: gunicorn (==21.2.0) ; extra == 'server'
+Requires-Dist: ruamel.yaml (<0.18.4,>=0.15) ; extra == 'server'
 Requires-Dist: werkzeug (<3,>=2.0) ; extra == 'server'
-Requires-Dist: flask-cors (==3.0.10) ; extra == 'server'
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-Requires-Dist: celery (<6,>=5.1.0) ; extra == 'server'
 Requires-Dist: wes-service (<5,>=4.0.0) ; extra == 'server'
-Requires-Dist: ruamel.yaml (<0.17.22,>=0.15) ; extra == 'server'
 Provides-Extra: wdl
-Requires-Dist: miniwdl (==1.10.0) ; extra == 'wdl'
+Requires-Dist: miniwdl (==1.11.1) ; extra == 'wdl'
 Requires-Dist: wdlparse (==0.1.0) ; extra == 'wdl'
+Requires-Dist: graphlib-backport (==1.0) ; (python_version < "3.9") and extra == 'wdl'
 

toil-6.1.0a1.dist-info/RECORD

@@ -0,0 +1,237 @@
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+toil/toilState.py,sha256=EIfKb8DSfm33DNBXZIXAa_TZJdkMcygGI3CmdWp0sEY,14907
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+toil/batchSystems/awsBatch.py,sha256=aPxHzBsf_9PCQuEkkRz5wrNOwh4Yf2Wr0jaP1M6SYmQ,25296
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{toil-5.12.0.dist-info → toil-6.1.0a1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.0)
+Generator: bdist_wheel (0.38.4)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{toil-5.12.0.dist-info → toil-6.1.0a1.dist-info}/entry_points.txt

@@ -6,5 +6,4 @@ cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]
 toil = toil.utils.toilMain:main
 toil-cwl-runner = toil.cwl.cwltoil:main [cwl]
 toil-wdl-runner = toil.wdl.wdltoil:main [wdl]
-toil-wdl-runner-old = toil.wdl.toilwdl:main [wdl]
 toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]