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

toil/utils/toilDebugJob.py

@@ -14,7 +14,11 @@
 """Debug tool for running a toil job locally."""
 import logging
 
+import pprint
+import sys
+
 from toil.common import Config, Toil, parser_with_common_options
+from toil.jobStores.fileJobStore import FileJobStore
 from toil.statsAndLogging import set_logging_from_options
 from toil.utils.toilDebugFile import printContentsOfJobStore
 from toil.worker import workerScript
@@ -23,28 +27,51 @@ logger = logging.getLogger(__name__)
 
 
 def main() -> None:
-    parser = parser_with_common_options(jobstore_option=True)
-    parser.add_argument("jobID", nargs=1,
+    parser = parser_with_common_options(jobstore_option=True, prog="toil debug-job")
+    parser.add_argument("jobID", type=str, nargs='?', default=None,
                         help="The job store id of a job within the provided jobstore to run by itself.")
-    parser.add_argument("--printJobInfo", nargs=1,
-                        help="Return information about this job to the user including preceding jobs, "
-                             "inputs, outputs, and runtime from the last known run.")
+    parser.add_argument("--printJobInfo", type=str,
+                        help="Dump debugging info about this job ID")
 
     options = parser.parse_args()
     set_logging_from_options(options)
-    config = Config()
+
+    jobStore = Toil.resumeJobStore(options.jobStore)
+    # Get the config with the workflow ID from the job store
+    config = jobStore.config
+    # But override its options
     config.setOptions(options)
 
-    jobStore = Toil.resumeJobStore(config.jobStore)
+    did_something = False
 
     if options.printJobInfo:
-        printContentsOfJobStore(jobStorePath=config.jobStore, nameOfJob=options.printJobInfo)
+        if isinstance(jobStore, FileJobStore):
+            # List all its files if we can
+            printContentsOfJobStore(job_store=jobStore, job_id=options.printJobInfo)
+        # Print the job description itself
+        job_desc = jobStore.load_job(options.printJobInfo)
+        print(f"Job: {job_desc}")
+        pprint.pprint(job_desc.__dict__)
+
+        did_something = True
 
     # TODO: Option to print list of successor jobs
     # TODO: Option to run job within python debugger, allowing step through of arguments
     # idea would be to have option to import pdb and set breakpoint at the start of the user's code
 
-    jobID = options.jobID[0]
-    logger.debug(f"Running the following job locally: {jobID}")
-    workerScript(jobStore, config, jobID, jobID, redirectOutputToLogFile=False)
-    logger.debug(f"Finished running: {jobID}")
+    if options.jobID is not None:
+        # We actually want to run a job.
+
+        jobID = options.jobID
+        logger.debug(f"Running the following job locally: {jobID}")
+        workerScript(jobStore, config, jobID, jobID, redirectOutputToLogFile=False)
+        logger.debug(f"Finished running: {jobID}")
+        # Even if the job fails, the worker script succeeds unless something goes wrong with it internally.
+
+        did_something = True
+
+    if not did_something:
+        # Somebody forgot to tell us to do anything.
+        # Show the usage instructions.
+        parser.print_help()
+        sys.exit(1)

toil/utils/toilDestroyCluster.py

@@ -21,7 +21,7 @@ from toil.statsAndLogging import set_logging_from_options
 logger = logging.getLogger(__name__)
 
 def main() -> None:
-    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
+    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False, prog="toil destroy-cluster")
     options = parser.parse_args()
     set_logging_from_options(options)
 

toil/utils/toilKill.py

@@ -25,7 +25,7 @@ logger = logging.getLogger(__name__)
 
 
 def main() -> None:
-    parser = parser_with_common_options()
+    parser = parser_with_common_options(prog="toil kill")
     parser.add_argument('--force', action='store_true',
                         help="Send SIGKILL to the leader process if local.")
     options = parser.parse_args()

toil/utils/toilLaunchCluster.py

@@ -37,9 +37,10 @@ def create_tags_dict(tags: List[str]) -> Dict[str, str]:
 
 
 def main() -> None:
-    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
+    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False, prog="toil launch-cluster")
     parser.add_argument("-T", "--clusterType", dest="clusterType",
-                        choices=['mesos', 'kubernetes'], default='mesos',
+                        choices=['mesos', 'kubernetes'],
+                        default=None,  # TODO: change default to "kubernetes" when we are ready.
                         help="Cluster scheduler to use.")
     parser.add_argument("--leaderNodeType", dest="leaderNodeType", required=True,
                         help="Non-preemptible node type to use for the cluster leader.")
@@ -160,6 +161,16 @@ def main() -> None:
         raise RuntimeError(f'Please provide a value for --zone or set a default in the '
                            f'TOIL_{options.provisioner.upper()}_ZONE environment variable.')
 
+    if options.clusterType == "mesos":
+        logger.warning('You are using a Mesos cluster, which is no longer recommended as Toil is '
+                       'transitioning to Kubernetes-based clusters. Consider switching to '
+                       '--clusterType=kubernetes instead.')
+
+    if options.clusterType is None:
+        logger.warning('Argument --clusterType is not set... using "mesos". '
+                       'In future versions of Toil, the default cluster scheduler will be '
+                       'set to "kubernetes" if the cluster type is not specified.')
+        options.clusterType = "mesos"
 
     logger.info('Creating cluster %s...', options.clusterName)
 

toil/utils/toilMain.py

@@ -5,7 +5,7 @@ import textwrap
 import types
 from typing import Any, Dict
 
-import pkg_resources
+from importlib.metadata import version as metadata_version
 
 from toil.version import version
 
@@ -47,6 +47,7 @@ def get_or_die(module: types.ModuleType, name: str) -> Any:
 def loadModules() -> Dict[str, types.ModuleType]:
     # noinspection PyUnresolvedReferences
     from toil.utils import toilClean  # noqa
+    from toil.utils import toilConfig  # noqa
     from toil.utils import toilDebugFile  # noqa
     from toil.utils import toilDebugJob  # noqa
     from toil.utils import toilDestroyCluster  # noqa
@@ -77,6 +78,6 @@ def printHelp(modules: Dict[str, types.ModuleType]) -> None:
 
 def printVersion() -> None:
     try:
-        print(pkg_resources.get_distribution('toil').version)
+        print(metadata_version('toil'))
     except:
         print(f'Version gathered from toil.version: {version}')

toil/utils/toilRsyncCluster.py

@@ -23,7 +23,7 @@ logger = logging.getLogger(__name__)
 
 
 def main() -> None:
-    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
+    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False, prog="toil rsync-cluster")
     parser.add_argument("--insecure", dest='insecure', action='store_true', required=False,
                         help="Temporarily disable strict host key checking.")
     parser.add_argument("args", nargs=argparse.REMAINDER, help="Arguments to pass to"

toil/utils/toilSshCluster.py

@@ -25,7 +25,7 @@ logger = logging.getLogger(__name__)
 
 
 def main() -> None:
-    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
+    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False, prog="toil ssh-cluster")
     parser.add_argument("--insecure", action='store_true',
                         help="Temporarily disable strict host key checking.")
     parser.add_argument("--sshOption", dest='sshOptions', default=[], action='append',