Fix Toil subcommand usage to include the subcommand

src/toil/common.py

@@ -640,9 +640,9 @@ def generate_config(filepath: str) -> None:
 
 
 def parser_with_common_options(
-    provisioner_options: bool = False, jobstore_option: bool = True
+    provisioner_options: bool = False, jobstore_option: bool = True, prog: Optional[str] = None
 ) -> ArgParser:
-    parser = ArgParser(prog="Toil", formatter_class=ArgumentDefaultsHelpFormatter)
+    parser = ArgParser(prog=prog or "Toil", formatter_class=ArgumentDefaultsHelpFormatter)
 
     if provisioner_options:
         add_provisioner_options(parser)

src/toil/utils/toilClean.py

@@ -24,7 +24,7 @@
 def main() -> None:
     parser = parser_with_common_options(jobstore_option=True)
 
-    options = parser.parse_args()
+    options = parser.parse_args(prog="toil clean")
     set_logging_from_options(options)
     try:
         jobstore = Toil.getJobStore(options.jobStore)

src/toil/utils/toilDebugFile.py

@@ -87,7 +87,7 @@ def printContentsOfJobStore(job_store: FileJobStore, job_id: Optional[str] = Non
 
 
 def main() -> None:
-    parser = parser_with_common_options(jobstore_option=True)
+    parser = parser_with_common_options(jobstore_option=True, prog="toil debug-file")
     parser.add_argument("--localFilePath",
                         nargs=1,
                         help="Location to which to copy job store files.")

src/toil/utils/toilDebugJob.py

@@ -26,7 +26,7 @@
 
 
 def main() -> None:
-    parser = parser_with_common_options(jobstore_option=True)
+    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", type=str,

src/toil/utils/toilDestroyCluster.py

@@ -22,7 +22,7 @@
 
 def main() -> None:
     parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
-    options = parser.parse_args()
+    options = parser.parse_args(prog="toil destroy-cluster")
     set_logging_from_options(options)
 
     logger.info('Destroying cluster %s', options.clusterName)

src/toil/utils/toilKill.py

@@ -25,7 +25,7 @@
 
 
 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()

src/toil/utils/toilLaunchCluster.py

@@ -37,7 +37,7 @@ 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=None,  # TODO: change default to "kubernetes" when we are ready.

src/toil/utils/toilRsyncCluster.py

@@ -23,7 +23,7 @@
 
 
 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"

src/toil/utils/toilSshCluster.py

@@ -25,7 +25,7 @@
 
 
 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',

src/toil/utils/toilStats.py

@@ -640,7 +640,7 @@ def add_stats_options(parser: ArgumentParser) -> None:
 
 def main() -> None:
     """Reports stats on the workflow, use with --stats option to toil."""
-    parser = parser_with_common_options()
+    parser = parser_with_common_options(prog="toil stats")
     add_stats_options(parser)
     options = parser.parse_args()
 

src/toil/utils/toilStatus.py

@@ -317,7 +317,7 @@ def traverseJobGraph(
 
 def main() -> None:
     """Reports the state of a Toil workflow."""
-    parser = parser_with_common_options()
+    parser = parser_with_common_options(prog="toil status")
     parser.add_argument("--failIfNotComplete", action="store_true",
                         help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
                         default=False)