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

toil/options/cwl.py

@@ -0,0 +1,336 @@
+import os
+from argparse import ArgumentParser
+
+from configargparse import SUPPRESS
+
+from toil.version import baseVersion
+
+
+def add_cwl_options(parser: ArgumentParser, suppress: bool = True) -> None:
+    """
+    Add CWL options to the parser. This only adds nonpositional CWL arguments.
+
+    :param parser: Parser to add options to
+    :param suppress: Suppress help output
+    :return: None
+    """
+    suppress_help = SUPPRESS if suppress else None
+    parser.add_argument("--not-strict", action="store_true", help=suppress_help)
+    parser.add_argument(
+        "--enable-dev",
+        action="store_true",
+        help=suppress_help or suppress_help or "Enable loading and running development versions of CWL",
+    )
+    parser.add_argument(
+        "--enable-ext",
+        action="store_true",
+        help=suppress_help or "Enable loading and running 'cwltool:' extensions to the CWL standards.",
+        default=False,
+    )
+    parser.add_argument("--quiet", dest="quiet", action="store_true", default=False, help=suppress_help)
+    parser.add_argument("--basedir", type=str, help=suppress_help)  # TODO: Might be hard-coded?
+    parser.add_argument("--outdir", type=str, default=None, help=suppress_help)
+    parser.add_argument("--version", action="version", version=baseVersion,
+                        help=suppress_help or "show program's version number and exit")
+    parser.add_argument(
+        "--log-dir",
+        type=str,
+        default="",
+        help=suppress_help or "Log your tools stdout/stderr to this location outside of container",
+    )
+    # this is as a result of suppressed help statements not working well with mutually_exclusive_groups, which will
+    # cause an assertion error
+    # https://github.com/python/cpython/issues/62090
+    dockergroup = parser.add_mutually_exclusive_group() if not suppress_help else parser.add_argument_group()
+    dockergroup.add_argument(
+        "--user-space-docker-cmd",
+        help=suppress_help or "(Linux/OS X only) Specify a user space docker command (like "
+                              "udocker or dx-docker) that will be used to call 'pull' and 'run'",
+    )
+    dockergroup.add_argument(
+        "--singularity",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Use Singularity runtime for running containers. "
+                              "Requires Singularity v2.6.1+ and Linux with kernel version v3.18+ or "
+                              "with overlayfs support backported.",
+    )
+    dockergroup.add_argument(
+        "--podman",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Use Podman runtime for running containers. ",
+    )
+    dockergroup.add_argument(
+        "--no-container",
+        action="store_true",
+        help=suppress_help or "Do not execute jobs in a "
+                              "Docker container, even when `DockerRequirement` "
+                              "is specified under `hints`.",
+    )
+    dockergroup.add_argument(
+        "--leave-container",
+        action="store_false",
+        default=True,
+        help=suppress_help or "Do not delete Docker container used by jobs after they exit",
+        dest="rm_container",
+    )
+    extra_dockergroup = parser.add_argument_group()
+    extra_dockergroup.add_argument(
+        "--custom-net",
+        help=suppress_help or "Specify docker network name to pass to docker run command",
+    )
+    cidgroup = parser.add_argument_group(
+        "Options for recording the Docker container identifier into a file."
+    )
+    cidgroup.add_argument(
+        # Disabled as containerid is now saved by default
+        "--record-container-id",
+        action="store_true",
+        default=False,
+        help=suppress_help or SUPPRESS,
+        dest="record_container_id",
+    )
+
+    cidgroup.add_argument(
+        "--cidfile-dir",
+        type=str,
+        help=suppress_help or "Store the Docker container ID into a file in the specified directory.",
+        default=None,
+        dest="cidfile_dir",
+    )
+
+    cidgroup.add_argument(
+        "--cidfile-prefix",
+        type=str,
+        help=suppress_help or "Specify a prefix to the container ID filename. "
+                              "Final file name will be followed by a timestamp. "
+                              "The default is no prefix.",
+        default=None,
+        dest="cidfile_prefix",
+    )
+
+    parser.add_argument(
+        "--preserve-environment",
+        type=str,
+        nargs="+",
+        help=suppress_help or "Preserve specified environment variables when running"
+                              " CommandLineTools",
+        metavar=("VAR1 VAR2"),
+        default=("PATH",),
+        dest="preserve_environment",
+    )
+    parser.add_argument(
+        "--preserve-entire-environment",
+        action="store_true",
+        help=suppress_help or "Preserve all environment variable when running CommandLineTools.",
+        default=False,
+        dest="preserve_entire_environment",
+    )
+    parser.add_argument(
+        "--destBucket",
+        type=str,
+        help=suppress_help or "Specify a cloud bucket endpoint for output files.",
+    )
+    parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=suppress_help)
+    parser.add_argument("--beta-dependencies-directory", default=None, help=suppress_help)
+    parser.add_argument("--beta-use-biocontainers", default=None, action="store_true", help=suppress_help)
+    parser.add_argument("--beta-conda-dependencies", default=None, action="store_true", help=suppress_help)
+    parser.add_argument(
+        "--tmpdir-prefix",
+        type=str,
+        help=suppress_help or "Path prefix for temporary directories",
+        default=None,
+    )
+    parser.add_argument(
+        "--tmp-outdir-prefix",
+        type=str,
+        help=suppress_help or "Path prefix for intermediate output directories",
+        default=None,
+    )
+    parser.add_argument(
+        "--force-docker-pull",
+        action="store_true",
+        default=False,
+        dest="force_docker_pull",
+        help=suppress_help or "Pull latest docker image even if it is locally present",
+    )
+    parser.add_argument(
+        "--no-match-user",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Disable passing the current uid to `docker run --user`",
+    )
+    parser.add_argument(
+        "--no-read-only",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Do not set root directory in the container as read-only",
+    )
+    parser.add_argument(
+        "--strict-memory-limit",
+        action="store_true",
+        help=suppress_help or "When running with "
+                              "software containers and the Docker engine, pass either the "
+                              "calculated memory allocation from ResourceRequirements or the "
+                              "default of 1 gigabyte to Docker's --memory option.",
+    )
+    parser.add_argument(
+        "--strict-cpu-limit",
+        action="store_true",
+        help=suppress_help or "When running with "
+                              "software containers and the Docker engine, pass either the "
+                              "calculated cpu allocation from ResourceRequirements or the "
+                              "default of 1 core to Docker's --cpu option. "
+                              "Requires docker version >= v1.13.",
+    )
+    parser.add_argument(
+        "--relax-path-checks",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Relax requirements on path names to permit "
+                              "spaces and hash characters.",
+        dest="relax_path_checks",
+    )
+    parser.add_argument(
+        "--default-container",
+        help=suppress_help or "Specify a default docker container that will be "
+                              "used if the workflow fails to specify one.",
+    )
+    parser.add_argument(
+        "--disable-validate",
+        dest="do_validate",
+        action="store_false",
+        default=True,
+        help=suppress_help or SUPPRESS,
+    )
+    parser.add_argument(
+        "--fast-parser",
+        dest="fast_parser",
+        action="store_true",
+        default=False,
+        help=suppress_help or SUPPRESS,
+    )
+    # same workaround as dockergroup
+    checkgroup = parser.add_mutually_exclusive_group() if not suppress_help else parser.add_argument_group()
+    checkgroup.add_argument(
+        "--compute-checksum",
+        action="store_true",
+        default=True,
+        help=suppress_help or "Compute checksum of contents while collecting outputs",
+        dest="compute_checksum",
+    )
+    checkgroup.add_argument(
+        "--no-compute-checksum",
+        action="store_false",
+        help=suppress_help or "Do not compute checksum of contents while collecting outputs",
+        dest="compute_checksum",
+    )
+
+    parser.add_argument(
+        "--eval-timeout",
+        help=suppress_help or "Time to wait for a Javascript expression to evaluate before giving "
+                              "an error, default 20s.",
+        type=float,
+        default=20,
+    )
+    parser.add_argument(
+        "--overrides",
+        type=str,
+        default=None,
+        help=suppress_help or "Read process requirement overrides from file.",
+    )
+
+    parser.add_argument(
+        "--mpi-config-file",
+        type=str,
+        default=None,
+        help=suppress_help or "Platform specific configuration for MPI (parallel "
+                              "launcher, its flag etc). See the cwltool README "
+                              "section 'Running MPI-based tools' for details of the format: "
+                              "https://github.com/common-workflow-language/cwltool#running-mpi-based-tools-that-need-to-be-launched",
+    )
+    parser.add_argument(
+        "--bypass-file-store",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Do not use Toil's file store and assume all "
+                              "paths are accessible in place from all nodes.",
+        dest="bypass_file_store",
+    )
+    parser.add_argument(
+        "--reference-inputs",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Do not copy remote inputs into Toil's file "
+        "store and assume they are accessible in place from "
+        "all nodes.",
+        dest="reference_inputs",
+    )
+    parser.add_argument(
+        "--disable-streaming",
+        action="store_true",
+        default=False,
+        help=suppress_help or "Disable file streaming for files that have 'streamable' flag True",
+        dest="disable_streaming",
+    )
+
+    provgroup = parser.add_argument_group(
+        "Options for recording provenance information of the execution"
+    )
+    provgroup.add_argument(
+        "--provenance",
+        help=suppress_help or "Save provenance to specified folder as a "
+                              "Research Object that captures and aggregates "
+                              "workflow execution and data products.",
+        type=str,
+    )
+
+    provgroup.add_argument(
+        "--enable-user-provenance",
+        default=False,
+        action="store_true",
+        help=suppress_help or "Record user account info as part of provenance.",
+        dest="user_provenance",
+    )
+    provgroup.add_argument(
+        "--disable-user-provenance",
+        default=False,
+        action="store_false",
+        help=suppress_help or "Do not record user account info in provenance.",
+        dest="user_provenance",
+    )
+    provgroup.add_argument(
+        "--enable-host-provenance",
+        default=False,
+        action="store_true",
+        help=suppress_help or "Record host info as part of provenance.",
+        dest="host_provenance",
+    )
+    provgroup.add_argument(
+        "--disable-host-provenance",
+        default=False,
+        action="store_false",
+        help=suppress_help or "Do not record host info in provenance.",
+        dest="host_provenance",
+    )
+    provgroup.add_argument(
+        "--orcid",
+        help=suppress_help or "Record user ORCID identifier as part of "
+                              "provenance, e.g. https://orcid.org/0000-0002-1825-0097 "
+                              "or 0000-0002-1825-0097. Alternatively the environment variable "
+                              "ORCID may be set.",
+        dest="orcid",
+        default=os.environ.get("ORCID", ""),
+        type=str,
+    )
+    provgroup.add_argument(
+        "--full-name",
+        help=suppress_help or "Record full name of user as part of provenance, "
+                              "e.g. Josiah Carberry. You may need to use shell quotes to preserve "
+                              "spaces. Alternatively the environment variable CWL_FULL_NAME may "
+                              "be set.",
+        dest="cwl_full_name",
+        default=os.environ.get("CWL_FULL_NAME", ""),
+        type=str,
+    )

toil/options/wdl.py

@@ -0,0 +1,32 @@
+from argparse import ArgumentParser
+
+from configargparse import SUPPRESS
+
+
+def add_wdl_options(parser: ArgumentParser, suppress: bool = True) -> None:
+    """
+    Add WDL options to a parser. This only adds nonpositional WDL arguments
+    :param parser: Parser to add options to
+    :param suppress: Suppress help output
+    :return: None
+    """
+    suppress_help = SUPPRESS if suppress else None
+    # include arg names without a wdl specifier if suppress is False
+    # this is to avoid possible duplicate options in custom toil scripts, ex outputFile can be a common argument name
+    output_dialect_arguments = ["--wdlOutputDialect"] + (["--outputDialect"] if not suppress else [])
+    parser.add_argument(*output_dialect_arguments, dest="output_dialect", type=str, default='cromwell',
+                        choices=['cromwell', 'miniwdl'],
+                        help=suppress_help or ("JSON output format dialect. 'cromwell' just returns the workflow's "
+                                               "output values as JSON, while 'miniwdl' nests that under an 'outputs' "
+                                               "key, and includes a 'dir' key where files are written."))
+    output_directory_arguments = ["--wdlOutputDirectory"] + (["--outputDirectory", "-o"] if not suppress else [])
+    parser.add_argument(*output_directory_arguments, dest="output_directory", type=str, default=None,
+                        help=suppress_help or (
+                            "Directory or URI prefix to save output files at. By default a new directory is created "
+                            "in the current directory."))
+    output_file_arguments = ["--wdlOutputFile"] + (["--outputFile", "-m"] if not suppress else [])
+    parser.add_argument(*output_file_arguments, dest="output_file", type=str, default=None,
+                        help=suppress_help or "File or URI to save output JSON to.")
+    reference_inputs_arguments = ["--wdlReferenceInputs"] + (["--referenceInputs"] if not suppress else [])
+    parser.add_argument(*reference_inputs_arguments, dest="reference_inputs", type=bool, default=False,
+                        help=suppress_help or "Pass input files by URL")

toil/provisioners/abstractProvisioner.py

@@ -15,7 +15,6 @@ import configparser
 import json
 import logging
 import os.path
-import platform
 import subprocess
 import tempfile
 import textwrap
@@ -477,15 +476,13 @@ class AbstractProvisioner(ABC):
         raise NotImplementedError
 
     @abstractmethod
-    def getNodeShape(self, instance_type: str, preemptible=False):
+    def getNodeShape(self, instance_type: str, preemptible=False) -> Shape:
         """
         The shape of a preemptible or non-preemptible node managed by this provisioner. The node
         shape defines key properties of a machine, such as its number of cores or the time
         between billing intervals.
 
         :param str instance_type: Instance type name to return the shape of.
-
-        :rtype: Shape
         """
         raise NotImplementedError
 

toil/provisioners/aws/__init__.py

@@ -13,18 +13,15 @@
 # limitations under the License.
 import datetime
 import logging
-import os
 from collections import namedtuple
 from operator import attrgetter
 from statistics import mean, stdev
-from typing import Any, List, Optional
+from typing import List, Optional
 
 from toil.lib.aws import (get_aws_zone_from_boto,
                           get_aws_zone_from_environment,
                           get_aws_zone_from_environment_region,
-                          get_aws_zone_from_metadata,
-                          running_on_ec2,
-                          zone_to_region)
+                          get_aws_zone_from_metadata)
 
 logger = logging.getLogger(__name__)
 
@@ -146,7 +143,7 @@ def optimize_spot_bid(boto2_ec2, instance_type, spot_bid, zone_options: List[str
     the instance in a sensible zone.
 
     :param zone_options: The collection of allowed zones to consider, within
-    the region associated with the Boto2 connection.
+        the region associated with the Boto2 connection.
     """
     spot_history = _get_spot_history(boto2_ec2, instance_type)
     if spot_history:

toil/provisioners/aws/awsProvisioner.py

@@ -98,6 +98,12 @@ _S3_BUCKET_MAX_NAME_LEN = 63
 # The suffix of the S3 bucket associated with the cluster
 _S3_BUCKET_INTERNAL_SUFFIX = '--internal'
 
+# prevent removal of these imports
+str(boto.ec2)
+str(boto.iam)
+str(boto.vpc)
+
+
 
 def awsRetryPredicate(e):
     if isinstance(e, socket.gaierror):

toil/provisioners/clusterScaler.py

@@ -32,12 +32,13 @@ from toil.batchSystems.abstractBatchSystem import (AbstractBatchSystem,
                                                    AbstractScalableBatchSystem,
                                                    NodeInfo)
 from toil.bus import ClusterDesiredSizeMessage, ClusterSizeMessage
-from toil.common import Config, defaultTargetTime
+from toil.common import Config
+from toil.options.common import defaultTargetTime
 from toil.job import JobDescription, ServiceJobDescription
 from toil.lib.conversions import bytes2human, human2bytes
 from toil.lib.retry import old_retry
 from toil.lib.threading import ExceptionalThread
-from toil.lib.throttle import LocalThrottle, throttle
+from toil.lib.throttle import throttle
 from toil.provisioners.abstractProvisioner import AbstractProvisioner, Shape
 
 if TYPE_CHECKING:

toil/provisioners/gceProvisioner.py

@@ -26,7 +26,7 @@ from libcloud.compute.types import Provider
 
 from toil.jobStores.googleJobStore import GoogleJobStore
 from toil.lib.conversions import human2bytes
-from toil.lib.util.compatibility import compat_bytes_recursive
+from toil.lib.compatibility import compat_bytes_recursive
 from toil.provisioners import NoSuchClusterException
 from toil.provisioners.abstractProvisioner import AbstractProvisioner, Shape
 from toil.provisioners.node import Node
@@ -197,7 +197,7 @@ class GCEProvisioner(AbstractProvisioner):
 
         logger.debug('Launched leader')
 
-    def getNodeShape(self, instance_type: str, preemptible=False):
+    def getNodeShape(self, instance_type: str, preemptible=False) -> Shape:
         # TODO: read this value only once
         sizes = self._gceDriver.list_sizes(location=self._zone)
         sizes = [x for x in sizes if x.name == instance_type]

toil/realtimeLogger.py

@@ -168,7 +168,8 @@ class RealtimeLogger(metaclass=RealtimeLoggerMetaclass):
     def _stopLeader(cls) -> None:
         """Stop the server on the leader."""
         with cls.lock:
-            assert cls.initialized > 0
+            if cls.initialized == 0:
+                raise RuntimeError("Can't stop the server on the leader as the leader was never initialized.")
             cls.initialized -= 1
             if cls.initialized == 0:
                 if cls.loggingServer:

toil/resource.py

@@ -23,27 +23,25 @@ from collections import namedtuple
 from contextlib import closing
 from io import BytesIO
 from pydoc import locate
-from tempfile import mkdtemp
+from types import ModuleType
+from typing import (IO,
+                    TYPE_CHECKING,
+                    BinaryIO,
+                    Callable,
+                    Optional,
+                    Sequence,
+                    Type)
 from urllib.error import HTTPError
 from urllib.request import urlopen
 from zipfile import ZipFile
 
-from typing import (TYPE_CHECKING,
-                    Optional,
-                    Callable,
-                    IO,
-                    Type,
-                    Sequence,
-                    BinaryIO)
-
 from toil import inVirtualEnv
+from toil.lib.io import mkdtemp
 from toil.lib.iterables import concat
 from toil.lib.memoize import strict_bool
 from toil.lib.retry import ErrorCondition, retry
 from toil.version import exactPython
 
-from types import ModuleType
-
 if TYPE_CHECKING:
     from toil.jobStores.abstractJobStore import AbstractJobStore
 
@@ -117,7 +115,8 @@ class Resource(namedtuple('Resource', ('name', 'pathHash', 'url', 'contentHash')
             # .. and register its location in an environment variable such that child processes
             # can find it.
             os.environ[cls.rootDirPathEnvName] = resourceRootDirPath
-        assert os.path.isdir(resourceRootDirPath)
+        if not os.path.isdir(resourceRootDirPath):
+            raise RuntimeError("Resource root path is not a directory.")
 
     @classmethod
     def cleanSystem(cls) -> None:
@@ -152,7 +151,9 @@ class Resource(namedtuple('Resource', ('name', 'pathHash', 'url', 'contentHash')
             return None
         else:
             self = cls.unpickle(s)
-            assert self.pathHash == pathHash
+            if self.pathHash != pathHash:
+                raise RuntimeError("The Resource's path is incorrect.")
+
             return self
 
     def download(self, callback: Optional[Callable[[str], None]] = None) -> None:
@@ -243,7 +244,8 @@ class Resource(namedtuple('Resource', ('name', 'pathHash', 'url', 'contentHash')
         with closing(urlopen(self.url)) as content:
             buf = content.read()
         contentHash = hashlib.md5(buf)
-        assert contentHash.hexdigest() == self.contentHash
+        if contentHash.hexdigest() != self.contentHash:
+            raise RuntimeError("The Resource's contents is incorrect.")
         dstFile.write(buf)
 
 
@@ -323,7 +325,8 @@ class VirtualEnvResource(DirectoryResource):
 
     @classmethod
     def _load(cls, path: str) -> BytesIO:
-        assert os.path.basename(path) == 'site-packages'
+        if os.path.basename(path) != 'site-packages':
+            raise RuntimeError("An incorrect path was passed through.")
         bytesIO = BytesIO()
         with ZipFile(file=bytesIO, mode='w') as zipFile:
             for dirName, _, fileList in os.walk(path):
@@ -404,7 +407,8 @@ class ModuleDescriptor(namedtuple('ModuleDescriptor', ('dirPath', 'name', 'fromV
                 nameList = [filePath.pop()]
                 for package in reversed(module.__package__.split('.')):
                     dirPathTail = filePath.pop()
-                    assert dirPathTail == package
+                    if dirPathTail != package:
+                        raise RuntimeError("Incorrect path to package.")
                     nameList.append(dirPathTail)
                 name = '.'.join(reversed(nameList))
                 dirPath = os.path.sep.join(filePath)
@@ -421,7 +425,8 @@ class ModuleDescriptor(namedtuple('ModuleDescriptor', ('dirPath', 'name', 'fromV
 
             for package in reversed(name.split('.')):
                 dirPathTail = filePath.pop()
-                assert dirPathTail == package
+                if dirPathTail != package:
+                    raise RuntimeError("Incorrect path to package.")
             dirPath = os.path.abspath(os.path.sep.join(filePath))
         absPrefix = os.path.abspath(sys.prefix)
         inVenv = inVirtualEnv()
@@ -591,7 +596,8 @@ class ModuleDescriptor(namedtuple('ModuleDescriptor', ('dirPath', 'name', 'fromV
 
     @classmethod
     def fromCommand(cls, command: Sequence[str]) -> "ModuleDescriptor":
-        assert len(command) == 3
+        if len(command) != 3:
+            raise RuntimeError("Incorrect number of arguments (Expected 3).")
         return cls(dirPath=command[0], name=command[1], fromVirtualEnv=strict_bool(command[2]))
 
     def makeLoadable(self) -> "ModuleDescriptor":

toil/server/app.py

@@ -14,12 +14,11 @@
 import argparse
 import logging
 import os
-from typing import Type
 
 import connexion  # type: ignore
+from configargparse import ArgumentParser
 
 from toil.lib.aws import get_current_aws_region, running_on_ec2, running_on_ecs
-from toil.lib.misc import get_public_ip
 from toil.server.wes.toil_backend import ToilBackend
 from toil.server.wsgi_app import run_app
 from toil.version import version
@@ -28,7 +27,7 @@ logger = logging.getLogger(__name__)
 
 
 def parser_with_server_options() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(description="Toil server mode.")
+    parser = ArgumentParser(description="Toil server mode.")
 
     parser.add_argument("--debug", action="store_true", default=False,
                         help="Enable debug mode.")

toil/server/cli/wes_cwl_runner.py

@@ -1,4 +1,3 @@
-import argparse
 import json
 import logging
 import os
@@ -13,6 +12,7 @@ from urllib.parse import urldefrag, urljoin, urlparse
 import requests
 import ruamel.yaml
 import schema_salad
+from configargparse import ArgumentParser
 from wes_client.util import WESClient  # type: ignore
 from wes_client.util import wes_reponse as wes_response
 
@@ -147,7 +147,7 @@ class WESClientWithWorkflowEngineParameters(WESClient):  # type: ignore
 
         :param workflow_params_file: The URL or path to the CWL input file.
         """
-        loader = schema_salad.ref_resolver.Loader(
+        loader = schema_salad.ref_resolver.Loader(  # type:ignore
             {"location": {"@type": "@id"}, "path": {"@type": "@id"}}
         )
 
@@ -396,7 +396,7 @@ def submit_run(client: WESClientWithWorkflowEngineParameters,
         input_file,
         attachments=attachments,
         workflow_engine_parameters=engine_options)
-    return run_result.get("run_id", None)
+    return str(run_result["run_id"])
 
 
 def poll_run(client: WESClientWithWorkflowEngineParameters, run_id: str) -> bool:
@@ -425,7 +425,7 @@ def print_logs_and_exit(client: WESClientWithWorkflowEngineParameters, run_id: s
 
 
 def main() -> None:
-    parser = argparse.ArgumentParser(description="A CWL runner that runs workflows through WES.")
+    parser = ArgumentParser(description="A CWL runner that runs workflows through WES.")
 
     # the first two positional arguments are the CWL file and its input file
     parser.add_argument("cwl_file", type=str)

toil/server/utils.py

@@ -193,7 +193,7 @@ class AbstractStateStore:
     This is a key-value store, with keys namespaced by workflow ID. Concurrent
     access from multiple threads or processes is safe and globally consistent.
 
-    Keys and workflow IDs are restricted to [-a-zA-Z0-9_], because backends may
+    Keys and workflow IDs are restricted to ``[-a-zA-Z0-9_]``, because backends may
     use them as path or URL components.
 
     Key values are either a string, or None if the key is not set.