toil 5.12.0__tar.gz → 6.1.0__tar.gz

toil-6.1.0/PKG-INFO

@@ -0,0 +1,123 @@
+Metadata-Version: 2.1
+Name: toil
+Version: 6.1.0
+Summary: Pipeline management software for clusters.
+Home-page: https://github.com/DataBiosphere/toil
+Author: Benedict Paten and the Toil community
+Author-email: toil-community@googlegroups.com
+License: Apache License v2.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: Linux
+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
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: System :: Distributed Computing
+Classifier: Topic :: Utilities
+Requires-Python: >=3.8
+License-File: LICENSE
+Requires-Dist: dill<0.4,>=0.3.2
+Requires-Dist: requests<3,>=2
+Requires-Dist: docker<8,>=6.1.0
+Requires-Dist: urllib3<3,>=1.26.0
+Requires-Dist: python-dateutil
+Requires-Dist: psutil<6,>=3.0.1
+Requires-Dist: PyPubSub<5,>=4.0.3
+Requires-Dist: addict<2.5,>=2.2.1
+Requires-Dist: pytz>=2012
+Requires-Dist: enlighten<2,>=1.5.2
+Requires-Dist: configargparse<2,>=1.7
+Requires-Dist: ruamel.yaml>=0.15
+Requires-Dist: pyyaml<7,>=6
+Requires-Dist: typing-extensions<5,>=4.6.2
+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: moto<5,>=4.1.11; extra == "aws"
+Provides-Extra: cwl
+Requires-Dist: cwltool==3.1.20240112164112; extra == "cwl"
+Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "cwl"
+Requires-Dist: galaxy-tool-util<23; extra == "cwl"
+Requires-Dist: galaxy-util<23; extra == "cwl"
+Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "cwl"
+Requires-Dist: ruamel.yaml.clib>=0.2.6; extra == "cwl"
+Requires-Dist: networkx!=2.8.1,<4; extra == "cwl"
+Requires-Dist: CacheControl[filecache]; 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"
+Provides-Extra: kubernetes
+Requires-Dist: kubernetes<22,>=12.0.1; extra == "kubernetes"
+Requires-Dist: kubernetes-stubs==v22.6.0post1; extra == "kubernetes"
+Requires-Dist: types-urllib3; extra == "kubernetes"
+Requires-Dist: types-PyYAML; extra == "kubernetes"
+Requires-Dist: idna>=2; extra == "kubernetes"
+Provides-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"
+Provides-Extra: server
+Requires-Dist: connexion[swagger-ui]<3,>=2.10.0; extra == "server"
+Requires-Dist: flask<3,>=2.0; extra == "server"
+Requires-Dist: werkzeug<3,>=2.0; extra == "server"
+Requires-Dist: flask-cors==4.0.0; extra == "server"
+Requires-Dist: gunicorn==21.2.0; extra == "server"
+Requires-Dist: celery<6,>=5.1.0; extra == "server"
+Requires-Dist: wes-service<5,>=4.0.0; extra == "server"
+Requires-Dist: ruamel.yaml<0.19,>=0.15; extra == "server"
+Provides-Extra: htcondor
+Requires-Dist: htcondor<11,>=10.2.0.post1; sys_platform != "darwin" and extra == "htcondor"
+Provides-Extra: mesos
+Requires-Dist: pymesos<0.4,>=0.3.15; python_version < "3.11" and extra == "mesos"
+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==3.1.20240112164112; extra == "all"
+Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "all"
+Requires-Dist: galaxy-tool-util<23; extra == "all"
+Requires-Dist: galaxy-util<23; extra == "all"
+Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "all"
+Requires-Dist: ruamel.yaml.clib>=0.2.6; extra == "all"
+Requires-Dist: networkx!=2.8.1,<4; extra == "all"
+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: google-auth<3,>=2.18.1; extra == "all"
+Requires-Dist: kubernetes<22,>=12.0.1; extra == "all"
+Requires-Dist: kubernetes-stubs==v22.6.0post1; extra == "all"
+Requires-Dist: types-urllib3; extra == "all"
+Requires-Dist: types-PyYAML; extra == "all"
+Requires-Dist: idna>=2; extra == "all"
+Requires-Dist: miniwdl==1.11.1; extra == "all"
+Requires-Dist: wdlparse==0.1.0; extra == "all"
+Requires-Dist: graphlib-backport==1.0; python_version < "3.9" and 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"
+Requires-Dist: flask-cors==4.0.0; extra == "all"
+Requires-Dist: gunicorn==21.2.0; extra == "all"
+Requires-Dist: celery<6,>=5.1.0; extra == "all"
+Requires-Dist: wes-service<5,>=4.0.0; extra == "all"
+Requires-Dist: ruamel.yaml<0.19,>=0.15; extra == "all"
+Requires-Dist: pymesos<0.4,>=0.3.15; python_version < "3.11" and extra == "all"

toil-6.1.0/requirements-cwl.txt

@@ -0,0 +1,8 @@
+cwltool==3.1.20240112164112
+schema-salad>=8.4.20230128170514,<9
+galaxy-tool-util<23
+galaxy-util<23
+ruamel.yaml>=0.15,<=0.19
+ruamel.yaml.clib>=0.2.6
+networkx!=2.8.1,<4
+CacheControl[filecache]

toil-6.1.0/requirements-dev.txt

@@ -0,0 +1,29 @@
+pytest>=6.2.1,<9
+pytest-cov>=2.12.1,<5
+pytest-timeout>=1.4.2,<3
+stubserver>=1.1,<2
+setuptools>=65.5.1,<70
+sphinx>=7,<8
+sphinx-autoapi>=2.1.1,<3
+# astroid 3 won't work until some sphinx-autoapi release after 2.1.1
+astroid>=2.15,<3
+sphinx-autodoc-typehints>=1.24.0,<3
+sphinxcontrib-autoprogram==0.1.8
+cwltest>=2.2.20211116163652
+mypy==1.8.0
+types-requests
+types-setuptools
+types-boto<2.49.18.20240205
+types-pytz
+flake8>=3.8.4,<8
+flake8-bugbear>=20.11.1,<25
+black
+isort
+pydocstyle
+autoflake
+isort
+diff_cover
+lxml
+docutils>=0.16,<0.21
+pyupgrade
+pytest-xdist

toil-6.1.0/requirements-mesos.txt

@@ -0,0 +1 @@
+pymesos>=0.3.15,<0.4 ; python_version < '3.11'

{toil-5.12.0 → toil-6.1.0}/requirements-server.txt

@@ -1,8 +1,8 @@
 connexion[swagger-ui]>=2.10.0, <3
 flask>=2.0,<3
 werkzeug>=2.0,<3
-flask-cors==3.0.10
-gunicorn==20.1.0
+flask-cors==4.0.0
+gunicorn==21.2.0
 celery>=5.1.0, <6
 wes-service>=4.0.0, <5
-ruamel.yaml>=0.15,<0.17.22
+ruamel.yaml>=0.15,<0.19

toil-6.1.0/requirements-wdl.txt

@@ -0,0 +1,3 @@
+miniwdl==1.11.1
+wdlparse==0.1.0
+graphlib-backport==1.0 ; python_version < '3.9'

{toil-5.12.0 → toil-6.1.0}/requirements.txt

@@ -1,13 +1,15 @@
 dill>=0.3.2, <0.4
 requests>=2, <3
-docker>=3.7.2, <6
+docker>=6.1.0, <8
 # Work around https://github.com/docker/docker-py/issues/3113
-urllib3>=1.26.0, <2.0.0
+urllib3>=1.26.0,<3
 python-dateutil
 psutil >= 3.0.1, <6
-py-tes>=0.4.2,<1
 PyPubSub >=4.0.3, <5
 addict>=2.2.1, <2.5
 pytz>=2012
 enlighten>=1.5.2, <2
-typing-extensions
+configargparse>=1.7,<2
+ruamel.yaml>=0.15
+pyyaml>=6,<7
+typing-extensions>=4.6.2, <5

{toil-5.12.0 → toil-6.1.0}/setup.cfg

@@ -23,13 +23,12 @@ markers =
 	local_cuda
 	lsf
 	mesos
-	parasol
+	online
 	rsync
 	server_mode
 	slow
 	slurm
 	singularity
-	tes
 	torque
 	wes_server
 	cwl_small_log_dir
@@ -62,10 +61,6 @@ no_warn_no_return = True
 [mypy-toil.cwl.*]
 strict = True
 
-[mypy-tes]
-ignore_errors = True
-follow_imports = skip
-
 [egg_info]
 tag_build = 
 tag_date = 0

{toil-5.12.0 → toil-6.1.0}/setup.py

@@ -11,8 +11,10 @@
 # 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 imp
+# import imp
 import os
+import types
+from importlib.machinery import SourceFileLoader
 from tempfile import NamedTemporaryFile
 
 from setuptools import find_packages, setup
@@ -47,13 +49,13 @@ def run_setup():
     # to how wheels work, so it is not included in all and
     # must be explicitly installed as an extra
     all_reqs = []
+
     non_htcondor_extras = [
         "aws",
         "cwl",
         "encryption",
         "google",
         "kubernetes",
-        "mesos",
         "wdl",
         "server"
     ]
@@ -62,8 +64,9 @@ def run_setup():
         all_reqs += extras_require[extra]
     # We exclude htcondor from "all" because it can't be on Mac
     extras_require['htcondor:sys_platform!="darwin"'] = get_requirements("htcondor")
+    extras_require['mesos'] = get_requirements("mesos")
+    all_reqs += get_requirements("mesos")
     extras_require["all"] = all_reqs
-
     setup(
         name='toil',
         version=version.distVersion,
@@ -82,10 +85,10 @@ def run_setup():
           'Operating System :: MacOS :: MacOS X',
           'Operating System :: POSIX',
           'Operating System :: POSIX :: Linux',
-          'Programming Language :: Python :: 3.7',
           'Programming Language :: Python :: 3.8',
           'Programming Language :: Python :: 3.9',
           'Programming Language :: Python :: 3.10',
+          'Programming Language :: Python :: 3.11',
           'Topic :: Scientific/Engineering',
           'Topic :: Scientific/Engineering :: Bio-Informatics',
           'Topic :: Scientific/Engineering :: Astronomy',
@@ -95,7 +98,7 @@ def run_setup():
           'Topic :: System :: Distributed Computing',
           'Topic :: Utilities'],
         license="Apache License v2.0",
-        python_requires=">=3.7",
+        python_requires=">=3.8",
         install_requires=install_requires,
         extras_require=extras_require,
         package_dir={'': 'src'},
@@ -113,7 +116,6 @@ def run_setup():
                 'cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]',
                 '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]',
                 '_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]',
                 '_toil_contained_executor = toil.batchSystems.contained_executor:executor']})
@@ -146,7 +148,10 @@ def import_version():
     #     return SourceFileLoader('toil.version', path='src/toil/version.py').load_module()
     #
     # Because SourceFileLoader will error and load "src/toil/__init__.py" .
-    return imp.load_source('toil.version', 'src/toil/version.py')
+    loader = SourceFileLoader('toil.version', 'src/toil/version.py')
+    mod = types.ModuleType(loader.name)
+    loader.exec_module(mod)
+    return mod
 
 
 version = import_version()

{toil-5.12.0 → toil-6.1.0}/src/toil/__init__.py

@@ -20,6 +20,7 @@ import sys
 import time
 from datetime import datetime
 from typing import TYPE_CHECKING, Optional, Tuple
+
 import requests
 from pytz import timezone
 
@@ -106,7 +107,8 @@ def toilPackageDirPath() -> str:
     The return value is guaranteed to end in '/toil'.
     """
     result = os.path.dirname(os.path.realpath(__file__))
-    assert result.endswith('/toil')
+    if not result.endswith('/toil'):
+        raise RuntimeError("The top-level toil package is not named Toil.")
     return result
 
 
@@ -132,7 +134,8 @@ def resolveEntryPoint(entryPoint: str) -> str:
             # opposed to being included via --system-site-packages). For clusters this means that
             # if Toil is installed in a virtualenv on the leader, it must be installed in
             # a virtualenv located at the same path on each worker as well.
-            assert os.access(path, os.X_OK)
+            if not os.access(path, os.X_OK):
+                raise RuntimeError("Cannot access the Toil virtualenv. If installed in a virtualenv on a cluster, make sure that the virtualenv path is the same for the leader and workers.")
             return path
     # Otherwise, we aren't in a virtualenv, or we're in a virtualenv but Toil
     # came in via --system-site-packages, or we think the virtualenv might not
@@ -238,7 +241,8 @@ def customInitCmd() -> str:
 
 def _check_custom_bash_cmd(cmd_str):
     """Ensure that the Bash command doesn't contain invalid characters."""
-    assert not re.search(r'[\n\r\t]', cmd_str), f'"{cmd_str}" contains invalid characters (newline and/or tab).'
+    if re.search(r'[\n\r\t]', cmd_str):
+        raise RuntimeError(f'"{cmd_str}" contains invalid characters (newline and/or tab).')
 
 
 def lookupEnvVar(name: str, envName: str, defaultValue: str) -> str:
@@ -370,11 +374,10 @@ def requestCheckRegularDocker(origAppliance: str, registryName: str, imageName:
     separate check is done for docker.io images.
 
     :param origAppliance: The full url of the docker image originally
-                          specified by the user (or the default).
-                           e.g. ``quay.io/ucsc_cgl/toil:latest``
-    :param registryName: The url of a docker image's registry.  e.g. ``quay.io``
-    :param imageName: The image, including path and excluding the tag. e.g. ``ucsc_cgl/toil``
-    :param tag: The tag used at that docker image's registry.  e.g. ``latest``
+        specified by the user (or the default). For example, ``quay.io/ucsc_cgl/toil:latest``.
+    :param registryName: The url of a docker image's registry. For example, ``quay.io``.
+    :param imageName: The image, including path and excluding the tag. For example, ``ucsc_cgl/toil``.
+    :param tag: The tag used at that docker image's registry. For example, ``latest``.
     :raises: ApplianceImageNotFound if no match is found.
     :return: Return True if match found.
     """
@@ -399,9 +402,9 @@ def requestCheckDockerIo(origAppliance: str, imageName: str, tag: str) -> bool:
     URL is based on the docker v2 schema.  Requires that an access token be fetched first.
 
     :param origAppliance: The full url of the docker image originally
-                          specified by the user (or the default).  e.g. "ubuntu:latest"
-    :param imageName: The image, including path and excluding the tag. e.g. "ubuntu"
-    :param tag: The tag used at that docker image's registry.  e.g. "latest"
+        specified by the user (or the default). For example, ``ubuntu:latest``.
+    :param imageName: The image, including path and excluding the tag. For example, ``ubuntu``.
+    :param tag: The tag used at that docker image's registry. For example, ``latest``.
     :raises: ApplianceImageNotFound if no match is found.
     :return: Return True if match found.
     """
@@ -548,7 +551,8 @@ try:
             So if we ever want to refresh, Boto 3 wants to refresh too.
             """
             # This should only happen if we have expiring credentials, which we should only get from boto3
-            assert (self._boto3_resolver is not None)
+            if self._boto3_resolver is None:
+                raise RuntimeError("The Boto3 resolver should not be None.")
 
             self._obtain_credentials_from_cache_or_boto3()
 
@@ -612,7 +616,8 @@ try:
                         content = f.read()
                         if content:
                             record = content.split('\n')
-                            assert len(record) == 4
+                            if len(record) != 4:
+                                raise RuntimeError("Number of cached credentials is not 4.")
                             self._access_key = record[0]
                             self._secret_key = record[1]
                             self._security_token = record[2]

{toil-5.12.0 → toil-6.1.0}/src/toil/batchSystems/abstractBatchSystem.py

@@ -15,19 +15,19 @@ import enum
 import logging
 import os
 import shutil
+import time
 from abc import ABC, abstractmethod
 from argparse import ArgumentParser, _ArgumentGroup
 from contextlib import contextmanager
 from threading import Condition
-import time
 from typing import (Any,
                     ContextManager,
                     Dict,
-                    List,
-                    Set,
                     Iterator,
+                    List,
                     NamedTuple,
                     Optional,
+                    Set,
                     Union,
                     cast)
 
@@ -37,6 +37,7 @@ from toil.common import Config, Toil, cacheDirName
 from toil.deferred import DeferredFunctionManager
 from toil.fileStores.abstractFileStore import AbstractFileStore
 from toil.job import JobDescription, ParsedRequirement, Requirer
+from toil.lib.memoize import memoize
 from toil.resource import Resource
 
 logger = logging.getLogger(__name__)
@@ -58,13 +59,28 @@ class BatchJobExitReason(enum.IntEnum):
     MEMLIMIT: int = 6
     """Job hit batch system imposed memory limit."""
 
+    @classmethod
+    def to_string(cls, value: int) -> str:
+        """
+        Convert to human-readable string.
+
+        Given an int that may be or may be equal to a value from the enum,
+        produce the string value of its matching enum entry, or a stringified
+        int.
+        """
+        try:
+            return cls(value).name
+        except ValueError:
+            return str(value)
+
 class UpdatedBatchJobInfo(NamedTuple):
     jobID: int
     exitStatus: int
     """
     The exit status (integer value) of the job. 0 implies successful.
 
-    EXIT_STATUS_UNAVAILABLE_VALUE is used when the exit status is not available (e.g. job is lost).
+    EXIT_STATUS_UNAVAILABLE_VALUE is used when the exit status is not available
+    (e.g. job is lost, or otherwise died but actual exit code was not reported).
     """
 
     exitReason: Optional[BatchJobExitReason]
@@ -106,6 +122,8 @@ class AbstractBatchSystem(ABC):
     @abstractmethod
     def supportsWorkerCleanup(cls) -> bool:
         """
+        Whether this batch system supports worker cleanup.
+
         Indicates whether this batch system invokes
         :meth:`BatchSystemSupport.workerCleanup` after the last job for a
         particular workflow invocation finishes. Note that the term *worker*
@@ -119,7 +137,9 @@ class AbstractBatchSystem(ABC):
 
     def setUserScript(self, userScript: Resource) -> None:
         """
-        Set the user script for this workflow. This method must be called before the first job is
+        Set the user script for this workflow.
+
+        This method must be called before the first job is
         issued to this batch system, and only if :meth:`.supportsAutoDeployment` returns True,
         otherwise it will raise an exception.
 
@@ -134,7 +154,6 @@ class AbstractBatchSystem(ABC):
         bus, so that it can send informational messages about the jobs it is
         running to other Toil components.
         """
-        pass
 
     @abstractmethod
     def issueBatchJob(self, jobDesc: JobDescription, job_environment: Optional[Dict[str, str]] = None) -> int:
@@ -263,7 +282,6 @@ class AbstractBatchSystem(ABC):
             setOption(option_name, parsing_function=None, check_function=None, default=None, env=None)
             returning nothing, used to update run configuration as a side effect.
         """
-        pass
 
     def getWorkerContexts(self) -> List[ContextManager[Any]]:
         """
@@ -372,7 +390,7 @@ class BatchSystemSupport(AbstractBatchSystem):
         :param name: the environment variable to be set on the worker.
 
         :param value: if given, the environment variable given by name will be set to this value.
-        if None, the variable's current value will be used as the value on the worker
+            If None, the variable's current value will be used as the value on the worker
 
         :raise RuntimeError: if value is None and the name cannot be found in the environment
         """
@@ -392,6 +410,7 @@ class BatchSystemSupport(AbstractBatchSystem):
         # We do in fact send messages to the message bus.
         self._outbox = message_bus.outbox()
 
+    @memoize
     def get_batch_logs_dir(self) -> str:
         """
         Get the directory where the backing batch system should save its logs.
@@ -404,6 +423,9 @@ class BatchSystemSupport(AbstractBatchSystem):
         """
         if self.config.batch_logs_dir:
             # Use what is specified
+            if not os.path.isdir(self.config.batch_logs_dir):
+                # But if it doesn't exist, make it exist
+                os.makedirs(self.config.batch_logs_dir, exist_ok=True)
             return self.config.batch_logs_dir
         # And if nothing is specified use the workDir.
         return Toil.getToilWorkDir(self.config.workDir)
@@ -430,7 +452,7 @@ class BatchSystemSupport(AbstractBatchSystem):
         file_name: str = f'toil_{self.config.workflowID}.{toil_job_id}.{cluster_job_id}.{std}.log'
         logs_dir: str = self.get_batch_logs_dir()
         return os.path.join(logs_dir, file_name)
-    
+
     def format_std_out_err_glob(self, toil_job_id: int) -> str:
         """
         Get a glob string that will match all file paths generated by format_std_out_err_path for a job.
@@ -438,11 +460,13 @@ class BatchSystemSupport(AbstractBatchSystem):
         file_glob: str = f'toil_{self.config.workflowID}.{toil_job_id}.*.log'
         logs_dir: str = self.get_batch_logs_dir()
         return os.path.join(logs_dir, file_glob)
-        
+
     @staticmethod
     def workerCleanup(info: WorkerCleanupInfo) -> None:
         """
-        Cleans up the worker node on batch system shutdown. Also see :meth:`supportsWorkerCleanup`.
+        Cleans up the worker node on batch system shutdown.
+
+        Also see :meth:`supportsWorkerCleanup`.
 
         :param WorkerCleanupInfo info: A named tuple consisting of all the relevant information
                for cleaning up the worker.
@@ -498,8 +522,10 @@ class NodeInfo:
 
 class AbstractScalableBatchSystem(AbstractBatchSystem):
     """
-    A batch system that supports a variable number of worker nodes. Used by :class:`toil.
-    provisioners.clusterScaler.ClusterScaler` to scale the number of worker nodes in the cluster
+    A batch system that supports a variable number of worker nodes.
+
+    Used by :class:`toil.provisioners.clusterScaler.ClusterScaler`
+    to scale the number of worker nodes in the cluster
     up or down depending on overall load.
     """
 

{toil-5.12.0 → toil-6.1.0}/src/toil/batchSystems/abstractGridEngineBatchSystem.py

@@ -17,13 +17,13 @@ from abc import ABCMeta, abstractmethod
 from datetime import datetime
 from queue import Empty, Queue
 from threading import Lock, Thread
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 from toil.batchSystems.abstractBatchSystem import (BatchJobExitReason,
                                                    UpdatedBatchJobInfo)
 from toil.batchSystems.cleanup_support import BatchSystemCleanupSupport
-from toil.bus import ExternalBatchIdMessage
-from toil.job import JobDescription, AcceleratorRequirement
+from toil.bus import ExternalBatchIdMessage, get_job_kind
+from toil.job import AcceleratorRequirement
 from toil.lib.misc import CalledProcessErrorStderr
 
 logger = logging.getLogger(__name__)
@@ -225,23 +225,20 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport):
             return activity
 
         def _handle_job_status(
-            self, job_id: int, status: Union[int, None], activity: bool
+            self, job_id: int, status: Union[int, Tuple[int, Optional[BatchJobExitReason]], None], activity: bool
         ) -> bool:
             """
             Helper method for checkOnJobs to handle job statuses
             """
             if status is not None:
+                if isinstance(status, int):
+                    code = status
+                    reason = None
+                else:
+                    code, reason = status
                 self.updatedJobsQueue.put(
                     UpdatedBatchJobInfo(
-                        jobID=job_id, exitStatus=status, exitReason=None, wallTime=None
-                    )
-                )
-                self.forgetJob(job_id)
-                return True
-            if status is not None and isinstance(status, BatchJobExitReason):
-                self.updatedJobsQueue.put(
-                    UpdatedBatchJobInfo(
-                        jobID=job_id, exitStatus=1, exitReason=status, wallTime=None
+                        jobID=job_id, exitStatus=code, exitReason=reason, wallTime=None
                     )
                 )
                 self.forgetJob(job_id)
@@ -279,9 +276,9 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport):
                 logger.error("GridEngine like batch system failure", exc_info=ex)
                 raise
 
-        def coalesce_job_exit_codes(self, batch_job_id_list: list) -> list:
+        def coalesce_job_exit_codes(self, batch_job_id_list: list) -> List[Union[int, Tuple[int, Optional[BatchJobExitReason]], None]]:
             """
-            Returns exit codes for a list of jobs.
+            Returns exit codes and possibly exit reasons for a list of jobs, or None if they are running.
 
             Called by AbstractGridEngineWorker.checkOnJobs().
 
@@ -351,16 +348,19 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport):
             raise NotImplementedError()
 
         @abstractmethod
-        def getJobExitCode(self, batchJobID):
+        def getJobExitCode(self, batchJobID) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]:
             """
-            Returns job exit code or an instance of abstractBatchSystem.BatchJobExitReason.
-            if something else happened other than the job exiting.
-            Implementation-specific; called by AbstractGridEngineWorker.checkOnJobs()
+            Returns job exit code and possibly an instance of abstractBatchSystem.BatchJobExitReason.
 
-            :param string batchjobID: batch system job ID
+            Returns None if the job is still running.
+
+            If the job is not running but the exit code is not available, it
+            will be EXIT_STATUS_UNAVAILABLE_VALUE. Implementation-specific;
+            called by AbstractGridEngineWorker.checkOnJobs().
 
-            :rtype: int|toil.batchSystems.abstractBatchSystem.BatchJobExitReason: exit code int
-                    or BatchJobExitReason if something else happened other than job exiting.
+            The exit code will only be 0 if the job affirmatively succeeded.
+
+            :param string batchjobID: batch system job ID
             """
             raise NotImplementedError()
 
@@ -407,10 +407,10 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport):
             else:
                 gpus = jobDesc.accelerators
 
-            self.newJobsQueue.put((jobID, jobDesc.cores, jobDesc.memory, jobDesc.command, jobDesc.get_job_kind(),
+            self.newJobsQueue.put((jobID, jobDesc.cores, jobDesc.memory, jobDesc.command, get_job_kind(jobDesc.get_names()),
                                    job_environment, gpus))
             logger.debug("Issued the job command: %s with job id: %s and job name %s", jobDesc.command, str(jobID),
-                         jobDesc.get_job_kind())
+                         get_job_kind(jobDesc.get_names()))
         return jobID
 
     def killBatchJobs(self, jobIDs):