toil 9.1.1__py3-none-any.whl → 9.2.0__py3-none-any.whl

toil/worker.py

@@ -28,9 +28,9 @@ import sys
 import threading
 import time
 import traceback
-from collections.abc import Iterator
+from collections.abc import Callable, Iterator
 from contextlib import contextmanager
-from typing import Any, Callable, Optional
+from typing import Any
 
 from configargparse import ArgParser
 
@@ -62,9 +62,10 @@ class StatsDict(MagicExpando):
 
     jobs: list[MagicExpando]
 
+
 def nextChainable(
     predecessor: JobDescription, job_store: AbstractJobStore, config: Config
-) -> Optional[JobDescription]:
+) -> JobDescription | None:
     """
     Returns the next chainable job's JobDescription after the given predecessor
     JobDescription, if one exists, or None if the chain must terminate.
@@ -167,6 +168,7 @@ def nextChainable(
     # Made it through! This job is chainable.
     return successor
 
+
 def unstick_worker(interval: float = 120, timeout: float = 120) -> None:
     """
     Thread function that tries to prevent the process from getting stuck.
@@ -189,7 +191,7 @@ def unstick_worker(interval: float = 120, timeout: float = 120) -> None:
     # Figure out our process ID
     pid = os.getpid()
 
-    child: Optional[subprocess.Popen[bytes]] = None
+    child: subprocess.Popen[bytes] | None = None
 
     def clean_up_child() -> None:
         """
@@ -233,7 +235,9 @@ def unstick_worker(interval: float = 120, timeout: float = 120) -> None:
             )
         except FileNotFoundError:
             # If there isn't an lsof, don't try and use it.
-            logger.info("lsof is not available. We will not be able to use it to unstick a stuck Toil leader.")
+            logger.info(
+                "lsof is not available. We will not be able to use it to unstick a stuck Toil leader."
+            )
             return
         try:
             child.wait(timeout=timeout)
@@ -247,19 +251,23 @@ def unstick_worker(interval: float = 120, timeout: float = 120) -> None:
         if child.returncode != 0:
             # Something went wrong, which is suspicious. Either it failed or it
             # timed out and could not be killed promptly.
-            logger.warning("Could not list open files on ourselves. Return code: %s", child.returncode)
+            logger.warning(
+                "Could not list open files on ourselves. Return code: %s",
+                child.returncode,
+            )
 
         # Wait the interval.
         time.sleep(interval)
 
+
 def workerScript(
     job_store: AbstractJobStore,
     config: Config,
     job_name: str,
     job_store_id: str,
     redirect_output_to_log_file: bool = True,
-    local_worker_temp_dir: Optional[str] = None,
-    debug_flags: Optional[set[str]] = None,
+    local_worker_temp_dir: str | None = None,
+    debug_flags: set[str] | None = None,
 ) -> int:
     """
     Worker process script, runs a job.
@@ -575,9 +583,7 @@ def workerScript(
                     caching=config.caching,
                 )
                 try:
-                    with job._executor(
-                        stats=statsDict, fileStore=fileStore
-                    ):
+                    with job._executor(stats=statsDict, fileStore=fileStore):
                         with deferredFunctionManager.open() as defer:
                             with fileStore.open(job):
                                 # Get the next block function to wait on committing this job
@@ -978,7 +984,7 @@ def in_contexts(contexts: list[str]) -> Iterator[None]:
                 yield
 
 
-def main(argv: Optional[list[str]] = None) -> None:
+def main(argv: list[str] | None = None) -> None:
     if argv is None:
         argv = sys.argv
     # Parse our command line

{toil-9.1.1.dist-info → toil-9.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toil
-Version: 9.1.1
+Version: 9.2.0
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -16,11 +16,11 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Astronomy
@@ -29,7 +29,7 @@ Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: System :: Distributed Computing
 Classifier: Topic :: Utilities
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: dill<0.4,>=0.3.2
@@ -40,7 +40,6 @@ Requires-Dist: python-dateutil
 Requires-Dist: psutil<8,>=6.1.0
 Requires-Dist: PyPubSub<5,>=4.0.3
 Requires-Dist: addict<2.5,>=2.2.1
-Requires-Dist: backports.zoneinfo[tzdata]; python_version < "3.9"
 Requires-Dist: enlighten<2,>=1.5.2
 Requires-Dist: configargparse<2,>=1.7
 Requires-Dist: ruamel.yaml>=0.15
@@ -55,11 +54,11 @@ Requires-Dist: mypy-boto3-s3<2,>=1.28.3.post2; extra == "aws"
 Requires-Dist: moto<6,>=5.0.3; extra == "aws"
 Requires-Dist: ec2_metadata<3,>=2.14.0; extra == "aws"
 Provides-Extra: cwl
-Requires-Dist: cwltool==3.1.20250715140722; extra == "cwl"
+Requires-Dist: cwltool==3.1.20260108082145; extra == "cwl"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "cwl"
 Requires-Dist: galaxy-tool-util<26; extra == "cwl"
 Requires-Dist: galaxy-util<26; extra == "cwl"
-Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "cwl"
+Requires-Dist: ruamel.yaml<=0.19.1,>=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"
@@ -77,15 +76,14 @@ Requires-Dist: types-urllib3; extra == "kubernetes"
 Requires-Dist: types-PyYAML; extra == "kubernetes"
 Requires-Dist: idna>=2; extra == "kubernetes"
 Provides-Extra: wdl
-Requires-Dist: miniwdl==1.13.0; extra == "wdl"
+Requires-Dist: miniwdl==1.13.1; 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]<4,>=3; extra == "server"
 Requires-Dist: flask<4,>=3; extra == "server"
 Requires-Dist: werkzeug<4,>=3; extra == "server"
 Requires-Dist: flask-cors<7,>=5.0.1; extra == "server"
-Requires-Dist: gunicorn<24,>=23.0.0; extra == "server"
+Requires-Dist: gunicorn<26,>=23.0.0; extra == "server"
 Requires-Dist: celery<6,>=5.4.0; extra == "server"
 Requires-Dist: wes-service<6,>=5.0.0; extra == "server"
 Requires-Dist: ruamel.yaml<1,>=0.18.7; extra == "server"
@@ -99,11 +97,11 @@ Requires-Dist: mypy-boto3-iam<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: mypy-boto3-s3<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: moto<6,>=5.0.3; extra == "all"
 Requires-Dist: ec2_metadata<3,>=2.14.0; extra == "all"
-Requires-Dist: cwltool==3.1.20250715140722; extra == "all"
+Requires-Dist: cwltool==3.1.20260108082145; extra == "all"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "all"
 Requires-Dist: galaxy-tool-util<26; extra == "all"
 Requires-Dist: galaxy-util<26; extra == "all"
-Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "all"
+Requires-Dist: ruamel.yaml<=0.19.1,>=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"
@@ -117,14 +115,13 @@ 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==1.13.0; extra == "all"
+Requires-Dist: miniwdl==1.13.1; 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]<4,>=3; extra == "all"
 Requires-Dist: flask<4,>=3; extra == "all"
 Requires-Dist: werkzeug<4,>=3; extra == "all"
 Requires-Dist: flask-cors<7,>=5.0.1; extra == "all"
-Requires-Dist: gunicorn<24,>=23.0.0; extra == "all"
+Requires-Dist: gunicorn<26,>=23.0.0; extra == "all"
 Requires-Dist: celery<6,>=5.4.0; extra == "all"
 Requires-Dist: wes-service<6,>=5.0.0; extra == "all"
 Requires-Dist: ruamel.yaml<1,>=0.18.7; extra == "all"