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

toil/test/wdl/wdltoil_test_kubernetes.py

@@ -1,7 +1,7 @@
+import logging
 import unittest
 from uuid import uuid4
 
-import logging
 import pytest
 
 from toil.provisioners import cluster_factory
@@ -12,9 +12,9 @@ from toil.test.wdl.wdltoil_test import (
     WDL_CONFORMANCE_TEST_REPO,
 )
 
-
 logger = logging.getLogger(__name__)
 
+
 @integrative
 @slow
 @pytest.mark.timeout(1800)

toil/toilState.py

@@ -13,7 +13,6 @@
 # limitations under the License.
 import logging
 import time
-from typing import Optional
 
 from toil.bus import JobUpdatedMessage, MessageBus
 from toil.job import CheckpointJobDescription, JobDescription
@@ -102,7 +101,7 @@ class ToilState:
     def load_workflow(
         self,
         rootJob: JobDescription,
-        jobCache: Optional[dict[str, JobDescription]] = None,
+        jobCache: dict[str, JobDescription] | None = None,
     ) -> None:
         """
         Load the workflow rooted at the given job.
@@ -207,7 +206,7 @@ class ToilState:
         start_time = time.time()
         wait_time = 0.1
         initially_known = job_id in self.__job_database
-        new_truth: Optional[JobDescription] = None
+        new_truth: JobDescription | None = None
         while True:
             try:
                 new_truth = self.__job_store.load_job(job_id)

toil/utils/toilDebugFile.py

@@ -16,7 +16,6 @@ import argparse
 import logging
 import os.path
 import sys
-from typing import Optional
 
 from toil.common import Config, Toil, parser_with_common_options
 from toil.jobStores.fileJobStore import FileJobStore
@@ -51,16 +50,12 @@ def fetchJobStoreFiles(jobStore: FileJobStore, options: argparse.Namespace) -> N
             )
             jobStore.read_file(
                 jobStoreFileID,
-                os.path.join(
-                    options.localFilePath, os.path.basename(jobStoreFileID)
-                ),
+                os.path.join(options.localFilePath, os.path.basename(jobStoreFileID)),
                 symlink=options.useSymlinks,
             )
 
 
-def printContentsOfJobStore(
-    job_store: FileJobStore, job_id: Optional[str] = None
-) -> None:
+def printContentsOfJobStore(job_store: FileJobStore, job_id: str | None = None) -> None:
     """
     Fetch a list of all files contained in the job store if nameOfJob is not
     declared, otherwise it only prints out the names of files for that specific
@@ -100,7 +95,7 @@ def main() -> None:
         "--localFilePath",
         type=str,
         default=".",
-        help="Location to which to copy job store files."
+        help="Location to which to copy job store files.",
     )
     parser.add_argument(
         "--fetch",

toil/utils/toilDebugJob.py

@@ -18,7 +18,6 @@ import os
 import pprint
 import sys
 from pathlib import Path
-from typing import Optional
 
 from toil.common import Toil, parser_with_common_options
 from toil.job import FilesDownloadedStoppingPointReached
@@ -163,7 +162,7 @@ def main() -> None:
             # And tell the job to just download files
             debug_flags.add("download_only")
         # We might need to reconstruct a container environment.
-        host_and_job_paths: Optional[list[tuple[str, str]]] = None
+        host_and_job_paths: list[tuple[str, str]] | None = None
         # Track if the run succeeded without error
         run_succeeded = False
 

toil/utils/toilLaunchCluster.py

@@ -15,7 +15,6 @@
 
 import logging
 import os
-from typing import Union
 
 from toil import applianceSelf
 from toil.common import parser_with_common_options
@@ -217,7 +216,7 @@ def main() -> None:
 
     # This holds either ints to launch static nodes, or tuples of ints
     # specifying ranges to launch managed auto-scaling nodes, for each type.
-    nodeCounts: list[Union[int, tuple[int, int]]] = []
+    nodeCounts: list[int | tuple[int, int]] = []
 
     if (worker_node_types != [] or worker_node_ranges != []) and not (
         worker_node_types != [] and worker_node_ranges != []

toil/utils/toilSshCluster.py

@@ -23,6 +23,7 @@ from toil.statsAndLogging import set_logging_from_options
 
 logger = logging.getLogger(__name__)
 
+
 def have_ipv6() -> bool:
     """
     Return True if the IPv6 loopback interface is useable.
@@ -40,6 +41,7 @@ def have_ipv6() -> bool:
             pass
     return False
 
+
 def main() -> None:
     parser = parser_with_common_options(
         provisioner_options=True, jobstore_option=False, prog="toil ssh-cluster"

toil/utils/toilStats.py

@@ -17,8 +17,9 @@ import logging
 import math
 import sys
 from argparse import ArgumentParser, Namespace
+from collections.abc import Callable
 from functools import partial
-from typing import Any, Callable, Optional, TextIO, Union
+from typing import Any, TextIO
 
 from toil.common import Config, Toil, parser_with_common_options
 from toil.job import Job
@@ -98,7 +99,7 @@ class ColumnWidths:
                 print("%s %s %d" % (c, f, self.get_width(c, f)))
 
 
-def pad_str(s: str, field: Optional[int] = None) -> str:
+def pad_str(s: str, field: int | None = None) -> str:
     """Pad the beginning of a string with spaces, if necessary."""
     if field is None or len(s) >= field:
         return s
@@ -106,31 +107,27 @@ def pad_str(s: str, field: Optional[int] = None) -> str:
         return " " * (field - len(s)) + s
 
 
-def pretty_space(k: float, field: Optional[int] = None, alone: bool = False) -> str:
+def pretty_space(k: float, field: int | None = None, alone: bool = False) -> str:
     """Given input k as kibibytes, return a nicely formatted string."""
     # If we don't have a header to say bytes, include the B.
     trailer = "B" if alone else ""
     if k < 1024:
-        return pad_str("{:g}Ki{}".format(k, trailer), field)
+        return pad_str(f"{k:g}Ki{trailer}", field)
     if k < (1024 * 1024):
-        return pad_str("{:.1f}Mi{}".format(k / 1024.0, trailer), field)
+        return pad_str(f"{k / 1024.0:.1f}Mi{trailer}", field)
     if k < (1024 * 1024 * 1024):
-        return pad_str("{:.1f}Gi{}".format(k / 1024.0 / 1024.0, trailer), field)
+        return pad_str(f"{k / 1024.0 / 1024.0:.1f}Gi{trailer}", field)
     if k < (1024 * 1024 * 1024 * 1024):
-        return pad_str(
-            "{:.1f}Ti{}".format(k / 1024.0 / 1024.0 / 1024.0, trailer), field
-        )
+        return pad_str(f"{k / 1024.0 / 1024.0 / 1024.0:.1f}Ti{trailer}", field)
     if k < (1024 * 1024 * 1024 * 1024 * 1024):
-        return pad_str(
-            "{:.1f}Pi{}".format(k / 1024.0 / 1024.0 / 1024.0 / 1024.0, trailer), field
-        )
+        return pad_str(f"{k / 1024.0 / 1024.0 / 1024.0 / 1024.0:.1f}Pi{trailer}", field)
 
     # due to https://stackoverflow.com/questions/47149154
     assert False
 
 
 def pretty_time(
-    t: float, field: Optional[int] = None, unit: str = "s", alone: bool = False
+    t: float, field: int | None = None, unit: str = "s", alone: bool = False
 ) -> str:
     """
     Given input t as seconds, return a nicely formatted string.
@@ -194,7 +191,7 @@ def report_unit(unit: str) -> str:
 def report_time(
     t: float,
     options: Namespace,
-    field: Optional[int] = None,
+    field: int | None = None,
     unit: str = "s",
     alone: bool = False,
 ) -> str:
@@ -206,13 +203,13 @@ def report_time(
     if field is not None:
         assert field >= len(unit_text)
         return "%*.2f%s" % (field - len(unit_text), t, unit_text)
-    return "{:.2f}{}".format(t, unit_text)
+    return f"{t:.2f}{unit_text}"
 
 
 def report_space(
     k: float,
     options: Namespace,
-    field: Optional[int] = None,
+    field: int | None = None,
     unit: str = "KiB",
     alone: bool = False,
 ) -> str:
@@ -238,7 +235,7 @@ def report_space(
 
 
 def report_number(
-    n: Union[int, float, None], field: Optional[int] = None, nan_value: str = "NaN"
+    n: int | float | None, field: int | None = None, nan_value: str = "NaN"
 ) -> str:
     """
     Given a number, report back the correct format as string.
@@ -257,7 +254,7 @@ def report(
     v: float,
     category: str,
     options: Namespace,
-    field: Optional[int] = None,
+    field: int | None = None,
     alone=False,
 ) -> str:
     """
@@ -283,7 +280,7 @@ def sprint_tag(
     key: str,
     tag: Expando,
     options: Namespace,
-    columnWidths: Optional[ColumnWidths] = None,
+    columnWidths: ColumnWidths | None = None,
 ) -> str:
     """Generate a pretty-print ready string from a JTTag()."""
     if columnWidths is None:
@@ -404,9 +401,7 @@ def sort_jobs(jobTypes: list[Any], options: Namespace) -> list[Any]:
     if options.sortCategory in CATEGORIES:
         return sorted(
             jobTypes,
-            key=lambda tag: getattr(
-                tag, "{}_{}".format(sortField, options.sortCategory)
-            ),
+            key=lambda tag: getattr(tag, f"{sortField}_{options.sortCategory}"),
             reverse=options.sort == "decending",
         )
     elif options.sortCategory == "alpha":
@@ -491,7 +486,7 @@ def build_element(
 
     def assertNonnegative(i: float, name: str) -> float:
         if i < 0:
-            raise RuntimeError("Negative value {} reported for {}".format(i, name))
+            raise RuntimeError(f"Negative value {i} reported for {name}")
         else:
             return float(i)
 
@@ -509,7 +504,7 @@ def build_element(
                 float(item.get(category_key, defaults[category])), category
             )
             values.append(category_value)
-    
+
     excess_cpu_items = 0
     for index in range(0, len(item_values[CATEGORIES[0]])):
         # For each item, compute the computed categories

toil/utils/toilStatus.py

@@ -15,7 +15,7 @@
 import logging
 import os
 import sys
-from typing import Any, Optional
+from typing import Any
 
 from toil.bus import replay_message_bus
 from toil.common import Toil, parser_with_common_options
@@ -29,7 +29,7 @@ logger = logging.getLogger(__name__)
 class ToilStatus:
     """Tool for reporting on job status."""
 
-    def __init__(self, jobStoreName: str, specifiedJobs: Optional[list[str]] = None):
+    def __init__(self, jobStoreName: str, specifiedJobs: list[str] | None = None):
         self.jobStoreName = jobStoreName
         self.jobStore = Toil.resumeJobStore(jobStoreName)
 
@@ -42,7 +42,9 @@ class ToilStatus:
                 self.jobsToReport = self.traverseJobGraph(rootJob)
             except JobException:
                 # Root job isn't set.
-                logger.warning("Workflow does not have a root job (yet? anymore?). Cannot look for jobs.")
+                logger.warning(
+                    "Workflow does not have a root job (yet? anymore?). Cannot look for jobs."
+                )
                 self.jobsToReport = []
 
         else:
@@ -60,19 +62,14 @@ class ToilStatus:
             """
             Change a job ID into a GraphViz node name.
             """
-            replacements = [
-                ("_", "_u_"),
-                ("/", "_s_"),
-                ("-", "_d_")
-            ]
+            replacements = [("_", "_u_"), ("/", "_s_"), ("-", "_d_")]
             result = job_id
             for char, replacement in replacements:
                 result = result.replace(char, replacement)
             return result
+
         id_strings = [str(job.jobStoreID) for job in self.jobsToReport]
-        jobsToNodeNames = {
-            s: id_to_name(s) for s in id_strings
-        }
+        jobsToNodeNames = {s: id_to_name(s) for s in id_strings}
 
         # Print the nodes
         for job in set(self.jobsToReport):
@@ -81,7 +78,7 @@ class ToilStatus:
                     jobsToNodeNames[str(job.jobStoreID)],
                     job.jobName,
                     job.displayName,
-                    "black" if job.has_body() else "green"
+                    "black" if job.has_body() else "green",
                 )
             )
 
@@ -359,8 +356,8 @@ class ToilStatus:
     def traverseJobGraph(
         self,
         rootJob: JobDescription,
-        jobsToReport: Optional[list[JobDescription]] = None,
-        foundJobStoreIDs: Optional[set[str]] = None,
+        jobsToReport: list[JobDescription] | None = None,
+        foundJobStoreIDs: set[str] | None = None,
     ) -> list[JobDescription]:
         """
         Find all current jobs in the jobStore and return them as an Array.

toil/version.py

@@ -1,14 +1,14 @@
-baseVersion = '9.1.1'
+baseVersion = '9.2.0'
 cgcloudVersion = '1.6.0a1.dev393'
-version = '9.1.1-f654a3c80f5318ae2ec2e5ecb278a05e1e844a58'
-cacheTag = 'cache-local-py3.9'
-mainCacheTag = 'cache-master-py3.9'
-distVersion = '9.1.1'
-exactPython = 'python3.9'
-python = 'python3.9'
-dockerTag = '9.1.1-f654a3c80f5318ae2ec2e5ecb278a05e1e844a58-py3.9'
-currentCommit = 'f654a3c80f5318ae2ec2e5ecb278a05e1e844a58'
+version = '9.2.0-03ecbc5c4965941b0d87c26cc2d09415dbeb670c'
+cacheTag = 'cache-local-py3.10'
+mainCacheTag = 'cache-master-py3.10'
+distVersion = '9.2.0'
+exactPython = 'python3.10'
+python = 'python3.10'
+dockerTag = '9.2.0-03ecbc5c4965941b0d87c26cc2d09415dbeb670c-py3.10'
+currentCommit = '03ecbc5c4965941b0d87c26cc2d09415dbeb670c'
 dockerRegistry = 'quay.io/ucsc_cgl'
 dockerName = 'toil'
 dirty = False
-cwltool_version = '3.1.20250715140722'
+cwltool_version = '3.1.20260108082145'