From c79809a920bc9a775803e5e6af7d8bb9ef4be206 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 2 Jan 2025 13:34:24 -0800
Subject: [PATCH] type stubs: upgrade for newer stricter mypy 1.14

https://typing.readthedocs.io/en/latest/spec/enums.html#defining-members
---
 .../pubsub/core/topictreetraverser.pyi         | 18 +++++++-----------
 src/toil/batchSystems/abstractBatchSystem.py   | 18 +++++++++---------
 2 files changed, 16 insertions(+), 20 deletions(-)

diff --git a/contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi b/contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi
index e181cb776b..71eb5ad39a 100644
--- a/contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi
+++ b/contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi
@@ -1,19 +1,15 @@
+from .topicobj import Topic as Topic
 from enum import IntEnum
-
-from _typeshed import Incomplete
-
-from .topicobj import Topic
+from typing import Optional
 
 class ITopicTreeVisitor: ...
 
 class TreeTraversal(IntEnum):
-    DEPTH: Incomplete
-    BREADTH: Incomplete
-    MAP: Incomplete
+    DEPTH = 0
+    BREADTH = 1
+    MAP = 2
 
 class TopicTreeTraverser:
-    def __init__(self, visitor: ITopicTreeVisitor = ...) -> None: ...
+    def __init__(self, visitor: Optional[ITopicTreeVisitor] = None) -> None: ...
     def setVisitor(self, visitor: ITopicTreeVisitor) -> None: ...
-    def traverse(
-        self, topicObj: Topic, how: TreeTraversal = ..., onlyFiltered: bool = ...
-    ) -> None: ...
+    def traverse(self, topicObj: Topic, how: TreeTraversal = ..., onlyFiltered: bool = True) -> None: ...
diff --git a/src/toil/batchSystems/abstractBatchSystem.py b/src/toil/batchSystems/abstractBatchSystem.py
index e2e50d5bee..9ccee35371 100644
--- a/src/toil/batchSystems/abstractBatchSystem.py
+++ b/src/toil/batchSystems/abstractBatchSystem.py
@@ -39,23 +39,23 @@
 
 
 class BatchJobExitReason(enum.IntEnum):
-    FINISHED: int = 1
+    FINISHED = 1
     """Successfully finished."""
-    FAILED: int = 2
+    FAILED = 2
     """Job finished, but failed."""
-    LOST: int = 3
+    LOST = 3
     """Preemptable failure (job's executing host went away)."""
-    KILLED: int = 4
+    KILLED = 4
     """Job killed before finishing."""
-    ERROR: int = 5
+    ERROR = 5
     """Internal error."""
-    MEMLIMIT: int = 6
+    MEMLIMIT = 6
     """Job hit batch system imposed memory limit."""
-    MISSING: int = 7
+    MISSING = 7
     """Job disappeared from the scheduler without actually stopping, so Toil killed it."""
-    MAXJOBDURATION: int = 8
+    MAXJOBDURATION = 8
     """Job ran longer than --maxJobDuration, so Toil killed it."""
-    PARTITION: int = 9
+    PARTITION = 9
     """Job was not able to talk to the leader via the job store, so Toil declared it failed."""
 
     @classmethod