type fixes

Author: mr-c

src/toil/lib/aws/s3.py

@@ -16,7 +16,7 @@
 import itertools
 import logging
 import urllib.parse
-from collections.abc import Iterator
+from collections.abc import Iterator, MutableSequence
 from contextlib import contextmanager
 from datetime import timedelta
 from io import BytesIO
@@ -31,6 +31,7 @@
 from mypy_boto3_s3.literals import BucketLocationConstraintType
 from mypy_boto3_s3.service_resource import Bucket
 from mypy_boto3_s3.type_defs import (
+    CompletedPartTypeDef,
     GetObjectOutputTypeDef,
     HeadObjectOutputTypeDef,
     ListMultipartUploadsOutputTypeDef,
@@ -291,7 +292,7 @@ def readFrom(self, readable: IO[Any]) -> None:
             Bucket=self.bucket_name, Key=self.file_id, **self.encryption_args
         )
         upload_id = response["UploadId"]
-        parts = []
+        parts: MutableSequence[CompletedPartTypeDef] = []
         try:
             for part_num in itertools.count():
                 logger.debug(
@@ -327,7 +328,7 @@ def readFrom(self, readable: IO[Any]) -> None:
             # Encryption information is not needed here because the upload was
             # not started with a checksum.
             response = self.s3_client.complete_multipart_upload(
-                Bucket=self.bucket_name,  # type: ignore
+                Bucket=self.bucket_name,
                 Key=self.file_id,
                 UploadId=upload_id,
                 MultipartUpload={"Parts": parts},

src/toil/lib/docker.py

@@ -23,14 +23,14 @@
 import requests
 
 import docker
-from docker.errors import (
-    ContainerError,  # type: ignore[import-not-found]
+from docker.errors import (  # type: ignore[import-not-found]
+    ContainerError,
     ImageNotFound,
     NotFound,
     create_api_error_from_http_exception,
 )
-from docker.utils.socket import (
-    consume_socket_output,  # type: ignore[import-not-found]
+from docker.utils.socket import (  # type: ignore[import-not-found]
+    consume_socket_output,
     demux_adaptor,
 )
 from toil.lib.accelerators import get_host_accelerator_numbers

src/toil/wdl/wdltoil.py

@@ -217,24 +217,12 @@ class FileDigester(Protocol):
     def __call__(self, __f: ReadableFileObj, __alg_name: str) -> hashlib._Hash: ...
 
 
-try:
-    # Don't do a direct conditional import to the final name here because then
-    # the polyfill needs *exactly* the signature of file_digest, and not just
-    # one that can accept all calls we make in the file, or MyPy will complain.
-    #
-    # We need to tell MyPy we expect this import to fail, when typechecking on
-    # pythons that don't have it. But we also need to tell it that it is fine
-    # if it succeeds, for Pythons that do have it.
-    #
-    # TODO: Change to checking sys.version_info because MyPy understands that
-    # better?
-    from hashlib import (
-        file_digest as file_digest_impl,
-    )  # type: ignore[attr-defined,unused-ignore]
+if sys.version_info >= (3, 11):
+    from hashlib import file_digest as file_digest_impl
 
     file_digest: FileDigester = file_digest_impl
-except ImportError:
-    # Polyfill file_digest from 3.11+
+else:
+
     def file_digest_fallback_impl(f: ReadableFileObj, alg_name: str) -> hashlib._Hash:
         BUFFER_SIZE = 1024 * 1024
         hasher = hashlib.new(alg_name)