diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 671f30d82e16..9e7bf7d561a7 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -864,7 +864,7 @@ def find_conversion_destination_for_dataset_by_extensions(
             ext = dataset_or_ext
             dataset = None
 
-        accepted_datatypes: List["Data"] = []
+        accepted_datatypes: List[Data] = []
         for accepted_format in accepted_formats:
             if isinstance(accepted_format, str):
                 accepted_datatype = self.get_datatype_by_extension(accepted_format)
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 231a88f234f8..d83e430e00ac 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -1,28 +1,28 @@
 aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
-anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
-ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
+anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
+ase==3.23.0 ; python_version >= "3.8" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
 axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
 babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
-backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
+backports-tarfile==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
 boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
 botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
-codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
+codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
+coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -34,10 +34,10 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
 exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
+fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
+fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-galaxy-release-util==0.1.9 ; python_version >= "3.8" and python_version < "3.13"
+galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
 graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -86,7 +86,7 @@ pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
+pkginfo==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
 platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
 playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -125,22 +125,22 @@ rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
+requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
+responses==0.25.2 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-rucio-clients==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
+rucio-clients==34.4.2 ; python_version >= "3.9" and python_version < "3.13"
 s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
-scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
+scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -157,7 +157,7 @@ sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_versio
 statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13"
 tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
-testfixtures==8.2.0 ; python_version >= "3.8" and python_version < "3.13"
+testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
 text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -167,14 +167,14 @@ trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
+watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
 werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
+zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 805eda6a8a58..9cd22f68931b 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -4,4 +4,4 @@ flake8-bugbear==24.4.26
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.4.4
+ruff==0.4.8
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index f25d7b6a27c7..7a0e084d61a0 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -11,8 +11,8 @@ aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
 amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
 aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
-annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
+annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
+anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
 apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13"
 appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
 arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -37,7 +37,7 @@ botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
@@ -50,8 +50,8 @@ cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
-conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
+conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
 cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13"
 cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
@@ -70,7 +70,7 @@ fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
-fsspec==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
+fsspec==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
 future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -113,7 +113,7 @@ msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 networkx==2.5 ; python_version >= "3.8" and python_version < "3.13"
-nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
+nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
 oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -127,16 +127,16 @@ pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
-prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
+prompt-toolkit==3.0.46 ; python_version >= "3.8" and python_version < "3.13"
 prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
 psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
 pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
+pydantic[email]==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
 pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -164,17 +164,17 @@ repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
 requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
-requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
+requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
 routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-s3fs==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
+s3fs==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
 shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -193,16 +193,16 @@ tenacity==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
 tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
+tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13"
 tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
 ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13"
+uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13"
 uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
 vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
@@ -212,6 +212,6 @@ whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
 yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
+zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13"
 zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
 zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index a18d0745af0d..7f5ddd202f6e 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,17 +1,17 @@
-annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.34.108 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.34.94 ; python_version >= "3.8" and python_version < "3.13"
+annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.34.122 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.34.122 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
-mypy-boto3-s3==1.34.105 ; python_version >= "3.8" and python_version < "3.13"
+mypy-boto3-s3==1.34.120 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13"
+types-awscrt==0.20.11 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -27,4 +27,4 @@ types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
 types-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
 types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13"
 types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 33b405bb5916..ad289ee51d0f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7989,8 +7989,8 @@ def __init__(self):
         self._inputs_by_name = None
         # Injected attributes
         # TODO: code using these should be refactored to not depend on these non-persistent fields
-        self.module: Optional["WorkflowModule"]
-        self.state: Optional["DefaultToolState"]
+        self.module: Optional[WorkflowModule]
+        self.state: Optional[DefaultToolState]
         self.upgrade_messages: Optional[Dict]
 
     @reconstructor
diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
index 14d8d6b73cec..bffb0de77794 100644
--- a/lib/galaxy/model/tags.py
+++ b/lib/galaxy/model/tags.py
@@ -61,7 +61,7 @@ def __init__(self, sa_session: galaxy_scoped_session, galaxy_session=None) -> No
         self.item_tag_assoc_info: Dict[str, ItemTagAssocInfo] = {}
         # Can't include type annotation in signature, because lagom will attempt to look up
         # GalaxySession, but can't find it due to the circular import
-        self.galaxy_session: Optional["GalaxySession"] = galaxy_session
+        self.galaxy_session: Optional[GalaxySession] = galaxy_session
 
     def create_tag_handler_session(self, galaxy_session: Optional["GalaxySession"]):
         # Creates a transient tag handler that avoids repeated flushes
@@ -502,7 +502,7 @@ class GalaxyTagHandlerSession(GalaxyTagHandler):
 
     def __init__(self, sa_session, galaxy_session: Optional["GalaxySession"]):
         super().__init__(sa_session, galaxy_session)
-        self.created_tags: Dict[str, "Tag"] = {}
+        self.created_tags: Dict[str, Tag] = {}
 
     def _get_tag(self, tag_name):
         """Get tag from cache or database."""
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
index d4f2157f82d5..c870829bf994 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
@@ -74,7 +74,7 @@ def install_data_managers(
         repository,
         repository_tools_tups,
     ) -> List["DataManagerInterface"]:
-        rval: List["DataManagerInterface"] = []
+        rval: List[DataManagerInterface] = []
         if "data_manager" in metadata_dict:
             tpm = tool_panel_manager.ToolPanelManager(self.app)
             repository_tools_by_guid = {}
diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 1b760e317871..e37335d829f0 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -252,7 +252,7 @@ def contents(
             raise exceptions.RequestParameterInvalidException(
                 "Parameter instance_type not being 'history' is not yet implemented."
             )
-        hdca: "HistoryDatasetCollectionAssociation" = self.collection_manager.get_dataset_collection_instance(
+        hdca: HistoryDatasetCollectionAssociation = self.collection_manager.get_dataset_collection_instance(
             trans, "history", hdca_id
         )
 
diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
index 0854502842aa..54ef988f990c 100644
--- a/lib/galaxy/webapps/galaxy/services/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -697,7 +697,7 @@ def bulk_operation(
         history = self.history_manager.get_mutable(history_id, trans.user, current_history=trans.history)
         filters = self.history_contents_filters.parse_query_filters(filter_query_params)
         self._validate_bulk_operation_params(payload, trans.user, trans)
-        contents: List["HistoryItem"]
+        contents: List[HistoryItem]
         if payload.items:
             contents = self._get_contents_by_item_list(
                 trans,
@@ -1366,7 +1366,7 @@ def _apply_operation_to_item(
     def _get_contents_by_item_list(
         self, trans, history: History, items: List[HistoryContentItem]
     ) -> List["HistoryItem"]:
-        contents: List["HistoryItem"] = []
+        contents: List[HistoryItem] = []
 
         dataset_items = filter(lambda item: item.history_content_type == HistoryContentType.dataset, items)
         datasets_ids = (dataset.id for dataset in dataset_items)
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index ebc1bdf5ffe9..934f973db689 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -423,7 +423,7 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
             modules.NoReplacement,
             model.DatasetCollectionInstance,
             List[model.DatasetCollectionInstance],
-            "HistoryItem",
+            HistoryItem,
         ] = modules.NO_REPLACEMENT
         prefixed_name = input_dict["name"]
         multiple = input_dict["multiple"]
diff --git a/pyproject.toml b/pyproject.toml
index 2f7355735122..f18cdb08b436 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -126,7 +126,7 @@ uvloop = "*"
 WebOb = "*"
 Whoosh = "*"
 zipstream-new = "*"
-s3fs = "*"
+s3fs = ">=2023.1.0"
 
 [tool.poetry.group.dev.dependencies]
 ase = ">=3.18.1"