diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 0be0caf9a3fd..b55d2289c810 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -36,9 +36,8 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.12"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12"
 fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
-fonttools==4.45.1 ; python_version >= "3.8" and python_version < "3.12"
+fonttools==4.46.0 ; python_version >= "3.8" and python_version < "3.12"
 frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
-future==0.18.3 ; python_version >= "3.8" and python_version < "3.12"
 galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.12"
 greenlet==3.0.1 ; python_version >= "3.8" and python_version < "3.12"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -46,7 +45,7 @@ httpcore==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
 httpx==0.25.2 ; python_version >= "3.8" and python_version < "3.12"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.12"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.12"
-importlib-metadata==6.9.0 ; python_version >= "3.8" and python_version < "3.12"
+importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12"
 importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10"
 iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12"
@@ -73,7 +72,7 @@ msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12"
 multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
 myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
-nh3==0.2.14 ; python_version >= "3.8" and python_version < "3.12"
+nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.12"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.12"
@@ -82,14 +81,14 @@ pathspec==0.11.2 ; python_version >= "3.8" and python_version < "3.12"
 pillow==10.1.0 ; python_version >= "3.8" and python_version < "3.12"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.12"
 pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.12"
-platformdirs==4.0.0 ; python_version >= "3.8" and python_version < "3.12"
+platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.12"
 playwright==1.40.0 ; python_version >= "3.8" and python_version < "3.12"
 pluggy==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.12"
 prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.12"
 prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12"
 psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12" and sys_platform != "cygwin"
-psycopg==3.1.13 ; python_version >= "3.8" and python_version < "3.12"
+psycopg==3.1.14 ; python_version >= "3.8" and python_version < "3.12"
 pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12"
 pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.12"
 pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.12"
@@ -99,7 +98,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.12"
 pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.12"
 pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
 pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.12"
-pytest-asyncio==0.21.1 ; python_version >= "3.8" and python_version < "3.12"
+pytest-asyncio==0.23.2 ; python_version >= "3.8" and python_version < "3.12"
 pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
 pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.12"
 pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -131,7 +130,7 @@ schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version <
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.11.4 ; python_version >= "3.9" and python_version < "3.12"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "linux"
-selenium==4.15.2 ; python_version >= "3.8" and python_version < "3.12"
+selenium==4.16.0 ; python_version >= "3.8" and python_version < "3.12"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
 setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -155,7 +154,7 @@ toml==0.10.2 ; python_version >= "3.8" and python_version < "3.12"
 tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
 trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.12"
 trio==0.23.1 ; python_version >= "3.8" and python_version < "3.12"
-tuspy==1.0.1 ; python_version >= "3.8" and python_version < "3.12"
+tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
 twill==3.2.1 ; python_version >= "3.8" and python_version < "3.12"
 twine==4.0.2 ; python_version >= "3.8" and python_version < "3.12"
 typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -168,5 +167,5 @@ wcwidth==0.2.12 ; python_version >= "3.8" and python_version < "3.12"
 werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.12"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
 wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
-yarl==1.9.3 ; python_version >= "3.8" and python_version < "3.12"
+yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12"
 zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 95966290773c..18619fe4d38f 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,7 +1,7 @@
 attrs==23.1.0
 flake8==6.1.0
-flake8-bugbear==23.11.28
+flake8-bugbear==23.12.2
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.1.0
-ruff==0.1.6
+ruff==0.1.7
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 87940aa7e3ed..b262a3faf2cc 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -1,6 +1,6 @@
-a2wsgi==1.8.0 ; python_version >= "3.8" and python_version < "3.12"
+a2wsgi==1.9.0 ; python_version >= "3.8" and python_version < "3.12"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.12"
-aiobotocore==2.7.0 ; python_version >= "3.8" and python_version < "3.12"
+aiobotocore==2.8.0 ; python_version >= "3.8" and python_version < "3.12"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.12"
 aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.12"
 aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.12"
@@ -30,7 +30,7 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.12"
 boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.12"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.12"
-botocore==1.31.64 ; python_version >= "3.8" and python_version < "3.12"
+botocore==1.33.1 ; python_version >= "3.8" and python_version < "3.12"
 bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12"
@@ -51,7 +51,7 @@ conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3
 cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12"
 cwl-upgrader==1.2.10 ; python_version >= "3.8" and python_version < "3.12"
 cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.12"
-cwltool==3.1.20231114134824 ; python_version >= "3.8" and python_version < "3.12"
+cwltool==3.1.20231207110929 ; python_version >= "3.8" and python_version < "3.12"
 decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.12"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.12"
 deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -69,7 +69,7 @@ fastapi==0.98.0 ; python_version >= "3.8" and python_version < "3.12"
 filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12"
 frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.12"
-fsspec==2023.10.0 ; python_version >= "3.8" and python_version < "3.12"
+fsspec==2023.12.1 ; python_version >= "3.8" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.8" and python_version < "3.12"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.12"
 galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.12"
@@ -86,8 +86,8 @@ h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
 h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.12"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.12"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.12"
-importlib-metadata==6.9.0 ; python_version >= "3.8" and python_version < "3.12"
-importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.12"
+importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12"
+importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9"
 isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.12"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12"
 jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.12"
@@ -103,10 +103,10 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.12"
 markdown==3.5.1 ; python_version >= "3.8" and python_version < "3.12"
 markupsafe==2.1.3 ; python_version >= "3.8" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.12"
-mercurial==6.6 ; python_version >= "3.8" and python_version < "3.12"
+mercurial==6.6.1 ; python_version >= "3.8" and python_version < "3.12"
 mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.12"
 mrcfile==1.4.3 ; python_version >= "3.8" and python_version < "3.12"
-msal==1.25.0 ; python_version >= "3.8" and python_version < "3.12"
+msal==1.26.0 ; python_version >= "3.8" and python_version < "3.12"
 msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12"
 multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -122,7 +122,7 @@ paramiko==3.3.1 ; python_version >= "3.8" and python_version < "3.12"
 parsley==1.3 ; python_version >= "3.8" and python_version < "3.12"
 paste==3.7.1 ; python_version >= "3.8" and python_version < "3.12"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.12"
-pebble==5.0.4 ; python_version >= "3.8" and python_version < "3.12"
+pebble==5.0.5 ; python_version >= "3.8" and python_version < "3.12"
 pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.12"
 prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12"
@@ -154,9 +154,9 @@ python-multipart==0.0.6 ; python_version >= "3.8" and python_version < "3.12"
 python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.12"
 pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.12"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12"
-pyzmq==25.1.1 ; python_version >= "3.8" and python_version < "3.12"
+pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.12"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.12"
-referencing==0.31.1 ; python_version >= "3.8" and python_version < "3.12"
+referencing==0.32.0 ; python_version >= "3.8" and python_version < "3.12"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.12"
 regex==2023.10.3 ; python_version >= "3.8" and python_version < "3.12"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.12"
@@ -171,7 +171,7 @@ rpds-py==0.13.2 ; python_version >= "3.8" and python_version < "3.12"
 rsa==4.9 ; python_version >= "3.8" and python_version < "3.12"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8"
 ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12"
-s3fs==2023.10.0 ; python_version >= "3.8" and python_version < "3.12"
+s3fs==2023.12.1 ; python_version >= "3.8" and python_version < "3.12"
 schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12"
 setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12"
@@ -180,6 +180,7 @@ six==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
 sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12"
 social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12"
+spython==0.3.11 ; python_version >= "3.8" and python_version < "3.12"
 sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12"
 sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12"
@@ -194,7 +195,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
 tornado==6.4 ; python_version >= "3.8" and python_version < "3.12"
 tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.12"
-tuspy==1.0.1 ; python_version >= "3.8" and python_version < "3.12"
+tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12"
 tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12"
 typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12"
 tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12"
@@ -210,7 +211,7 @@ webob==1.8.7 ; python_version >= "3.8" and python_version < "3.12"
 whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.12"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
 yacman==0.9.2 ; python_version >= "3.8" and python_version < "3.12"
-yarl==1.9.3 ; python_version >= "3.8" and python_version < "3.12"
+yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12"
 zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12"
 zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.12"
 zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.12"