Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -22,7 +22,7 @@ charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.7 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
@@ -33,7 +33,7 @@ darker==1.7.2 ; python_version >= "3.7" and python_version < "3.12"
 defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12"
 docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
-exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.12"
+exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.12"
 filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
 fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
 fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -124,7 +124,7 @@ ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
 schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12"
 scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
-scipy==1.11.1 ; python_version >= "3.9" and python_version < "3.12"
+scipy==1.11.2 ; python_version >= "3.9" and python_version < "3.12"
 secretstorage==3.3.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
 selenium==4.11.2 ; python_version >= "3.7" and python_version < "3.12"
 seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
 mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
-ruff==0.0.284
+ruff==0.0.285
 typing_extensions==4.7.1
 zipp==3.15.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -7,7 +7,7 @@ aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12"
 aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12"
 aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
-alembic==1.11.2 ; python_version >= "3.7" and python_version < "3.12"
+alembic==1.11.3 ; python_version >= "3.7" and python_version < "3.12"
 amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
 anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12"
 apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -43,7 +43,7 @@ circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.7 ; python_version >= "3.7" and python_version < "3.12"
 cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
@@ -64,7 +64,7 @@ docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
 ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
 email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12"
-exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.11"
+exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.11"
 fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
 fastapi==0.98.0 ; python_version >= "3.7" and python_version < "3.12"
 filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -112,7 +112,7 @@ numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.25.2 ; python_version >= "3.9" and python_version < "3.12"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
-orjson==3.9.4 ; python_version >= "3.7" and python_version < "3.12"
+orjson==3.9.5 ; python_version >= "3.7" and python_version < "3.12"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -182,7 +182,7 @@ starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
 starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12"
 supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
 svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
-tenacity==8.2.2 ; python_version >= "3.7" and python_version < "3.12"
+tenacity==8.2.3 ; python_version >= "3.7" and python_version < "3.12"
 tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12"
 tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
 tornado==6.2 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -10,7 +10,7 @@ types-bleach==6.0.0.4
 types-boto==2.49.18.9
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
-types-docutils==0.20.0.1
+types-docutils==0.20.0.3
 types-Markdown==3.4.2.10
 types-paramiko==3.3.0.0
 types-pkg-resources==0.1.3