Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,8 +1,9 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=dev
-aiohappyeyeballs==2.4.4
+aiohappyeyeballs==2.4.4 ; python_full_version < '3.9'
+aiohappyeyeballs==2.4.6 ; python_full_version >= '3.9'
 aiohttp==3.10.11 ; python_full_version < '3.9'
-aiohttp==3.11.11 ; python_full_version >= '3.9'
+aiohttp==3.11.12 ; python_full_version >= '3.9'
 aiosignal==1.3.1 ; python_full_version < '3.9'
 aiosignal==1.3.2 ; python_full_version >= '3.9'
 alabaster==0.7.13 ; python_full_version < '3.9'
@@ -50,7 +51,7 @@ exceptiongroup==1.2.2 ; python_full_version < '3.11'
 filelock==3.16.1 ; python_full_version < '3.9'
 filelock==3.17.0 ; python_full_version >= '3.9'
 fluent-logger==0.11.1
-fonttools==4.55.8
+fonttools==4.56.0
 frozenlist==1.5.0
 galaxy-release-util==0.2.0
 graylint==1.1.1
@@ -95,7 +96,7 @@ matplotlib==3.10.0 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2
 mdurl==0.1.2
 mirakuru==2.5.2 ; python_full_version < '3.9'
-mirakuru==2.5.3 ; python_full_version >= '3.9'
+mirakuru==2.6.0 ; python_full_version >= '3.9'
 mistune==3.0.2
 more-itertools==10.5.0 ; python_full_version < '3.9' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 more-itertools==10.6.0 ; python_full_version >= '3.9' and platform_machine != 'ppc64le' and platform_machine != 's390x'
@@ -112,7 +113,7 @@ onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 packaging==24.2
 pathspec==0.12.1
-pbr==6.1.0 ; python_full_version >= '3.9'
+pbr==6.1.1 ; python_full_version >= '3.9'
 pillow==10.4.0 ; python_full_version < '3.9'
 pillow==11.1.0 ; python_full_version >= '3.9'
 pkce==1.0.3

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.9.4
+ruff==0.9.5

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,9 +5,10 @@ adal==1.2.7
 aiobotocore==2.19.0
 aiodataloader==0.4.0
 aiofiles==24.1.0
-aiohappyeyeballs==2.4.4
+aiohappyeyeballs==2.4.4 ; python_full_version < '3.9'
+aiohappyeyeballs==2.4.6 ; python_full_version >= '3.9'
 aiohttp==3.10.11 ; python_full_version < '3.9'
-aiohttp==3.11.11 ; python_full_version >= '3.9'
+aiohttp==3.11.12 ; python_full_version >= '3.9'
 aioitertools==0.12.0
 aiosignal==1.3.1 ; python_full_version < '3.9'
 aiosignal==1.3.2 ; python_full_version >= '3.9'
@@ -116,7 +117,7 @@ kombu==5.4.2
 lagom==2.7.5
 legacy-cgi==2.6.2 ; python_full_version >= '3.13'
 lxml==5.3.0
-mako==1.3.8
+mako==1.3.9
 markdown==3.7
 markdown-it-py==3.0.0
 markupsafe==2.1.5 ; python_full_version < '3.9'
@@ -140,7 +141,7 @@ oauthlib==3.2.2
 orjson==3.10.15
 oyaml==1.0
 packaging==24.2
-paramiko==3.5.0
+paramiko==3.5.1
 parsley==1.3
 paste==3.10.1
 pastedeploy==3.1.0
@@ -172,7 +173,7 @@ pynacl==1.5.0
 pyparsing==3.1.4 ; python_full_version < '3.9'
 pyparsing==3.2.1 ; python_full_version >= '3.9'
 pyreadline3==3.5.4 ; sys_platform == 'win32'
-pysam==0.22.1
+pysam==0.23.0
 python-dateutil==2.9.0.post0
 python-magic==0.4.27
 python-multipart==0.0.20
@@ -215,7 +216,7 @@ sniffio==1.3.1
 social-auth-core==4.5.4
 sortedcontainers==2.4.0
 spython==0.3.14
-sqlalchemy==2.0.37
+sqlalchemy==2.0.38
 sqlitedict==2.1.0
 sqlparse==0.5.3
 starlette==0.44.0 ; python_full_version < '3.9'

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

@@ -1,13 +1,14 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.36.12
-botocore-stubs==1.36.12
+boto3-stubs==1.36.16
+botocore-stubs==1.36.16
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==44.0.0
 lxml-stubs==0.5.1
-mypy==1.14.1
-mypy-boto3-s3==1.36.9
+mypy==1.14.1 ; python_full_version < '3.9'
+mypy==1.15.0 ; python_full_version >= '3.9'
+mypy-boto3-s3==1.36.15
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.10.6