update dependencies

Author: elichad

lib/galaxy/dependencies/dev-requirements.txt

@@ -46,7 +46,7 @@ fonttools==4.57.0
 frozenlist==1.6.0
 galaxy-release-util==0.2.0
 graylint==1.1.1
-greenlet==3.2.0
+greenlet==3.2.1
 h11==0.14.0
 html5lib==1.1
 httpcore==1.0.8
@@ -67,12 +67,12 @@ jeepney==0.9.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' a
 jinja2==3.1.6
 jmespath==1.0.1
 jsonschema==4.23.0
-jsonschema-specifications==2024.10.1
+jsonschema-specifications==2025.4.1
 junit-xml==1.9
 keyring==25.6.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.4.7 ; python_full_version < '3.10'
 kiwisolver==1.4.8 ; python_full_version >= '3.10'
-lxml==5.3.2
+lxml==5.4.0
 markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
 markupsafe==3.0.2
@@ -82,10 +82,10 @@ mdit-py-plugins==0.4.2
 mdurl==0.1.2
 mirakuru==2.6.0
 mistune==3.0.2
-more-itertools==10.6.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
+more-itertools==10.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.0
 multidict==6.4.3
-mypy-extensions==1.0.0
+mypy-extensions==1.1.0
 myst-parser==3.0.1 ; python_full_version < '3.10'
 myst-parser==4.0.1 ; python_full_version >= '3.10'
 nh3==0.2.21
@@ -94,7 +94,8 @@ numpy==2.2.5 ; python_full_version >= '3.10'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2
-packaging==24.2
+packaging==24.2 ; python_full_version < '3.10'
+packaging==25.0 ; python_full_version >= '3.10'
 pathspec==0.12.1
 pbr==6.1.1
 pfzy==0.3.4
@@ -105,7 +106,7 @@ playwright==1.51.0
 pluggy==1.5.0
 port-for==0.7.4
 prettytable==3.16.0
-prompt-toolkit==3.0.50
+prompt-toolkit==3.0.51
 propcache==0.3.1
 psutil==7.0.0 ; sys_platform != 'cygwin'
 psycopg==3.2.6
@@ -144,11 +145,11 @@ requests-cache==1.2.1
 requests-toolbelt==1.0.0
 responses==0.25.7
 rfc3986==2.0.0
-rich==14.0.0
+rich==13.9.4
 rich-click==1.8.8
 roc-validator==0.4.2 ; python_full_version < '3.9.20'
 roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
-roc-validator==0.6.3 ; python_full_version >= '3.10'
+roc-validator==0.6.4 ; python_full_version >= '3.10'
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
 rpds-py==0.24.0
 ruamel-yaml==0.18.10
@@ -161,7 +162,7 @@ scipy==1.15.2 ; python_full_version >= '3.10'
 secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 selenium==4.31.0
 seletools==1.5.0
-setuptools==79.0.0
+setuptools==79.0.1
 six==1.17.0
 sniffio==1.3.1
 snowballstemmer==2.2.0

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

@@ -1,5 +1,5 @@
 attrs==25.3.0
-flake8==7.1.2
+flake8==7.2.0
 flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.13.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -71,7 +71,7 @@ fs==2.4.16
 fsspec==2025.3.2
 future==1.0.0
 gravity==1.0.7
-greenlet==3.2.0 ; (python_full_version < '3.14' and platform_machine == 'AMD64') or (python_full_version < '3.14' and platform_machine == 'WIN32') or (python_full_version < '3.14' and platform_machine == 'aarch64') or (python_full_version < '3.14' and platform_machine == 'amd64') or (python_full_version < '3.14' and platform_machine == 'ppc64le') or (python_full_version < '3.14' and platform_machine == 'win32') or (python_full_version < '3.14' and platform_machine == 'x86_64')
+greenlet==3.2.1 ; (python_full_version < '3.14' and platform_machine == 'AMD64') or (python_full_version < '3.14' and platform_machine == 'WIN32') or (python_full_version < '3.14' and platform_machine == 'aarch64') or (python_full_version < '3.14' and platform_machine == 'amd64') or (python_full_version < '3.14' and platform_machine == 'ppc64le') or (python_full_version < '3.14' and platform_machine == 'win32') or (python_full_version < '3.14' and platform_machine == 'x86_64')
 gunicorn==23.0.0
 gxformat2==0.20.0
 h11==0.14.0
@@ -88,13 +88,13 @@ jinja2==3.1.6
 jmespath==1.0.1
 jsonref==1.1.0
 jsonschema==4.23.0
-jsonschema-specifications==2024.10.1
+jsonschema-specifications==2025.4.1
 kombu==5.5.3
 lagom==2.7.5
 legacy-cgi==2.6.3 ; python_full_version >= '3.13'
 limits==4.2 ; python_full_version < '3.10'
-limits==5.0.0 ; python_full_version >= '3.10'
-lxml==5.3.2
+limits==5.1.0 ; python_full_version >= '3.10'
+lxml==5.4.0
 mako==1.3.10
 markdown==3.8
 markdown-it-py==3.0.0
@@ -106,7 +106,7 @@ mrcfile==1.5.4
 msal==1.32.0
 msgpack==1.1.0
 multidict==6.4.3
-mypy-extensions==1.0.0
+mypy-extensions==1.1.0
 networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version >= '3.10'
 nodeenv==1.9.1
@@ -115,7 +115,8 @@ numpy==2.2.5 ; python_full_version >= '3.10'
 oauthlib==3.2.2
 orjson==3.10.16
 oyaml==1.0
-packaging==24.2
+packaging==24.2 ; python_full_version < '3.10'
+packaging==25.0 ; python_full_version >= '3.10'
 paramiko==3.5.1
 parsley==1.3
 paste==3.10.1
@@ -161,7 +162,7 @@ requests==2.32.3
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 requests-unixsocket==0.4.1
-rich==14.0.0
+rich==13.9.4
 rich-argparse==1.7.0
 rocrate==0.13.0
 routes==2.5.1
@@ -170,7 +171,7 @@ ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
 s3fs==2025.3.2
 schema-salad==8.9.20250408123006
-setuptools==79.0.0
+setuptools==79.0.1
 setuptools-scm==5.0.2
 six==1.17.0
 slowapi==0.1.9

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

@@ -1,18 +1,18 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.37.38
-botocore-stubs==1.37.38
+boto3-stubs==1.38.1
+botocore-stubs==1.38.1
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==44.0.2
 lxml-stubs==0.5.1
 mypy==1.15.0
-mypy-boto3-s3==1.37.24
-mypy-extensions==1.0.0
+mypy-boto3-s3==1.38.0
+mypy-extensions==1.1.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.11.3
 pydantic-core==2.33.1
-setuptools==79.0.0
+setuptools==79.0.1
 tomli==2.2.1 ; python_full_version < '3.11'
 types-awscrt==0.26.1
 types-bleach==6.2.0.20241123
@@ -28,7 +28,7 @@ types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20250402
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.0.20250328 ; python_full_version >= '3.10'
-types-s3transfer==0.11.5
+types-s3transfer==0.12.0
 types-setuptools==79.0.0.20250422
 types-six==1.17.0.20250403
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'