Merge pull request #19418 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -20,8 +20,8 @@ backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine !=
 backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
 black==24.8.0 ; python_full_version < '3.9'
 black==24.10.0 ; python_full_version >= '3.9'
-boto3==1.35.93
-botocore==1.35.93
+boto3==1.36.1
+botocore==1.36.1
 build==1.2.2.post1
 cachecontrol==0.14.2
 certifi==2024.12.14
@@ -93,7 +93,8 @@ mdurl==0.1.2
 mirakuru==2.5.2 ; python_full_version < '3.9'
 mirakuru==2.5.3 ; python_full_version >= '3.9'
 mistune==3.0.2
-more-itertools==10.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
+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'
 msgpack==1.1.0
 multidict==6.1.0
 mypy-extensions==1.0.0
@@ -124,7 +125,7 @@ prettytable==3.12.0 ; python_full_version >= '3.9'
 propcache==0.2.0 ; python_full_version < '3.9'
 propcache==0.2.1 ; python_full_version >= '3.9'
 psutil==6.1.1 ; sys_platform != 'cygwin'
-psycopg==3.2.3
+psycopg==3.2.4
 pycparser==2.22
 pyee==12.0.0
 pygithub==2.5.0
@@ -161,19 +162,20 @@ rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
 rdflib==7.1.2 ; python_full_version >= '3.9'
 readme-renderer==43.0 ; python_full_version < '3.9'
 readme-renderer==44.0 ; python_full_version >= '3.9'
-referencing==0.35.1 ; python_full_version >= '3.9'
+referencing==0.35.1 ; python_version < '0'
+referencing==0.36.1 ; python_full_version >= '3.9'
 requests==2.32.3
 requests-toolbelt==1.0.0
-responses==0.25.5
+responses==0.25.6
 rfc3986==2.0.0
 rich==13.9.4
 rpds-py==0.20.1 ; python_version < '0'
 rpds-py==0.22.3 ; python_full_version >= '3.9'
 ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.9' and platform_python_implementation == 'CPython'
 ruamel-yaml-clib==0.2.12 ; python_full_version >= '3.9' and python_full_version < '3.13' and platform_python_implementation == 'CPython'
-rucio-clients==36.0.0.post2 ; python_full_version >= '3.9'
-s3transfer==0.10.4
+rucio-clients==36.1.0 ; python_full_version >= '3.9'
+s3transfer==0.11.1
 schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
 schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
 scipy==1.10.1 ; python_full_version < '3.9'
@@ -228,7 +230,7 @@ wcwidth==0.2.13
 websocket-client==1.8.0
 werkzeug==3.0.6 ; python_full_version < '3.9'
 werkzeug==3.1.3 ; python_full_version >= '3.9'
-wrapt==1.17.1
+wrapt==1.17.2
 wsproto==1.2.0
 yarl==1.15.2 ; python_full_version < '3.9'
 yarl==1.18.3 ; python_full_version >= '3.9'

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==0.9.1
+ruff==0.9.2

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-hashes --no-dev
 a2wsgi==1.10.8
 adal==1.2.7
-aiobotocore==2.17.0
+aiobotocore==2.18.0
 aiodataloader==0.4.0
 aiofiles==24.1.0
 aiohappyeyeballs==2.4.4
@@ -37,7 +37,7 @@ bleach==6.1.0 ; python_full_version < '3.9'
 bleach==6.2.0 ; python_full_version >= '3.9'
 boltons==24.1.0
 boto==2.49.0
-botocore==1.35.93
+botocore==1.36.1
 bx-python==0.13.0
 cachecontrol==0.14.2
 celery==5.4.0
@@ -112,15 +112,15 @@ jsonschema-specifications==2023.12.1 ; python_full_version < '3.9'
 jsonschema-specifications==2024.10.1 ; python_full_version >= '3.9'
 kombu==5.4.2
 lagom==2.7.5
-legacy-cgi==2.6.1 ; python_full_version >= '3.13'
+legacy-cgi==2.6.2 ; python_full_version >= '3.13'
 lxml==5.3.0
 mako==1.3.8
 markdown==3.7
 markdown-it-py==3.0.0
 markupsafe==2.1.5 ; python_full_version < '3.9'
 markupsafe==3.0.2 ; python_full_version >= '3.9'
 mdurl==0.1.2
-mercurial==6.9
+mercurial==6.9.1
 mistune==3.0.2
 mrcfile==1.5.3
 msal==1.31.1
@@ -182,7 +182,8 @@ pyzmq==26.2.0
 rdflib==6.3.2 ; python_full_version < '3.8.1'
 rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
 rdflib==7.1.2 ; python_full_version >= '3.9'
-referencing==0.35.1
+referencing==0.35.1 ; python_full_version < '3.9'
+referencing==0.36.1 ; python_full_version >= '3.9'
 refgenconf==0.12.2
 regex==2024.11.6
 repoze-lru==0.7
@@ -245,7 +246,7 @@ wcwidth==0.2.13
 webencodings==0.5.1
 webob==1.8.9
 whoosh==2.7.4
-wrapt==1.17.1
+wrapt==1.17.2
 yacman==0.9.3
 yarl==1.15.2 ; python_full_version < '3.9'
 yarl==1.18.3 ; python_full_version >= '3.9'

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

@@ -1,13 +1,13 @@
 # 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==1.35.97
-botocore-stubs==1.35.97
+boto3-stubs==1.36.2
+botocore-stubs==1.36.2
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==44.0.0
 lxml-stubs==0.5.1
 mypy==1.14.1
-mypy-boto3-s3==1.35.93
+mypy-boto3-s3==1.36.0
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.10.5
@@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20241230
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.0.20241016 ; python_full_version >= '3.10'
-types-s3transfer==0.10.4
+types-s3transfer==0.11.1
 types-setuptools==75.8.0.20250110
 types-six==1.17.0.20241205
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'