Merge pull request #21104 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: nsoranzo

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,7 +1,7 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=dev
 aiohappyeyeballs==2.6.1
-aiohttp==3.13.0
+aiohttp==3.13.1
 aiosignal==1.4.0
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
@@ -18,29 +18,31 @@ boto3==1.40.49
 botocore==1.40.49
 build==1.3.0
 cachecontrol==0.14.3
-cachetools==6.2.0
+cachetools==6.2.1
 cattrs==25.3.0
 certifi==2025.10.5
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
-charset-normalizer==3.4.3
+charset-normalizer==3.4.4
 click==8.1.8 ; python_full_version < '3.10'
 click==8.3.0 ; python_full_version >= '3.10'
 codespell==2.4.1
 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
-colorlog==6.9.0
+colorlog==6.10.1
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.7
-cryptography==46.0.2
+coverage==7.10.7 ; python_full_version < '3.10'
+coverage==7.11.0 ; python_full_version >= '3.10'
+cryptography==46.0.3
 cwltest==2.6.20250818005349
 cycler==0.12.1
 darker==3.0.0
 darkgraylib==2.4.0
 decorator==5.2.1
 defusedxml==0.7.1
 docutils==0.21.2
-dogpile-cache==1.4.1
+dogpile-cache==1.4.1 ; python_full_version < '3.10'
+dogpile-cache==1.5.0 ; python_full_version >= '3.10'
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.19.1 ; python_full_version < '3.10'
@@ -56,14 +58,16 @@ html5rdf==1.2.1 ; python_full_version >= '3.10'
 httpcore==1.0.9
 httpx==0.28.1
 id==1.5.0
-idna==3.10
+idna==3.11
 imagesize==1.4.1
 importlib-metadata==8.7.0 ; python_full_version < '3.12'
 importlib-resources==6.5.2 ; python_full_version < '3.10'
-iniconfig==2.1.0
+iniconfig==2.1.0 ; python_full_version < '3.10'
+iniconfig==2.3.0 ; python_full_version >= '3.10'
 inquirerpy==0.3.4
 isodate==0.7.2 ; python_full_version < '3.11'
-isort==6.1.0
+isort==6.1.0 ; python_full_version < '3.10'
+isort==7.0.0 ; python_full_version >= '3.10'
 jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-context==6.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-functools==4.3.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
@@ -99,7 +103,7 @@ myst-parser==4.0.1 ; python_full_version >= '3.10'
 nh3==0.3.1
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.3 ; python_full_version >= '3.11'
+numpy==2.3.4 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
@@ -108,7 +112,8 @@ packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
 pathspec==0.12.1
 pfzy==0.3.4
-pillow==11.3.0
+pillow==11.3.0 ; python_full_version < '3.10'
+pillow==12.0.0 ; python_full_version >= '3.10'
 pkce==1.0.3
 platformdirs==4.4.0 ; python_full_version < '3.10'
 platformdirs==4.5.0 ; python_full_version >= '3.10'
@@ -119,8 +124,8 @@ port-for==1.0.0 ; python_full_version >= '3.10'
 prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.4.1
-psutil==7.1.0 ; sys_platform != 'cygwin'
-psycopg==3.2.10
+psutil==7.1.2 ; sys_platform != 'cygwin'
+psycopg==3.2.12
 pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
 pyee==13.0.0
 pygithub==2.8.1
@@ -147,27 +152,29 @@ pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.2.0
 python-slugify==8.0.4
-pytokens==0.1.10
+pytokens==0.2.0
 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.3
 rdflib==7.2.1
 readme-renderer==44.0
-referencing==0.36.2
+referencing==0.36.2 ; python_full_version < '3.10'
+referencing==0.37.0 ; python_full_version >= '3.10'
 requests==2.32.5
 requests-cache==1.2.1
 requests-toolbelt==1.0.0
 responses==0.25.8
 rfc3986==2.0.0
 rich==13.9.4
-rich-click==1.9.3
+rich-click==1.9.4
 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==0.7.3 ; python_full_version >= '3.10'
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
-rpds-py==0.27.1
-ruamel-yaml==0.18.15
+rpds-py==0.27.1 ; python_full_version < '3.10'
+rpds-py==0.28.0 ; python_full_version >= '3.10'
+ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.3.0
+rucio-clients==38.4.0
 s3transfer==0.14.0
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
@@ -176,7 +183,7 @@ scipy==1.16.2 ; python_full_version >= '3.11'
 secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 secretstorage==3.4.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.36.0 ; python_full_version >= '3.10'
+selenium==4.38.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -197,18 +204,18 @@ statsd==4.0.1
 stevedore==5.5.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
-testfixtures==9.1.0 ; python_full_version >= '3.11'
+testfixtures==9.2.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.3.0 ; python_full_version <= '3.11'
-total-perspective-vortex==3.1.1
+total-perspective-vortex==3.1.2
 trio==0.31.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
 twine==6.2.0
-types-cachetools==6.2.0.20250827
+types-cachetools==6.2.0.20251022
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.4.20250913 ; python_full_version >= '3.10'
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.14.0
+ruff==0.14.2

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,17 +5,18 @@ adal==1.2.7
 aiobotocore==2.25.0
 aiofiles==25.1.0
 aiohappyeyeballs==2.6.1
-aiohttp==3.13.0
+aiohttp==3.13.1
 aioitertools==0.12.0
 aiosignal==1.4.0
-alembic==1.16.5
+alembic==1.16.5 ; python_full_version < '3.10'
+alembic==1.17.0 ; python_full_version >= '3.10'
 amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.11.0
 apispec==6.8.4
 appdirs==1.4.4
 arcp==0.2.1
-argcomplete==3.6.2
+argcomplete==3.6.3
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
 attrs==25.4.0
@@ -33,11 +34,11 @@ boto==2.49.0
 botocore==1.40.49
 bx-python==0.14.0
 cachecontrol==0.14.3
-cachetools==6.2.0
+cachetools==6.2.1
 celery==5.5.3
 certifi==2025.10.5
 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
-charset-normalizer==3.4.3
+charset-normalizer==3.4.4
 circus==0.19.0
 click==8.1.8 ; python_full_version < '3.10'
 click==8.3.0 ; python_full_version >= '3.10'
@@ -49,7 +50,7 @@ cloudbridge==3.2.0
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
-cryptography==46.0.2
+cryptography==46.0.3
 ct3==3.4.0
 cwl-upgrader==1.2.12
 cwl-utils==0.40
@@ -75,23 +76,24 @@ frozenlist==1.8.0
 fs==2.4.16
 fsspec==2025.9.0
 future==1.0.0
-google-api-core==2.26.0
+google-api-core==2.27.0
 google-auth==2.41.1
-google-cloud-batch==0.17.37
-googleapis-common-protos==1.70.0
+google-cloud-batch==0.18.0
+googleapis-common-protos==1.71.0
 gravity==1.1.1
 greenlet==3.2.4 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
-grpcio==1.75.1
-grpcio-status==1.75.1
+grpcio==1.76.0
+grpcio-status==1.76.0
 gunicorn==23.0.0
 gxformat2==0.21.0
 h11==0.16.0
 h5grove==2.3.0
-h5py==3.14.0
+h5py==3.14.0 ; python_full_version < '3.10'
+h5py==3.15.1 ; python_full_version >= '3.10'
 httpcore==1.0.9
 httpx==0.28.1
 humanfriendly==10.0
-idna==3.10
+idna==3.11
 ijson==3.4.0.post0
 importlib-metadata==8.7.0 ; python_full_version < '3.10'
 importlib-resources==6.5.2 ; python_full_version < '3.12'
@@ -106,7 +108,7 @@ jsonschema==4.25.1
 jsonschema-specifications==2025.9.1
 kombu==5.5.4
 lagom==2.7.7
-legacy-cgi==2.6.3 ; python_full_version >= '3.13'
+legacy-cgi==2.6.4 ; python_full_version >= '3.13'
 limits==4.2 ; python_full_version < '3.10'
 limits==5.6.0 ; python_full_version >= '3.10'
 lxml==6.0.2
@@ -129,10 +131,10 @@ nodejs-wheel==22.20.0
 nodejs-wheel-binaries==22.20.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.3 ; python_full_version >= '3.11'
+numpy==2.3.4 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 openpyxl==3.1.5
-orjson==3.11.3
+orjson==3.11.4
 oyaml==1.0
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
@@ -141,19 +143,20 @@ parsley==1.3
 paste==3.10.1
 pastedeploy==3.1.0
 pebble==5.1.3
-pillow==11.3.0
+pillow==11.3.0 ; python_full_version < '3.10'
+pillow==12.0.0 ; python_full_version >= '3.10'
 prompt-toolkit==3.0.52
 propcache==0.4.1
 proto-plus==1.26.1
-protobuf==6.32.1
+protobuf==6.33.0
 prov==1.5.1
-psutil==7.1.0
+psutil==7.1.2
 pulsar-galaxy-lib==0.15.11
 pyasn1==0.6.1
 pyasn1-modules==0.4.2
 pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
-pydantic==2.12.2
+pydantic==2.12.3
 pydantic-core==2.41.4
 pydantic-tes==0.2.0
 pydot==4.0.1
@@ -177,21 +180,23 @@ pytz==2025.2
 pyyaml==6.0.3
 pyzmq==27.1.0
 rdflib==7.2.1
-referencing==0.36.2
+referencing==0.36.2 ; python_full_version < '3.10'
+referencing==0.37.0 ; python_full_version >= '3.10'
 refgenconf==0.12.2
-regex==2025.9.18
+regex==2025.10.23
 repoze-lru==0.7
 requests==2.32.5
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 requests-unixsocket==0.4.1
 rich==13.9.4
 rich-argparse==1.7.1
-rocrate==0.14.0
+rocrate==0.14.2
 routes==2.5.1
-rpds-py==0.27.1
+rpds-py==0.27.1 ; python_full_version < '3.10'
+rpds-py==0.28.0 ; python_full_version >= '3.10'
 rsa==4.9.1
-ruamel-yaml==0.18.15
+ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 s3fs==2025.9.0
 schema-salad==8.9.20250723145140
@@ -213,7 +218,7 @@ tenacity==9.1.2
 text-unidecode==1.3
 tifffile==2024.8.30 ; python_full_version < '3.10'
 tifffile==2025.5.10 ; python_full_version == '3.10.*'
-tifffile==2025.10.4 ; python_full_version >= '3.11'
+tifffile==2025.10.16 ; python_full_version >= '3.11'
 tinydb==4.8.2
 tomli==2.3.0 ; python_full_version < '3.11'
 tornado==6.5.2
@@ -227,8 +232,8 @@ tzlocal==5.3.1
 ubiquerg==0.8.1
 urllib3==1.26.20 ; python_full_version < '3.10'
 urllib3==2.5.0 ; python_full_version >= '3.10'
-uvicorn==0.37.0
-uvloop==0.21.0
+uvicorn==0.38.0
+uvloop==0.22.1
 vine==5.1.0
 wcwidth==0.2.14
 webencodings==0.5.1