diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 14da16802153..442c4fc3d686 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -13,22 +13,22 @@ anyio==4.8.0 ; python_full_version >= '3.9' ase==3.23.0 ; python_full_version < '3.9' ase==3.24.0 ; python_full_version >= '3.9' async-timeout==5.0.1 ; python_full_version < '3.11' -attrs==24.3.0 +attrs==25.1.0 axe-selenium-python==2.1.6 -babel==2.16.0 +babel==2.17.0 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x' 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' +black==25.1.0 ; python_full_version >= '3.9' boto3==1.36.3 botocore==1.36.3 build==1.2.2.post1 cachecontrol==0.14.2 -certifi==2024.12.14 +certifi==2025.1.31 cffi==1.17.1 charset-normalizer==3.4.1 click==8.1.8 -codespell==2.4.0 +codespell==2.4.1 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32' contourpy==1.1.1 ; python_full_version < '3.9' contourpy==1.3.0 ; python_full_version == '3.9.*' @@ -42,15 +42,15 @@ darker==2.1.1 darkgraylib==1.2.1 decorator==5.1.1 ; python_full_version >= '3.9' defusedxml==0.7.1 -deprecated==1.2.17 +deprecated==1.2.18 docutils==0.20.1 ; python_full_version < '3.9' docutils==0.21.2 ; python_full_version >= '3.9' -dogpile-cache==1.3.3 ; python_full_version >= '3.9' +dogpile-cache==1.3.4 ; python_full_version >= '3.9' 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==4.55.6 +fonttools==4.55.8 frozenlist==1.5.0 galaxy-release-util==0.2.0 graylint==1.1.1 @@ -68,7 +68,8 @@ importlib-resources==6.5.2 ; python_full_version == '3.9.*' iniconfig==2.0.0 isodate==0.6.1 ; python_full_version < '3.9' isodate==0.7.2 ; python_full_version >= '3.9' and python_full_version < '3.11' -isort==5.13.2 +isort==5.13.2 ; python_full_version < '3.9' +isort==6.0.0 ; python_full_version >= '3.9' 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==4.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' @@ -118,18 +119,19 @@ pkce==1.0.3 pkgutil-resolve-name==1.3.10 ; python_version < '0' platformdirs==4.3.6 playwright==1.48.0 ; python_full_version < '3.9' -playwright==1.49.1 ; python_full_version >= '3.9' +playwright==1.50.0 ; python_full_version >= '3.9' pluggy==1.5.0 port-for==0.7.3 ; python_full_version < '3.9' port-for==0.7.4 ; python_full_version >= '3.9' prettytable==3.11.0 ; python_full_version < '3.9' -prettytable==3.13.0 ; python_full_version >= '3.9' +prettytable==3.14.0 ; 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==3.2.4 pycparser==2.22 -pyee==12.0.0 +pyee==12.0.0 ; python_full_version < '3.9' +pyee==12.1.1 ; python_full_version >= '3.9' pygithub==2.5.0 pygments==2.19.1 pyjwt==2.9.0 ; python_full_version < '3.9' @@ -150,13 +152,13 @@ pytest-json-report==1.5.0 pytest-metadata==3.1.1 pytest-mock==3.14.0 pytest-playwright==0.5.2 ; python_full_version < '3.9' -pytest-playwright==0.6.2 ; python_full_version >= '3.9' +pytest-playwright==0.7.0 ; python_full_version >= '3.9' pytest-postgresql==6.1.1 pytest-shard==0.1.2 python-dateutil==2.9.0.post0 python-irodsclient==3.0.0 python-slugify==8.0.4 -pytz==2024.2 ; python_full_version < '3.9' +pytz==2025.1 ; python_full_version < '3.9' pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32' pyyaml==6.0.2 rdflib==6.3.2 ; python_full_version < '3.8.1' @@ -165,7 +167,7 @@ rdflib==7.1.3 ; 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_version < '0' -referencing==0.36.1 ; python_full_version >= '3.9' +referencing==0.36.2 ; python_full_version >= '3.9' requests==2.32.3 requests-toolbelt==1.0.0 responses==0.25.6 @@ -176,7 +178,7 @@ 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==36.1.0 ; python_full_version >= '3.9' +rucio-clients==36.2.0 ; python_full_version >= '3.9' s3transfer==0.11.2 schema-salad==8.7.20241010092723 ; python_full_version < '3.9' schema-salad==8.8.20241206093842 ; python_full_version >= '3.9' diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 1f9281d0f932..9a102aa00ab4 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ -attrs==24.3.0 +attrs==25.1.0 flake8==7.1.1 flake8-bugbear==24.12.12 mccabe==0.7.0 pycodestyle==2.12.1 pyflakes==3.2.0 -ruff==0.9.3 +ruff==0.9.4 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 08b68b960e7e..b1076d85d81e 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -23,8 +23,8 @@ arcp==0.2.1 argcomplete==3.5.3 async-timeout==5.0.1 ; python_full_version < '3.11' attmap==0.13.2 -attrs==24.3.0 -babel==2.16.0 +attrs==25.1.0 +babel==2.17.0 backports-zoneinfo==0.2.1 ; python_full_version < '3.9' bagit==1.8.1 bagit-profile==1.3.1 @@ -35,13 +35,13 @@ billiard==4.2.1 bioblend==1.4.0 bleach==6.1.0 ; python_full_version < '3.9' bleach==6.2.0 ; python_full_version >= '3.9' -boltons==24.1.0 +boltons==25.0.0 boto==2.49.0 botocore==1.36.3 bx-python==0.13.0 cachecontrol==0.14.2 celery==5.4.0 -certifi==2024.12.14 +certifi==2025.1.31 cffi==1.17.1 charset-normalizer==3.4.1 circus==0.18.0 @@ -74,19 +74,19 @@ dparse==0.6.4 edam-ontology==1.25.2 email-validator==2.2.0 exceptiongroup==1.2.2 ; python_full_version < '3.11' -fastapi-slim==0.115.7 +fastapi-slim==0.115.8 filelock==3.16.1 ; python_full_version < '3.9' filelock==3.17.0 ; python_full_version >= '3.9' fissix==24.4.24 ; python_full_version >= '3.13' frozenlist==1.5.0 fs==2.4.16 fsspec==2024.10.0 ; python_full_version < '3.9' -fsspec==2024.12.0 ; python_full_version >= '3.9' +fsspec==2025.2.0 ; python_full_version >= '3.9' future==1.0.0 galaxy2cwl==0.1.4 ; python_full_version < '3.9' graphene==3.4.3 graphene-sqlalchemy==3.0.0rc2 -graphql-core==3.2.5 +graphql-core==3.2.6 graphql-relay==3.2.0 gravity==1.0.7 greenlet==3.1.1 ; (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') @@ -178,14 +178,14 @@ python-magic==0.4.27 python-multipart==0.0.20 python-slugify==8.0.4 python3-openid==3.2.0 -pytz==2024.2 +pytz==2025.1 pyyaml==6.0.2 -pyzmq==26.2.0 +pyzmq==26.2.1 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==7.1.3 ; python_full_version >= '3.9' referencing==0.35.1 ; python_full_version < '3.9' -referencing==0.36.1 ; python_full_version >= '3.9' +referencing==0.36.2 ; python_full_version >= '3.9' refgenconf==0.12.2 regex==2024.11.6 repoze-lru==0.7 @@ -204,7 +204,7 @@ 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' s3fs==2024.10.0 ; python_full_version < '3.9' -s3fs==2024.12.0 ; python_full_version >= '3.9' +s3fs==2025.2.0 ; python_full_version >= '3.9' schema-salad==8.7.20241010092723 ; python_full_version < '3.9' schema-salad==8.8.20241206093842 ; python_full_version >= '3.9' setuptools==75.3.0 ; python_full_version < '3.9' diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index d5151bc89459..68967ed1590d 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,19 +1,19 @@ # 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==1.36.6 -botocore-stubs==1.36.6 +boto3-stubs==1.36.12 +botocore-stubs==1.36.12 cffi==1.17.1 ; platform_python_implementation != 'PyPy' cryptography==44.0.0 lxml-stubs==0.5.1 mypy==1.14.1 -mypy-boto3-s3==1.36.0 +mypy-boto3-s3==1.36.9 mypy-extensions==1.0.0 pycparser==2.22 ; platform_python_implementation != 'PyPy' pydantic==2.10.6 pydantic-core==2.27.2 tomli==2.2.1 ; python_full_version < '3.11' -types-awscrt==0.23.7 +types-awscrt==0.23.9 types-bleach==6.2.0.20241123 types-boto==2.49.18.20241019 types-contextvars==2.4.7.3