diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 99d499db3e54..39cf4dca07ca 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -2,7 +2,7 @@ aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13" aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13" -anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13" +anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13" ase==3.23.0 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -11,8 +11,8 @@ babel==2.16.0 ; python_version >= "3.8" and python_version < "3.13" backports-tarfile==1.2.0 ; python_version >= "3.8" and python_version < "3.12" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" black==24.8.0 ; python_version >= "3.8" and python_version < "3.13" -boto3==1.35.16 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.35.16 ; python_version >= "3.8" and python_version < "3.13" +boto3==1.35.23 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13" build==1.2.2 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13" @@ -35,7 +35,7 @@ deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13" docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" dogpile-cache==1.3.3 ; python_version >= "3.9" and python_version < "3.13" exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11" -filelock==3.16.0 ; python_version >= "3.8" and python_version < "3.13" +filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13" fonttools==4.53.1 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" @@ -45,7 +45,7 @@ greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13" httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13" -idna==3.9 ; python_version >= "3.8" and python_version < "3.13" +idna==3.10 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.10" @@ -61,7 +61,7 @@ jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13" jsonschema==4.23.0 ; python_version >= "3.9" and python_version < "3.13" junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13" -keyring==25.3.0 ; python_version >= "3.8" and python_version < "3.13" +keyring==25.4.1 ; python_version >= "3.8" and python_version < "3.13" kiwisolver==1.4.7 ; python_version >= "3.8" and python_version < "3.13" lxml==5.3.0 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" @@ -90,13 +90,13 @@ pbr==6.1.0 ; python_version >= "3.9" and python_version < "3.13" pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13" -platformdirs==4.3.3 ; python_version >= "3.8" and python_version < "3.13" +platformdirs==4.3.6 ; python_version >= "3.8" and python_version < "3.13" playwright==1.47.0 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13" prettytable==3.11.0 ; python_version >= "3.8" and python_version < "3.13" psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" -psycopg==3.2.1 ; python_version >= "3.8" and python_version < "3.13" +psycopg==3.2.2 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13" pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -142,9 +142,9 @@ scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10" scipy==1.14.1 ; python_version >= "3.10" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" -selenium==4.24.0 ; python_version >= "3.8" and python_version < "3.13" +selenium==4.25.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==74.1.2 ; python_version >= "3.8" and python_version < "3.13" +setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index c450b5097b08..2b00c5ee134d 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.8.19 mccabe==0.7.0 pycodestyle==2.12.1 pyflakes==3.2.0 -ruff==0.6.5 +ruff==0.6.6 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index deb48ead5b11..518105f7c0ce 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -2,7 +2,7 @@ a2wsgi==1.10.7 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.15.0 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.15.1 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13" aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -13,7 +13,7 @@ alembic==1.13.2 ; python_version >= "3.8" and python_version < "3.13" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13" annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" -anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13" +anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13" apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13" appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13" arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13" @@ -34,8 +34,8 @@ bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.35.16 ; python_version >= "3.8" and python_version < "3.13" -bx-python==0.12.0 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13" +bx-python==0.13.0 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13" @@ -66,8 +66,8 @@ dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13" edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13" email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11" -fastapi-slim==0.114.2 ; python_version >= "3.8" and python_version < "3.13" -filelock==3.16.0 ; python_version >= "3.8" and python_version < "3.13" +fastapi-slim==0.115.0 ; python_version >= "3.8" and python_version < "3.13" +filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13" fsspec==2024.9.0 ; python_version >= "3.8" and python_version < "3.13" @@ -86,7 +86,7 @@ h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" h5grove==2.3.0 ; python_version >= "3.8" and python_version < "3.13" h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" -idna==3.9 ; python_version >= "3.8" and python_version < "3.13" +idna==3.10 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.9" isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13" @@ -97,7 +97,7 @@ jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13" jsonschema==4.23.0 ; python_version >= "3.8" and python_version < "3.13" -kombu==5.4.1 ; python_version >= "3.8" and python_version < "3.13" +kombu==5.4.2 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" lxml==5.3.0 ; python_version >= "3.8" and python_version < "3.13" mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13" @@ -121,7 +121,7 @@ oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" orjson==3.10.7 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" packaging==24.1 ; python_version >= "3.8" and python_version < "3.13" -paramiko==3.4.1 ; python_version >= "3.8" and python_version < "3.13" +paramiko==3.5.0 ; python_version >= "3.8" and python_version < "3.13" parsley==1.3 ; python_version >= "3.8" and python_version < "3.13" paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13" pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13" @@ -135,10 +135,10 @@ psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic-core==2.23.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.9.1 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.9.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.9.2 ; python_version >= "3.8" and python_version < "3.13" pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13" pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13" pyfaidx==0.8.1.2 ; python_version >= "3.8" and python_version < "3.13" @@ -149,7 +149,7 @@ pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13" pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13" pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13" -pyreadline3==3.4.3 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13" +pyreadline3==3.5.4 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13" pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13" python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13" @@ -176,14 +176,14 @@ ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" s3fs==2024.9.0 ; python_version >= "3.8" and python_version < "3.13" schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==74.1.2 ; python_version >= "3.8" and python_version < "3.13" +setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13" shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" -spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13" -sqlalchemy==2.0.34 ; python_version >= "3.8" and python_version < "3.13" +spython==0.3.14 ; python_version >= "3.8" and python_version < "3.13" +sqlalchemy==2.0.35 ; python_version >= "3.8" and python_version < "3.13" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" sqlparse==0.5.1 ; python_version >= "3.8" and python_version < "3.13" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 4398146f2329..c23cbbbedc24 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,15 +1,15 @@ annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" -boto3-stubs[s3]==1.35.19 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.35.19 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.35.24 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.35.24 ; python_version >= "3.8" and python_version < "3.13" cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13" lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13" -mypy-boto3-s3==1.35.16 ; python_version >= "3.8" and python_version < "3.13" +mypy-boto3-s3==1.35.22 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" mypy==1.11.2 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" -pydantic-core==2.23.3 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.9.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" types-awscrt==0.21.5 ; python_version >= "3.8" and python_version < "3.13" types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13" @@ -19,12 +19,12 @@ types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13" types-docutils==0.21.0.20240907 ; python_version >= "3.8" and python_version < "3.13" types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13" types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13" -types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13" +types-paramiko==3.5.0.20240918 ; python_version >= "3.8" and python_version < "3.13" types-python-dateutil==2.9.0.20240906 ; python_version >= "3.8" and python_version < "3.13" -types-pyyaml==6.0.12.20240808 ; python_version >= "3.8" and python_version < "3.13" +types-pyyaml==6.0.12.20240917 ; python_version >= "3.8" and python_version < "3.13" types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13" types-s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13" -types-setuptools==74.1.0.20240907 ; python_version >= "3.8" and python_version < "3.13" +types-setuptools==75.1.0.20240917 ; python_version >= "3.8" and python_version < "3.13" types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13" types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"