diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 50e5db6dc2ef..1258d2e754e2 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -40,10 +40,10 @@ exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11" 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==4.54.1 ; python_version >= "3.8" and python_version < "3.13" -frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" +frozenlist==1.5.0 ; python_version >= "3.8" and python_version < "3.13" galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13" graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13" -greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" +greenlet==3.1.1 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" httpcore==1.0.6 ; python_version >= "3.8" and python_version < "3.13" httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13" @@ -93,7 +93,7 @@ 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==4.3.6 ; python_version >= "3.8" and python_version < "3.13" -playwright==1.47.0 ; python_version >= "3.8" and python_version < "3.13" +playwright==1.48.0 ; 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" @@ -134,7 +134,7 @@ requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13" rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13" -rich==13.9.2 ; python_version >= "3.8" and python_version < "3.13" +rich==13.9.3 ; python_version >= "3.8" and python_version < "3.13" rpds-py==0.20.0 ; python_version >= "3.9" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" @@ -181,7 +181,7 @@ urllib3[socks]==1.26.20 ; python_version >= "3.8" and python_version < "3.13" watchdog==4.0.2 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13" -werkzeug==3.0.4 ; python_version >= "3.8" and python_version < "3.13" +werkzeug==3.0.6 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13" yarl==1.15.2 ; 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 0f3613e5155a..60d87b7dfddb 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==0.7.0 +ruff==0.7.1 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3894ee456644..91752afea326 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -65,11 +65,11 @@ 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==0.115.2 ; python_version >= "3.8" and python_version < "3.13" +fastapi-slim==0.115.3 ; 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" +frozenlist==1.5.0 ; 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" +fsspec==2024.10.0 ; python_version >= "3.8" and python_version < "3.13" future==1.0.0 ; python_version >= "3.8" and python_version < "3.13" galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13" graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13" @@ -77,7 +77,7 @@ graphene==3.4 ; python_version >= "3.8" and python_version < "3.13" graphql-core==3.2.5 ; python_version >= "3.8" and python_version < "3.13" graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13" gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13" -greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8" +greenlet==3.1.1 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8" gunicorn==23.0.0 ; python_version >= "3.8" and python_version < "3.13" gxformat2==0.20.0 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" @@ -99,7 +99,7 @@ jsonschema==4.23.0 ; 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" +mako==1.3.6 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown==3.7 ; python_version >= "3.8" and python_version < "3.13" markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" @@ -117,7 +117,7 @@ numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==2.0.2 ; python_version >= "3.9" and python_version < "3.10" numpy==2.1.2 ; python_version >= "3.10" and python_version < "3.13" 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" +orjson==3.10.10 ; 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==3.5.0 ; python_version >= "3.8" and python_version < "3.13" @@ -167,13 +167,13 @@ requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13" requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" -rich==13.9.2 ; python_version >= "3.8" and python_version < "3.13" +rich==13.9.3 ; python_version >= "3.8" and python_version < "3.13" rocrate==0.11.0 ; python_version >= "3.8" and python_version < "3.13" routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13" rpds-py==0.20.0 ; python_version >= "3.8" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" 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" +s3fs==2024.10.0 ; python_version >= "3.8" and python_version < "3.13" schema-salad==8.7.20241010092723 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" setuptools==75.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -187,7 +187,7 @@ 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" starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13" -starlette==0.40.0 ; python_version >= "3.8" and python_version < "3.13" +starlette==0.41.0 ; python_version >= "3.8" and python_version < "3.13" supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13" svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13" tenacity==9.0.0 ; python_version >= "3.8" and python_version < "3.13" @@ -208,7 +208,7 @@ uvloop==0.21.0 ; python_version >= "3.8" and python_version < "3.13" vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13" -webob==1.8.8 ; python_version >= "3.8" and python_version < "3.13" +webob==1.8.9 ; python_version >= "3.8" and python_version < "3.13" whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" yacman==0.9.3 ; 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 328c76785427..30501dcbe567 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,19 +1,19 @@ annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" -boto3-stubs[s3]==1.35.44 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.35.44 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.35.49 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.35.49 ; 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==43.0.3 ; 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==1.35.42 ; python_version >= "3.8" and python_version < "3.13" +mypy-boto3-s3==1.35.46 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -mypy==1.12.0 ; python_version >= "3.8" and python_version < "3.13" +mypy==1.13.0 ; 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==2.23.4 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11" -types-awscrt==0.22.0 ; python_version >= "3.8" and python_version < "3.13" +types-awscrt==0.23.0 ; python_version >= "3.8" and python_version < "3.13" types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13" -types-boto==2.49.18.20240806 ; python_version >= "3.8" and python_version < "3.13" +types-boto==2.49.18.20241019 ; python_version >= "3.8" and python_version < "3.13" types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13" types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13" types-docutils==0.21.0.20241005 ; python_version >= "3.8" and python_version < "3.13" @@ -24,7 +24,7 @@ types-python-dateutil==2.9.0.20241003 ; python_version >= "3.8" and python_versi 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==0.10.3 ; python_version >= "3.8" and python_version < "3.13" -types-setuptools==75.2.0.20241019 ; python_version >= "3.8" and python_version < "3.13" +types-setuptools==75.2.0.20241025 ; python_version >= "3.8" and python_version < "3.13" types-six==1.16.21.20241009 ; 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"