From 223b71cac4c4eb91cce10e897047dc387d86ce95 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 17 Jan 2026 03:34:36 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 25 +++++----- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 46 ++++++++++--------- .../dependencies/pinned-test-requirements.txt | 11 +++-- .../pinned-typecheck-requirements.txt | 10 ++-- 5 files changed, 50 insertions(+), 44 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 27795b9c9c4..a5fcd8d28a9 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -46,7 +46,8 @@ darker==3.0.0 darkgraylib==2.4.1 decorator==5.2.1 defusedxml==0.7.1 -docutils==0.21.2 +docutils==0.21.2 ; python_full_version < '3.11' +docutils==0.22.4 ; python_full_version >= '3.11' 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' @@ -77,7 +78,7 @@ isodate==0.7.2 ; python_full_version < '3.11' 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==6.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x' +jaraco-context==6.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' jaraco-functools==4.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' jeepney==0.9.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux' jinja2==3.1.6 @@ -91,9 +92,10 @@ junit-xml==1.9 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' kiwisolver==1.4.7 ; python_full_version < '3.10' kiwisolver==1.4.9 ; python_full_version >= '3.10' -librt==0.7.7 ; platform_python_implementation != 'PyPy' +librt==0.7.8 ; platform_python_implementation != 'PyPy' lxml==6.0.2 -markdown-it-py==3.0.0 +markdown-it-py==3.0.0 ; python_full_version < '3.11' +markdown-it-py==4.0.0 ; python_full_version >= '3.11' markdown-it-reporter==0.0.2 markupsafe==3.0.3 matplotlib==3.9.4 ; python_full_version < '3.10' @@ -110,11 +112,12 @@ multidict==6.7.0 mypy==1.19.1 mypy-extensions==1.1.0 myst-parser==3.0.1 ; python_full_version < '3.10' -myst-parser==4.0.1 ; python_full_version >= '3.10' +myst-parser==4.0.1 ; python_full_version == '3.10.*' +myst-parser==5.0.0 ; python_full_version >= '3.11' nh3==0.3.2 numpy==2.0.2 ; python_full_version < '3.10' numpy==2.2.6 ; python_full_version == '3.10.*' -numpy==2.4.0 ; python_full_version >= '3.11' +numpy==2.4.1 ; python_full_version >= '3.11' onedatafilerestclient==21.2.5.2 outcome==1.3.0.post0 owlrl==6.0.2 ; python_full_version < '3.10' @@ -186,7 +189,6 @@ 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==0.8.0 ; python_full_version >= '3.10' roman-numerals==4.1.0 ; python_full_version >= '3.11' -roman-numerals-py==4.1.0 ; python_full_version >= '3.11' rpds-py==0.27.1 ; python_full_version < '3.10' rpds-py==0.30.0 ; python_full_version >= '3.10' ruamel-yaml==0.18.17 @@ -197,7 +199,7 @@ s3transfer==0.16.0 ; python_full_version >= '3.10' schema-salad==8.9.20251102115403 scipy==1.13.1 ; python_full_version < '3.10' scipy==1.15.3 ; python_full_version == '3.10.*' -scipy==1.16.3 ; python_full_version >= '3.11' +scipy==1.17.0 ; 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==3.5.0 ; 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' @@ -209,8 +211,9 @@ snowballstemmer==3.0.1 sortedcontainers==2.4.0 sphinx==7.4.7 ; python_full_version < '3.10' sphinx==8.1.3 ; python_full_version == '3.10.*' -sphinx==8.2.3 ; python_full_version >= '3.11' -sphinx-rtd-theme==3.0.2 +sphinx==9.0.4 ; python_full_version == '3.11.*' +sphinx==9.1.0 ; python_full_version >= '3.12' +sphinx-rtd-theme==3.1.0 sphinxcontrib-applehelp==2.0.0 sphinxcontrib-devhelp==2.0.0 sphinxcontrib-htmlhelp==2.1.0 @@ -227,7 +230,7 @@ testfixtures==10.0.0 ; 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' +tomli==2.4.0 ; python_full_version <= '3.11' total-perspective-vortex==3.1.3 trio==0.31.0 ; python_full_version < '3.10' trio==0.32.0 ; python_full_version >= '3.10' diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 3f544c31cea..ff1ebcc5b0d 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/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==0.14.11 +ruff==0.14.13 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 49ae3d1cf55..a2f63503124 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -11,11 +11,11 @@ aiohttp==3.13.3 aioitertools==0.13.0 aiosignal==1.4.0 alembic==1.16.5 ; python_full_version < '3.10' -alembic==1.18.0 ; python_full_version >= '3.10' +alembic==1.18.1 ; python_full_version >= '3.10' amqp==5.3.1 annotated-doc==0.0.4 annotated-types==0.7.0 -anthropic==0.75.0 +anthropic==0.76.0 anyio==4.12.1 apispec==6.8.4 ; python_full_version < '3.10' apispec==6.9.0 ; python_full_version >= '3.10' @@ -72,7 +72,7 @@ cwl-upgrader==1.2.14 ; python_full_version >= '3.10' cwl-utils==0.40 cwltool==3.1.20251031082601 ; python_full_version < '3.10' cwltool==3.1.20260108082145 ; python_full_version >= '3.10' -cyclopts==4.4.4 ; python_full_version >= '3.10' +cyclopts==4.5.0 ; python_full_version >= '3.10' defusedxml==0.7.1 deprecated==1.3.1 deprecation==2.1.0 @@ -83,7 +83,8 @@ dnspython==2.7.0 ; python_full_version < '3.10' dnspython==2.8.0 ; python_full_version >= '3.10' docopt==0.6.2 docstring-parser==0.17.0 -docutils==0.21.2 +docutils==0.21.2 ; python_full_version < '3.11' +docutils==0.22.4 ; python_full_version >= '3.11' dparse==0.6.4 edam-ontology==1.25.3 email-validator==2.3.0 @@ -94,7 +95,7 @@ executing==2.2.1 ; python_full_version >= '3.10' fakeredis==2.33.0 ; python_full_version >= '3.10' fastapi==0.128.0 fastavro==1.12.1 ; sys_platform != 'emscripten' -fastmcp==2.14.2 ; python_full_version >= '3.10' +fastmcp==2.14.3 ; python_full_version >= '3.10' filelock==3.19.1 ; python_full_version < '3.10' filelock==3.20.3 ; python_full_version >= '3.10' fissix==24.4.24 @@ -103,14 +104,14 @@ fs==2.4.16 fsspec==2025.10.0 ; python_full_version < '3.10' fsspec==2026.1.0 ; python_full_version >= '3.10' future==1.0.0 -genai-prices==0.0.50 +genai-prices==0.0.51 google-api-core==2.29.0 google-auth==2.47.0 google-cloud-batch==0.20.0 google-genai==1.47.0 ; python_full_version < '3.10' -google-genai==1.57.0 ; python_full_version >= '3.10' +google-genai==1.59.0 ; python_full_version >= '3.10' googleapis-common-protos==1.72.0 -gravity @ git+https://github.com/nsoranzo/gravity.git@a60c911e61c784d37d3eb334c1c68288d2c06ef3 +gravity @ git+https://github.com/nsoranzo/gravity.git@7c5f457424658ee904694f5566e61b562bce7ed6 greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64') greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64') griffe==1.14.0 ; python_full_version < '3.10' @@ -140,7 +141,7 @@ isa-rwval==0.10.11 isal==1.8.0 isodate==0.7.2 ; python_full_version < '3.11' jaraco-classes==3.4.0 ; python_full_version >= '3.10' -jaraco-context==6.0.2 ; python_full_version >= '3.10' +jaraco-context==6.1.0 ; python_full_version >= '3.10' jaraco-functools==4.4.0 ; python_full_version >= '3.10' jeepney==0.9.0 ; python_full_version >= '3.10' and sys_platform == 'linux' jinja2==3.1.6 @@ -157,14 +158,15 @@ lagom==2.7.7 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' -logfire==4.17.0 ; python_full_version >= '3.10' -logfire-api==4.17.0 +logfire==4.19.0 ; python_full_version >= '3.10' +logfire-api==4.19.0 lupa==2.6 ; python_full_version >= '3.10' lxml==6.0.2 mako==1.3.10 markdown==3.9 ; python_full_version < '3.10' markdown==3.10 ; python_full_version >= '3.10' -markdown-it-py==3.0.0 +markdown-it-py==3.0.0 ; python_full_version < '3.11' +markdown-it-py==4.0.0 ; python_full_version >= '3.11' markupsafe==3.0.3 mcp==1.25.0 ; python_full_version >= '3.10' mdurl==0.1.2 @@ -186,7 +188,7 @@ 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==2.4.0 ; python_full_version >= '3.11' +numpy==2.4.1 ; python_full_version >= '3.11' oauthlib==3.3.1 openai==2.15.0 openapi-pydantic==0.5.1 ; python_full_version >= '3.10' @@ -215,12 +217,12 @@ pebble==5.1.3 pillow==11.3.0 ; python_full_version < '3.10' pillow==12.1.0 ; python_full_version >= '3.10' platformdirs==4.5.1 ; python_full_version >= '3.10' -prometheus-client==0.23.1 ; python_full_version >= '3.10' +prometheus-client==0.24.1 ; python_full_version >= '3.10' prompt-toolkit==3.0.52 propcache==0.4.1 proto-plus==1.27.0 protobuf==5.29.5 ; python_full_version < '3.10' -protobuf==6.33.3 ; python_full_version >= '3.10' +protobuf==6.33.4 ; python_full_version >= '3.10' prov==1.5.1 psutil==7.2.1 pulsar-galaxy-lib==0.15.13 @@ -232,14 +234,14 @@ pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementat pycryptodome==3.23.0 pydantic==2.12.5 pydantic-ai==0.8.1 ; python_full_version < '3.10' -pydantic-ai==1.41.0 ; python_full_version >= '3.10' +pydantic-ai==1.44.0 ; python_full_version >= '3.10' pydantic-ai-slim==0.8.1 ; python_full_version < '3.10' -pydantic-ai-slim==1.41.0 ; python_full_version >= '3.10' +pydantic-ai-slim==1.44.0 ; python_full_version >= '3.10' pydantic-core==2.41.5 pydantic-evals==0.8.1 ; python_full_version < '3.10' -pydantic-evals==1.41.0 ; python_full_version >= '3.10' +pydantic-evals==1.44.0 ; python_full_version >= '3.10' pydantic-graph==0.8.1 ; python_full_version < '3.10' -pydantic-graph==1.41.0 ; python_full_version >= '3.10' +pydantic-graph==1.44.0 ; python_full_version >= '3.10' pydantic-settings==2.11.0 ; python_full_version < '3.10' pydantic-settings==2.12.0 ; python_full_version >= '3.10' pydantic-tes==0.2.0 @@ -275,7 +277,7 @@ rdflib==7.5.0 ; python_full_version >= '3.10' redis==7.1.0 ; python_full_version >= '3.10' referencing==0.36.2 refgenconf==0.12.2 -regex==2025.11.3 +regex==2026.1.15 repoze-lru==0.7 requests==2.32.5 requests-oauthlib==2.0.0 @@ -320,11 +322,11 @@ 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==2025.12.20 ; python_full_version >= '3.11' +tifffile==2026.1.14 ; python_full_version >= '3.11' tiktoken==0.12.0 ; python_full_version >= '3.10' tinydb==4.8.2 tokenizers==0.22.2 ; sys_platform != 'emscripten' -tomli==2.3.0 ; python_full_version < '3.11' +tomli==2.4.0 ; python_full_version < '3.11' tornado==6.5.4 tqdm==4.67.1 tuspy==1.1.0 diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt index 26712a40139..fa5eae9337a 100644 --- a/lib/galaxy/dependencies/pinned-test-requirements.txt +++ b/lib/galaxy/dependencies/pinned-test-requirements.txt @@ -69,9 +69,10 @@ jsonschema-specifications==2025.9.1 junit-xml==1.9 kiwisolver==1.4.7 ; python_full_version < '3.10' kiwisolver==1.4.9 ; python_full_version >= '3.10' -librt==0.7.7 ; platform_python_implementation != 'PyPy' +librt==0.7.8 ; platform_python_implementation != 'PyPy' lxml==6.0.2 -markdown-it-py==3.0.0 +markdown-it-py==3.0.0 ; python_full_version < '3.11' +markdown-it-py==4.0.0 ; python_full_version >= '3.11' markupsafe==3.0.3 matplotlib==3.9.4 ; python_full_version < '3.10' matplotlib==3.10.8 ; python_full_version >= '3.10' @@ -85,7 +86,7 @@ mypy==1.19.1 mypy-extensions==1.1.0 numpy==2.0.2 ; python_full_version < '3.10' numpy==2.2.6 ; python_full_version == '3.10.*' -numpy==2.4.0 ; python_full_version >= '3.11' +numpy==2.4.1 ; python_full_version >= '3.11' onedatafilerestclient==21.2.5.2 outcome==1.3.0.post0 owlrl==6.0.2 ; python_full_version < '3.10' @@ -157,7 +158,7 @@ s3transfer==0.16.0 ; python_full_version >= '3.10' schema-salad==8.9.20251102115403 scipy==1.13.1 ; python_full_version < '3.10' scipy==1.15.3 ; python_full_version == '3.10.*' -scipy==1.16.3 ; python_full_version >= '3.11' +scipy==1.17.0 ; python_full_version >= '3.11' selenium==4.32.0 ; python_full_version < '3.10' selenium==4.39.0 ; python_full_version >= '3.10' seletools==1.5.0 @@ -173,7 +174,7 @@ testfixtures==10.0.0 ; 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' +tomli==2.4.0 ; python_full_version <= '3.11' total-perspective-vortex==3.1.3 trio==0.31.0 ; python_full_version < '3.10' trio==0.32.0 ; python_full_version >= '3.10' diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index a9dc627a5af..f2a936e6ec3 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,11 +1,11 @@ # This file was autogenerated by uv via the following command: # uv export --frozen --no-annotate --no-hashes --only-group=typecheck annotated-types==0.7.0 -boto3-stubs==1.42.25 -botocore-stubs==1.42.25 +boto3-stubs==1.42.30 +botocore-stubs==1.42.30 cffi==2.0.0 ; platform_python_implementation != 'PyPy' cryptography==46.0.3 -librt==0.7.7 ; platform_python_implementation != 'PyPy' +librt==0.7.8 ; platform_python_implementation != 'PyPy' lxml-stubs==0.5.1 mypy==1.19.1 mypy-boto3-s3==1.42.21 @@ -14,8 +14,8 @@ pathspec==1.0.3 pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy' pydantic==2.12.5 pydantic-core==2.41.5 -tomli==2.3.0 ; python_full_version < '3.11' -types-awscrt==0.30.0 +tomli==2.4.0 ; python_full_version < '3.11' +types-awscrt==0.31.1 types-bleach==6.3.0.20251115 types-boto==2.49.18.20241019 types-contextvars==2.4.7.3