Merge pull request #21606 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: nsoranzo

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'

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

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

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'

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