Merge pull request #20779 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: mvdbeek

lib/galaxy/dependencies/dev-requirements.txt

@@ -6,7 +6,7 @@ aiosignal==1.4.0
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
 anyio==4.10.0
-ase==3.25.0
+ase==3.26.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.3.0
 axe-selenium-python==2.1.6
@@ -20,7 +20,7 @@ cachecontrol==0.14.3
 cattrs==25.1.1
 certifi==2025.8.3
 cffi==1.17.1
-charset-normalizer==3.4.2
+charset-normalizer==3.4.3
 click==8.1.8 ; python_full_version < '3.10'
 click==8.2.1 ; python_full_version >= '3.10'
 codespell==2.4.1
@@ -29,7 +29,7 @@ colorlog==6.9.0
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.2
+coverage==7.10.3
 cryptography==45.0.6
 cwltest==2.6.20250314152537
 cycler==0.12.1
@@ -41,9 +41,9 @@ docutils==0.21.2
 dogpile-cache==1.2.2
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
-filelock==3.18.0
+filelock==3.19.1
 fluent-logger==0.11.1
-fonttools==4.59.0
+fonttools==4.59.1
 frozenlist==1.7.0
 galaxy-release-util==0.3.1
 graylint==1.1.1
@@ -73,20 +73,21 @@ jsonschema-specifications==2025.4.1
 junit-xml==1.9
 keyring==25.6.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.4.7 ; python_full_version < '3.10'
-kiwisolver==1.4.8 ; python_full_version >= '3.10'
+kiwisolver==1.4.9 ; python_full_version >= '3.10'
 lxml==5.4.0
 markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
 markupsafe==3.0.2
 matplotlib==3.9.4 ; python_full_version < '3.10'
 matplotlib==3.10.5 ; python_full_version >= '3.10'
-mdit-py-plugins==0.4.2
+mdit-py-plugins==0.4.2 ; python_full_version < '3.10'
+mdit-py-plugins==0.5.0 ; python_full_version >= '3.10'
 mdurl==0.1.2
 mirakuru==2.6.1
 mistune==3.0.2
 more-itertools==10.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.1
-multidict==6.6.3
+multidict==6.6.4
 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'
@@ -101,7 +102,7 @@ owlrl==7.1.4 ; python_full_version >= '3.10'
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
 pathspec==0.12.1
-pbr==6.1.1
+pbr==7.0.0
 pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
@@ -167,7 +168,7 @@ scipy==1.15.3 ; python_full_version == '3.10.*'
 scipy==1.16.1 ; python_full_version >= '3.11'
 secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.34.2 ; python_full_version >= '3.10'
+selenium==4.35.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 setuptools==80.9.0
 six==1.17.0

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==0.12.8
+ruff==0.12.9

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.10
 adal==1.2.7
-aiobotocore==2.24.0
+aiobotocore==2.24.1
 aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.12.15
@@ -36,7 +36,7 @@ cachecontrol==0.14.3
 celery==5.5.3
 certifi==2025.8.3
 cffi==1.17.1
-charset-normalizer==3.4.2
+charset-normalizer==3.4.3
 circus==0.19.0
 click==8.1.8 ; python_full_version < '3.10'
 click==8.2.1 ; python_full_version >= '3.10'
@@ -66,7 +66,7 @@ email-validator==2.2.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 fastapi-slim==0.116.1
-filelock==3.18.0
+filelock==3.19.1
 fissix==24.4.24
 frozenlist==1.7.0
 fs==2.4.16
@@ -110,7 +110,7 @@ mistune==3.0.2
 mrcfile==1.5.4
 msal==1.33.0
 msgpack==1.1.1
-multidict==6.6.3
+multidict==6.6.4
 mypy-extensions==1.1.0
 networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version == '3.10.*'
@@ -121,7 +121,7 @@ numpy==2.2.6 ; python_full_version == '3.10.*'
 numpy==2.3.2 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 openpyxl==3.1.5
-orjson==3.11.1
+orjson==3.11.2
 oyaml==1.0
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
@@ -143,7 +143,7 @@ pydantic-core==2.33.2
 pydantic-tes==0.2.0
 pydot==4.0.1
 pyeventsystem==0.1.0
-pyfaidx==0.8.1.4
+pyfaidx==0.8.2
 pygments==2.19.2
 pyjwt==2.10.1
 pykwalify==1.8.0
@@ -187,7 +187,7 @@ sniffio==1.3.1
 social-auth-core==4.7.0
 sortedcontainers==2.4.0
 spython==0.3.14
-sqlalchemy==2.0.42
+sqlalchemy==2.0.43
 sqlparse==0.5.3
 starlette==0.47.2
 starlette-context==0.4.0
@@ -218,7 +218,7 @@ wcwidth==0.2.13
 webencodings==0.5.1
 webob==1.8.9
 whoosh==2.7.4
-wrapt==1.17.2
+wrapt==1.17.3
 yacman==0.9.3
 yarl==1.20.1
 zipp==3.23.0 ; python_full_version < '3.10'

lib/galaxy/dependencies/pinned-test-requirements.txt

@@ -4,7 +4,7 @@ aiohappyeyeballs==2.6.1
 aiohttp==3.12.15
 aiosignal==1.4.0
 anyio==4.10.0
-ase==3.25.0
+ase==3.26.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.3.0
 axe-selenium-python==2.1.6
@@ -14,25 +14,25 @@ cachecontrol==0.14.3
 cattrs==25.1.1
 certifi==2025.8.3
 cffi==1.17.1 ; implementation_name != 'pypy' and os_name == 'nt'
-charset-normalizer==3.4.2
+charset-normalizer==3.4.3
 click==8.1.8 ; python_full_version < '3.10'
 click==8.2.1 ; python_full_version >= '3.10'
 colorama==0.4.6 ; sys_platform == 'win32'
 colorlog==6.9.0
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.2
+coverage==7.10.3
 cwltest==2.6.20250314152537
 cycler==0.12.1
 decorator==5.2.1
 defusedxml==0.7.1
 dogpile-cache==1.2.2
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
-filelock==3.18.0
+filelock==3.19.1
 fluent-logger==0.11.1
-fonttools==4.59.0
+fonttools==4.59.1
 frozenlist==1.7.0
 greenlet==3.2.4
 h11==0.16.0
@@ -52,7 +52,7 @@ jsonschema==4.25.0
 jsonschema-specifications==2025.4.1
 junit-xml==1.9
 kiwisolver==1.4.7 ; python_full_version < '3.10'
-kiwisolver==1.4.8 ; python_full_version >= '3.10'
+kiwisolver==1.4.9 ; python_full_version >= '3.10'
 lxml==5.4.0
 markdown-it-py==3.0.0
 markupsafe==3.0.2
@@ -62,7 +62,7 @@ mdurl==0.1.2
 mirakuru==2.6.1
 mistune==3.0.2
 msgpack==1.1.1
-multidict==6.6.3
+multidict==6.6.4
 mypy-extensions==1.1.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
@@ -73,7 +73,7 @@ owlrl==6.0.2 ; python_full_version < '3.10'
 owlrl==7.1.4 ; python_full_version >= '3.10'
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
-pbr==6.1.1
+pbr==7.0.0
 pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
@@ -129,7 +129,7 @@ scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
 scipy==1.16.1 ; python_full_version >= '3.11'
 selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.34.2 ; python_full_version >= '3.10'
+selenium==4.35.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 setuptools==80.9.0
 six==1.17.0

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -1,7 +1,7 @@
 # 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==1.40.6
+boto3-stubs==1.40.11
 botocore-stubs==1.38.46
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==45.0.6
@@ -14,12 +14,12 @@ pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.11.7
 pydantic-core==2.33.2
 tomli==2.2.1 ; python_full_version < '3.11'
-types-awscrt==0.27.5
+types-awscrt==0.27.6
 types-bleach==6.2.0.20250809
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
-types-docutils==0.21.0.20250809
+types-docutils==0.22.0.20250814
 types-html5lib==1.1.11.20250809
 types-markdown==3.8.0.20250809
 types-paramiko==4.0.0.20250809