Merge pull request #20732 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: nsoranzo

lib/galaxy/dependencies/dev-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=dev
 aiohappyeyeballs==2.6.1
-aiohttp==3.12.14
+aiohttp==3.12.15
 aiosignal==1.4.0
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
@@ -15,28 +15,28 @@ backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine !=
 black==25.1.0
 boto3==1.39.8
 botocore==1.39.8
-build==1.2.2.post1
+build==1.3.0
 cachecontrol==0.14.3
 cattrs==25.1.1
 certifi==2025.7.14
 cffi==1.17.1
 charset-normalizer==3.4.2
 click==8.1.8 ; python_full_version < '3.10'
-click==8.2.1 ; python_full_version >= '3.10'
+click==8.2.2 ; python_full_version >= '3.10'
 codespell==2.4.1
 colorama==0.4.6 ; os_name == 'nt' or 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'
-coverage==7.10.0
+contourpy==1.3.2 ; python_full_version == '3.10.*'
+contourpy==1.3.3 ; python_full_version >= '3.11'
+coverage==7.10.1
 cryptography==45.0.5
 cwltest==2.6.20250314152537
 cycler==0.12.1
 darker==2.1.1
 darkgraylib==1.2.1
 decorator==5.2.1
 defusedxml==0.7.1
-deprecated==1.2.18
 docutils==0.21.2
 dogpile-cache==1.2.2
 enum-tools==0.12.0 ; python_full_version >= '3.10'
@@ -45,7 +45,7 @@ filelock==3.18.0
 fluent-logger==0.11.1
 fonttools==4.59.0
 frozenlist==1.7.0
-galaxy-release-util==0.3.0
+galaxy-release-util==0.3.1
 graylint==1.1.1
 greenlet==3.2.3
 h11==0.16.0
@@ -79,7 +79,7 @@ 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==3.10.3 ; python_full_version >= '3.10'
+matplotlib==3.10.5 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2
 mdurl==0.1.2
 mirakuru==2.6.1
@@ -97,7 +97,7 @@ numpy==2.3.2 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
-owlrl==7.1.3 ; 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'
 pathspec==0.12.1
@@ -116,7 +116,7 @@ psutil==7.0.0 ; sys_platform != 'cygwin'
 psycopg==3.2.9
 pycparser==2.22
 pyee==13.0.0
-pygithub==2.6.1
+pygithub==2.7.0
 pygments==2.19.2
 pyjwt==2.10.1
 pynacl==1.5.0
@@ -164,7 +164,7 @@ s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
-scipy==1.16.0 ; python_full_version >= '3.11'
+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'
@@ -209,7 +209,6 @@ wcwidth==0.2.13
 webencodings==0.5.1 ; python_full_version < '3.10'
 websocket-client==1.8.0
 werkzeug==3.1.3
-wrapt==1.17.2
 wsproto==1.2.0
 yarl==1.20.1
 zipp==3.23.0 ; python_full_version < '3.12'

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==0.12.5
+ruff==0.12.7

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,7 +5,7 @@ adal==1.2.7
 aiobotocore==2.23.2
 aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
-aiohttp==3.12.14
+aiohttp==3.12.15
 aioitertools==0.12.0
 aiosignal==1.4.0
 alembic==1.16.4
@@ -31,15 +31,15 @@ bleach==6.2.0
 boltons==25.0.0
 boto==2.49.0
 botocore==1.39.8
-bx-python==0.13.0
+bx-python==0.14.0
 cachecontrol==0.14.3
 celery==5.5.3
 certifi==2025.7.14
 cffi==1.17.1
 charset-normalizer==3.4.2
 circus==0.19.0
 click==8.1.8 ; python_full_version < '3.10'
-click==8.2.1 ; python_full_version >= '3.10'
+click==8.2.2 ; python_full_version >= '3.10'
 click-didyoumean==0.3.1
 click-plugins==1.1.1.2
 click-repl==0.3.0
@@ -128,7 +128,7 @@ paramiko==3.5.1
 parsley==1.3
 paste==3.10.1
 pastedeploy==3.1.0
-pebble==5.1.2
+pebble==5.1.3
 pillow==11.3.0
 prompt-toolkit==3.0.51
 propcache==0.3.2
@@ -163,7 +163,7 @@ pyzmq==27.0.0
 rdflib==7.1.4
 referencing==0.36.2
 refgenconf==0.12.2
-regex==2024.11.6
+regex==2025.7.34
 repoze-lru==0.7
 requests==2.32.4
 requests-oauthlib==2.0.0
@@ -186,7 +186,7 @@ sniffio==1.3.1
 social-auth-core==4.7.0
 sortedcontainers==2.4.0
 spython==0.3.14
-sqlalchemy==2.0.40
+sqlalchemy==2.0.42
 sqlparse==0.5.3
 starlette==0.47.2
 starlette-context==0.4.0

lib/galaxy/dependencies/pinned-test-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=test
 aiohappyeyeballs==2.6.1
-aiohttp==3.12.14
+aiohttp==3.12.15
 aiosignal==1.4.0
 anyio==4.9.0
 ase==3.25.0
@@ -16,12 +16,13 @@ certifi==2025.7.14
 cffi==1.17.1 ; implementation_name != 'pypy' and os_name == 'nt'
 charset-normalizer==3.4.2
 click==8.1.8 ; python_full_version < '3.10'
-click==8.2.1 ; python_full_version >= '3.10'
+click==8.2.2 ; 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'
-coverage==7.10.0
+contourpy==1.3.2 ; python_full_version == '3.10.*'
+contourpy==1.3.3 ; python_full_version >= '3.11'
+coverage==7.10.1
 cwltest==2.6.20250314152537
 cycler==0.12.1
 decorator==5.2.1
@@ -56,7 +57,7 @@ lxml==5.4.0
 markdown-it-py==3.0.0
 markupsafe==3.0.2
 matplotlib==3.9.4 ; python_full_version < '3.10'
-matplotlib==3.10.3 ; python_full_version >= '3.10'
+matplotlib==3.10.5 ; python_full_version >= '3.10'
 mdurl==0.1.2
 mirakuru==2.6.1
 mistune==3.0.2
@@ -69,7 +70,7 @@ numpy==2.3.2 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
-owlrl==7.1.3 ; 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
@@ -126,7 +127,7 @@ s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
-scipy==1.16.0 ; python_full_version >= '3.11'
+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'
 seletools==1.5.0

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

@@ -1,35 +1,35 @@
 # 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==1.39.14
+boto3-stubs==1.40.1
 botocore-stubs==1.38.46
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==45.0.5
 lxml-stubs==0.5.1
-mypy==1.17.0
-mypy-boto3-s3==1.39.5
+mypy==1.17.1
+mypy-boto3-s3==1.40.0
 mypy-extensions==1.1.0
 pathspec==0.12.1
 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==0.27.4
+types-awscrt==0.27.5
 types-bleach==6.2.0.20250514
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
-types-docutils==0.21.0.20250722
+types-docutils==0.21.0.20250728
 types-html5lib==1.1.11.20250708
 types-markdown==3.8.0.20250708
-types-paramiko==3.5.0.20250708
+types-paramiko==3.5.0.20250801
 types-python-dateutil==2.9.0.20250708
 types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20250516
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.4.20250611 ; python_full_version >= '3.10'
 types-s3transfer==0.13.0
-types-setuptools==80.9.0.20250529
+types-setuptools==80.9.0.20250801
 types-six==1.17.0.20250515
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
 typing-extensions==4.14.1