Merge pull request #18982 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

doc/source/conf.py

@@ -162,9 +162,6 @@ def setup(app):
     "navigation_depth": 2,
 }
 
-# Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = []
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 # html_title = None

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,7 +1,7 @@
 --extra-index-url https://wheels.galaxyproject.org/simple
 
 aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.10 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
 anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -13,13 +13,13 @@ babel==2.16.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 black==24.8.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
-build==1.2.2 ; python_version >= "3.8" and python_version < "3.13"
+boto3==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
+build==1.2.2.post1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
-charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
+charset-normalizer==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
@@ -83,7 +83,7 @@ myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.18 ; python_version >= "3.8" and python_version < "3.13"
 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==2.1.1 ; python_version >= "3.10" and python_version < "3.13"
+numpy==2.1.2 ; python_version >= "3.10" and python_version < "3.13"
 onedatafilerestclient==21.2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -97,6 +97,7 @@ playwright==1.47.0 ; 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"
+propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13"
 psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
 psycopg==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
@@ -138,7 +139,7 @@ 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"
 rucio-clients==35.4.0 ; python_version >= "3.9" and python_version < "3.13"
-s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
+s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10"
@@ -151,7 +152,7 @@ six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-sphinx-rtd-theme==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+sphinx-rtd-theme==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 sphinx==7.1.2 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-applehelp==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -165,7 +166,7 @@ stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.13"
 tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
 testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
 text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
-tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
+tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13"
 toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.2 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
 trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -183,5 +184,5 @@ 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"
 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==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
+yarl==1.15.0 ; python_version >= "3.8" and python_version < "3.13"
 zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,11 +2,11 @@
 
 a2wsgi==1.10.7 ; python_version >= "3.8" and python_version < "3.13"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.15.1 ; python_version >= "3.8" and python_version < "3.13"
+aiobotocore==2.15.2 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13"
 aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.10 ; python_version >= "3.8" and python_version < "3.13"
 aioitertools==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alembic==1.13.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -17,7 +17,7 @@ anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
 apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13"
 appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
 arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
-argcomplete==3.5.0 ; python_version >= "3.8" and python_version < "3.13"
+argcomplete==3.5.1 ; python_version >= "3.8" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13"
 attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -34,13 +34,13 @@ bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
 boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.35.36 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.13.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
-charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
+charset-normalizer==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
 circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
 click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -51,11 +51,11 @@ cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
-conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
+conda-package-streaming==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
 cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
 cwl-utils==0.34 ; python_version >= "3.8" and python_version < "3.13"
-cwltool==3.1.20240909164951 ; python_version >= "3.8" and python_version < "3.13"
+cwltool==3.1.20241007082533 ; python_version >= "3.8" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -116,7 +116,7 @@ networkx==3.1 ; python_version >= "3.8" and python_version < "3.13"
 nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13"
 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==2.1.1 ; python_version >= "3.10" and python_version < "3.13"
+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"
 oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -130,6 +130,7 @@ pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13"
 pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.48 ; python_version >= "3.8" and python_version < "3.13"
+propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13"
 prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
 psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
@@ -141,7 +142,7 @@ pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
 pydantic[email]==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
 pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pyfaidx==0.8.1.2 ; python_version >= "3.8" and python_version < "3.13"
+pyfaidx==0.8.1.3 ; python_version >= "3.8" and python_version < "3.13"
 pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
 pyjwt==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
 pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -177,7 +178,6 @@ s3fs==2024.9.0 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13"
-shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -193,7 +193,7 @@ 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"
 tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
-tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
+tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11"
 tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13"
 tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13"
@@ -204,7 +204,7 @@ tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13"
 tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
 ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
 urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
-uvicorn==0.31.0 ; python_version >= "3.8" and python_version < "3.13"
+uvicorn==0.31.1 ; python_version >= "3.8" and python_version < "3.13"
 uvloop==0.20.0 ; 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"
@@ -213,7 +213,7 @@ webob==1.8.8 ; 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"
-yarl==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
+yarl==1.15.0 ; python_version >= "3.8" and python_version < "3.13"
 zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13"
 zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
 zstandard==0.23.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -1,8 +1,8 @@
 --extra-index-url https://wheels.galaxyproject.org/simple
 
 annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.35.34 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.35.34 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.35.39 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.35.39 ; 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==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -25,8 +25,8 @@ types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3
 types-python-dateutil==2.9.0.20241003 ; python_version >= "3.8" and python_version < "3.13"
 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==0.10.2 ; 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==75.1.0.20240917 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20240513 ; 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"