Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -20,8 +20,9 @@ charset-normalizer==3.3.2 ; 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")
-contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13"
+contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9"
+contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
+coverage[toml]==7.5.4 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -33,7 +34,7 @@ deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
 exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
+filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
 fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -45,7 +46,7 @@ httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
 httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-metadata==7.2.1 ; python_version >= "3.8" and python_version < "3.13"
 importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
 iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -71,17 +72,17 @@ mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
-more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
+more-itertools==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
 onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
+packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -92,7 +93,7 @@ playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
-psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
+psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
 psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -126,21 +127,21 @@ readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.25.2 ; python_version >= "3.8" and python_version < "3.13"
+responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.1 ; 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==34.4.2 ; python_version >= "3.9" and python_version < "3.13"
+rucio-clients==34.4.3 ; python_version >= "3.9" and python_version < "3.13"
 s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; 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 < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.1.0 ; 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"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -169,10 +170,11 @@ twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
+urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
+urllib3[socks]==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
 watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
+websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
 werkzeug==3.0.3 ; 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"

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

@@ -1,7 +1,7 @@
 attrs==23.2.0
-flake8==7.0.0
+flake8==7.1.0
 flake8-bugbear==24.4.26
 mccabe==0.7.0
-pycodestyle==2.11.1
+pycodestyle==2.12.0
 pyflakes==3.2.0
-ruff==0.4.8
+ruff==0.4.10

lib/galaxy/dependencies/pinned-requirements.txt

@@ -16,7 +16,7 @@ anyio==4.4.0 ; 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==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
+argcomplete==3.4.0 ; 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==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -64,10 +64,10 @@ docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
 edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
-email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
+email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
 fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
+filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
 fsspec==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -79,15 +79,15 @@ graphene==3.3 ; python_version >= "3.8" and python_version < "3.13"
 graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
 graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
-greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32")
+greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8"
 gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13"
 gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-metadata==7.2.1 ; python_version >= "3.8" and python_version < "3.13"
 importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9"
 isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
 isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -105,31 +105,31 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mercurial==6.7.3 ; python_version >= "3.8" and python_version < "3.13"
+mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
 mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13"
+msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 networkx==2.5 ; 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==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
 oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
-orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13"
+orjson==3.10.5 ; python_version >= "3.8" and python_version < "3.13"
 oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
+packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
 paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
-prompt-toolkit==3.0.46 ; python_version >= "3.8" and python_version < "3.13"
+prompt-toolkit==3.0.47 ; python_version >= "3.8" and python_version < "3.13"
 prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
-psutil==5.9.8 ; 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"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -174,22 +174,22 @@ ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 s3fs==2024.6.0 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.1.0 ; 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"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.31 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
 starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13"
 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==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
+tenacity==8.4.1 ; 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"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
@@ -201,7 +201,7 @@ typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; 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==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
+urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
 uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13"
 uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
 vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -1,6 +1,6 @@
 annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.34.122 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.34.122 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -11,7 +11,7 @@ pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platfo
 pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.20.11 ; python_version >= "3.8" and python_version < "3.13"
+types-awscrt==0.20.12 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"