Merge pull request galaxyproject#18904 from galaxybot/dev_auto_update…

…_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,5 +1,5 @@
-aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13"
+aiohappyeyeballs==2.4.2 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.8 ; 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"
@@ -37,7 +37,7 @@ dogpile-cache==1.3.3 ; python_version >= "3.9" and python_version < "3.13"
 exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.16.1 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.53.1 ; python_version >= "3.8" and python_version < "3.13"
+fonttools==4.54.1 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13"
 graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -54,7 +54,7 @@ isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-context==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-functools==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-functools==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
 jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -96,15 +96,15 @@ 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"
 psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
-psycopg==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
+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"
 pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
 pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
 pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
-pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
+pyproject-hooks==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
 pytest-asyncio==0.23.8 ; python_version >= "3.8" and python_version < "3.13"
 pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -135,7 +135,7 @@ rich==13.8.1 ; python_version >= "3.8" and python_version < "3.13"
 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==35.3.0 ; python_version >= "3.9" 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"
 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"
@@ -172,7 +172,7 @@ tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.1.1 ; 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"
+tzdata==2024.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
 urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
 urllib3[socks]==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
 watchdog==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -181,5 +181,5 @@ 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==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
+yarl==1.13.1 ; 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-lint-requirements.txt

@@ -4,4 +4,4 @@ flake8-bugbear==24.8.19
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.6.6
+ruff==0.6.8

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,11 +5,11 @@ 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"
 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==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13"
+aiohappyeyeballs==2.4.2 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.8 ; 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==1.13.2 ; python_version >= "3.8" and python_version < "3.13"
+alembic==1.13.3 ; python_version >= "3.8" and python_version < "3.13"
 amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
 aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
 annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -29,7 +29,7 @@ bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
 bcrypt==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
 bdbag==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
 beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13"
-billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
+billiard==4.2.1 ; python_version >= "3.8" and python_version < "3.13"
 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"
@@ -84,13 +84,14 @@ gunicorn==23.0.0 ; python_version >= "3.8" and python_version < "3.13"
 gxformat2==0.20.0 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 h5grove==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
-h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
+h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.9"
+h5py==3.12.1 ; python_version >= "3.9" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.10 ; python_version >= "3.8" and python_version < "3.13"
 importlib-metadata==8.5.0 ; python_version >= "3.8" and python_version < "3.13"
 importlib-resources==6.4.5 ; python_version >= "3.8" and python_version < "3.9"
 isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13"
-isal==1.7.0 ; python_version >= "3.8" and python_version < "3.13"
+isal==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
 jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -129,7 +130,7 @@ pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
 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==3.0.47 ; python_version >= "3.8" and python_version < "3.13"
+prompt-toolkit==3.0.48 ; 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"
@@ -153,7 +154,7 @@ pyreadline3==3.5.4 ; sys_platform == "win32" and python_version >= "3.8" and pyt
 pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
-python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
+python-multipart==0.0.12 ; python_version >= "3.8" and python_version < "3.13"
 python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pytz==2024.2 ; python_version >= "3.8" and python_version < "3.13"
 pyyaml==6.0.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -188,7 +189,7 @@ sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.5.1 ; 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==0.38.5 ; python_version >= "3.8" and python_version < "3.13"
+starlette==0.38.6 ; 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==9.0.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -200,11 +201,11 @@ tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 tuswsgi==0.5.5 ; 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"
+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==0.30.6 ; python_version >= "3.8" and python_version < "3.13"
+uvicorn==0.31.0 ; 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 +214,7 @@ 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==1.11.1 ; python_version >= "3.8" and python_version < "3.13"
+yarl==1.13.1 ; 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

@@ -1,6 +1,6 @@
 annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.35.24 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.35.24 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.35.29 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.35.29 ; 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"
@@ -19,7 +19,7 @@ types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
 types-docutils==0.21.0.20240907 ; python_version >= "3.8" and python_version < "3.13"
 types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13"
 types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13"
-types-paramiko==3.5.0.20240918 ; python_version >= "3.8" and python_version < "3.13"
+types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.9.0.20240906 ; 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"

lib/galaxy/dependencies/update.sh

@@ -88,8 +88,8 @@ split_requirement () {
 # For some packages there is no recent version that works on all Python versions
 # supported by Galaxy, so Poetry resorts to an old version. Here we replace any
 # such requirement with multiple Python-version-specific requirements.
-# Packages which specify a maximum Python version pin:
 split_requirement contourpy
+split_requirement h5py
 split_requirement matplotlib
 split_requirement numpy
 split_requirement scipy