Merge pull request #20139 from galaxybot/dev_auto_update_dependencies

Author: mvdbeek

lib/galaxy/dependencies/dev-requirements.txt

@@ -13,22 +13,23 @@ axe-selenium-python==2.1.6
 babel==2.17.0
 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 black==25.1.0
-boto3==1.37.1
-botocore==1.37.1
+boto3==1.37.3
+botocore==1.37.3
 build==1.2.2.post1
-cachecontrol==0.14.2
+cachecontrol==0.14.3
 cattrs==24.1.3
 certifi==2025.4.26
 cffi==1.17.1
-charset-normalizer==3.4.1
-click==8.1.8
+charset-normalizer==3.4.2
+click==8.1.8 ; python_full_version < '3.10'
+click==8.2.0 ; 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==7.8.0
-cryptography==44.0.2
+cryptography==45.0.2
 cwltest==2.6.20250314152537
 cycler==0.12.1
 darker==2.1.1
@@ -37,24 +38,24 @@ decorator==5.2.1
 defusedxml==0.7.1
 deprecated==1.2.18
 docutils==0.21.2
-dogpile-cache==1.3.4
+dogpile-cache==1.2.2
 enum-tools==0.12.0 ; python_full_version >= '3.10'
-exceptiongroup==1.2.2 ; python_full_version < '3.11'
+exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.18.0
 fluent-logger==0.11.1
-fonttools==4.57.0
+fonttools==4.58.0
 frozenlist==1.6.0
 galaxy-release-util==0.2.0
 graylint==1.1.1
-greenlet==3.2.1
+greenlet==3.2.2
 h11==0.16.0
 html5lib==1.1
 httpcore==1.0.9
 httpx==0.28.1
 id==1.5.0
 idna==3.10
 imagesize==1.4.1
-importlib-metadata==8.6.1 ; python_full_version < '3.12'
+importlib-metadata==8.7.0 ; python_full_version < '3.12'
 importlib-resources==6.5.2 ; python_full_version < '3.10'
 iniconfig==2.1.0
 inquirerpy==0.3.4
@@ -77,20 +78,20 @@ 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==3.10.1 ; python_full_version >= '3.10'
+matplotlib==3.10.3 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2
 mdurl==0.1.2
 mirakuru==2.6.0
 mistune==3.0.2
 more-itertools==10.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.0
-multidict==6.4.3
+multidict==6.4.4
 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'
 nh3==0.2.21
 numpy==2.0.2 ; python_full_version < '3.10'
-numpy==2.2.5 ; python_full_version >= '3.10'
+numpy==2.2.6 ; python_full_version >= '3.10'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2
@@ -101,17 +102,17 @@ pbr==6.1.1
 pfzy==0.3.4
 pillow==11.2.1
 pkce==1.0.3
-platformdirs==4.3.7
-playwright==1.51.0
-pluggy==1.5.0
+platformdirs==4.3.8
+playwright==1.52.0
+pluggy==1.6.0
 port-for==0.7.4
 prettytable==3.16.0
 prompt-toolkit==3.0.51
 propcache==0.3.1
 psutil==7.0.0 ; sys_platform != 'cygwin'
-psycopg==3.2.6
+psycopg==3.2.9
 pycparser==2.22
-pyee==12.1.1
+pyee==13.0.0
 pygithub==2.6.1
 pygments==2.19.1
 pyjwt==2.10.1
@@ -130,7 +131,7 @@ pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.14.0
 pytest-playwright==0.7.0
-pytest-postgresql==7.0.1
+pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.1.0
@@ -149,23 +150,23 @@ rich==13.9.4
 rich-click==1.8.8
 roc-validator==0.4.2 ; python_full_version < '3.9.20'
 roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
-roc-validator==0.6.5 ; python_full_version >= '3.10'
+roc-validator==0.7.0 ; python_full_version >= '3.10'
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
-rpds-py==0.24.0
+rpds-py==0.25.0
 ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
-rucio-clients==36.5.0
+rucio-clients==37.3.0
 s3transfer==0.11.3
 schema-salad==8.9.20250408123006
 scipy==1.13.1 ; python_full_version < '3.10'
-scipy==1.15.2 ; python_full_version >= '3.10'
+scipy==1.15.3 ; python_full_version >= '3.10'
 secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
-selenium==4.31.0
+selenium==4.32.0
 seletools==1.5.0
-setuptools==79.0.1
+setuptools==80.7.1
 six==1.17.0
 sniffio==1.3.1
-snowballstemmer==2.2.0
+snowballstemmer==3.0.1
 sortedcontainers==2.4.0
 sphinx==7.4.7 ; python_full_version < '3.10'
 sphinx==8.1.3 ; python_full_version == '3.10.*'

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.13.0
 pyflakes==3.3.2
-ruff==0.11.7
+ruff==0.11.10

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.8
 adal==1.2.7
-aiobotocore==2.21.1
+aiobotocore==2.22.0
 aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.11.18
@@ -12,7 +12,7 @@ alembic==1.15.2
 amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.9.0
-apispec==6.8.1
+apispec==6.8.2
 appdirs==1.4.4
 arcp==0.2.1
 argcomplete==3.6.2
@@ -30,15 +30,16 @@ bioblend==1.5.0
 bleach==6.2.0
 boltons==25.0.0
 boto==2.49.0
-botocore==1.37.1
+botocore==1.37.3
 bx-python==0.13.0
-cachecontrol==0.14.2
+cachecontrol==0.14.3
 celery==5.5.2
 certifi==2025.4.26
 cffi==1.17.1
-charset-normalizer==3.4.1
+charset-normalizer==3.4.2
 circus==0.19.0
-click==8.1.8
+click==8.1.8 ; python_full_version < '3.10'
+click==8.2.0 ; python_full_version >= '3.10'
 click-didyoumean==0.3.1
 click-plugins==1.1.1
 click-repl==0.3.0
@@ -47,7 +48,7 @@ cloudbridge==3.2.0
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
 conda-package-streaming==0.11.0
-cryptography==44.0.2
+cryptography==45.0.2
 ct3==3.4.0
 cwl-upgrader==1.2.12
 cwl-utils==0.37
@@ -62,7 +63,7 @@ docutils==0.21.2
 dparse==0.6.4
 edam-ontology==1.25.2
 email-validator==2.2.0
-exceptiongroup==1.2.2 ; python_full_version < '3.11'
+exceptiongroup==1.3.0 ; python_full_version < '3.11'
 fastapi-slim==0.115.12
 filelock==3.18.0
 fissix==24.4.24
@@ -71,17 +72,17 @@ fs==2.4.16
 fsspec==2025.3.2
 future==1.0.0
 gravity==1.0.7
-greenlet==3.2.1 ; (python_full_version < '3.14' and platform_machine == 'AMD64') or (python_full_version < '3.14' and platform_machine == 'WIN32') or (python_full_version < '3.14' and platform_machine == 'aarch64') or (python_full_version < '3.14' and platform_machine == 'amd64') or (python_full_version < '3.14' and platform_machine == 'ppc64le') or (python_full_version < '3.14' and platform_machine == 'win32') or (python_full_version < '3.14' and platform_machine == 'x86_64')
+greenlet==3.2.2 ; (python_full_version < '3.14' and platform_machine == 'AMD64') or (python_full_version < '3.14' and platform_machine == 'WIN32') or (python_full_version < '3.14' and platform_machine == 'aarch64') or (python_full_version < '3.14' and platform_machine == 'amd64') or (python_full_version < '3.14' and platform_machine == 'ppc64le') or (python_full_version < '3.14' and platform_machine == 'win32') or (python_full_version < '3.14' and platform_machine == 'x86_64')
 gunicorn==23.0.0
 gxformat2==0.20.0
 h11==0.16.0
-httpcore==1.0.9
-httpx==0.28.1
 h5grove==2.3.0
 h5py==3.13.0
+httpcore==1.0.9
+httpx==0.28.1
 humanfriendly==10.0
 idna==3.10
-importlib-metadata==8.6.1
+importlib-metadata==8.7.0 ; python_full_version < '3.10'
 importlib-resources==6.5.2 ; python_full_version < '3.12'
 isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef
 isal==1.7.2
@@ -95,27 +96,27 @@ kombu==5.5.3
 lagom==2.7.5
 legacy-cgi==2.6.3 ; python_full_version >= '3.13'
 limits==4.2 ; python_full_version < '3.10'
-limits==5.1.0 ; python_full_version >= '3.10'
+limits==5.2.0 ; python_full_version >= '3.10'
 lxml==5.4.0
 mako==1.3.10
 markdown==3.8
 markdown-it-py==3.0.0
 markupsafe==3.0.2
 mdurl==0.1.2
-mercurial==7.0.1
+mercurial==7.0.2
 mistune==3.0.2
 mrcfile==1.5.4
 msal==1.32.3
 msgpack==1.1.0
-multidict==6.4.3
+multidict==6.4.4
 mypy-extensions==1.1.0
 networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version >= '3.10'
 nodeenv==1.9.1
 numpy==2.0.2 ; python_full_version < '3.10'
-numpy==2.2.5 ; python_full_version >= '3.10'
+numpy==2.2.6 ; python_full_version >= '3.10'
 oauthlib==3.2.2
-orjson==3.10.16
+orjson==3.10.18
 oyaml==1.0
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
@@ -131,13 +132,13 @@ prov==1.5.1
 psutil==7.0.0
 pulsar-galaxy-lib==0.15.7
 pycparser==2.22
-pycryptodome==3.22.0
-pydantic==2.11.3
-pydantic-core==2.33.1
+pycryptodome==3.23.0
+pydantic==2.11.4
+pydantic-core==2.33.2
 pydantic-tes==0.2.0
 pydot==2.0.0
 pyeventsystem==0.1.0
-pyfaidx==0.8.1.3
+pyfaidx==0.8.1.4
 pygments==2.19.1
 pyjwt==2.10.1
 pykwalify==1.8.0
@@ -168,17 +169,17 @@ rich==13.9.4
 rich-argparse==1.7.0
 rocrate==0.13.0
 routes==2.5.1
-rpds-py==0.24.0
+rpds-py==0.25.0
 ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
 s3fs==2025.3.2
 schema-salad==8.9.20250408123006
-setuptools==79.0.1
+setuptools==80.7.1
 setuptools-scm==5.0.2
 six==1.17.0
 slowapi==0.1.9
 sniffio==1.3.1
-social-auth-core==4.6.0
+social-auth-core==4.6.1
 sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.40
@@ -191,10 +192,10 @@ svgwrite==1.4.3
 tenacity==9.1.2
 text-unidecode==1.3
 tifffile==2024.8.30 ; python_full_version < '3.10'
-tifffile==2025.3.30 ; python_full_version >= '3.10'
+tifffile==2025.5.10 ; python_full_version >= '3.10'
 tinydb==4.8.2
 tomli==2.2.1 ; python_full_version < '3.11'
-tornado==6.4.2
+tornado==6.5
 tqdm==4.67.1
 tuspy==1.1.0
 tuswsgi==0.5.5
@@ -215,6 +216,6 @@ whoosh==2.7.4
 wrapt==1.17.2
 yacman==0.9.3
 yarl==1.20.0
-zipp==3.21.0
+zipp==3.21.0 ; python_full_version < '3.10'
 zipstream-new==1.1.8
 zstandard==0.23.0

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

@@ -1,36 +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==1.38.3
-botocore-stubs==1.38.3
+boto3-stubs==1.38.18
+botocore-stubs==1.38.18
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
-cryptography==44.0.2
+cryptography==45.0.2
 lxml-stubs==0.5.1
 mypy==1.15.0
 mypy-boto3-s3==1.38.0
 mypy-extensions==1.1.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
-pydantic==2.11.3
-pydantic-core==2.33.1
-setuptools==79.0.1
+pydantic==2.11.4
+pydantic-core==2.33.2
 tomli==2.2.1 ; python_full_version < '3.11'
-types-awscrt==0.26.1
-types-bleach==6.2.0.20241123
+types-awscrt==0.27.2
+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==0.21.0.20241128
-types-html5lib==1.1.11.20241018
+types-docutils==0.21.0.20250516
+types-html5lib==1.1.11.20250516
 types-markdown==3.8.0.20250415
-types-paramiko==3.5.0.20240928
-types-python-dateutil==2.9.0.20241206
+types-paramiko==3.5.0.20250516
+types-python-dateutil==2.9.0.20250516
 types-python-slugify==8.0.2.20240310
-types-pyyaml==6.0.12.20250402
+types-pyyaml==6.0.12.20250516
 types-requests==2.31.0.6 ; python_full_version < '3.10'
-types-requests==2.32.0.20250328 ; python_full_version >= '3.10'
+types-requests==2.32.0.20250515 ; python_full_version >= '3.10'
 types-s3transfer==0.12.0
-types-setuptools==79.0.0.20250422
-types-six==1.17.0.20250403
+types-setuptools==80.7.0.20250516
+types-six==1.17.0.20250515
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
 typing-extensions==4.13.2
 typing-inspection==0.4.0

packages/app/setup.cfg

@@ -72,7 +72,7 @@ install_requires =
     refgenconf>=0.12.0
     regex
     requests
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     sqlitedict
     starlette
     svgwrite

packages/data/setup.cfg

@@ -58,7 +58,7 @@ install_requires =
     pysam>=0.21
     rocrate
     social-auth-core>=4.5.0
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     tifffile
     typing-extensions
 packages = find: