Update Python dependencies

by running `make update-dependencies`.

Author: galaxybot

lib/galaxy/dependencies/dev-requirements.txt

@@ -29,7 +29,7 @@ colorlog==6.9.0
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.4
+coverage==7.10.6
 cryptography==45.0.6
 cwltest==2.6.20250818005349
 cycler==0.12.1
@@ -38,12 +38,12 @@ darkgraylib==1.2.1
 decorator==5.2.1
 defusedxml==0.7.1
 docutils==0.21.2
-dogpile-cache==1.2.2
+dogpile-cache==1.4.0
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.19.1
 fluent-logger==0.11.1
-fonttools==4.59.1
+fonttools==4.59.2
 frozenlist==1.7.0
 galaxy-release-util==0.3.1
 graylint==1.1.1
@@ -68,6 +68,8 @@ jaraco-functools==4.3.0 ; platform_machine != 'ppc64le' and platform_machine !=
 jeepney==0.9.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 jinja2==3.1.6
 jmespath==1.0.1
+jsonpatch==1.33
+jsonpointer==3.0.0
 jsonschema==4.25.1
 jsonschema-specifications==2025.4.1
 junit-xml==1.9
@@ -79,7 +81,7 @@ 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==3.10.5 ; python_full_version >= '3.10'
+matplotlib==3.10.6 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2 ; python_full_version < '3.10'
 mdit-py-plugins==0.5.0 ; python_full_version >= '3.10'
 mdurl==0.1.2
@@ -102,16 +104,15 @@ 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
-pbr==7.0.1
 pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
-platformdirs==4.3.8
-playwright==1.54.0
+platformdirs==4.4.0
+playwright==1.55.0
 pluggy==1.6.0
 port-for==0.7.4
 prettytable==3.16.0
-prompt-toolkit==3.0.51
+prompt-toolkit==3.0.52
 propcache==0.3.2
 psutil==7.0.0 ; sys_platform != 'cygwin'
 psycopg==3.2.9
@@ -139,7 +140,7 @@ pytest-playwright==0.7.0
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
-python-irodsclient==3.1.1
+python-irodsclient==3.2.0
 python-slugify==8.0.4
 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.2
@@ -157,20 +158,18 @@ 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==0.7.3 ; python_full_version >= '3.10'
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
-rpds-py==0.27.0
+rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==37.7.1
+rucio-clients==38.0.0
 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==1.16.1 ; 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==4.35.0 ; python_full_version >= '3.10'
+selenium==4.32.0
 seletools==1.5.0
-setuptools==80.9.0
 six==1.17.0
 sniffio==1.3.1
 snowballstemmer==3.0.1
@@ -187,7 +186,7 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 statsd==4.0.1
-stevedore==5.4.1
+stevedore==5.5.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
 testfixtures==9.1.0 ; python_full_version >= '3.11'
@@ -200,7 +199,7 @@ trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3
 twine==6.1.0
-typing-extensions==4.14.1
+typing-extensions==4.15.0
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==1.26.20 ; 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==2.14.0
 pyflakes==3.4.0
-ruff==0.12.10
+ruff==0.12.11

lib/galaxy/dependencies/pinned-requirements.txt

@@ -8,7 +8,7 @@ aiohappyeyeballs==2.6.1
 aiohttp==3.12.15
 aioitertools==0.12.0
 aiosignal==1.4.0
-alembic==1.16.4
+alembic==1.16.5
 amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.10.0
@@ -62,7 +62,7 @@ docopt==0.6.2
 docutils==0.21.2
 dparse==0.6.4
 edam-ontology==1.25.2
-email-validator==2.2.0
+email-validator==2.3.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 fastapi-slim==0.116.1
@@ -121,7 +121,7 @@ numpy==2.2.6 ; python_full_version == '3.10.*'
 numpy==2.3.2 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 openpyxl==3.1.5
-orjson==3.11.2
+orjson==3.11.3
 oyaml==1.0
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
@@ -131,7 +131,7 @@ paste==3.10.1
 pastedeploy==3.1.0
 pebble==5.1.3
 pillow==11.3.0
-prompt-toolkit==3.0.51
+prompt-toolkit==3.0.52
 propcache==0.3.2
 prov==1.5.1
 psutil==7.0.0
@@ -164,7 +164,7 @@ pyzmq==27.0.2
 rdflib==7.1.4
 referencing==0.36.2
 refgenconf==0.12.2
-regex==2025.7.34
+regex==2025.8.29
 repoze-lru==0.7
 requests==2.32.5
 requests-oauthlib==2.0.0
@@ -174,7 +174,7 @@ rich==13.9.4
 rich-argparse==1.7.1
 rocrate==0.14.0
 routes==2.5.1
-rpds-py==0.27.0
+rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 s3fs==2025.7.0
@@ -189,22 +189,22 @@ sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.43
 sqlparse==0.5.3
-starlette==0.47.2
+starlette==0.47.3
 starlette-context==0.4.0
-supervisor==4.2.5
+supervisor==4.3.0
 svgwrite==1.4.3
 tenacity==9.1.2
 text-unidecode==1.3
 tifffile==2024.8.30 ; python_full_version < '3.10'
 tifffile==2025.5.10 ; python_full_version == '3.10.*'
-tifffile==2025.6.11 ; python_full_version >= '3.11'
+tifffile==2025.8.28 ; python_full_version >= '3.11'
 tinydb==4.8.2
 tomli==2.2.1 ; python_full_version < '3.11'
 tornado==6.5.2
 tqdm==4.67.1
 tuspy==1.1.0
 tuswsgi==0.5.5
-typing-extensions==4.14.1
+typing-extensions==4.15.0
 typing-inspection==0.4.1
 tzdata==2025.2
 tzlocal==5.3.1

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

@@ -22,17 +22,17 @@ colorlog==6.9.0
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.4
+coverage==7.10.6
 cwltest==2.6.20250818005349
 cycler==0.12.1
 decorator==5.2.1
 defusedxml==0.7.1
-dogpile-cache==1.2.2
+dogpile-cache==1.4.0
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.19.1
 fluent-logger==0.11.1
-fonttools==4.59.1
+fonttools==4.59.2
 frozenlist==1.7.0
 greenlet==3.2.4
 h11==0.16.0
@@ -48,6 +48,8 @@ inquirerpy==0.3.4
 isodate==0.7.2 ; python_full_version < '3.11'
 jinja2==3.1.6
 jmespath==1.0.1
+jsonpatch==1.33
+jsonpointer==3.0.0
 jsonschema==4.25.1
 jsonschema-specifications==2025.4.1
 junit-xml==1.9
@@ -57,7 +59,7 @@ lxml==5.4.0
 markdown-it-py==3.0.0
 markupsafe==3.0.2
 matplotlib==3.9.4 ; python_full_version < '3.10'
-matplotlib==3.10.5 ; python_full_version >= '3.10'
+matplotlib==3.10.6 ; python_full_version >= '3.10'
 mdurl==0.1.2
 mirakuru==2.6.1
 mistune==3.0.2
@@ -73,16 +75,15 @@ owlrl==6.0.2 ; 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==7.0.1
 pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
-platformdirs==4.3.8
-playwright==1.54.0
+platformdirs==4.4.0
+playwright==1.55.0
 pluggy==1.6.0
 port-for==0.7.4
 prettytable==3.16.0
-prompt-toolkit==3.0.51
+prompt-toolkit==3.0.52
 propcache==0.3.2
 psutil==7.0.0 ; sys_platform != 'cygwin'
 psycopg==3.2.9
@@ -106,7 +107,7 @@ pytest-playwright==0.7.0
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
-python-irodsclient==3.1.1
+python-irodsclient==3.2.0
 python-slugify==8.0.4
 pyyaml==6.0.2
 rdflib==7.1.4
@@ -119,24 +120,22 @@ rich-click==1.8.9
 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==0.7.3 ; python_full_version >= '3.10'
-rpds-py==0.27.0
+rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==37.7.1
+rucio-clients==38.0.0
 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==1.16.1 ; python_full_version >= '3.11'
-selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.35.0 ; python_full_version >= '3.10'
+selenium==4.32.0
 seletools==1.5.0
-setuptools==80.9.0
 six==1.17.0
 sniffio==1.3.1
 sortedcontainers==2.4.0
 statsd==4.0.1
-stevedore==5.4.1
+stevedore==5.5.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
 testfixtures==9.1.0 ; python_full_version >= '3.11'
@@ -148,7 +147,7 @@ trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3
-typing-extensions==4.14.1
+typing-extensions==4.15.0
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==1.26.20 ; python_full_version < '3.10'

lib/galaxy/dependencies/pinned-typecheck-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=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.40.16
+boto3-stubs==1.40.21
 botocore-stubs==1.38.46
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==45.0.6
@@ -32,6 +32,6 @@ types-s3transfer==0.13.0
 types-setuptools==80.9.0.20250822
 types-six==1.17.0.20250515
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
-typing-extensions==4.14.1
+typing-extensions==4.15.0
 typing-inspection==0.4.1
 urllib3==2.5.0 ; python_full_version >= '3.10'