Update Python dependencies

by running `make update-dependencies`.

Author: galaxybot

lib/galaxy/dependencies/dev-requirements.txt

@@ -18,7 +18,7 @@ boto3==1.40.18
 botocore==1.40.18
 build==1.3.0
 cachecontrol==0.14.3
-cachetools==5.5.2
+cachetools==6.2.0
 cattrs==25.2.0
 certifi==2025.8.3
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
@@ -32,7 +32,7 @@ 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==7.10.7
-cryptography==46.0.1
+cryptography==46.0.2
 cwltest==2.6.20250818005349
 cycler==0.12.1
 darker==3.0.0
@@ -45,7 +45,7 @@ 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==4.60.0
+fonttools==4.60.1
 frozenlist==1.7.0
 galaxy-release-util==0.3.1
 greenlet==3.2.4
@@ -62,7 +62,7 @@ importlib-resources==6.5.2 ; python_full_version < '3.10'
 iniconfig==2.1.0
 inquirerpy==0.3.4
 isodate==0.7.2 ; python_full_version < '3.11'
-isort==6.0.1
+isort==6.1.0
 jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-context==6.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-functools==4.3.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
@@ -80,7 +80,7 @@ kiwisolver==1.4.9 ; python_full_version >= '3.10'
 lxml==6.0.2
 markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
-markupsafe==3.0.2
+markupsafe==3.0.3
 matplotlib==3.9.4 ; 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'
@@ -112,7 +112,8 @@ pkce==1.0.3
 platformdirs==4.4.0
 playwright==1.55.0
 pluggy==1.6.0
-port-for==0.7.4
+port-for==0.7.4 ; python_full_version < '3.10'
+port-for==1.0.0 ; python_full_version >= '3.10'
 prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.3.2
@@ -164,7 +165,7 @@ roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
 rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.2.0
+rucio-clients==38.3.0
 s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
@@ -173,7 +174,7 @@ scipy==1.16.2 ; python_full_version >= '3.11'
 secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 secretstorage==3.4.0 ; python_full_version >= '3.10' and 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==4.36.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -200,7 +201,7 @@ tinydb==4.8.2
 toml==0.10.2
 tomli==2.2.1 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.0
-trio==0.30.0
+trio==0.31.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
@@ -209,7 +210,7 @@ types-cachetools==6.2.0.20250827
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.4.20250913 ; python_full_version >= '3.10'
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
-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==0.13.2
+ruff==0.13.3

lib/galaxy/dependencies/pinned-requirements.txt

@@ -20,10 +20,10 @@ async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
 attrs==25.3.0
 babel==2.17.0
-bagit==1.8.1
+bagit==1.9.0
 bagit-profile==1.3.1
 bcrypt==5.0.0
-bdbag==1.7.5
+bdbag==1.8.0
 beaker==1.13.0
 billiard==4.2.2
 bioblend==1.6.0
@@ -33,7 +33,7 @@ boto==2.49.0
 botocore==1.40.18
 bx-python==0.14.0
 cachecontrol==0.14.3
-cachetools==5.5.2
+cachetools==6.2.0
 celery==5.5.3
 certifi==2025.8.3
 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
@@ -49,7 +49,7 @@ cloudbridge==3.2.0
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
-cryptography==46.0.1
+cryptography==46.0.2
 ct3==3.4.0
 cwl-upgrader==1.2.12
 cwl-utils==0.40
@@ -67,15 +67,15 @@ edam-ontology==1.25.2
 email-validator==2.3.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
-fastapi-slim==0.117.1
+fastapi-slim==0.118.0
 filelock==3.19.1
 fissix==24.4.24
 frozenlist==1.7.0
 fs==2.4.16
 fsspec==2025.9.0
 future==1.0.0
-google-api-core==2.25.1
-google-auth==2.40.3
+google-api-core==2.25.2
+google-auth==2.41.1
 google-cloud-batch==0.17.37
 googleapis-common-protos==1.70.0
 gravity==1.1.1
@@ -107,12 +107,12 @@ kombu==5.5.4
 lagom==2.7.7
 legacy-cgi==2.6.3 ; python_full_version >= '3.13'
 limits==4.2 ; python_full_version < '3.10'
-limits==5.5.0 ; python_full_version >= '3.10'
+limits==5.6.0 ; python_full_version >= '3.10'
 lxml==6.0.2
 mako==1.3.10
 markdown==3.9
 markdown-it-py==3.0.0
-markupsafe==3.0.2
+markupsafe==3.0.3
 mdurl==0.1.2
 mercurial==7.1.1
 mistune==3.0.2
@@ -195,7 +195,6 @@ ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_impl
 s3fs==2025.9.0
 schema-salad==8.9.20250723145140
 setuptools==80.9.0
-setuptools-scm==9.2.0
 six==1.17.0
 slowapi==0.1.9
 sniffio==1.3.1
@@ -212,15 +211,15 @@ 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==2025.9.20 ; python_full_version >= '3.11'
+tifffile==2025.9.30 ; 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-inspection==0.4.1
+typing-extensions==4.15.0
+typing-inspection==0.4.2
 tzdata==2025.2
 tzlocal==5.3.1
 ubiquerg==0.8.1

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

@@ -12,7 +12,7 @@ backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 boto3==1.40.18
 botocore==1.40.18
 cachecontrol==0.14.3
-cachetools==5.5.2
+cachetools==6.2.0
 cattrs==25.2.0
 certifi==2025.8.3
 cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt'
@@ -34,7 +34,7 @@ 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==4.60.0
+fonttools==4.60.1
 frozenlist==1.7.0
 greenlet==3.2.4
 h11==0.16.0
@@ -59,7 +59,7 @@ kiwisolver==1.4.7 ; python_full_version < '3.10'
 kiwisolver==1.4.9 ; python_full_version >= '3.10'
 lxml==6.0.2
 markdown-it-py==3.0.0
-markupsafe==3.0.2
+markupsafe==3.0.3
 matplotlib==3.9.4 ; python_full_version < '3.10'
 matplotlib==3.10.6 ; python_full_version >= '3.10'
 mdurl==0.1.2
@@ -85,7 +85,8 @@ pkce==1.0.3
 platformdirs==4.4.0
 playwright==1.55.0
 pluggy==1.6.0
-port-for==0.7.4
+port-for==0.7.4 ; python_full_version < '3.10'
+port-for==1.0.0 ; python_full_version >= '3.10'
 prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.3.2
@@ -127,14 +128,14 @@ roc-validator==0.7.3 ; python_full_version >= '3.10'
 rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.2.0
+rucio-clients==38.3.0
 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==1.16.2 ; python_full_version >= '3.11'
 selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.35.0 ; python_full_version >= '3.10'
+selenium==4.36.0 ; python_full_version >= '3.10'
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -149,15 +150,15 @@ tinydb==4.8.2
 toml==0.10.2
 tomli==2.2.1 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.0
-trio==0.30.0
+trio==0.31.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
 types-cachetools==6.2.0.20250827
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.4.20250913 ; python_full_version >= '3.10'
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
-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

@@ -1,10 +1,10 @@
 # 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==1.40.40
+boto3-stubs==1.40.45
 botocore-stubs==1.40.33
 cffi==2.0.0 ; platform_python_implementation != 'PyPy'
-cryptography==46.0.1
+cryptography==46.0.2
 lxml-stubs==0.5.1
 mypy==1.18.2
 mypy-boto3-s3==1.40.26
@@ -32,6 +32,6 @@ types-s3transfer==0.13.1
 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-inspection==0.4.1
+typing-extensions==4.15.0
+typing-inspection==0.4.2
 urllib3==2.5.0 ; python_full_version >= '3.10'