Update Python dependencies

by running `make update-dependencies`.

Author: galaxybot

lib/galaxy/dependencies/dev-requirements.txt

@@ -13,8 +13,8 @@ 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==1.38.46
-botocore==1.38.46
+boto3==1.39.8
+botocore==1.39.8
 build==1.2.2.post1
 cachecontrol==0.14.3
 cattrs==25.1.1
@@ -28,7 +28,7 @@ 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==7.9.2
+coverage==7.10.0
 cryptography==45.0.5
 cwltest==2.6.20250314152537
 cycler==0.12.1
@@ -93,7 +93,7 @@ myst-parser==4.0.1 ; python_full_version >= '3.10'
 nh3==0.3.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.1 ; python_full_version >= '3.11'
+numpy==2.3.2 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
@@ -106,7 +106,7 @@ pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
 platformdirs==4.3.8
-playwright==1.53.0
+playwright==1.54.0
 pluggy==1.6.0
 port-for==0.7.4
 prettytable==3.16.0
@@ -159,9 +159,9 @@ roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
 rpds-py==0.26.0
 ruamel-yaml==0.18.14
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==37.7.0
+rucio-clients==37.7.1
 s3transfer==0.13.1
-schema-salad==8.9.20250408123006
+schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
 scipy==1.16.0 ; python_full_version >= '3.11'

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==0.12.4
+ruff==0.12.5

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.10
 adal==1.2.7
-aiobotocore==2.23.1
+aiobotocore==2.23.2
 aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.12.14
@@ -30,7 +30,7 @@ bioblend==1.6.0
 bleach==6.2.0
 boltons==25.0.0
 boto==2.49.0
-botocore==1.38.46
+botocore==1.39.8
 bx-python==0.13.0
 cachecontrol==0.14.3
 celery==5.5.3
@@ -51,8 +51,8 @@ conda-package-streaming==0.12.0
 cryptography==45.0.5
 ct3==3.4.0
 cwl-upgrader==1.2.12
-cwl-utils==0.38
-cwltool==3.1.20250110105449
+cwl-utils==0.39
+cwltool==3.1.20250715140722
 defusedxml==0.7.1
 deprecated==1.2.18
 deprecation==2.1.0
@@ -107,7 +107,7 @@ mdurl==0.1.2
 mercurial==7.0.3
 mistune==3.0.2
 mrcfile==1.5.4
-msal==1.32.3
+msal==1.33.0
 msgpack==1.1.1
 multidict==6.6.3
 mypy-extensions==1.1.0
@@ -117,18 +117,18 @@ networkx==3.5 ; python_full_version >= '3.11'
 nodeenv==1.9.1
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.1 ; python_full_version >= '3.11'
+numpy==2.3.2 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 openpyxl==3.1.5
-orjson==3.11.0
+orjson==3.11.1
 oyaml==1.0
 packaging==24.2 ; python_full_version < '3.10'
 packaging==25.0 ; python_full_version >= '3.10'
 paramiko==3.5.1
 parsley==1.3
 paste==3.10.1
 pastedeploy==3.1.0
-pebble==5.1.1
+pebble==5.1.2
 pillow==11.3.0
 prompt-toolkit==3.0.51
 propcache==0.3.2
@@ -140,7 +140,7 @@ pycryptodome==3.23.0
 pydantic==2.11.7
 pydantic-core==2.33.2
 pydantic-tes==0.2.0
-pydot==2.0.0
+pydot==4.0.1
 pyeventsystem==0.1.0
 pyfaidx==0.8.1.4
 pygments==2.19.2
@@ -177,7 +177,7 @@ rpds-py==0.26.0
 ruamel-yaml==0.18.14
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 s3fs==2025.7.0
-schema-salad==8.9.20250408123006
+schema-salad==8.9.20250723145140
 setuptools==80.9.0
 setuptools-scm==8.3.1
 six==1.17.0
@@ -189,7 +189,7 @@ spython==0.3.14
 sqlalchemy==2.0.40
 sqlitedict==2.1.0
 sqlparse==0.5.3
-starlette==0.47.1
+starlette==0.47.2
 starlette-context==0.4.0
 supervisor==4.2.5
 svgwrite==1.4.3

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

@@ -8,8 +8,8 @@ ase==3.25.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.3.0
 axe-selenium-python==2.1.6
-boto3==1.38.46
-botocore==1.38.46
+boto3==1.39.8
+botocore==1.39.8
 cachecontrol==0.14.3
 cattrs==25.1.1
 certifi==2025.7.14
@@ -21,7 +21,7 @@ colorama==0.4.6 ; 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==7.9.2
+coverage==7.10.0
 cwltest==2.6.20250314152537
 cycler==0.12.1
 decorator==5.2.1
@@ -65,7 +65,7 @@ multidict==6.6.3
 mypy-extensions==1.1.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
-numpy==2.3.1 ; python_full_version >= '3.11'
+numpy==2.3.2 ; python_full_version >= '3.11'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==6.0.2 ; python_full_version < '3.10'
@@ -77,7 +77,7 @@ pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
 platformdirs==4.3.8
-playwright==1.53.0
+playwright==1.54.0
 pluggy==1.6.0
 port-for==0.7.4
 prettytable==3.16.0
@@ -121,9 +121,9 @@ roc-validator==0.7.3 ; python_full_version >= '3.10'
 rpds-py==0.26.0
 ruamel-yaml==0.18.14
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==37.7.0
+rucio-clients==37.7.1
 s3transfer==0.13.1
-schema-salad==8.9.20250408123006
+schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
 scipy==1.16.0 ; python_full_version >= '3.11'

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==1.39.9
+boto3-stubs==1.39.14
 botocore-stubs==1.38.46
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==45.0.5
@@ -19,7 +19,7 @@ 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==0.21.0.20250715
+types-docutils==0.21.0.20250722
 types-html5lib==1.1.11.20250708
 types-markdown==3.8.0.20250708
 types-paramiko==3.5.0.20250708