Merge pull request #20869 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -13,11 +13,11 @@ 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==1.39.11
-botocore==1.39.11
+boto3==1.40.18
+botocore==1.40.18
 build==1.3.0
 cachecontrol==0.14.3
-cattrs==25.1.1
+cattrs==25.2.0
 certifi==2025.8.3
 cffi==1.17.1
 charset-normalizer==3.4.3
@@ -30,11 +30,11 @@ 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==7.10.6
-cryptography==45.0.6
+cryptography==45.0.7
 cwltest==2.6.20250818005349
 cycler==0.12.1
-darker==2.1.1
-darkgraylib==1.2.1
+darker==3.0.0
+darkgraylib==2.4.0
 decorator==5.2.1
 defusedxml==0.7.1
 docutils==0.21.2
@@ -46,7 +46,6 @@ fluent-logger==0.11.1
 fonttools==4.59.2
 frozenlist==1.7.0
 galaxy-release-util==0.3.1
-graylint==1.1.1
 greenlet==3.2.4
 h11==0.16.0
 html5lib==1.1 ; python_full_version < '3.10'
@@ -87,7 +86,7 @@ mdit-py-plugins==0.5.0 ; python_full_version >= '3.10'
 mdurl==0.1.2
 mirakuru==2.6.1
 mistune==3.0.2
-more-itertools==10.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
+more-itertools==10.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.1
 multidict==6.6.4
 mypy-extensions==1.1.0
@@ -118,7 +117,7 @@ psutil==7.0.0 ; sys_platform != 'cygwin'
 psycopg==3.2.9
 pycparser==2.22
 pyee==13.0.0
-pygithub==2.7.0
+pygithub==2.8.1
 pygments==2.19.2
 pyjwt==2.10.1
 pynacl==1.5.0
@@ -135,7 +134,7 @@ pytest-html==4.1.1
 pytest-httpserver==1.1.3
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
-pytest-mock==3.14.1
+pytest-mock==3.15.0
 pytest-playwright==0.7.0
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
@@ -161,7 +160,7 @@ roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
 rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.0.0
+rucio-clients==38.1.0
 s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
@@ -198,7 +197,7 @@ trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3
-twine==6.1.0
+twine==6.2.0
 typing-extensions==4.15.0
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1

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==0.12.11
+ruff==0.12.12

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==2.24.1
+aiobotocore==2.24.2
 aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.12.15
@@ -30,9 +30,10 @@ bioblend==1.6.0
 bleach==6.2.0
 boltons==25.0.0
 boto==2.49.0
-botocore==1.39.11
+botocore==1.40.18
 bx-python==0.14.0
 cachecontrol==0.14.3
+cachetools==5.5.2
 celery==5.5.3
 certifi==2025.8.3
 cffi==1.17.1
@@ -48,7 +49,7 @@ cloudbridge==3.2.0
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
-cryptography==45.0.6
+cryptography==45.0.7
 ct3==3.4.0
 cwl-upgrader==1.2.12
 cwl-utils==0.39
@@ -70,10 +71,16 @@ filelock==3.19.1
 fissix==24.4.24
 frozenlist==1.7.0
 fs==2.4.16
-fsspec==2025.7.0
+fsspec==2025.9.0
 future==1.0.0
+google-api-core==2.25.1
+google-auth==2.40.3
+google-cloud-batch==0.17.36
+googleapis-common-protos==1.70.0
 gravity==1.1.1
 greenlet==3.2.4 ; (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')
+grpcio==1.74.0
+grpcio-status==1.74.0
 gunicorn==23.0.0
 gxformat2==0.20.0
 h11==0.16.0
@@ -101,7 +108,7 @@ limits==4.2 ; python_full_version < '3.10'
 limits==5.5.0 ; python_full_version >= '3.10'
 lxml==5.4.0
 mako==1.3.10
-markdown==3.8.2
+markdown==3.9
 markdown-it-py==3.0.0
 markupsafe==3.0.2
 mdurl==0.1.2
@@ -133,9 +140,13 @@ pebble==5.1.3
 pillow==11.3.0
 prompt-toolkit==3.0.52
 propcache==0.3.2
+proto-plus==1.26.1
+protobuf==6.32.0
 prov==1.5.1
 psutil==7.0.0
-pulsar-galaxy-lib==0.15.9
+pulsar-galaxy-lib==0.15.10
+pyasn1==0.6.1
+pyasn1-modules==0.4.2
 pycparser==2.22
 pycryptodome==3.23.0
 pydantic==2.11.7
@@ -143,7 +154,7 @@ pydantic-core==2.33.2
 pydantic-tes==0.2.0
 pydot==4.0.1
 pyeventsystem==0.1.0
-pyfaidx==0.9.0.1
+pyfaidx==0.9.0.3
 pygments==2.19.2
 pyjwt==2.10.1
 pykwalify==1.8.0
@@ -164,7 +175,7 @@ pyzmq==27.0.2
 rdflib==7.1.4
 referencing==0.36.2
 refgenconf==0.12.2
-regex==2025.8.29
+regex==2025.9.1
 repoze-lru==0.7
 requests==2.32.5
 requests-oauthlib==2.0.0
@@ -175,9 +186,10 @@ rich-argparse==1.7.1
 rocrate==0.14.0
 routes==2.5.1
 rpds-py==0.27.1
+rsa==4.9.1
 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
+s3fs==2025.9.0
 schema-salad==8.9.20250723145140
 setuptools==80.9.0
 setuptools-scm==9.2.0

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

@@ -8,10 +8,10 @@ ase==3.26.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.3.0
 axe-selenium-python==2.1.6
-boto3==1.39.11
-botocore==1.39.11
+boto3==1.40.18
+botocore==1.40.18
 cachecontrol==0.14.3
-cattrs==25.1.1
+cattrs==25.2.0
 certifi==2025.8.3
 cffi==1.17.1 ; implementation_name != 'pypy' and os_name == 'nt'
 charset-normalizer==3.4.3
@@ -102,7 +102,7 @@ pytest-html==4.1.1
 pytest-httpserver==1.1.3
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
-pytest-mock==3.14.1
+pytest-mock==3.15.0
 pytest-playwright==0.7.0
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
@@ -123,7 +123,7 @@ roc-validator==0.7.3 ; python_full_version >= '3.10'
 rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.0.0
+rucio-clients==38.1.0
 s3transfer==0.13.1
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; 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==1.40.21
-botocore-stubs==1.38.46
+boto3-stubs==1.40.25
+botocore-stubs==1.40.25
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
-cryptography==45.0.6
+cryptography==45.0.7
 lxml-stubs==0.5.1
 mypy==1.17.1
 mypy-boto3-s3==1.40.0
@@ -21,14 +21,14 @@ types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
 types-docutils==0.22.0.20250822
 types-html5lib==1.1.11.20250809
-types-markdown==3.8.0.20250809
+types-markdown==3.9.0.20250906
 types-paramiko==4.0.0.20250822
 types-python-dateutil==2.9.0.20250822
 types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20250822
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.4.20250809 ; python_full_version >= '3.10'
-types-s3transfer==0.13.0
+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'