Merge pull request #21005 from galaxybot/dev_auto_update_dependencies (064866f6) · Commits · NDIP / Galaxy

lib/galaxy/dependencies/dev-requirements.txt

+11 −10

Original line number	Diff line number	Diff line
		@@ -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

+1 −1

Original line number	Diff line number	Diff line
		@@ -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

+12 −13

Original line number	Diff line number	Diff line
		@@ -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

+9 −8

Original line number	Diff line number	Diff line
		@@ -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
		@@ -149,7 +150,7 @@ 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
		@@ -157,7 +158,7 @@ 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-typecheck-requirements.txt

+4 −4

Original line number	Diff line number	Diff line
		# 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'