Merge pull request #20905 from galaxybot/dev_auto_update_dependencies (286fd6e6) · Commits · NDIP / Galaxy

lib/galaxy/dependencies/dev-requirements.txt

+17 −15

Original line number	Diff line number	Diff line
		@@ -19,7 +19,7 @@ build==1.3.0
		cachecontrol==0.14.3
		cattrs==25.2.0
		certifi==2025.8.3
		cffi==1.17.1
		cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
		charset-normalizer==3.4.3
		click==8.1.8 ; python_full_version < '3.10'
		click==8.2.1 ; python_full_version >= '3.10'
		@@ -38,7 +38,7 @@ darkgraylib==2.4.0
		decorator==5.2.1
		defusedxml==0.7.1
		docutils==0.21.2
		dogpile-cache==1.4.0
		dogpile-cache==1.4.1
		enum-tools==0.12.0 ; python_full_version >= '3.10'
		exceptiongroup==1.3.0 ; python_full_version < '3.11'
		filelock==3.19.1
		@@ -70,12 +70,12 @@ jmespath==1.0.1
		jsonpatch==1.33
		jsonpointer==3.0.0
		jsonschema==4.25.1
		jsonschema-specifications==2025.4.1
		jsonschema-specifications==2025.9.1
		junit-xml==1.9
		keyring==25.6.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
		kiwisolver==1.4.7 ; python_full_version < '3.10'
		kiwisolver==1.4.9 ; python_full_version >= '3.10'
		lxml==5.4.0
		lxml==6.0.1
		markdown-it-py==3.0.0
		markdown-it-reporter==0.0.2
		markupsafe==3.0.2
		@@ -95,7 +95,7 @@ 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==2.3.2 ; python_full_version >= '3.11'
		numpy==2.3.3 ; python_full_version >= '3.11'
		onedatafilerestclient==21.2.5.2
		outcome==1.3.0.post0
		owlrl==6.0.2 ; python_full_version < '3.10'
		@@ -114,13 +114,13 @@ prettytable==3.16.0
		prompt-toolkit==3.0.52
		propcache==0.3.2
		psutil==7.0.0 ; sys_platform != 'cygwin'
		psycopg==3.2.9
		pycparser==2.22
		psycopg==3.2.10
		pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
		pyee==13.0.0
		pygithub==2.8.1
		pygments==2.19.2
		pyjwt==2.10.1
		pynacl==1.5.0
		pynacl==1.6.0
		pyparsing==3.2.3
		pyproject-hooks==1.2.0
		pyshacl==0.26.0 ; python_full_version < '3.10'
		@@ -129,13 +129,13 @@ pysocks==1.7.1
		pytest==7.4.4
		pytest-asyncio==0.23.8
		pytest-base-url==2.1.0
		pytest-cov==6.2.1
		pytest-cov==7.0.0
		pytest-html==4.1.1
		pytest-httpserver==1.1.3
		pytest-json-report==1.5.0
		pytest-metadata==3.1.1
		pytest-mock==3.15.0
		pytest-playwright==0.7.0
		pytest-playwright==0.7.1
		pytest-postgresql==7.0.2
		pytest-shard==0.1.2
		python-dateutil==2.9.0.post0
		@@ -165,9 +165,11 @@ 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
		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'
		seletools==1.5.0
		six==1.17.0
		sniffio==1.3.1
		@@ -196,9 +198,9 @@ tomli==2.2.1 ; python_full_version <= '3.11'
		trio==0.30.0
		trio-websocket==0.12.2
		tuspy==1.1.0
		twill==3.3
		twill==3.3.1
		twine==6.2.0
		typing-extensions==4.15.0
		typing-extensions==4.14.1
		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==0.12.12
		ruff==0.13.0

lib/galaxy/dependencies/pinned-requirements.txt

+17 −16

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ alembic==1.16.5
		amqp==5.3.1
		annotated-types==0.7.0
		anyio==4.10.0
		apispec==6.8.2
		apispec==6.8.3
		appdirs==1.4.4
		arcp==0.2.1
		argcomplete==3.6.2
		@@ -36,7 +36,7 @@ cachecontrol==0.14.3
		cachetools==5.5.2
		celery==5.5.3
		certifi==2025.8.3
		cffi==1.17.1
		cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
		charset-normalizer==3.4.3
		circus==0.19.0
		click==8.1.8 ; python_full_version < '3.10'
		@@ -52,13 +52,14 @@ conda-package-streaming==0.12.0
		cryptography==45.0.7
		ct3==3.4.0
		cwl-upgrader==1.2.12
		cwl-utils==0.39
		cwl-utils==0.40
		cwltool==3.1.20250715140722
		defusedxml==0.7.1
		deprecated==1.2.18
		deprecation==2.1.0
		dictobj==0.4
		dnspython==2.7.0
		dnspython==2.7.0 ; python_full_version < '3.10'
		dnspython==2.8.0 ; python_full_version >= '3.10'
		docopt==0.6.2
		docutils==0.21.2
		dparse==0.6.4
		@@ -94,25 +95,25 @@ importlib-metadata==8.7.0 ; python_full_version < '3.10'
		importlib-resources==6.5.2 ; python_full_version < '3.12'
		invoke==2.2.0
		isa-rwval==0.10.11
		isal==1.7.2
		isal==1.8.0
		isodate==0.7.2 ; python_full_version < '3.11'
		jinja2==3.1.6
		jmespath==1.0.1
		jsonref==1.1.0
		jsonschema==4.25.1
		jsonschema-specifications==2025.4.1
		jsonschema-specifications==2025.9.1
		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'
		lxml==5.4.0
		lxml==6.0.1
		mako==1.3.10
		markdown==3.9
		markdown-it-py==3.0.0
		markupsafe==3.0.2
		mdurl==0.1.2
		mercurial==7.1
		mercurial==7.1.1
		mistune==3.0.2
		mrcfile==1.5.4
		msal==1.33.0
		@@ -125,7 +126,7 @@ 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==2.3.2 ; python_full_version >= '3.11'
		numpy==2.3.3 ; python_full_version >= '3.11'
		oauthlib==3.3.1
		openpyxl==3.1.5
		orjson==3.11.3
		@@ -141,15 +142,15 @@ pillow==11.3.0
		prompt-toolkit==3.0.52
		propcache==0.3.2
		proto-plus==1.26.1
		protobuf==6.32.0
		protobuf==6.32.1
		prov==1.5.1
		psutil==7.0.0
		pulsar-galaxy-lib==0.15.10
		pyasn1==0.6.1
		pyasn1-modules==0.4.2
		pycparser==2.22
		pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
		pycryptodome==3.23.0
		pydantic==2.11.7
		pydantic==2.11.8
		pydantic-core==2.33.2
		pydantic-tes==0.2.0
		pydot==4.0.1
		@@ -159,7 +160,7 @@ pygments==2.19.2
		pyjwt==2.10.1
		pykwalify==1.8.0
		pylibmagic==0.5.0
		pynacl==1.5.0
		pynacl==1.6.0
		pyparsing==3.2.3
		pypng==0.20220715.0
		pyreadline3==3.5.4 ; sys_platform == 'win32'
		@@ -171,7 +172,7 @@ python-slugify==8.0.4
		python3-openid==3.2.0
		pytz==2025.2
		pyyaml==6.0.2
		pyzmq==27.0.2
		pyzmq==27.1.0
		rdflib==7.1.4
		referencing==0.36.2
		refgenconf==0.12.2
		@@ -209,14 +210,14 @@ 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==2025.8.28 ; python_full_version >= '3.11'
		tifffile==2025.9.9 ; 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==4.15.0
		typing-extensions==4.14.1
		typing-inspection==0.4.1
		tzdata==2025.2
		tzlocal==5.3.1

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

+14 −13

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ botocore==1.40.18
		cachecontrol==0.14.3
		cattrs==25.2.0
		certifi==2025.8.3
		cffi==1.17.1 ; implementation_name != 'pypy' and os_name == 'nt'
		cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt'
		charset-normalizer==3.4.3
		click==8.1.8 ; python_full_version < '3.10'
		click==8.2.1 ; python_full_version >= '3.10'
		@@ -27,7 +27,7 @@ cwltest==2.6.20250818005349
		cycler==0.12.1
		decorator==5.2.1
		defusedxml==0.7.1
		dogpile-cache==1.4.0
		dogpile-cache==1.4.1
		enum-tools==0.12.0 ; python_full_version >= '3.10'
		exceptiongroup==1.3.0 ; python_full_version < '3.11'
		filelock==3.19.1
		@@ -51,11 +51,11 @@ jmespath==1.0.1
		jsonpatch==1.33
		jsonpointer==3.0.0
		jsonschema==4.25.1
		jsonschema-specifications==2025.4.1
		jsonschema-specifications==2025.9.1
		junit-xml==1.9
		kiwisolver==1.4.7 ; python_full_version < '3.10'
		kiwisolver==1.4.9 ; python_full_version >= '3.10'
		lxml==5.4.0
		lxml==6.0.1
		markdown-it-py==3.0.0
		markupsafe==3.0.2
		matplotlib==3.9.4 ; python_full_version < '3.10'
		@@ -68,7 +68,7 @@ multidict==6.6.4
		mypy-extensions==1.1.0
		numpy==2.0.2 ; python_full_version < '3.10'
		numpy==2.2.6 ; python_full_version == '3.10.*'
		numpy==2.3.2 ; python_full_version >= '3.11'
		numpy==2.3.3 ; python_full_version >= '3.11'
		onedatafilerestclient==21.2.5.2
		outcome==1.3.0.post0
		owlrl==6.0.2 ; python_full_version < '3.10'
		@@ -86,8 +86,8 @@ prettytable==3.16.0
		prompt-toolkit==3.0.52
		propcache==0.3.2
		psutil==7.0.0 ; sys_platform != 'cygwin'
		psycopg==3.2.9
		pycparser==2.22 ; implementation_name != 'pypy' and os_name == 'nt'
		psycopg==3.2.10
		pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt'
		pyee==13.0.0
		pygments==2.19.2
		pyparsing==3.2.3
		@@ -97,13 +97,13 @@ pysocks==1.7.1
		pytest==7.4.4
		pytest-asyncio==0.23.8
		pytest-base-url==2.1.0
		pytest-cov==6.2.1
		pytest-cov==7.0.0
		pytest-html==4.1.1
		pytest-httpserver==1.1.3
		pytest-json-report==1.5.0
		pytest-metadata==3.1.1
		pytest-mock==3.15.0
		pytest-playwright==0.7.0
		pytest-playwright==0.7.1
		pytest-postgresql==7.0.2
		pytest-shard==0.1.2
		python-dateutil==2.9.0.post0
		@@ -128,8 +128,9 @@ 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
		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'
		seletools==1.5.0
		six==1.17.0
		sniffio==1.3.1
		@@ -146,8 +147,8 @@ tomli==2.2.1 ; python_full_version <= '3.11'
		trio==0.30.0
		trio-websocket==0.12.2
		tuspy==1.1.0
		twill==3.3
		typing-extensions==4.15.0
		twill==3.3.1
		typing-extensions==4.14.1
		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

+9 −9

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==1.40.25
		botocore-stubs==1.40.25
		cffi==1.17.1 ; platform_python_implementation != 'PyPy'
		boto3-stubs==1.40.30
		botocore-stubs==1.40.30
		cffi==2.0.0 ; platform_python_implementation != 'PyPy'
		cryptography==45.0.7
		lxml-stubs==0.5.1
		mypy==1.17.1
		mypy-boto3-s3==1.40.0
		mypy==1.18.1
		mypy-boto3-s3==1.40.26
		mypy-extensions==1.1.0
		pathspec==0.12.1
		pycparser==2.22 ; platform_python_implementation != 'PyPy'
		pydantic==2.11.7
		pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
		pydantic==2.11.8
		pydantic-core==2.33.2
		tomli==2.2.1 ; python_full_version < '3.11'
		types-awscrt==0.27.6
		@@ -27,11 +27,11 @@ 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-requests==2.32.4.20250913 ; python_full_version >= '3.10'
		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==4.15.0
		typing-extensions==4.14.1
		typing-inspection==0.4.1
		urllib3==2.5.0 ; python_full_version >= '3.10'