diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 1d5dd3f2073c..43199986755e 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -12,7 +12,7 @@ babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12" billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" black==23.3.0 ; python_version >= "3.7" and python_version < "3.12" bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12" -build==0.10.0 ; python_version >= "3.7" and python_version < "3.12" +build==1.0.3 ; python_version >= "3.7" and python_version < "3.12" cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12" cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" @@ -22,18 +22,18 @@ charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -click==8.1.6 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.7 ; python_version >= "3.7" and python_version < "3.12" codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12" -cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" -cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12" +cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12" +cwltest==2.3.20230825125225 ; python_version >= "3.7" and python_version < "3.12" cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12" darker==1.7.2 ; python_version >= "3.7" and python_version < "3.12" defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12" -docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12" -exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.12" +docutils==0.19 ; python_version >= "3.7" and python_version < "3.12" +exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.12" filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12" fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12" fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12" @@ -55,7 +55,7 @@ jeepney==0.8.0 ; python_version >= "3.7" and python_version < "3.12" and sys_pla jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12" keyring==24.1.1 ; python_version >= "3.7" and python_version < "3.12" -kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12" +kiwisolver==1.4.5 ; python_version >= "3.7" and python_version < "3.12" kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12" markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -106,10 +106,10 @@ pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12" pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12" pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12" pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12" -pytest==7.4.0 ; python_version >= "3.7" and python_version < "3.12" +pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.12" python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12" -pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12" +pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12" pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32" pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12" rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -124,7 +124,7 @@ ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12" scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" -scipy==1.11.1 ; python_version >= "3.9" and python_version < "3.12" +scipy==1.11.2 ; python_version >= "3.9" and python_version < "3.12" secretstorage==3.3.3 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" selenium==4.11.2 ; python_version >= "3.7" and python_version < "3.12" seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.12" @@ -133,7 +133,7 @@ six==1.16.0 ; python_version >= "3.7" and python_version < "3.12" sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12" snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.12" sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" -sphinx-rtd-theme==1.2.2 ; python_version >= "3.7" and python_version < "3.12" +sphinx-rtd-theme==2.0.0rc2 ; python_version >= "3.7" and python_version < "3.12" sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.12" sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" @@ -146,8 +146,8 @@ statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12" testfixtures==7.1.0 ; python_version >= "3.7" and python_version < "3.12" tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12" toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12" -tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" -trio-websocket==0.10.3 ; python_version >= "3.7" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.7" and python_full_version <= "3.11.0a6" +trio-websocket==0.10.4 ; python_version >= "3.7" and python_version < "3.12" trio==0.22.2 ; python_version >= "3.7" and python_version < "3.12" tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12" twill==3.1 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index cc18b68332c8..6be9098761b4 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -5,6 +5,6 @@ importlib-metadata==4.2.0 mccabe==0.7.0 pycodestyle==2.9.1 pyflakes==2.5.0 -ruff==0.0.284 +ruff==0.0.287 typing_extensions==4.7.1 zipp==3.15.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index f754ad8be393..82bb0f72517b 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,5 +1,3 @@ ---extra-index-url https://wheels.galaxyproject.org/simple - a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12" adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12" aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12" @@ -7,7 +5,7 @@ aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12" aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12" aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12" aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12" -alembic==1.11.2 ; python_version >= "3.7" and python_version < "3.12" +alembic==1.12.0 ; python_version >= "3.7" and python_version < "3.12" amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12" apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12" @@ -43,9 +41,9 @@ circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -click==8.1.6 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.7 ; python_version >= "3.7" and python_version < "3.12" cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12" -cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +cloudbridge==3.2.0 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12" conda-package-streaming==0.9.0 ; python_version >= "3.7" and python_version < "3.12" @@ -53,19 +51,18 @@ cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12" cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12" cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12" cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12" -cython==3.0.0 ; python_version >= "3.7" and python_version < "3.12" -decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12" +cython==3.0.2 ; python_version >= "3.7" and python_version < "3.12" defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12" dictobj==0.4 ; python_version >= "3.7" and python_version < "3.12" dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.12" docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.12" -docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12" +docutils==0.19 ; python_version >= "3.7" and python_version < "3.12" dparse==0.6.3 ; python_version >= "3.7" and python_version < "3.12" ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12" edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12" email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12" -exceptiongroup==1.1.2 ; python_version >= "3.7" and python_version < "3.11" +exceptiongroup==1.1.3 ; python_version >= "3.7" and python_version < "3.11" fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12" fastapi==0.98.0 ; python_version >= "3.7" and python_version < "3.12" filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12" @@ -76,7 +73,7 @@ future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12" galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12" gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12" -greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "win32" or platform_machine == "WIN32" or platform_machine == "AMD64" or platform_machine == "amd64" or platform_machine == "x86_64" or platform_machine == "ppc64le" or platform_machine == "aarch64") and python_version < "3.12" +greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12" gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12" gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.12" h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" @@ -86,7 +83,7 @@ humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.12" idna==3.4 ; python_version >= "3.7" and python_version < "3.12" importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.12" importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.12" -isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.12" +isa-rwval==0.10.1 ; python_version >= "3.7" and python_version < "3.12" isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12" jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" jmespath==1.0.1 ; python_version >= "3.7" and python_version < "3.12" @@ -100,20 +97,20 @@ markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12" markdown==3.4.4 ; python_version >= "3.7" and python_version < "3.12" markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12" mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12" -mercurial==6.5.1 ; python_version >= "3.7" and python_version < "3.12" +mercurial==6.5.2 ; python_version >= "3.7" and python_version < "3.12" mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12" mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12" msal==1.23.0 ; python_version >= "3.7" and python_version < "3.12" msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.12" multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12" mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12" -networkx==2.5 ; python_version >= "3.7" and python_version < "3.12" +networkx==2.6.3 ; python_version >= "3.7" and python_version < "3.12" nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12" numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==1.25.2 ; python_version >= "3.9" and python_version < "3.12" oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12" -orjson==3.9.4 ; python_version >= "3.7" and python_version < "3.12" +orjson==3.9.7 ; python_version >= "3.7" and python_version < "3.12" oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12" packaging==23.1 ; python_version >= "3.7" and python_version < "3.12" paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.12" @@ -125,7 +122,7 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9 prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12" prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12" psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" -pulsar-galaxy-lib==0.15.3 ; python_version >= "3.7" and python_version < "3.12" +pulsar-galaxy-lib==0.15.4 ; python_version >= "3.7" and python_version < "3.12" pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.12" pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" pycryptodome==3.18.0 ; python_version >= "3.7" and python_version < "3.12" @@ -151,7 +148,7 @@ python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12" python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12" python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12" python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12" -pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12" +pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12" pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12" pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12" rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -183,9 +180,10 @@ starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12" starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12" supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12" svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12" -tenacity==8.2.2 ; python_version >= "3.7" and python_version < "3.12" +tenacity==8.2.3 ; python_version >= "3.7" and python_version < "3.12" tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12" tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" tornado==6.2 ; python_version >= "3.7" and python_version < "3.12" tqdm==4.66.1 ; python_version >= "3.7" and python_version < "3.12" tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index ea39387ec32a..fd731d24da41 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,22 +1,22 @@ -cffi==1.15.1 -cryptography==41.0.3 -mypy==1.4.1 -mypy-extensions==1.0.0 -pycparser==2.21 -pydantic==1.10.12 -tomli==2.0.1 -typed-ast==1.5.5 -types-bleach==6.0.0.4 -types-boto==2.49.18.9 -types-contextvars==2.4.7.3 -types-dataclasses==0.6.6 -types-docutils==0.20.0.1 -types-Markdown==3.4.2.10 -types-paramiko==3.3.0.0 -types-pkg-resources==0.1.3 -types-python-dateutil==2.8.19.14 -types-PyYAML==6.0.12.11 -types-requests==2.31.0.2 -types-six==1.16.21.9 -types-urllib3==1.26.25.14 -typing_extensions==4.7.1 +cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" +cryptography==41.0.3 ; python_version >= "3.7" and python_version < "3.12" +mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12" +mypy==1.4.1 ; python_version >= "3.7" and python_version < "3.12" +pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" +pydantic==1.10.12 ; python_version >= "3.7" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" +typed-ast==1.5.5 ; python_version >= "3.7" and python_version < "3.8" +types-bleach==6.0.0.4 ; python_version >= "3.7" and python_version < "3.12" +types-boto==2.49.18.9 ; python_version >= "3.7" and python_version < "3.12" +types-contextvars==2.4.7.3 ; python_version >= "3.7" and python_version < "3.12" +types-dataclasses==0.6.6 ; python_version >= "3.7" and python_version < "3.12" +types-docutils==0.20.0.3 ; python_version >= "3.7" and python_version < "3.12" +types-markdown==3.4.2.10 ; python_version >= "3.7" and python_version < "3.12" +types-paramiko==3.3.0.0 ; python_version >= "3.7" and python_version < "3.12" +types-pkg-resources==0.1.3 ; python_version >= "3.7" and python_version < "3.12" +types-python-dateutil==2.8.19.14 ; python_version >= "3.7" and python_version < "3.12" +types-pyyaml==6.0.12.11 ; python_version >= "3.7" and python_version < "3.12" +types-requests==2.31.0.2 ; python_version >= "3.7" and python_version < "3.12" +types-six==1.16.21.9 ; python_version >= "3.7" and python_version < "3.12" +types-urllib3==1.26.25.14 ; python_version >= "3.7" and python_version < "3.12" +typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12"